Title of Invention

"ISOPENTENYL TRANSFERASE SEQUENCES AND METHODS OF USE"

Abstract Methods and compositions for modulating plant development are provided. Polynucleotide sequences and amino acid sequences encoding isopentenyl transferase (IPT) polypeptides are provided. The sequences can be used in a variety of methods including modulating root development, modulating floral development, modulating leaf and/or shoot development, modulating senescence, modulating seed size and/or weight, and modulating tolerance of plants to abiotic stress. Polynucleotides comprising an IPT promoter are also provided. The promoter can be used to regulate expression of a sequence of interest. Transformed plants, plant cell, tissues, and seed are also provided.
Full Text ISOPENTENYL TRANSFERASE SEQUENCES AND METHODS OF USE
FIELD OF THE INVENTION
The invention relates to the field of genetic manipulation of plants,
particularly the modulation of gene activity to affect plant development and growth.
BACKGROUND OF THE INVENTION
Cytokinins are a class of N6 substituted purine derivative plant hormones
that regulate cell division and influence a large number of developmental events,
such as shoot development, sink strength, root branching, control of apical
dominance in the shoot, leaf development, chloroplast development, and leaf
senescence (Mok et al. (1994) Cytokinins. Chemistry, Action and Function. CRC
Press, Boca Raton, FLA, pp. 155-166; Morgan (1984) Advanced Plant Physiology
ed. MB., Pitman, London, UK, pp53-75; and Letham (1994) Annual Review of
Plant Physiol 34:163-197). In maize, cytokinins (CK) play an important role in
establishing seed size, decreasing tip kernel abortion, and increasing seed set
during unfavorable environmental conditions (Cheikh et al. (1994) Plant Physiol.
106: 45-51;. Dietrich et al. (1995) Plant Physiol Biochem 33:327-36). Active
cytokinin pools are regulated by rates of synthesis and degradation.
Until recently, roots were believed to be the major site of cytokinin
biosynthesis but evidence indicates that others tissues, such as shoot meristems
and developing seeds, also have high cytokinin biosynthetic activity. It has been
suggested that cytokinins are synthesized in restricted sites where cell
proliferation is active. The presence of several AtlPT genes in Arabidopsis and
their differential pattern of expression might serve this purpose.
The catabolic enzyme isopentenyl transferase (IPT) directs the synthesis of
cytokinins and plays a major role in controlling cytokinin levels in plant tissues. ,
Multiple routes have been proposed for cytokinin biosynthesis. Transfer RNA
degradation has been suggested to be a source of cytokinin, because some tRNA
molecules contain an isopentenyladenosine (iPA) residue at the site adjacent to
the anticodon (Swaminathan et al. (1977) -Biochemistry 16: 1355-1360). The
modification is catalyzed by tRNA isopentenyl transferase (tRNA IPT; EC 2.5.1.8),
'wh'lc'h '"has b'een identified in various organisms such as Escherichia coli,
Saccharomyces cerevisiae, Lactobacillus acidophilus, Homo sapiens, and Zea
mays (Bartz et al. (1972) Biochemie 54:31-39; Kline et al, (1969) Biochemistry
8:4361-4371; Holtz etal. (1975) Hoppe-Seyler's Z. Physiol. Chem 356:1459-1464;
Golovko et al. (2000) Gene 259:85-93; and, Holtz et al. (1979) Hoppe-Seyler's 2.
Physiol. Chem 359:89-101). However, this pathway is not considered to be the
main route for cytokinin synthesis (Chen et al. (1997) Physiol. Plant 101:665-673
and McGraw et al. (1995) Plant Hormones, Physiology, Biochemistry and
Molecular Biology. Ed. Davies, 98-117, Kluwer Academic Publishers, Dordrecht).
Another possible route of cytokinin formation is de novo biosynthesis of
iPMP by adenylate isopenteny! transferase (IPT; EC 2.5.1.27) with dimethylallyldiphosphate
(DMAPP), AMP, ATP, and ADP as substrates. Our current
knowledge of cytokinin biosynthesis in plants is largely deduced from studies on a
possible analogous system in Agrobacterium tumefaciens. Cells of A.
tumefaciens are able to infect certain plant species by inducing tumor formation in
host plant tissues (Van Montagu et al. (1982) Curr Top Microbiol Immunol 96: 237-
254; Hansen et al. (1999). Curr Top Microbiol Immunol 240:21-57). To do so, the
A. tumefaciens cells synthesize and secrete cytokinins which mediate the
transformation of normal host plant tissues into tumors or calli. This process is
facilitated by the A. tumefaciens tumor-inducing plasmid which contains genes
encoding the necessary enzyme and regulators for cytokinin biosynthesis.
Biochemical and genetic studies revealed that Gene 4 of the tumor-inducing
plasmid encodes an isopentenyl transferase (IPT), which converts AMP and
DMAPP into isopentenyladenosine-5'-monophosphate (iPMP), the active form of
cytokinins (Akiyoshi et al. (1984) Proc. Natl. Acad. Sci USA 87:5994-5998).
Overexpression of the Agrobacterium ipt gene in a variety of transgenic plants has
been shown to cause an increased level of cytokinins and elicit typical cytokinin
responses in the host plant (Hansen et al. (1999) Curr Top Microbiol Immunol
240:21-57). Therefore, it has been postulated that plant cells use machinery
similar to that of A. tumefaciens cells for cytokinin biosynthesis. Arabidopsis IPT
homologs have recently been identified in Arabidopsis and Petunia (Takei et al.
(2001) J. Biol. Chem. 276: 26405-26410 and Kakimoto (2001) Plant Cell Physiol.
42:677-685). Overexpression of the Arabidopsis IPT homologs in plants elevated
cytokinin levels and elicited typical cytokinin responses in planta and under tissue
culture conditions (Kakimoto (2001) Plant Cell Physiol. 42:677-685).
Arabicldpsis ipT "genes are members of a small multigene family of nine
different genes, two of which code for tRNA isopentenyl transferases, and seven
of which encode a gene product with a cytokinin biosynthetic function.
Biochemical analysis of the recombinant AtlPT4 protein showed that, in contrast to
the bacterial enzyme, the Arabidopsis enzyme uses ATP as a substrate instead of
AMP. Another plant IPT gene (Sho) was identified in Petunia hybrida using an
activation tagging strategy (Zubko et a/. (2002) The Plant Journal 29:797-808).
In view of the influence of cytokinins on a wide variety of plant
developmental processes, including root architecture, shoot and leaf development,
and seed set, the ability to manipulate cytokinin levels in higher plant cells, and
thereby drastically effect plant growth and productivity, offers significant
commercial value (Mok et a/. (1994) Cytokinins. Chemistry, Action and Function.
CRC Press, Boca Raton, FLA, pp. 155-166),
BRIEF SUMMARY OF THE INVENTION
Compositions and methods of the invention comprise and employ
isopentenyl transferase (IPT) polypeptides and polynucleotides that are involved in
modulating plant development, morphology, and physiology.
Compositions further include expression cassettes, plants, plant cells, and
seeds having the IPT sequences of the invention. The plants, plant cells, and
seeds of the invention may exhibit phenotypic changes, such as modulated
(increased or decreased) cytokinin levels; modulated floral development;
modulated root development; altered shoot to root ratio; increased seed size or an
increased seed weight; increased plant yield or plant vigor; maintained or
improved stress tolerance (e.g., increased or maintained size of the plant,
minimized tip kernel abortion, increased or maintained seed set); decreased shoot
growth; delayed senescence or an enhanced vegetative growth, all relative to a
plant, plant cell, or seed not modified per the invention.
Compositions of the invention also include IPT promoters, DNA constructs
comprising the IPT promoter operably linked to a nucleotide sequence of interest,
expression vectors, plants, plant cells, and seeds comprising these DNA
constructs.
Methods are provided for reducing or eliminating the activity of an IPT
polypeptide in a plant, comprising introducing into the plant a selected
'ploiyhuclebtide. in "specific methods, providing the polynucleotide decreases the
level of cytokinin in the plant and/or modulates root development of the plant.
Methods are also provided for increasing the level of an IPT polypeptide in
a plant comprising introducing into the plant a selected polyn. In specific methods,
expression of the IPT polynucleotide increases the level of a cytokinin in the plant;
maintains or improves the stress tolerance of the plant; maintains or increases the
size of the plant; minimizes seed abortion; increases or maintains seed set;
increases shoot growth; increases seed size or seed weight; increases plant yield
or plant vigor; modulates floral development; delays senescence; or increases leaf
growth.
Methods are also provided for regulating the expression of a nucleotide
sequence of interest. The method comprises introducing into a plant a DNA
construct comprising a heterologous nucleotide sequence of interest operably
linked to an IPT promoter of the invention.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 provides an alignment of cytokinin biosynthetic enzymes from
maize, petunia, and Arabidopsis. The amino acid sequences present in the
alignment include ZmlPTI (SEQ ID N0:23), ZmlPT2 (SEQ ID NO:2), ZmlPT4
(SEQ ID NO:6), ZmlPTS (SEQ ID N0:9), ZmlPT6 (SEQ ID N0:12), ZmlPTT (SEQ
ID NO:15), ZmlPTS (SEQ ID NO:18), AtlPTI (SEQ ID NO:29), AtlPTS (SEQ ID
N0:34), AtlPT4 (SEQ ID NO:30), AtlPTS (SEQ ID N0:35), AtlPT6 (SEQ ID
N0:36), AtlPT7 (SEQ ID NO:37), AtlPTS (SEQ ID NO:38) and Sho (SEQ ID
NO:31). Asterisks indicate amino acids conserved in many IPT proteins and the
underlined amino acids represent a putative ATP/GTP binding site.
Figure 2 provides a schematic of the structure of the ZmlPTI gene from
Mo17 (SEQ ID NO: 21). Coding regions are indicated by the thick arrows and the
CAATand a putative TATA box are shown.
Figure 3 provides an amino acid sequence alignment of ZmlPTI (SEQ ID
NO: 23, referred to as ZmlPT-Mo17) and a variant of ZmlPTI (SEQ ID NO:27,
referred to as ZmlPT-B73). The sequences have 98% amino acid sequence
identity. The consensus sequence for the ZmlPTI polypeptide is found in SEQ ID
NO: 39.
Figure 4 provides ppm values for- ZmlPTI in Lynx embryo libraries at
various days after pollination (DAP).
'Figure 5A snows tne detection of ZmlPTI in different maize organs using
RT-PCR.
Figure 5B shows the detection of ZmlPTI in developing kernels using RTPCR.
Figure 6 shows a Southern blot with B73 or Mo17 genomic DNA digested
by 3 different restriction enzymes. 40 y,g of genomic DNA was digested and run
on a 0.8% agarose gel and transferred to a nylon membrane. The ZmlPT2-B73
gene coding sequence was used as a probe.
Figure 7 shows a Northern blot and relative expression of the ZmlPT2 gene
in different vegetative organs and in whole kernels at different days after
pollination (DAP). Transcript levels were measured in leaves (L), stalks (S), roots
(R), and in whole kernels at 0, 5, 10, 15, 20 and 25 days after pollination, and
quantified relative to abundance of cyclophilin transcripts.
Figure 8 provides a Northern blots and relative expression of the ZmlPT2
gene in kernels at different days after pollination. Transcript levels were measured
in 0- to 5-DAP whole kernels and in 6- to 34-DAP kernels without pedicels, and
quantified relative to abundance of cyclophilin transcripts. Zeatin riboside levels
(the most abundant CK in corn kernels) were previously measured in the same
samples and are indicated by the solid line (Brugiere et al. (2003) Plant Phsyiol
132:1228-1240).
Figure 9 provides ppm values in Lynx embryo libraries forZmlPT2.
Figure 10 provides an alignment of the arnino acid sequences
corresponding to Arabidopsis IPT proteins (AtlPT), the petunia IPT protein (Sho)
and rice putative IPT proteins (OslPT). The sequences in the alignment are as
follows: OslPT6 (SEQ ID NO: 57); OslPT8 (SEQ ID NO: 41); OslPTIO (SEQ ID
NO: 59); OslPT11 (SEQ ID NO: 43); OslPT9 (SEQ ID NO: 61); OslPTS (SEQ ID
NO: 63); OslPT2 (SEQ ID NO: 46); OslPTI (SEQ ID NO: 49); OslPT5 (SEQ ID
NO: 52); OslPT4 (34394150) (SEQ ID NO: 66); OslPT7 (SEQ ID NO: 54); AtlPTI
(AB062607) (SEQ ID NO: 29); AtlPTS (AB062610) (SEQ ID NO: 34); AtlPT4
(AB062611) (SEQ ID NO: 30); AtlPTS (AB062608) (SEQ ID NO: 35); AtlPT6
(AB062612) (SEQ ID NO: 36); AtlPT7 (AB062613) (SEQ ID NO: 37); AtlPTS
(AB082614) (SEQ ID NO: 38); Sho (Petunia) (SEQ ID NO: 31); and, consensus
(SEQ ID NO: 67).
Figure 11 is a Northern blot that shows the relative expression of the
Zm/PT2 gene at different days after pollination in different parts of the kernels.
Transcript levels were measured in 0- to 25-DAP dissected kernels and quantified
relative to abundance of 18S RNA transcripts.
Figure 12 shows chromatograms related to the DMAPP::AMP isopentenyl
transferase activity of Agrobacterium and maize purified recombinant protein.
Figure 13 shows chromatograms related to further treatment of the reaction
products of Figure 12.
Figure 14 shows chromatograms related to the DMAPP::ATP isopentenyl
transferase activity of the maize purified recombinant protein.
Figure 15 is a Western blot of whole maize kernels at various days after
pollinations.
Figure 16 is a graphic representation of the TUSC results.
Figure 17 is a phylogenetic tree of plant IPT sequences.
DETAILED DESCRIPTION OF THE INVENTION
The present inventions now will be described more fully hereinafter with
reference to the accompanying drawings, in which some, but not all embodiments
of the invention are shown. Indeed, these inventions may be embodied in many
different forms and should not be construed as limited to the embodiments set
forth herein; rather, these embodiments are provided so that this disclosure will
satisfy applicable legal requirements. Like numbers refer to like elements
throughout.
Many modifications and other embodiments of the inventions set forth
herein will come to mind to one skilled in the art to which this invention pertains
having the benefit of the teachings presented in the foregoing descriptions and the
associated drawings. Therefore, it is to be understood that the invention is not to
be limited to the specific embodiments disclosed and that modifications and other
embodiments are intended to be included within the scope of the appended
claims. Although specific terms are employed herein, they are used in a generic
and descriptive sense only and not for purposes of limitation,
COMPOSITIONS
Compositions of the invention include isopentenyl transferase (IPT)
polypeptides and polynucleotides that are involved in modulating plant
development, morphology, and physiology. Compositions of the invention further
include IPT promoters that are capable of regulating transcription. In particular,
tne present invention provides for isolated polynucleotides comprising nucleotide
sequences encoding the amino acid sequences shown in SEQ ID NO: 2, 6, 9, 12,
15, 18, 23, 27, 41, 43, 46, 49, 52, 54, 57, 59, 61, 63, 66, and 77. Further provided
are isolated polypeptides having an amino acid sequence encoded by a
polynucleotide described herein, for example those set forth in SEQ ID NO: 1, 3,
4, 5, 7, 8, 10, 11, 13, 14, 16, 17, 19, 20, 21, 22, 24, 26, 28, 40, 42, 44, 47, 50, 53,
55, 58, 60, 62, 64, 45, 48, 51, 56, 65, 69, 70, 71, 72, 73, 74, or 77, Additional
compositions include the IPT promoter sequences set forth in SEQ ID NO: 25 or
75, and promoter sequences as further isolated and characterized from the 5'
regions provided herein for ZmlPT4 (SEQ ID NO: 5), ZmlPT5 (SEQ ID NO: 8),
ZmlPT6 (SEQ ID NO: 11), ZmlPT7 (SEQ ID NO: 14), ZmlPT8 (SEQ ID NO: 17),
ZmlPT9 (SEQ ID NO: 20), OslPTI (SEQ ID NO: 47), OslPT2 (SEQ ID NO: 44),
OslPTS (SEQ ID NO: 62), OslPT4 (SEQ ID NO: 64), OslPTS (SEQ ID NO: 50),
OslPT6 (SEQ ID NO: 55), OslPT7 (SEQ ID NO: 53), OslPTS (SEQ ID NO: 40),
OslPT9 (SEQ ID NO: 60), OslPTI 0 (SEQ ID NO: 58), and OslPT11 (SEQ ID NO:
42).
The isopentenyl transferase polypeptides of the invention share sequence
identity with members of the isopentenyl transferase family of proteins.
Polypeptides in the IPT family have been identified in various bacteria and in
Arabidopsis and Petunia. See, for example, (Kakimoto (2001) Plant Cell Physio.
42:677-658); Takei et al. (2001) The Journal of Biological Chemistry 276:26405-
26410; and Zubko et al. (2002) The Plant Journal 29:797-808). Members of the
IPT family are characterized by having the consensus sequence
GxTxxGK[ST]xxxxx[VLI]xxxxxxx[VLI][VLI]xxDxxQx{57,60}[VLI][VLI]xGG[ST] (SEQ
ID NO:32) (where x denotes any amino acid residue, [ ] any one of the amino
acids shown in [ ], and x{m,n} m to n amino acid residues in number). See,
Kakimoto et al. (2001) Plant Cell Physiol. 42:677-85 and Kakirnoto et al. (2003) J.
Plant Res. 116:233-9, both of which are herein incorporated by reference. IPT
family members may also have ATP/GTP binding sites. An amino acid alignment
of the maize IPT proteins along with Arabidopsis and petunia cytokinin
biosynthetic enzymes is provided in Figure 1, and an amino acid alignment of the
rice IPT proteins with Arabidopsis and petunia cytokinin biosynthetic enzymes is
provided in Figure 10. Asterisks indicate a consensus sequences found in many
cytokinin biosynthetic enzymes. The underlined amino acids indicate a putative
ATP/GTP binding domains.
'Isopentenyl transterase enzymes are involved in cytokinin biosynthesis,
therefore the IPT polypeptides of the invention have "cytokinin synthesis activity."
By "cytokinin synthesis activity" is intended enzymatic activity that generates
cytokinins, derivatives thereof, or any intermediates in the cytokinin synthesis
pathway. Cytokinin synthesis activity therefore includes, but is not limited to,
DMAPP:AMP isopentenyltransferase activity (the conversion of AMP (adenosine-
5'-monophosphate) and DMAPP into iPMP (isopentenyladenosine-5-
monophosphate)), DMAPP:ADP isopentenyltransferase activity (the conversion of
ADP (adenosine-5'-diphosphate) and DMAPP into iPDP (isopentenyladenosine-5-
diphosphate)); DMAPP:ATP isopentenyltransferase activity (the conversion of
ATP (adenosine-5'-triphosphate) and DMAPP into iPTP (isopentenyladenosine-51-
triphosphate)), and DMAPP:tRNA isopentenyltransferase activity (the modification
of cytoplasmic and/or mitrochondrial tRNAs to give isopentenyl). Cytokinin
synthesis activity can further include a substrate comprising a second side chain
precursor, other than DMAPP. Examples of side chain donors include compounds
of terpenoid origin. For example, the substrate could be hydroxymethylbutenyl
diphosphate (HMBPP) which would allow frans-zeatin riboside monophosphate
(ZMP) synthesis. See, for example, Astot et a/. (2000) Proc Natl Acad Sci
97:14778-14783 and Takei et a/. (2003) J Plant Res. 116(3):265-9.
Cytokinin synthesis activity further includes the synthesis of intermediates
involved in formation of ZMP. Methods to assay for the production of various
cytokinins and their intermediates can be found, for example, in Takei et al. (2001)
The Journal of Biological Chemistry 276:26405-26410, Zubo et a/. (2002) The
Plant Journal 29:797-808; Kakimoto et al. (2001) Plant Cell Physio. 42:677-658,
and Sun et al. (2003) Plant Physiology 737:167-176, each of which is herein
incorporated by reference. "Cytokinin synthesis activity" also includes any
alteration in a plant or plant cell phenotype that is characteristic of an increase in
cytokinin concentration. Such cytokinin specific effects are discussed elsewhere
herein and include, but are not limited to, enhanced shoot formation, reduced
apical dominance, delayed senescence, delayed flowering, increased leaf growth,
increased cytokinin levels in the plant, increased tolerance under stress,
minimization of tip kernel abortion, increased or maintained seed set under stress
conditions, and a decrease in root growth. Assays to measure or detect such
phenotypes are known. See, for example, Miyawaki et al. (2004) The Plant
Journal 37:128-138, Takei et al. (2001) The Journal of Biological Chemistry
, 2'uB'b"ef a! (2002) The Plant Journal 29:797-808; Kakimoto ef
a/. (2001) P/an? Ce// Pftys/o. 42:677-658, and Sun ef a/. (2003) Plant Physiology
131 .-167-176, each of which is herein incorporated by reference. Additional
phenotypes resulting from an increase in cytokinin synthesis activity in a plant are
discussed herein.
Compositions of the invention include IPT sequences that are involved in
cytokinin biosynthesis. In particular, the present invention provides for isolated
polynucleotides comprising nucleotide sequences encoding the amino acid
sequences shown in SEQ ID NO: 2, 6, 9,12,15, 18, 23, 27, 41,43, 46,49, 52, 54,
57, 59, 61, 63, 66, and 77. Further provided are polypeptides having an amino
acid sequence encoded by a polynucleotide described herein, for example those
set forth in SEQ ID NOS: 1, 3, 4, 5, 7, 8, 10, 11, 13,14, 16, 17,19, 20, 21, 22, 24,
26, 28, 40, 42, 44, 47, 50, 53, 55, 58, 60, 62, 64, 45, 48, 51, 56, 65, 69, 70, 71, 72,
73, or 74 and fragments and variants thereof. In addition, further provided are
promoter sequences, for example, the sequence set forth in SEQ ID NO: 25 or 75,
variants and fragments thereof.
The invention encompasses isolated or substantially purified polynucleotide
or protein compositions. An "isolated" or "purified" polynucleotide or protein, or
biologically active portion thereof, is substantially or essentially free from
components that normally accompany or interact with the polynucleotide or protein
as found in its naturally occurring environment. Thus, an isolated or purified
polynucleotide or protein is substantially free of other cellular material, or culture
medium when produced by recombinant techniques, or substantially free of
chemical precursors or other chemicals when chemically synthesized. Optimally,
an "isolated" polynucleotide is free of sequences (optimally protein encoding
sequences) that naturally flank the polynucleotide (i.e., sequences located at the
5' and 3' ends of the polynucleotide) in the genomic DNA of the organism from
which the polynucleotide is derived. For example, in various embodiments, the
isolated polynucleotide can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5
kb, or 0.1 kb of nucleotide sequence that naturally flank the polynucleotide in
genomic DNA of the cell from which the polynucleotide is derived. A protein that is
substantially free of cellular material includes preparations of protein having less
than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of contaminating protein.
When the protein of the invention or biologically active portion thereof is
recombinantly produced, optimally culture medium represents less than about
3b'%", 20%, 10%, 5%, or 1% (by dry weight) of chemical precursors or non-proteinof-
interest chemicals.
Fragments and variants of the disclosed polynucleotides and proteins
encoded thereby are also encompassed by the present invention. By "fragment"
is intended a portion of the polynucleotide or a portion of the amino acid sequence
and hence protein encoded thereby. Fragments of a polynucleotide may encode
protein fragments that retain the biological activity of the native protein and hence
have cytokinin synthesis activity. Alternatively, fragments of a polynucleotide that
are useful as hybridization probes generally do not encode fragment proteins
retaining biological activity. Thus, fragments of a nucleotide sequence may range
from at least about 20 nucleotides, about 50 nucleotides, about 100 nucleotides,
and up to the full-length polynucleotide encoding the proteins of the invention.
A fragment of an IPT polynucleotide that encodes a biologically active
portion of an IPT protein of the invention will encode at least 15, 25, 30, 50, 100,
150, 200, 225, 250, 275, 300, 310, 315, or 320 contiguous amino acids, or up to
the total number of amino acids present in a full-length IPT protein of the invention
(for example, 322, 364, 337, 338, 352, 388, 353, 352, 450, 590, 328, 325, 251,
427, 417, 585, 455, 344, and 347 amino acids for SEQ ID NO: 2, 6, 9, 12, 15, 18,
23, 27, 41, 43, 46, 49, 52, 54, 57, 59, 61, 63, and 66, respectively). Fragments of
an IPT polynucleotide that are useful as hybridization probes or PCR primers
generally need not encode a biologically active portion of an IPT protein.
Thus, a fragment of an IPT polynucleotide may encode a biologically active
portion of an IPT protein, or it may be a fragment that can be used as a
hybridization probe or PCR primer using methods disclosed below. A biologically
active portion of an IPT protein can be prepared by isolating a portion of one of the
IPT polynucleotides of the invention, expressing the encoded portion of the IPT
protein (e.g., by recombinant expression in vitro), and assessing the activity of the
encoded portion of the IPT protein. Polynucleotides that are fragments of an IPT
nucleotide sequence comprise at least 16, 20, 50, 75, 100, 150, 200, 250, 300,
350, 400, 450, 500, 550, 600, 650, 700, 800, 900, 950, or 965 contiguous
nucleotides, or up to the number of nucleotides present in a full-length IPT
polynucleotide disclosed herein (for example, 1495, 969, 2901, 2654, 1095, 4595,
1014, 1955, 1017, 1652, 1059, 3419, 1167, 1535, 3000, 1209, 1062, 1299, 1056,
4682, 8463, 4470, 4114, 2599, 1284, 5030, 8306, 7608, 5075, 4777, 984, 975,
753, 1254,1044, 1035,1284,1353, 1368,1758, and 1773 nucleotides for SEQ ID
"NO: 'i; 3, 4, 5, 7, 8, 10, 11, 13, 14, 16, 17, 19, 20, 21, 22, 24, 26, 28, 40, 42, 44,
47, 50, 53, 55, 58, 60, 62, 64, 45, 48, 51, 56, 65, 69, 70, 71, 72, 73, and 74,
respectively).
"Variants" is intended to mean substantially similar sequences. For
polynucleotides, a variant comprises a deletion and/or addition of one or more
nucleotides at one or more sites within the native polynucleotide and/or a
substitution of one or more nucleotides at one or more sites in the native
polynucleotide. As used herein, a "native" polynucleotide or polypeptide
comprises a naturally occurring nucleotide sequence or amino acid sequence,
respectively. For polynucleotides, conservative variants include those sequences
that, because of the degeneracy of the genetic code, encode the amino acid
sequence of one of the IPT polypeptides of the invention. Naturally occurring
variants such as these can be identified with the use of well-known molecular
biology techniques, as, for example, with polymerase chain reaction (PCR) and
hybridization techniques as outlined below. Variant polynucleotides also include
synthetically derived polynucleotide, such as those generated, for example, by
using site-directed mutagenesis but which still encode an IPT protein of the
invention. Generally, variants of a particular polynucleotide of the invention will
have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence
identity to that particular polynucleotide as determined by sequence alignment
programs and parameters described elsewhere herein.
Variants of a particular polynucleotide of the invention (i.e., the reference
polynucleotide) can also be evaluated by comparison of the percent sequence
identity between the polypeptide encoded by a variant polynucleotide and the
polypeptide encoded by the reference polynucleotide. Thus, for example, isolated
polynucleotides that encode a polypeptide with a given percent sequence identity
to the polypeptide of SEQ ID NO: 2, 6, 9,12, 15,18, 23, 27,41,43, 46, 49, 52, 54,
57, 59, 61, 63, 66, or 77 are disclosed, Percent sequence identity between any
two polypeptides can be calculated using sequence alignment programs and
parameters described elsewhere herein. Where any given pair of polynucleotides
of the invention is evaluated by comparison of the percent sequence identity
shared by the two polypeptides they encode, the percent sequence identity
between the two encoded polypeptides is at least about 40%, 45%, 50%, 55%,
"60'%'; 65%; 70%, 75%, 8Wo,"85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,
98%, 99% or more sequence identity,
"Variant" protein is intended to mean a protein derived from the native
protein by deletion or addition of one or more amino acids at one or more sites in
the native protein and/or substitution of one or more amino acids at one or more
sites in the native protein. Certain variant proteins encompassed by the present
invention are biologically active, that is they continue to possess the desired
biological activity of the native protein, that is, cytokinin synthesis activity, as
described herein. Such variants may result from, for example, genetic
polymorphism or from human manipulation. Biologically active variants of a native
IPT protein of the invention will have at least about 40%, 45%, 50%, 55%, 60%,
65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99% or more sequence identity to the amino acid sequence for the native protein
as determined by sequence alignment programs and parameters described
elsewhere herein. A biologically active variant of a protein of the invention may
differ from that protein by as few as 1-15 amino acid residues, as few as 1-10,
such as 6-10, as few as 5, as few as 4, 3,2, or even 1 amino acid residue.
The proteins of the invention may be altered in various ways including
amino acid substitutions, deletions, truncations, and insertions. Methods for such
manipulations are generally known in the art. For example, amino acid sequence
variants and fragments of the IPT proteins can be prepared by mutations in the
DNA. Methods for mutagenesis and polynucleotide alterations are well known in
the art. See, for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492;
Kunkel et a/. (1987) Methods in Enzymol. 154:367-382; U.S. Patent No.
4,873,192; Walker and Gaastra, eds. (1983) Techniques in Molecular Biology
(MacMillan Publishing Company, New York) and the references cited therein.
Guidance as to appropriate amino acid substitutions that do not affect biological
activity of the protein of interest may be found in the model of Dayhoff et a/. (1978)
Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Washington,
D.C.), herein incorporated by reference. Conservative substitutions, such as
exchanging one amino acid with another having similar properties, may be
optimal.
Thus, the genes and polynucleotides of the invention include both the
naturally occurring sequences as well as mutant forms. Likewise, the proteins of
the invention encompass naturally occurring proteins as well as variations and
modified forms thereof." "Such variants will continue to possess the desired IPT
activity. Obviously, the mutations that will be made in the DMA encoding the
variant must not place the sequence out of reading frame and optimally will not
create complementary regions that could produce secondary mRNA structure.
The deletions, insertions, and substitutions of the protein sequences
encompassed herein are not expected to produce radical changes in the
characteristics of the protein. However, when it is difficult to predict the exact
effect of the substitution, deletion, or insertion in advance of doing so, one skilled
in the art will appreciate that the effect will be evaluated by routine screening
assays. That is, the activity can be evaluated by assaying for cytokinin synthesis
activity. See, for example, Takei et al. (2001) The Journal of Biological Chemistry
276:26405-26410; Zubo et al. (2002) The Plant Journal 29:797-808; Kakimoto et
al. (2001) Plant Cell Physio. 42:677-658; Sun et al. (2003) Plant Physiology
737:167-176; and Miyawaki et al. (2004) The Plant Journal 37:128-138, all of
which are herein incorporated by reference.
Variant polynucleotides and proteins also encompass sequences and
proteins derived from a mutagenic and recombinogenic procedure such as DNA
shuffling. With such a procedure, one or more different IPT coding sequences can
be manipulated to create a new IPT polypeptide possessing the desired
properties. In this manner, libraries of recombinant polynucleotides are generated
from a population of related sequence polynucleotides comprising sequence
regions that have substantial sequence identity and can be homologously
recombined in vitro or in vivo. For example, using this approach, sequence motifs
encoding a domain of interest may be shuffled between the IPT gene of the
invention and other known IPT genes to obtain a new gene coding for a protein
with an improved property of interest, such as an Increased Km in the case of an
enzyme. Strategies for such DNA shuffling are known in the art. See, for
example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer
(1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438;
Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) Proc. Natl.
Acad. Sci. USA 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and
U.S. Patent Nos. 5,605,793 and 5,837,458.
The compositions of the invention also include isolated polynucleotides
comprising an IPT promoter nucleotide sequence as set forth in SEQ ID NO: 25 or
75, and promoter sequences as further isolated and characterized from the
regions 5' to the coding sequence provided as a part of SEQ ID NO: 5 (ZmlPT4),
SEQ ID NO: 8 (ZmiPTS), SEQ ID NO: 11 (ZmlPT6), SEQ ID NO: 14 (ZmlPTT),
SEQ ID NO: 17 (ZmiPTS), SEQ ID NO: 20 (ZmlPTS), SEQ ID NO: 47 (OslPTI),
SEQ ID NO: 44 (OslPT2), SEQ ID NO: 62 (OslPTS), SEQ ID NO: 64 (OslPT4),
SEQ ID NO: 50 (OslPTS), SEQ ID NO: 55 (OslPT6), SEQ ID NO: 53 (OslPT7),
SEQ ID NO: 40 (OslPTS), SEQ ID NO: 60 (OslPTS), SEQ ID NO: 58 (OslPTIO),
and SEQ ID NO: 42 (OslPT11).
By "promoter" is intended a regulatory region of DNA usually comprising a
TATA box capable of directing RNA polymerase II to initiate RNA synthesis at the
appropriate transcription initiation site for a particular polynucleotide sequence. A
promoter may additionally comprise other recognition sequences generally
positioned upstream or 5' to the TATA box, referred to as upstream promoter
elements, which influence the transcription initiation rate. The promoter
sequences of the present invention regulate (i.e., repress or activate) transcription.
It is recognized that additional domains can be added to the promoter
sequences of the invention and thereby modulate the level of expression, the
developmental timing of expression, or tissue type that expression occurs in. See
particularly, Australian Patent No. AU-A-77751/94 and U.S. Patent Nos. 5,466,785
and 5,635,618.
Fragments and variants of the disclosed IPT promoter polynucleotides are
also encompassed by the present invention. Fragments of a promoter
polynucieotide may retain biological activity and hence retain transcriptional
regulatory activity. Alternatively, fragments of a polynucleotide that are useful as
hybridization probes generally do not retain biological activity. Thus, fragments of
a promoter nucleotide sequence may range from at least about 20 nucleotides,
about 50 nucleotides, about 100 nucleotides, and up to the full-length
polynucleotide of the invention.
Thus, a fragment of an IPT promoter polynucleotide may encode a
biologically active portion of an IPT promoter, or it may be a fragment that can be
used as a hybridization probe or PCR primer using methods disclosed below. A
biologically active portion of the IPT promoter polynucleotides can be prepared by
isolating a portion of one of the IPT promoter polynucleotide of the invention, and
assessing the activity of the portion of the IPT promoter. Polynucleotides that are
fragments of an IPT promoter comprise at least 16,20, 50, 75, 100,150, 200, 250,
300, 350, 400, 450, 500, 550, 600, 650, 700, 800, 900, 1,000, 1,050, or 1,080
contiguous nucleotides, or up to the number of nucleotides present in a full-length
IPT promoter polynucleotide disclosed herein (for example, 1082 and 1920
nucleotides for SEQ ID NOS: 25 and 75, respectfully).
For a promoter polynucleotide, a variant comprises a deletion and/or
addition of one or more nucleotides at one or more internal sites within the native
polynucleotide and/or a substitution of one or more nucleotides at one or more
sites in the native polynucleotide. Generally, variants of a particular promoter
polynucleotide of the invention will have at least about 40%, 45%, 50%, 55%,
60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,
98%, 99% or more sequence identity to that particular polynucleotide as
determined by sequence alignment programs and parameters described
elsewhere herein.
Variant polynucleotides also encompass sequences derived from a
mutagenic and recombinogenic procedure such as DNA shuffling. With such a
procedure, one or more different promoter sequences can be manipulated to
create a new IPT promoter possessing the desired properties. Strategies for such
DNA shuffling are described elsewhere herein.
Methods are available in the art for determining if a promoter sequence
retains the ability to regulate transcription. Such activity can be measured by
Northern blot analysis. See, for example, Sambrook et a/. (1989) Molecular
Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press,
Plainview, New York), herein incorporated by reference. Alternatively, biological
activity of the promoter can be measured using assays specifically designed for
measuring the activity and/or level of the polypeptide being expressed from the
promoter. Such assays are known in the art. Also, known promoter elements can
be identified within a putative promoter sequence. For example, the IPT1
promoter (SEQ ID NO: 25) of the invention has a TATA-box at bp 688. A TATAbox
like sequence can be found 48 bp upstream of the transcription start site
(between bp 1035 and 1042). A potential CAAT box can be found between bp
929 and 932.
The polynucleotides of the invention (i.e., the IPT sequences and the IPT
promoter sequences) can be used to isolate corresponding sequences from other
organisms, particularly other plants, more particularly other monocots. In this
manner, methods such as PCR, hybridization, and the like can be used to identify
such sequences based on their sequence homology to the sequences set forth
herein; Sequen"ces'"'isolaled"1l5ased on their sequence identity to the entire IPT
sequences or the IPT promoter sequences set forth herein or to variants and
fragments thereof are encompassed by the present invention. Such sequences
include sequences that are orthologs of the disclosed sequences. "Orthologs" is
intended to mean genes derived from a common ancestral gene and which are
found in different species as a result of speciation. Genes found in different
species are considered orthologs when their nucleotide sequences and/or their
encoded protein sequences share at least 60%, 70%, 75%, 80%, 85%, 90%, 91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater sequence identity.
Functions of orthologs are often highly conserved among species. Thus, isolated
polynucleotides that encode for an IPT protein or comprise an IPT promoter
sequence and which hybridize under stringent conditions to the IPT sequences or
the IPT promoter sequences disclosed herein, or to variants or fragments or
complements thereof, are encompassed by the present invention.
In a PCR approach, oligonucleotide primers can be designed for use in
PCR reactions to amplify corresponding DNA sequences from cDNA or genomic
DNA extracted from any plant of interest. Methods for designing PCR primers and
PCR cloning are generally known in the art and are disclosed in Sambrook et a/.
(1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor
Laboratory Press, Plainview, New York). See also Innis et a/., eds. (1990) PCR
Protocols: A Guide to Methods and Applications (Academic Press, New York);
Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and
Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New
York). Known methods of PCR include, but are not limited to, methods using
paired primers, nested primers, single specific primers, degenerate primers, genespecific
primers, vector-specific primers, partially-mismatched primers, and the
like.
In hybridization techniques, all or part of a known polynucleotide is used as
a probe that selectively hybridizes to other corresponding polynucleotides present
in a population of cloned genomic DNA fragments or cDNA fragments (i.e.,
genomic or cDNA libraries) from a chosen organism. The hybridization probes
may be genomic DNA fragments, cDNA fragments, RNA fragments, or other
oligonucleotides, and may be labeled with a detectable group such as 32P, or any
other detectable marker. Thus, for example, probes for hybridization can be made
by labeling synthetic oligonucleotides based on the IPT polynucleotides or the IPT
sequences or me invention. Methods for preparation of probes for
hybridization and for construction of cDNA and genomic libraries are generally
known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A
Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, New
York).
For example, the entire IPT polynucleotide or the IPT promoter sequence
disclosed herein, or one or more portions thereof, may be used as a probe
capable of specifically hybridizing to corresponding IPT polynucleotides,
messenger RNAs, or promoter sequences. To achieve specific hybridization
under a variety of conditions, such probes include sequences that are unique
among IPT polynucleotide sequences or IPT promoter sequences and are
optimally at least about 10 nucleotides in length, and most optimally at least about
20 nucleotides in length. Such probes may be used to amplify corresponding IPT
polynucleotides or IPT promoters from a chosen plant by PCR. This technique
may be used to isolate additional coding sequences from a desired plant or as a
diagnostic assay to determine the presence of coding sequences in a plant.
Hybridization techniques include hybridization screening of plated DNA libraries
(either plaques or colonies; see, for example, Sambrook et al. (1989) Molecular
Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press,
Plainview, New York).
Hybridization of such sequences may be carried out under stringent
conditions. By "stringent conditions" or "stringent hybridization conditions" is
intended conditions under which a probe will hybridize to its target sequence to a
detectably greater degree than to other sequences (e.g., at least 2-fold over
background). Stringent conditions are sequence-dependent and will be different in
different circumstances. By controlling the stringency of the hybridization and/or
washing conditions, target sequences that are 100% complementary to the probe
can be identified (homologous probing). Alternatively, stringency conditions can
be adjusted to allow some mismatching in sequences so that lower degrees of
similarity are detected (heterologous probing). Generally, a probe is less than
about 1000 nucleotides in length, optimally less than 500 nucleotides in length.
Typically, stringent conditions will be those in which the salt concentration is
less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration
(or other salts) at pH 7.0 to 8.3 -and the temperature is at least about 30°C for
short probes (e.g., 10 to 50 nucleotides) and at least about 60°C for long probes
(e.g., greater man 5U nucieotides). Stringent conditions may also be achieved
with the addition of destabilizing agents such as formamide. Exemplary low
stringency conditions include hybridization with a buffer solution of 30 to 35%
formamide, 1 M NaCI, 1% SDS (sodium dodecyl sulphate) at 37°C, and a wash in
1X to 2X SSC (20X SSC * 3.0 M NaCI/0.3 M trisodium citrate) at 50 to 55°C.
Exemplary moderate stringency conditions include hybridization in 40 to 45%
formamide, 1.0 M NaCI, 1% SDS at 37°C, and a wash in 0.5X to 1X SSC at 55 to
60°C. Exemplary high stringency conditions include hybridization in 50%
formamide, 1 M NaCI, 1% SDS at 37°C, and a wash in 0.1X SSC at 60 to 65°C.
Optionally, wash buffers may comprise about 0.1% to about 1% SDS. Duration of
hybridization is generally less than about 24 hours, usually about 4 to about 12
hours. The duration of the wash time will be at least a length of time sufficient, to
reach equilibrium.
Specificity is typically the function of post-hybridization washes, the critical
factors being the ionic strength and temperature of the final wash solution. For
DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and
Wahl (1984) Anal, Biochem. 138:267-284: Tm = 81.5°C + 16.6 (log M) + 0.41
(%GC) - 0.61 (% form) - 500/L; where M is the molarity of monovalent cations,
%GC is the percentage of guanosine and cytosine nucieotides in the DNA, % form
is the percentage of formamide in the hybridization solution, and L is the length of
the hybrid in base pairs. The Tm is the temperature (under defined ionic strength
and pH) at which 50% of a complementary target sequence hybridizes to a
perfectly matched probe. Tm is reduced by about 1°C for each 1% of
mismatching; thus, Tm, hybridization, and/or wash conditions can be adjusted to
hybridize to sequences of the desired identity. For example, if sequences with
>90% identity are sought, the Tm can be decreased 10°C. Generally, stringent
conditions are selected to be about 5°C lower than the thermal melting point (Tm)
for the specific sequence and its complement at a defined ionic strength and pH.
However, severely stringent conditions can utilize a hybridization and/or wash at 1,
2, 3, or 4°C lower than the thermal melting point (Tm); moderately stringent
conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10°C lower than
the thermal melting point (Tm); low stringency conditions can utilize a hybridization
and/or wash at 11, 12, 13, 14, 15, or 20°C lower than the thermal melting point
(Tm). Using the equation, hybridization and wash compositions, and desired Tm,
those of ordinary skill will understand that variations in the stringency of
hybridization and/or wash solutions are inherently described. If the desired degree
of mismatching results in a Tm of less than 45°C (aqueous solution) or 32°C
(formarnide solution), it is optimal to increase the SSC concentration so that a
higher temperature can be used. An extensive guide to the hybridization of
nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry
and Molecular Biology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2
(Elsevier, New York); and Ausubel et al., eds. (1995) Current Protocols in
Molecular Biology, Chapter 2 (Greene Publishing and Wiley-lnterscience, New
York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d
ed., Cold Spring Harbor Laboratory Press, Plainview, New York).
The following terms are used to describe the sequence relationships
between two or more polynucleotides or polypeptides: (a) "reference sequence",
(b) "comparison window", (c) "sequence identity", and, (d) "percentage of
sequence identity."
(a) As used herein, "reference sequence" is a defined sequence used
as a basis for sequence comparison. A reference sequence may be a subset or
the entirety of a specified sequence; for example, as a segment of a full-length
cDNA or gene sequence, or the complete cDNA or gene sequence.
(b) As used herein, "comparison window" makes reference to a
contiguous and specified segment of a polynucleotide sequence, wherein the
polynucleotide sequence in the comparison window may comprise additions or
deletions (i.e., gaps) compared to the reference sequence (which does not
comprise additions or deletions) for optimal alignment of the two polynucleotides.
Generally, the comparison window is at least 20 contiguous nucleotides in length,
and optionally can be 30, 40, 50, 100, or longer. Those of skill in the art
understand that to avoid a high similarity to a reference sequence due to inclusion
of gaps in the polynucleotide sequence a gap penalty is typically introduced and is
subtracted from the number of matches.
Methods of alignment of sequences for comparison are well known in the
art. Thus, the determination of percent sequence identity between any two
sequences can be accomplished using a mathematical algorithm. Non-limiting
examples of such mathematical algorithms are the algorithm of Myers and Miller
(1988) CABIOS 4:11-17; the local alignment algorithm of Smith et al. (1981) Adv.
Appl. Math. 2:482; the global alignment algorithm of Needleman and Wunsch
(1970) J. Mo/. B/o/. 48:443-453; the search-for-local alignment method of Pearson
and Lipman (1988) Proc. Natl. Acad. Sci. 85:2444-2448; the algorithm of Karlin
and Altschul (1990) Proc. Natl. Acad. Scl. USA 872264, modified as in Karlin and
Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877.
Computer implementations of these mathematical algorithms can be
utilized for comparison of sequences to determine sequence identity. Such
implementations include, but are not limited to: CLUSTAL in the PC/Gene
program (available from Intelligenetics, Mountain View, California); the ALIGN
program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the
GCG Wisconsin Genetics Software Package, Version 10 (available from Accelrys
Inc., 9685 Scranton Road, San Diego, California, USA). Alignments using these
programs can be performed using the default parameters. The CLUSTAL
program is well described by Higgins et al. (1988) Gene 73:237-244 (1988);
Higgins et al. (1989) CABIOS 5:151-153; Corpet era/. (1988) Nucleic Acids Res.
16:10881-90; Huang et al. (1992) CABIOS 8:155-65; and Pearson et al. (1994)
Meth. Mol. Biol. 24:307-331. The ALIGN program is based on the algorithm of
Myers and Miller (1988) supra. A PAM120 weight residue table, a gap length
penalty of 12, and a gap penalty of 4 can be used with the ALIGN program when
comparing amino acid sequences. The BLAST programs of Altschul et al (1990)
J. Mol. Biol. 215:403 are based on the algorithm of Karlin and Altschul (1990)
supra. BLAST nucleotide searches can be performed with the BLASTN program,
score = 100, wordlength = 12, to obtain nucleotide sequences homologous to a
nucleotide sequence encoding a protein of the invention. BLAST protein searches
can be performed with the BLASTX program, score = 50, wordlength = 3, to obtain
amino acid sequences homologous to a protein or polypeptide of the invention.
To obtain gapped alignments for comparison purposes, Gapped BLAST (in
BLAST 2.0) can be utilized as described in Altschul et al. (1997) Nucleic Acids
Res. 25:3389. Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform
an iterated search that detects distant relationships between molecules. See
Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST,
the default parameters of the respective programs (e.g., BLASTN for nucleotide
sequences, BLASTX for proteins) can be used. See www.ncbi.nlm.nih.gov.
Alignment may also be performed manually by inspection. ,
Unless otherwise stated, sequence identity/similarity values provided herein
refer to the value obtained using GAP Version 10 using the following parameters:
% identity and % similarity for a nucleotide sequence using GAP Weight of 50 and
Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and %
similarity for an amino acid sequence using GAP Weight of 8 and Length Weight
of 2, and the BLOSUM62 scoring matrix; or any equivalent program thereof. By
"equivalent program" is intended any sequence comparison program that, for any
two sequences in question, generates an alignment having identical nucleotide or
amino acid residue matches and an identical percent sequence identity when
compared to the corresponding alignment generated by GAP Version 10.
GAP uses the algorithm of Needleman and Wunsch (1970) J. Mol. Bid.
48:443-453, to find the alignment of two complete sequences that maximizes the
number of matches and minimizes the number of gaps. GAP considers all
possible alignments and gap positions and creates the alignment with the largest
number of matched bases and the fewest gaps. It allows for the provision of a gap
creation penalty and a gap extension penalty in units of matched bases. GAP
must make a profit of gap creation penalty number of matches for each gap it
inserts. If a gap extension penalty greater than zero is chosen, GAP must, in
addition, make a profit for each gap inserted of the length of the gap times the gap
extension penalty. Default gap creation penalty values and gap extension penalty
values in Version 10 of the GCG Wisconsin Genetics Software Package for
protein sequences are 8 and 2, respectively. For nucleotide sequences the
default gap creation penalty is 50 while the default gap extension penalty is 3.
The gap creation and gap extension penalties can be expressed as an integer
selected from the group of integers consisting of from 0 to 200. Thus, for
example, the gap creation and gap extension penalties can be 0,1, 2, 3,4, 5, 6, 7,
8, 9,10, 15, 20, 25, 30, 35,40, 45, 50, 55, 60, 65 or greater.
GAP presents one member of the family of best alignments. There may be
many members of this family, but no other member has a better quality. GAP
displays four figures of merit for alignments: Quality, Ratio, Identity, and Similarity.
The Quality is the metric maximized in order to align the sequences. Ratio is the
quality divided by the number of bases in the shorter segment. Percent Identity is
the percent of the symbols that actually match. Percent Similarity is the percent of
the symbols that are similar. Symbols that are across from gaps are ignored. A
similarity is scored when the scoring matrix value for a pair of symbols is greater
than or equal to 0.50, the similarity threshold. The scoring matrix used in Version
10 of the GCG Wisconsin Genetics Software Package is BLOSUM62 (see
Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915).
(c) As used Herein,sequence identity" or "identity" in the context of two
polynucleotides or polypeptide sequences makes reference to the residues in the
two sequences that are the same when aligned for maximum correspondence
over a specified comparison window. When percentage of sequence identity is
used in reference to proteins it is recognized that residue positions which are not
identical often differ by conservative amino acid substitutions, where amino acid
residues are substituted for other amino acid residues with similar chemical
properties (e.g., charge or hydrophobicity) and therefore do not change the
functional properties of the molecule. When sequences differ in conservative
substitutions, the percent sequence identity may be adjusted upwards to correct
for the conservative nature of the substitution. Sequences that differ by such
conservative substitutions are said to have "sequence similarity" or "similarity".
Means for making this adjustment are well known to those of skill in the art.
Typically this involves scoring a conservative substitution as a partial rather than a
full mismatch, thereby increasing the percentage sequence identity. Thus, for
example, where an identical amino acid is given a score of 1 and a nonconservative
substitution is given a score of zero, a conservative substitution is
given a score between zero and 1. The scoring of conservative substitutions is
calculated, e.g., as implemented in the program PC/GENE (Intelligenetics,
Mountain View, California).
(d) As used herein, "percentage of sequence identity" means the value
determined by comparing two optimally aligned sequences over a comparison
window, wherein the portion of the polynucleotide sequence in the comparison
window may comprise additions or deletions (i.e., gaps) as compared to the
reference sequence (which does not comprise additions or deletions) for optimal
alignment of the two sequences. The percentage is calculated by determining the
number of positions at which the identical nucleic acid base or amino acid residue
occurs in both sequences to yield the number of matched positions, dividing the
number of matched positions by the total number of positions in the window of
comparison, and multiplying the result by 100 to yield the percentage of sequence
identity.
The invention further provides plants having altered levels and/or activities
of the IPT polypeptides of the invention. In some embodiments, the plants of the
invention have stably incorporated into their genome the IPT sequences of the
invention. In other embodiments, plants that are genetically modified at a genomic
locus encoding an IPT polypeptide of the invention are provided. By "native
genomic locus" is intended a naturally occurring genomic sequence. For some
embodiments, the genomic locus is set forth in SEQ ID NO: 21, 40, 42, 44, 47, 50,
53, 55, 58, 60, 62, or 64. The genomic locus may be modified to reduce or
eliminate the activity of the IPT polypeptide. The term "genetically modified" as
used herein refers to a plant or plant part that is modified in its genetic information
by the introduction of one or more foreign polynucleotides, and the insertion of the
foreign polynucleotide leads to a phenotypic change in the plant. By "phenotypic
change" is intended a measurable change in one or more cell functions. For
example, plants having a genetic modification at the genomic locus encoding the
IPT polypeptide can show reduced or eliminated expression or activity of the IPT
polypeptide. Various methods to generate such a genetically modified genomic
locus are described elsewhere herein, as are the variety of phenotypes that can
result from the modulation of the level/activity of the IPT sequences of the
invention.
The invention further provides plants having at least one DNA construct
comprising a heterologous nucleotide sequence of interest operably linked to the
IPT promoter of the invention. In further embodiments, the DNA construct is
stably integrated into the genome of the plant.
As used herein, the term plant includes reference to whole plants, plant
parts or organs (e.g. leaves, stems, roots), plant cells, and seeds and progeny of
same. Plant cell, as used herein, includes, without limitation, cells obtained from
or found in seeds, suspension cultures, embryos, meristematic regions, callus
tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen and mlcrospores,
as well as plant protoplasts and plant cell tissue cultures, plant calli, plant clumps,
and plant cells that are intact in plants or parts of plants such as embryos, pollen,
ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks,
roots, root tips, anthers, grain and the like. As used herein, "grain" refers to the
mature seed produced by commercial growers for purposes other than growing or
reproducing the species. Progeny, variants, and mutants of the regenerated
plants are also included within the scope of the invention, provided that these
parts comprise the introduced nucleic acid sequences.
METHODS
/. Providing Sequences
The sequences of the present invention can be introduced/expressed in a
host cell such as bacteria, yeast, insect, mammalian, or optimally plant cells. It is
expected that those of skill in the art are knowledgeable in the numerous systems
available for the introduction of a polypeptide or a nucleotide sequence of the
present invention into a host cell. No attempt to describe in detail the various
methods known for providing proteins in prokaryotes or eukaryotes will be made.
By "host cell" is meant a cell which comprises a heterologous nucleic acid
sequence of the invention. Host cells may be prokaryotic cells such as £ coli, or
eukaryotic cells such as yeast, insect, amphibian, or mammalian cells. Host cells
can also be monocotyledonous or dicotyledonous plant cells. In certain
embodiments, the monocotyledonous host cell is a maize host cell.
The use of the term "polynucleotide" is not intended to limit the present
invention to polynucleotides comprising DNA. Those of ordinary skill in the art will
recognize that polynucleotides can comprise ribonucleotides and combinations of
ribonucleotides and deoxyribonucleotides. Such deoxyribonucieotides and
ribonucleotides include both naturally occurring molecules and synthetic
analogues. The polynucleotides of the invention also encompass all forms of
sequences including, but not limited to, single-stranded forms, double-stranded
forms, hairpins, stem-and-loop structures, and the like.
The IPT polynucleotides or the IPT promoters of the invention can be
provided in expression cassettes for expression in the plant of interest. The
cassette will include 5' and 3' regulatory sequences operably linked to an IPT
polynucleotide of the invention. "Operably linked" is intended to mean a functional
linkage between two or more elements. For example, an operable linkage
between a polynucleotide of interest and a regulatory sequence (i.e., a promoter)
is a functional link that allows for expression of the polynucleotide of interest.
Operably linked elements may be contiguous or non-contiguous. When used to
refer to the joining of two protein coding regions, by operably linked is intended
that the coding regions are in the same reading frame. The cassette may
additionally contain at least one additional gene to be cotransformed into the
organism. Alternatively, the additional gene(s) can be provided on multiple
expression cassettes. An expression cassette may be provided with a plurality of
restriction sites and/or recombination sites for insertion of the IPT polynucleotide
"to be under the transcriptional regulation of the regulatory regions. The
expression cassette may additionally contain selectable marker genes.
In certain embodiments, the expression cassette will include in the 5'-3'
direction of transcription, a transcriptional and translational initiation region (i.e., a
promoter), an IPT polynucleotide of the invention, and a transcriptional and
translational termination region (i.e., termination region) functional in plants. The
regulatory regions (i.e., promoters, transcriptional regulatory regions, and
translational termination regions) and/or the IPT polynucleotide of the invention
may be native/analogous to the host cell or to each other. Alternatively, the
regulatory regions and/or the IPT polynucleotide of the invention may be
heterologous to the host cell or to each other. As used herein, "heterologous" in
reference to a sequence is a sequence that originates from a foreign species, or, if
from the same species, is substantially modified from its native form in
composition and/or genomic locus by deliberate human intervention. For
example, a promoter operably linked to a heterologous polynucleotide is from a
species different from the species from which the polynucleotide was derived, or, if
from the same/analogous species, one or both are substantially modified from
their original form and/or genomic locus, or the promoter is not the native promoter
for the operably-linked polynucleotide. As used herein, a chimeric gene comprises
a coding sequence operably linked to a transcription initiation region that is
heterologous to the coding sequence.
While heterologous promoters can be used to express the IPT sequences,
the native promoter sequences or other IPT promoters (e.g., SEQ ID NO: 25 or
75) may also be used. Such constructs can change expression levels of IPT
sequences in the plant or plant cell. Thus, the phenotype of the plant or plant cell
can be altered.
The termination region may be native with the transcriptional initiation
region, may be native with the operably-linked IPT polynucleotide of interest, may
be native with the plant host, or may be derived from another source (i.e., foreign
or heterologous with reference to the promoter), the IPT polynucleotide of interest,
the plant host, or any combination thereof. Convenient termination regions are
available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase
and nopaline synthase termination regions. See also Guerineau etal. (1991) Mol.
Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al.
(1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272;
"Muhroe et al. (1990) Gene 91:151-158; Ballas et al. (1989) Nucleic Acids Res.
17:7891-7903; and Joshi et al. (1987) Nucleic Acids Res. 15:9627-9639.
Where appropriate, the polynucleotides may be optimized for increased
expression in the transformed plant. That is, the polynucleotides can be
synthesized using plant-preferred codons for improved expression. See, for
example, Campbell and Gowri (1990) Plant Physiol. 92:1-11 for a discussion of
host-preferred codon usage. Methods are available in the art for synthesizing
plant-preferred genes. See, for example, U.S. Patent Nos. 5,380,831, and
5,436,391, and Murray et al. (1989) Nucleic Acids Res. 17:477-498, herein
incorporated by reference.
Additional sequence modifications are known to enhance gene expression
in a cellular host. These include elimination of sequences encoding spurious
polyadenylation signals, exon-intron splice site signals, transposon-like repeats,
and other such well-characterized sequences that may be deleterious to gene
expression. The G-C content of the sequence may be adjusted to levels average
for a given cellular host, as calculated by reference to known genes expressed in
the host cell. When possible, the sequence is modified to avoid predicted hairpin
secondary mRNA structures.
The expression cassettes may additionally contain 5' leader sequences.
Such leader sequences can act to enhance translation. Translation leaders are
known in the art and include: picornavirus leaders, for example, EMCV leader
(Encephalomyocarditis 5' noncoding region) (Elroy-Stein et al. (1989) Proc. Natl.
Acad. Sci. USA 86:6126-6130); potyvirus leaders, for example, TEV leader
(Tobacco Etch Virus) (Gallie et al. (1995) Gene 165(2):233-238), MDMV leader
(Maize Dwarf Mosaic Virus) (Virology 154:9-20), and human immunoglobulin
heavy-chain binding protein (BiP) (Macejak et al. (1991) Nature 353:90-94);
untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA
4) (Jobling et al. (1987) Nature 325:622-625); tobacco mosaic virus leader (TMV)
(Gallie et al. (1989) in Molecular Biology of RNA, ed. Cech (Liss, New Yprk), pp.
237-256); and maize chlorotic mottle virus leader (MCMV) (Lommel et al. (1991)
Virology 81:382-385). See also, Della-Cioppa ef a/. (1987) Plant Physiol.
84:965-968. Other methods known to enhance translation can also be utilized.
In preparing the expression cassette, the various DNA fragments may be
manipulated, so as to provide for the DNA sequences in the proper orientation
and, as appropriate, in the proper reading frame. Toward this end, adapters or
linkers" may "be" e'rn'plbye'd'Tololh the DNA fragments or other manipulations may be
involved to provide for convenient restriction sites, removal of superfluous DNA,
removal of restriction sites, or the like. For this purpose, in vitro mutagenesis,
primer repair, restriction, annealing, resubstitutions, e.g., transitions and
transversions, may be involved.
The expression cassette can also comprise a selectable marker gene for the
selection of transformed cells. Selectable marker genes are utilized for the selection
of transformed cells or tissues. Marker genes include genes encoding antibiotic
resistance, such as those encoding neomycin phosphotransferase II (NEO) and
hygromycin phosphotransferase (HPT), as well as genes conferring resistance to
herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones,
and 2,4-dichlorophenoxyacetate (2,4-D). Additional selectable markers include
phenotypic markers such as B-galactosidase and fluorescent proteins such as
green fluorescent protein (GFP) (Su et a/. (2004) Biotechnol Bioeng 85:610-9-and
Fetter ef al. (2004) Plant Cell 76:215-28), cyan fluorescent protein (CYP) (Bolte et
a/. (2004) J. Cell Science 117:943-54 and Kato ef al. (2002) Plant Physiol
729:913-42), and yellow fluorescent protein (PhiYFP™ from Evrogen, see, Bolte et
al. (2004) J, Cell Science 777:943-54). For additional selectable markers, see
generally, Yarranton (1992) Curr. Opin. Biotech. 3:506-511; Christopherson.ef al.
(1992) Proc. Natl. Acad. Sci. USA 89:6314-6318; Yao et al. (1992) Cell 71:63-72;
Reznikoff (1992) Mot. Micrvbiol. 6:2419-2422; Barkley et al. (1980) in The Operon,
pp. 177-220; Hu et al. (1987) Cell 48:555-566; Brown era/. (1987) Cell 49:603-612;
Figge et al. (1988) Cell 52:713-722; Deuschle et al. (1989) Proc. Natl. Acad. Act.
USA 86:5400-5404; Fuerst ef al. (1989) Proc. Natl. Acad. Sci. USA 86:2549-2553;
Deuschle ef al. (1990) Science 248:480-483; Gossen (1993) Ph.D. Thesis,
University of Heidelberg; Reines ef al. (1993) Proc. Natl. Acad. Sci. USA 90:1917-
1921; Labow ef al. (1990) Mol. Cell. Biol. 10:3343-3356; Zambretti ef al. (1992) Proc.
Natl. Acad. Sci. USA 89:3952-3956; Bairn ef al. (1991) Proc. Natl. Acad. Sci. USA
88:5072-5076; Wyborski ef al. (1991) Nucleic Adds Res. 19:4647-4653; Hillenand-
Wissrnan (1989) Topics Mol. Struc. Biol. 10:143-162; Degenkolb ef al. (1991)
Antimicrob. Agents Chemother. 35:1591-1595; Kleinschnidt ef al. (1988)
Biochemistry 27:1094-1104; Bonin (1993) Ph.D. Thesis, University of Heidelberg;
Gossen ef al. (1992) Proc. Natl. Acad. Sci. USA 89:5547-5551; Oliva ef al. (1992)
Antimicrob. Agents Chemother. 36:913-919; Hlavka et al. (1985) Handbook of
Experimental Pharmacology, Vol. 78 (Springer-Verlag, Berlin); Gill ef al. (1988)
"Nature 334:721-724! Such disclosures are herein incorporated by reference. The
above list of selectable marker genes is not meant to be limiting. Any selectable
marker gene can be used in the present invention.
A number of promoters can be used in the practice of the invention,
including the native promoter of the polynucleotide sequence of interest. The
promoters can be selected based on the desired outcome. The nucleic acids can
be combined with constitutive, inducible, tissue-preferred, or other promoters for
expression in plants,
Such constitutive promoters include, for example, the core promoter of the
Rsyn7 promoter and other constitutive promoters disclosed in WO 99/43838 and
U.S. Patent No. 6,072,050; the core CaMV 35S promoter (Odell ef a/. (1985)
Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171);
ubiquitin (Christensen etal. (1989) Plant Mol. Biol. 12:619-632 and Christensen et
al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last ef al. (1991) Theor. Appl.
Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS
promoter (U.S. Patent No. 5,659,026), and the like. Other constitutive promoters
include, for example, U.S. Patent, Nos. 5,608,149; 5,608,144; 5,604,121;
5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and 6,177,611.
Tissue-preferred promoters can be utilized to target enhanced IPT
expression within a particular plant tissue. Tissue-preferred promoters include
Yamamoto etal. (1997) Plant J. 12(2):255-265; Kawamata etal. (1997) Plant Cell
Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen Genet. 254(3):337-343;
Russell et al. (1997) Transgenic Res. 6(2): 157-168; Rinehart ef al. (1996) Plant
Physiol. 112(3): 1331-1341; Van Camp ef al. (1996) Plant Physiol. 112(2):525-535;
Canevascini et al. (1996) Plant Physiol. 112(2):513-524; Yamamoto ef al. (1994)
Plant Cell Physiol. 35(5):773-778; Lam (1994) Results Probl. Cell Differ. 20:181-
196; Orozco ef al. (1993) Plant Mol Biol. 23(6): 1129-1138; Matsuoka ef al. (1993)
Proc Natl. Acad. Sci. USA 90(20):9586-9590; and Guevara-Garcia ef al. (1993)
Plant J. 4(3):495-505. Such promoters can be modified, if necessary, for weak
expression. See, also, U.S. Patent Application No. 2003/0074698, herein
incorporated by reference.
Leaf-preferred promoters are known in the art. See, for example,
Yamamoto ef al. (1997) Plant J. 12(2):255-265; Kwon ef al. (1994) Plant Physiol.
105:357-67; Yamamoto ef al. (1994) Plant Cell Physiol-. 35(5):773-778; Gotor ef al.
(1993) Plant J. 3:509-18; Orozco ef al. (1993) Plant Mol. Biol. 23(6): 1129-1138;
Ba'szczynskl'lira/. "Cl"988)*W&c/. Acid Res. 16:4732; Mitra Qt al. (1994) P/anf
Molecular Biology 26:35-93; Kayaya et al. (1995) Molecular and General Genetics
248:668-674; and Matsuoka et al. (1993) Proc. Natl. Acad. Sci. USA 90(20):9586-
9590. Senecence regulated promoters are also of use, such as, SAM22 (Crowell
et al. (1992) Plant Mol. Biol. 78:459-466). See, also, U.S. Patent No. 5,589,052
herein incorporated by reference.
Root-preferred promoters are known and can be selected from the many
available from the literature or isolated de novo from various compatible species.
See, for example, Hire et al. (1992) Plant Mol. Biol. 20(2):207-218 (soybean rootspecific
glutamine synthetase gene); Keller and Baumgartner (1991) Plant Cell
3(10):1051-1061 (root-specific control element in the GRP 1.8 gene of French
bean); Sanger et al. (1990) Plant Mol. Biol. 14(3):433-443 (root-specific promoter
of the mannopine synthase (MAS) gene of Agrobacterium tumefaciens); and Miao
et al. (1991) Plant Cell 3(1):11-22 (full-length cDNA clone encoding cytosolic
glutamine synthetase (GS), which is expressed in roots and root nodules of
soybean). See also Bogusz et al. (1990) Plant Cell 2(7):633-641, where two rootspecific
promoters isolated from hemoglobin genes from the nitrogen-fixing
nonlegume Parasponia andersonii and the related non-nitrogen-fixing nonlegume
Trema tomentosa are described. The promoters of these genes were linked to a
(3-glucuronidase reporter gene and introduced into both the nonlegume Nicotiana
tabacum and the legume Lotus corniculatus, and in both instances root-specific
promoter activity was preserved. Leach and Aoyagi (1991) describe their analysis
of the promoters of the highly expressed rolC and rolD root-inducing genes of
Agrobacterium rhizogenes (see Plant Science (Limerick) 79(1):69-76). They
concluded that enhancer and tissue-preferred DNA determinants are dissociated
in those promoters. Teeri et al. (1989) used gene fusion to lacZ to show that the
Agrobacterium T-DNA gene encoding octopine synthase is especially active in the
epidermis of the root tip and that the TR21 gene is root specific in the intact plant
and stimulated by wounding in leaf tissue, an especially desirable combination of
characteristics for use with an insecticidal or larvicidal gene (see EMBO J.
8(2):343-350). The TR11 gene, fused to nptll (neomycin phosphotransferase II)
showed similar characteristics. Additional root-preferred promoters include the
VfENOD-GRP3 gene promoter (Kuster et al. (1995) Plant Mol. Biol. 29(4):759-
772); rolB promoter (Gapana et al. (1994) Plant Mol. Biol. 25(4):681-691; and the
CRWAQ81 root-preferred promoter with the ADH first intron (U.S. Patent
PMllcalion lu"05/d'097633):' See also U.S. Patent Nos. 5,837,876; 5,750,386;
5,633,363; 5,459,252; 5,401,836; 5,110,732; and 5,023,179.
"Seed-preferred" promoters refers to those promoters active during seed
development and may include expression in seed initials or related maternal
tissue. Such seed-preferred promoters include, but are not limited to, Cim1
(cytokinin-induced message); cZ19B1 (maize 19 kDa zein); milps (myo-inositol-1-
phosphate synthase) (see WO 00/11177 and U.S. Patent No. 6,225,529; herein
incorporated by reference). Gamma-zein is an endosperm-specific promoter.
Globulin-1 (Glob-1) is a representative embryo-specific promoter. For dicots,
seed-specific promoters include, but are not limited to, bean B-phaseolin, napin, (3-
conglycinin, soybean lectin, cruciferin, and the like. For monocots, seed-specific
promoters include, but are not limited to, maize 15 kDa zein, 22 kDa zein, 27 kDa
zein, gamma-zein, waxy, shrunken 1, shrunken 2, globulin 1, etc. See also WO
00/12733, where seed-preferred promoters from endl and end2 genes are
disclosed; herein incorporated by reference. Additional embryo specific promoters
are disclosed in Sato etal. (1996) Proc. Natl. Acad. Sci. 93:8117-8122; Nakase et
al. (1997) Plant J 12:235-46; and Postma-Haarsma etal. (1999) Plant Mol. Biol.
39:257-71. Additional endosperm specific promoters are disclosed in Albani et al.
(1984) EMBO 3:1405-15; Albani et al. (1999) Theor. Appl. Gen. 98:1253-62;
Albani et al. (1993) Plant J. 4:343-55; Mena et al. (1998) The Plant Journal
116:53-62, and Wu et al. (1998) Plant Cell Physiology 39:885-889.
Also of interest are promoters active in meristem regions, such as
developing inflorescence tissues, and promoters which drive expression at or
about the time of anthesis or early kernel development. This may include, for
example, the maize Zag promoters, including Zag1 and Zag2 (see Schmidt et al.
(1993) The Plant Cell 5:729-37; GenBank X80206; Theissen et al. (1995) Gene
156:155-166; and U.S. patent application 10/817,483); maize Zap promoter (also
known as ZmMADS; U.S. patent application 10/387,937; WO 03/078590); maize
ckx1-2 promoter (U.S. patent publication 2002-0152500 A1; WO 02/0078438);
maize eepl promoter (U.S. patent application 10/817,483); maize end2 promoter
(U.S. Patent 6,528,704 and U.S. patent application 10/310,191); maize led
promoter (U.S. patent application 09/718,754); maize F3.7 promoter (Baszczynski
et al., Maydica 42:189-201 (1997)); maize tb1 promoter (Hubbarda et al., Genetics
162: 1927-1935 (2002) and Wang et al. (1999) Nature 398:236-239); maize eep2
promoter (U.S. patent application 10/817,483); maize thioredoxinH promoter (U.S.
"provisional patent application 60/514,123); maize Zm40 promoter (U.S. Patent
6,403,862 and WO 01/2178); maize ml_IP15 promoter (U.S. Patent 6,479,734);
maize ESR promoter (U.S. patent application 10/786,679); rnaize PCNA2 promoter
(U.S. patent application 10/388,359); maize cytokinin oxidase promoters (U.S.
patent application 11/094,917); promoters disclosed in Weigal et al. (1992) Cell
69:843-859; Accession No. AJ131822; Accession No. Z71981; Accession No.
AF049870; and shoot-preferred promoters disclosed in McAvoy et al. (2003) Acta
Hort. (ISHS) 625:379-385. Other dividing cell or meristematic tissue-preferred
promoters that may be of interest have been disclosed in Ito et al. (1994) Plant
Mol. Biol. 24:863-878; Regad etal. (1995) Mo. Gen. Genet. 248:703-711; Shaul et
al. (1996) Pmc. Natl. Acad. Sci. 93:4868-4872; Ito et al. (1997) Plant J. 11:983-
992; and Trehin et al. (1997) Plant Mol. Biol. 35:667-672, all of which are hereby
incorporated by reference herein.
Inflorescence-preferred promoters include the promoter of chalcone
synthase (Van der Meer et al. (1990) Plant Mol. Biol. f 5:95-109), LAT52 (Twell et
al. (1989) Mol. Gen. Genet. 217:240-245), pollen specific genes (Albani et al
(1990) Plant Mol Biol. 15:605, Zm13 (Buerrero et al. (1993) Mol. Gen. Genet.
224:161-168), maize pollen-specific gene (Hamilton etal. (1992) Plant Mol. Biol.
18:211-218), sunflower pollen expressed gene (Baltz et al. (1992) The Plant
Journal 2:713-721), and B. napus pollen specific genes (Arnoldo et al. (1992) J.
Cell. Biochem, Abstract No. Y101204).
Stress-inducible promoters include salt/water stress-inducible promoters
such as P5CS (Zang et al. (1997) Plant Sciences 729:81-89); cold-inducible
promoters, such as, cor15a (Haj'ela et al. (1990) Plant Physiol. 93:1246-1252),
cor15b (Wlihelm et al. (1993) Plant Mol Biol 23:1073-1077), wsc120 (Ouellet et al.
(1998) FEBS Lett. 423-324-328), ci7 (Kirch et al. (1997) Plant Mol Biol. 33:897-
909), ci21A (Schneider et al. (1997) Plant Physiol. 773:335-45); drought-inducible
promoters, such as, Trg-31 (Chaudhary et al (1996) Plant Mol. Biol. 30:1247-57);
osmotic inducible promoters, such as, Rab17 (Vilardell et al. (1991) Plant Mol.
Biol. 77:985-93) and osmotin (Raghothama et al. (1993) Plant Mol Biol 23:1117-
28); and, heat inducible promoters, such as, heat shock proteins (Barros et al.
(1992) Plant Mol. 79:665-75; Marrs et al. (1993) Dev. Genet. 74:27-41), and
smHSP (Waters et al. (1996) J. Experimental Botany 47:325-338). Other stressinducible
promoters include rip2 (U.S. Patent No. 5,332,808 and U.S. Publication
Mb."'2003/0217393) "an'a "rd'2'9a (Yamaguchi-Shinozaki et al. (1993) Mol. Gen.
Genetics 236:331-340).
Stress-insensitive promoters can also be used in the methods of the
invention. This class of promoters, as well as representative examples, are fruther
described elsewhere herein.
Nitrogen-responsive promoters can also be used in the methods of the
invention. Such promoters include, but are not limited to, the 22 kDa Zein
promoter (Spena et al. (1982) EMBO J 1: 1589-1594 and Muller et al. (1995) J.
Plant Physiol 745:606-613); the 19 kDa zein promoter (Pedersen et al. (1982) Cell
29:1019-1025); the 14 kDa zeln promoter (Pedersen et al. (1986) J. Biol. Chem.
267:6279-6284), the b-32 promoter (Lohmer et al. (1991) EMBO J 70:617-624);
and the nitrite reductase (NiR) promoter (Rastogi et al. (1997) Plant Mol Biol.
34(3):465-76 and Sander et al. (1995) Plant Mol Biol. 27(1):165-77). For a review
of consensus sequences found in nitrogen-induced promoters, see for example,
Muller et al. (1997) The Plant Journal 72:281-291.
Chemically-regulated promoters can be used to modulate the expression of
a gene in a plant through the application of an exogenous chemical regulator.
Depending upon the objective, the promoter may be a chemically-inducible
promoter, where application of the chemical induces gene expression, or a
chemical-repressible promoter, where application of the chemical represses gene
expression. Chemical-inducible promoters are known in the art and include, but
are not limited to, the maize ln2-2 promoter, which is activated by
benzenesulfonamide herbicide safeners, the maize GST promoter, which is
activated by hydrophobic electrophilic compounds that are used as pre-emergent
herbicides, and the tobacco PR-1a promoter, which is activated by salicylic acid.
Other chemical-regulated promoters of interest include steroid-responsive
promoters (see, for example, the glucocorticoid-inducible promoter in Schena et
al. (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al. (1998)
Plant J. 14(2):247-257) and tetracycline-inducible and tetracycline-repressible
promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237,
and U.S. Patent Nos. 5,814,618 and 5,789,156), herein incorporated by reference.
A promoter induced by cytokinin, such as the ZmCkx1-2 promoter (U.S.
Patent 6,921,815, and pending U.S. patent application 11/074,144), may also be
jsed in the methods and compositions of the invention. Such a construct would
amplify biosynthesis of cytokinin occurring in developmental stages and/or tissues
"oflnterest. Other cytokihin-inducible promoters are described in pending U.S.
patent applications 11/094,917 and 60/627,394, all hereby incorporated by
reference.
Additional inducible promoters include heat shock promoters, such as
Gmhsp17.5-E (soybean) (Czarnecka et at, (1989) Mol Cell Biol. 9(8): 3457-3463);
APX1 gene promoter (Arabidopsis) (Storozhenko et al. (1998) Plant Physiol.
118(3): 1005-1014): Ha hspl7.7 G4 (Helianthus annuus) (Almoguera et al. (2002)
Plant Physiol. 129(1): 333-341; and Maize Hsp70 (Rochester et al. (1986) EMBO
J. 5: 451-8.
The methods of the invention involve introducing a polypeptide or
polynucleotide into a plant. "Introducing" is intended to mean presenting to the
plant the polynucleotide or polypeptide in such a manner that the sequence gains
access to the interior of a cell of the plant. The methods of the invention do not
depend on a particular method for introducing a sequence into a plant, only that
the polynucleotide or polypeptides gains access to the interior of at least one cell
of the plant. Methods for introducing polynucleotides or polypeptides into plants
are known in the art and include, but are not limited to, stable transformation
methods, transient transformation methods, and virus-mediated methods.
"Stable transformation" is intended to mean that the nucieotide construct of
interest introduced into a plant integrates into the genome of the plant and is
capable of being inherited by the progeny thereof. "Transient transformation" is
intended to mean that a sequence is introduced into the plant and is only
temporarily expressed or present in the plant.
Transformation protocols as well as protocols for introducing polypeptides
or polynucleotide sequences into plants may vary depending on the type of plant
or plant cell, i.e., monocot or dicot, targeted for transformation. Suitable methods
of introducing polypeptides and polynucleotides into plant cells include
microinjection (Crossway et al. (1986) Biotechniques 4:320-334), electroporation
(Riggs et al. (1986) Proc. Nail. Acad. Sci. USA 83:5602-5606), Agrobacteriummediated
transformation (U.S. Patent No. 5,563,055 and U.S. Patent No.
5,981,840), direct gene transfer (Paszkowski et al. (1984) EMBO J. 3:2717-2722),
and ballistic particle acceleration (see, for example, U.S. Patent Nos. 4,945,050;
U.S. Patent No. 5,879,918; U.S. Patent No. 5,886,244; and, 5,932,782; Tomes et
al. (1995) in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed.
Gamborg and Phillips (Springer-Verlag, Berlin); McCabe et al. (1988)
Biotechnology 6:923-926); and Led transformation (WO 00/28058). Also see
Weissinger et al. (1988) Ann. Rev. Genet. 22:421-477; Sanford et al. (1987)
Particulate Science and Technology 5:27-37 (onion); Christou et al. (1988) Plant
Physiol. 87:671-674 (soybean); McCabe et al. (1988) Bio/Technology 6:923-926
(soybean); Finer and McMullen (1991) In Vitro Cell Dev. Biol. 27P:175-182
(soybean); Singh etal. (1998) Theor. Appl. Genet. 96:319-324 (soybean); Datta et
al. (1990) Biotechnology 8:736-740 (rice); Hoque et al. (2005) Plant Cell Tissue &
Organ Culture 82(1) :45-55 (rice); Sreekala et al. (2005) Plant Cell Reports
24(2) :86-94 (rice); Klein et al. (1988) Proc. NatI. Acad. Sci. USA 85:4305-4309
(maize); Klein et al, (1988) Biotechnology 6:559-563 (maize); U.S. Patent Nos.
5,240,855; 5,322,783; and, 5,324,646; Klein et al. (1988) Plant Physiol.
91:440-444 (maize); Fromm et al. (1990) Biotechnology 8:833-839 (maize);
Hooykaas-Van Slogteren etal. (1984) Nature (London) 311:763-764; U.S. Patent
No. 5,736,369 (cereals); Bytebier er al. (1987) Proc. NatI. Acad. Sci. USA
84:5345-5349 (Liliaceae); De Wet ef al. (1985) in The Experimental Manipulation
of Ovule Tissues, ed. Chapman etal. (Longman, New York), pp. 197-209 (pollen);
Kaeppler et al. (1990) Plant Cell Reports 9:415-418 and Kaeppler et al. (1992)
Theor. Appl. Genet. 84:560-666 (whisker-mediated transformation); D'Halluin et al.
(1992) Plant Cell 4:1495-1505 (electroporation); Li et al. (1993) Plant Cell Reports
12:250-255 and Christou and Ford (1995) Annals of Botany 75:407-413 (rice);
Osjoda et al. (1996) Nature Biotechnology 14:745-750 (maize via Agrobacterium
tumefaciens); all of which are herein incorporated by reference.
In specific embodiments, the IPT sequences or the IPT promoter
sequences of the invention can be provided to a plant using a variety of transient
transformation methods. Such transient transformation methods include, but are
not limited to, the introduction of the IPT protein or IPT promoter or variants and
fragments thereof directly into the plant or the introduction of an IPT transcript into
the plant. Such methods include, for example, microinjection or particle
bombardment. See, for example, Crossway et al. (1986) Mol Gen. Genet.
202:179-185; Nomura et al. (1986) Plant Sci. 44:53-58; Hepler et al. (1994) Proc.
NatI. Acad. Sci. 91: 2176-2180 and Hush etal. (1994) The Journal of Cell Science
707:775-784, all of which are herein incorporated by reference. Alternatively, the
IPT polynucleotide or the IPT promoter can be transiently transformed into the
plant using techniques known in the art. Such techniques include viral vector
system and the precipitation of the polynucleotide in a manner that precludes
§ub'sequent""refease of "the' DMA. Thus, the transcription from the particle-bound
DMA can occur, but the frequency with which it is released to become integrated
into the genome is greatly reduced. Such methods include the use of particles
coated with polyethyenlimine (PEI; Sigma #P3143).
In other embodiments, the polynucleotide of the invention may be
introduced into plants by contacting plants with a virus or viral nucleic acids.
Generally, such methods involve incorporating a nucleotide construct of the
invention within a viral DNA or RNA molecule. It is recognized that an IPT
polynucleotide of the invention may be initially synthesized as part of a viral
polyprotein, which later may be processed by proteolysis in vivo or in vitro to
produce the desired recombinant protein. Further, it is recognized that promoters
useful for the invention also encompass promoters utilized for transcription by viral
RNA polymerases. Methods for introducing polynucleotides into plants and
expressing a protein encoded therein, involving viral DNA or RNA molecules, are
known in the art. See, for example, U.S. Patent Nos. 5,889,191, 5,889,190,
5,866,785, 5,589,367, 5,316,931, and Porta etal. (1996) Molecular Biotechnology
5:209-221; herein incorporated by reference.
Methods are known in the art for the targeted insertion of a polynucleotide
at a specific location in the plant genome. In one embodiment, the insertion of the
polynucleotide at a desired genomic location is achieved using a site-specific
recombination system. See, for example, W099/25821, WO99/25854,
WO99/25840, W099/25855, and WO99/25853, and US 6,187,994; 6,552,248;
6,624,297; 6,331,661; 6,262,341; 6,541,231; 6,664,108; 6,300,545; 6,528,700;
and 6,911,575, all of which are herein incorporated by reference. Briefly, the
polynucleotide of the invention can be contained in a transfer cassette flanked by
two non-recombinogenic recombination sites. The transfer cassette is introduced
into a plant having stably incorporated into its genome a target site which is
flanked by two non-recombinogenic recombination sites that correspond to the
sites of the transfer cassette. An appropriate recombinase is provided and the
transfer cassette is integrated at the target site. The polynucleotide of interest is
thereby integrated at a specific chromosomal position in the plant genome.
The cells that have been transformed may be grown into plants in
accordance with conventional ways. See, for example, McCormick et at. (1986)
Plant Cell Reports 5:81-84. These plants may then be grown, and pollinated with
either the same transformed strain or different strains, and the resulting progeny
having expression of the desired phenotypic characteristic identified. Two or more
generations may be grown to ensure that expression of the desired phenotypic
characteristic is stably maintained and inherited and then seeds harvested to
ensure that expression of the desired phenotypic characteristic has been
achieved, In this manner, the present invention provides transformed seed (also
referred to as "transgenic seed") having a polynucleotide of the invention, for
example, an expression cassette of the invention, stably incorporated into their
genome.
Pedigree breeding starts with the crossing of two genotypes, such as an
elite line of interest and one other inbred line having one or more desirable
characteristics (i.e., having stably incorporated a polynucleotide of the invention,
having a modulated activity and/or level of the polypeptide of the invention, etc)
which complements the elite line of interest. If the two original parents do not
provide all the desired characteristics, other sources can be included in the
breeding population. In the pedigree method, superior plants are selfed and
selected in successive filial generations. In the succeeding filial generations the
heterozygous condition gives way to homogeneous lines as a result of selfpollination
and selection. Typically in the pedigree method of breeding, five or
more successive filial generations of selfing and selection are practiced: F1 -» F2;
F2-> F3, F3 -> F4; F4 ~> F5, etc. After a sufficient amount of inbreeding,
successive filial generations will serve to increase seed of the developed inbred.
In specific embodiments, the inbred line comprises homozygous alleles at about
95% or more of its loci.
In addition to being used to create a backcross conversion, backcrossing
can also be used in combination with pedigree breeding to modify an elite line of
interest and a hybrid that is made using the modified elite line. Backcrossing can
be used to transfer one or more specifically desirable traits from one line, the
donor parent, to an inbred called the recurrent parent, which has overall good
agronomic characteristics yet lacks that desirable trait or traits. However, the
same procedure can be used to move the progeny toward the genotype of the
recurrent parent but at the same time retain many components of the nonrecurrent
parent by stopping the backcrossing at an early stage and proceeding
with selfing and selection. For example, an F1, such as a commercial hybrid, is
created. This commercial hybrid may be backcrossed to one of its parent lines to
create a BC1 or BC2. Progeny are selfed and selected so that the newly
"developed inbred has many or the attributes of the recurrent parent and yet
several of the desired attributes of the non-recurrent parent This approach
leverages the value and strengths of the recurrent parent for use in new hybrids
and breeding.
Therefore, an embodiment of this invention is a method of making a
backcross conversion of a maize inbred line of interest, comprising the steps of
crossing a plant of a maize inbred line of interest with a donor plant comprising a
mutant gene or transgene conferring a desired trait (i.e., a modulation in the level
of cytokinin (an increase or a decrease) or any plant phenotype resulting from the
modulated cytokinin level (such plant phenotypes are discussed elsewhere
herein)), selecting an F1 progeny plant comprising the mutant gene or transgene
conferring the desired trait, and backcrossing the selected F1 progeny plant to a
plant of the maize inbred line of interest. This method may further comprise the
step of obtaining a molecular marker profile of the maize inbred line of interest and
using the molecular marker profile to select for a progeny plant with the desired
trait and the molecular marker profile of the inbred line of interest. In the same
manner, this method may be used to produce F1 hybrid seed by adding a final
step of crossing the desired trait conversion of the maize inbred line of interest
with a different maize plant to make F1 hybrid maize seed comprising a mutant
gene or transgene conferring the desired trait.
Recurrent selection is a method used in a plant breeding program to
improve a population of plants. The method entails individual plants cross
pollinating with each other to form progeny. The progeny are grown and the
superior progeny selected by any number of selection methods, which include
individual plant, half-sib progeny, full-sib progeny, selfed progeny and topcrossing.
The selected progeny are cross-pollinated with each other to form progeny for
another population. This population is planted and again superior plants are
selected to cross pollinate with each other. Recurrent selection is a cyclical
process and therefore can be repeated as many times as desired. The objective
of recurrent selection is to improve the traits of a population. The improved
population can then be used as a source of breeding material to obtain inbred
lines to be used in hybrids or used as parents for a synthetic cultivar. A synthetic
cultivar is the resultant progeny formed by the intercrossing of several selected
inbreds.
'Mass selection is a useful technique when used in conjunction witn
molecular marker enhanced selection. In mass selection seeds from individuals
are selected based on phenotype and/or genotype. These selected seeds are
then bulked and used to grow the next generation. Bulk selection requires
growing a population of plants in a bulk plot, allowing the plants to self-pollinate,
harvesting the seed in bulk and then using a sample of the seed harvested in bulk
to plant the next generation. Instead of self pollination, directed pollination could
be used as part of the breeding program.
Mutation breeding is one of many methods that could be used to introduce
new traits into an elite line. Mutations that occur spontaneously or are artificially
induced can be useful sources of variability for a plant breeder. The goal of
artificial mutagenesis is to increase the rate of mutation for a desired
characteristic. Mutation rates can be increased by many different means including
temperature, long-term seed storage, tissue culture conditions, radiation such as
X-rays, Gamma rays (e.g., cobalt 60 or cesium 137), neutrons, (product of nuclear
fission by uranium 235 in an atomic reactor), Beta radiation (emitted from
radioisotopes such as phosphorus 32 or carbon 14), or ultraviolet radiation
(preferably from 2500 to 2900nm), or chemical mutagens (such as base
analogues (5-bromo-uracil), related compounds (8-ethoxy caffeine), antibiotics
(streptonigrin), alkylating agents (sulfur mustards, nitrogen mustards, epoxides,
ethylenamines, sulfates, sulfonates, sulfones, lactones), azide, hydroxylamine,
nitrous acid, or acridines. Once a desired trait is observed through mutagenesis
the trait may then be incorporated into existing germplasm by traditional breeding
techniques, such as backcrossing. Details of mutation breeding can be found in
"Principals of Cultivar Development," Fehr, 1993 Macmillan Publishing Company,
the disclosure of which is incorporated herein by reference. In addition, mutations
created in other lines may be used to produce a backcross conversion of elite
lines that comprises such mutations.
The present invention may be used for transformation of any plant species,
including, but not limited to, rnonocots and dicots. Examples of plant species of
interest include, but are not limited to, com (Zea mays), Brassica sp. (e.g., B. napus,
B. rapa, B, juncea), particularly those Brassica species useful as sources of seed oil,
alfalfa (Medicago sativa), rice (Oryza sativa), rye (Seca/e cereale), sorghum
(Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisatum glaucum),
proso millet (Pan/cum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine
coracanaj), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat
(Triticum aestivum], soybean (Glycine max), tobacco (Nicotiana tabacum), potato
(Solatium tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium
barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus); cassava
(Manihot esculenta), coffee (Coffea spp.), coconut (Cocos nucifera), pineapple
(Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea
(Camellia s/nens/s), banana (Musa spp.), avocado (Persea americana), fig (Ficus
casica), guava (Psidium guajava), mango (Mangifera indica), olive (O/ea europaea),
papaya (Can'ca papaya), cashew (Anacardium occidentale), macadamia
(Macadam/a integrifolia], almond (Prunus amygdalus), sugar beets (Beta vulgaris),
sugarcane (Saccharum spp.), oats, barley, vegetables, ornamentals, and conifers.
Vegetables include tomatoes (Lycopersicon esculentum), lettuce (e.g.,
Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis),
peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C.
sativus), cantaloupe (C. cantalupensis), and musk melon (C. me/o). Ornamentals
include azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus
(Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus
spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia
(Euphorbia pulcherrima), and chrysanthemum.
Conifers that may be employed in practicing the present invention include, for
example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii),
ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorts), and Monterey
pine (Pinus radiata); Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga
canadensis); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs
such as silver fir (Abies amabilis) and balsam fir (Abies balsamea)', and cedars such
as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis
nootkatensis). In specific embodiments, plants of the present invention are crop
plants (for example, corn, alfalfa, sunflower, Brassica, soybean, cotton, safflower,
peanut, sorghum, wheat, millet, tobacco, etc.). In other embodiments, com and
soybean plants are optimal, and in yet other embodiments corn plants are optimal.
Other plants of interest include grain plants that provide seeds of interest,
oil-seed plants, and leguminous plants. Seeds of interest include grain seeds,
such as maize, wheat, barley, rice, sorghum, rye, etc. Oil-seed plants include
cotton, soybean, safflower, sunflower, Brassica, maize, alfalfa, palm, coconut, etc.
Leguminous plants include beans and peas. Beans include guar, locust bean,
tenugreeK, soybean, garden Beans, cowpea, mungbean, lima | bean, fava bean,
lentils, chickpea, etc.
Typically, an intermediate host cell will be used in the practice of this
invention to increase the copy number of the cloning vector. With an increased
copy number, the vector containing the nucleic acid of interest'can be isolated in
significant quantities for introduction into the desired plant cells. In one
embodiment, plant promoters that do not cause expression of the polypeptide in
bacteria are employed.
Prokaryotes most frequently are represented by various strains of £ coli;
however, other microbial strains may also be used. Commonly used prokaryotic
control sequences which are defined herein to include promoters for transcription
initiation, optionally with an operator, along with ribosome binding sequences,
include such commonly used promoters as the beta lactamase (penicillinase) and
lactose (lac) promoter systems (Chang ef a/. (1977) Nature 198:1056), the
tryptophan (trp) promoter system (Goeddel et a/. (1980) Nucleic Acids Res.
8:4057) and the lambda derived P L promoter and N-gene ribosome binding site
(Shimatake et al. (1981) Nature 292:128). The inclusion of selection markers in
DNA vectors transfected in £ coli. is also useful. Examples of such markers
include genes specifying resistance to ampicillin, tetracycline, or chloramphenicol.
The vector is selected to allow introduction into the appropriate host cell.
Bacterial vectors are typically of plasmid or phage origin. Appropriate bacterial
cells are infected with phage vector particles or transfected with naked phage
vector DNA. If a plasmid vector is used, the bacterial cells are transfected with the
plasmid vector DNA. Expression systems for expressing a protein of the present
invention are available using Bacillus sp. and Salmonella (Palva ef al. (1983)
Gene 22:229-235); Mosbach et al. (1983) Nature 302:543-545).
A variety of eukaryotic expression systems such as yeast, insect cell lines,
plant and mammalian cells, are known to those of skill in the art. As explained
briefly below, a polynucleotide of the present invention can be expressed in these
eukaryotic systems. In some embodiments, transformed/transfected plant cells,
as discussed infra, are employed as expression systems for production of the
proteins of the instant invention.
Synthesis of heterologous polynucleotides in yeast is well known (Sherman
et al. (1982) Methods in Yeast Genetics, Cold Spring Harbor Laboratory). Two
widely utilized yeasts for production of eukaryotic proteins are Saccharomyces
cerews/ae ana Pichfa pastons. Vectors, strains, and protocols for expression in
Saccharomyces and Pichia are known in the art and available from commercial
suppliers (e.g., Invitrogen). Suitable vectors usually have expression control
sequences, such as promoters, including 3-phosphoglycerate kinase or alcohol
oxidase, and an origin of replication, termination sequences and the like as
desired. A protein of the present invention, once expressed, can be isolated from
yeast by lysing the cells and applying standard protein isolation techniques to the
lists. The monitoring of the purification process can be accomplished by using
Western blot techniques or radioimmunoassay or other standard immunoassay
techniques.
The sequences of the present invention can also be ligated to various
expression vectors for use in transfecting cell cultures of, for instance,
mammalian, insect, or plant origin. Illustrative cell cultures useful for the
production of the peptides are mammalian cells. A number of suitable host cell
lines capable of expressing intact proteins have been developed in the art, and
include the HEK293, BHK21, and CHO cell lines. Expression vectors for these
cells can include expression control sequences, such as an origin of replication, a
promoter (e.g. the CMV promoter, a HSV tk promoter or pgk (phosphoglycerate
kinase) promoter), an enhancer (Queen et a/. (1986) Immunol. Rev. 89:49), and
necessary processing information sites, such as ribosome binding sites, RNA
splice sites, polyadenylation sites (e.g., an SV40 large T Ag poly A addition site),
and transcriptional terminator sequences. Other animal cells useful for production
of proteins of the present invention are available, for instance, from the American
Type Culture Collection,
Appropriate vectors for expressing proteins of the present invention in
insect cells are usually derived from the SF9 baculovirus. Suitable insect cell lines
include mosquito larvae, silkworm, armyworm, moth and DrosophHa cell lines such
as a Schneider cell line (See, Schneider (1987) J. Embryol. Exp. Morphol. 27:353-
365).
As with yeast, when higher animal or plant host cells are employed,
polyadenylation or transcription terminator sequences are typically incorporated
into the vector. An example of a terminator sequence is the polyadenylation
sequence from the bovine growth hormone gene. Sequences for accurate splicing
of the transcript may also be included. An example of a splicing sequence is the
VP1 intron from SV40 (Sprague et a/. (1983) J. Virol. 45:773-781). Additionally,
gene sequences to control replication in the host cell may be incorporated into the
vector such as those found in bovine papilloma virus type-vectors (Saveria-Campo
(1985) DNA Cloning Vol. II a.Practical Approach, D.M. Glover, Ed., IRL Press,
Arlington, Virginia, pp. 213-238).
Animal and lower eukaryotic (e.g., yeast) host cells are competent or
rendered competent for transfection by various means. There are several wellknown
methods of introducing DNA into animal cells. These include: calcium
phosphate precipitation, fusion of the recipient cells with bacterial protoplasts
containing the DNA, treatment of the recipient cells with liposomes containing the
DNA, DEAE dextrin, electroporation, biolistics, and micro-injection of the DNA
directly into the cells. The transfected cells are cultured by means well known in
the art (Kuchler (1997) Biochemical Methods in Cell Culture and Virology,
Dowden, Hutchinson and Ross, Inc.).
//. Modulating the Concentration and/or Activity of an Isopentenvl
Trans/erase Polvpeotide
A method for modulating the concentration and/or activity of the polypeptide
of the present invention in a plant is provided. In general, concentration and/or
activity of the IPT polypeptide is increased or reduced by at least 1%, 5%, 10%,
20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% or more, relative to a native
control plant, plant part, or cell which does not comprise the introduced sequence.
Modulation of the concentration and/or activity may occur at one or more stages of
development. In specific embodiments, the polypeptides of the present invention
are modulated in monocots, such as maize.
The expression level of the IPT polypeptide may be measured directly, for
example, by assaying for the level of the IPT polypeptide in the plant, or indirectly,
for example, by measuring the cytokinin synthesis activity in the plant. Methods
for assaying for cytokinin synthesis activity are described elsewhere herein.
In specific embodiments, the polypeptide or the polynucleotide of the
invention is introduced into the plant cell. Subsequently, a plant cell having the
introduced sequence of the invention is selected using methods known to those of
skill in the art such as, but not limited to, Southern blot analysis, DNA sequencing,
PCR analysis, or phenotypic analysis. A plant or plant part altered or modified by
the foregoing embodiments is grown under plant forming- conditions for a time
sufficient to modulate the concentration and/or activity of polypeptides of the
" present invention in the plant".' Plant forming conditions are well known in the art
and discussed briefly elsewhere herein.
It is also recognized that the level and/or activity of the polypeptide may be
modulated by employing a polynucleotide that is not capable of directing, in a
transformed plant, the expression of a protein or an RNA. For example, the
polynucleotides of the invention may be used to design polynucleotide constructs
that can be employed in methods for altering or mutating a genomic nucleotide
sequence in an organism. Such polynucleotide constructs include, but are not
limited to, RNA:DNA vectors, RNA:DNA mutational vectors, RNA:DNA repair
vectors, mixed-duplex oligonucleotides, self-complementary RNA:DNA
oligonucleotides, and recombinogenic oligonucleobases. Such nucleotide
constructs and methods of use are known in the art. See, U.S. Patent Nos.
5,565,350; 5,731,181; 5,756,325; 5,760,012; 5,795,972; and 5,871,984; all of
which are herein incorporated by reference. See also, WO 98/49350, WO
99/07865, WO 99/25821, and Beetham et a/. (1999) Proc. Natl. Acad. Sci. USA
96:8774-8778; herein incorporated by reference.
It is therefore recognized that methods of the present invention do not
depend on the incorporation of the entire polynucleotide into the genome, only that
the plant or cell thereof is altered as a result of the introduction of the
polynucleotide into a cell. In one embodiment of the invention, the genome may
be altered following the introduction of a polynucleotide into a cell. For example,
the polynucleotide, or any part thereof, may incorporate into the genome of the
plant. Alterations to the genome include, but are not limited to, additions,
deletions, and substitutions of nucleotides into the genome. While the methods of
the present invention do not depend on additions, deletions, and substitutions of
any particular number of nucleotides, it is recognized that such additions,
deletions, or substitutions comprise at least one nucleotide.
It is further recognized that modulating the level and/or activity of the IPT
sequence can be performed to elicit the effects of the sequence only during
certain developmental stages and to switch the effect off in other stages where
expression is no longer desirable. Control of the IPT expression can be obtained
via the use of induclble or tissue-preferred promoters. Alternatively, the gene
could be inverted or deleted using site-specific recombinases, transposons or
recombination systems, which would also- turn on or off expression of the IPT
sequence.
A "subject plant" or" plant cell" is one in which genetic alteration, such as
transformation, has been effected as to a gene of interest, or is a plant or plant cell
which is descended from a plant or cell so altered and which comprises the
alteration. A "control" or "control plant" or "control plant cell" provides a reference
point for measuring changes in phenotype of the subject plant or plant cell.
A control plant or plant cell may comprise, for example: (a) a wild-type plant
or cell, i.e., of the same genotype as the starting material for the genetic alteration
which resulted in the subject plant or cell; (b) a plant or plant cell of the same
genotype as the starting material but which has been transformed with a null
construct (i.e. with a construct which has no known effect on the trait of interest,
such as a construct comprising a marker gene); (c) a plant or plant cell which is a
non-transformed segregant among progeny of a subject plant or plant cell; (d) a
plant or plant cell genetically identical to the subject plant or plant cell but which is
not exposed to conditions or stimuli that would induce expression of the gene of
interest; or (e) the subject plant or plant cell itself, under conditions in which the
gene of interest is not expressed.
In the present case, for example, changes in cytokinin levels, including
changes in absolute amounts of cytokinin, cytokinin ratios, cytokinin activity, or
cytokinin distribution, or changes in plant or plant cell phenotype, such as
flowering time, seed set, branching, senescence, stress tolerance, or root mass,
could be measured by comparing a subject plant or plant cell to a control plant or
plant cell.
A. Increasing the Activity and/or Concentration of an Isopentenyl
Transferase Polypeptide
Methods are provided to increase the activity and/or concentration of the
IPT polypeptide of the invention. An increase in the concentration and/or activity
of the IPT polypeptide of the invention can be achieved by providing to the plant
an IPT polypeptide. As discussed elsewhere herein, many methods are known in
the art for providing a polypeptide to a plant including, but not limited to, direct
introduction of the polypeptide into the plant, and introducing into the plant
(transiently or stably) a polynucleotide construct encoding a polypeptide having
cytokinin synthesis activity. It is also recognized that the methods of the invention
may employ a polynucleotide that is not capable of directing, in the transformed
plant, the expression of a protein or an RNA. Thus, the level and/or activity of an
fPT polypeptide may be increased by altering the gene encoding the IPT
polypeptide or its promoter. See, e.g., Kmiec, U.S. Patent 5,565,350; Zarling et
Ql, PCT/US93/03868. Therefore mutagenized plants that carry mutations in IPT
genes, where the mutations increase expression of the IPT gene or increase the
cytokinin synthesis activity of the encoded IPT polypeptide are provided. As
described elsewhere herein, methods to assay for an increase in protein
concentration or an increase in cytokinin synthesis activity are known.
B. Reducing the Activity and/or Concentration of an Isopentenyl
Transferase Polypeptide
Methods are provided to reduce or eliminate the activity and/or
concentration of the IPT polypeptide by transforming a plant cell with an
expression cassette that expresses a polynucleotide that inhibits the expression of
the IPT polypeptide. The polynucleotide may inhibit the expression of an IPT
polypeptide directly, by preventing translation of the IPT polypeptide messenger
RNA, or indirectly, by encoding a molecule that inhibits the transcription or
translation of an IPT polypeptide gene encoding an IPT polypeptide. Methods for
inhibiting or eliminating the expression of a gene in a plant are well known in the
art, and any such method may be used in the present invention to inhibit the
expression of the IPT polypeptides.
In accordance with the present invention, the expression of an IPT
polypeptide is inhibited if the level of the IPT polypeptide is statistically lower than
the level of the same IPT polypeptide in a plant that has not been genetically
modified or mutagenized to inhibit the expression of that IPT polypeptide. In
particular embodiments of the invention, the protein level of the IPT polypeptide in
a modified plant according to the invention is less than 95%, less than 90%, less
than 80%, less than 70%, less than 60%, less than 50%, less than 40%, less than
30%, less than 20%, less than 10%, or less than 5% of the protein level of the
same IPT polypeptide in a plant that is not a mutant or that has not been
genetically modified to inhibit the expression of that IPT polypeptide. The
expression level of the IPT polypeptide may be measured directly, for example, by
assaying for the level of the IPT polypeptide expressed in the cell or plant, or
indirectly, for example, by measuring the cytokinin synthesis activity in the cell or
plant. Methods for determining the cytokinin synthesis activity of the IPT
polypeptide are described elsewhere herein.
In other embodiments of the invention, the activity of one or more IPT
polypeptides is reduced or eliminated by transforming a plant cell with an
expression cassette comprising a polynucleotide encoding a polypeptide that
inhibits the activity of one or more IPT polypeptides. The cytokinin synthesis
activity of an IPT polypeptide is inhibited according to the present invention if the
cytokinin synthesis activity of the IPT polypeptide is statistically lower than the
cytokinin synthesis activity of the same IPT polypeptide in a plant that has not
been genetically modified to inhibit the cytokinin synthesis activity of that IPT
polypeptide. In particular embodiments of the invention, the cytokinin synthesis
activity of the IPT polypeptide in a modified plant according to the invention is less
than 95%, less than 90%, less than 80%, less than 70%, less than 60%, less than
50%, less than 40%, less than 30%, less than 20%, less than 10%, or less than
5% of the cytokinin synthesis activity of the same IPT polypeptide in a plant that
that has not been genetically modified to inhibit the expression of that IPT
polypeptide. The cytokinin synthesis activity of an IPT polypeptide is "eliminated"
according to the invention when it is not detectable by the assay methods
described elsewhere herein. Methods of determining the cytokinin synthesis
activity of an IPT polypeptide are described elsewhere herein.
In other embodiments, the activity of an IPT polypeptide may be reduced or
eliminated by disrupting the gene encoding the IPT polypeptide. The invention
encompasses mutagenized plants that carry mutations in IPT genes, where the
mutations reduce expression of the IPT gene or inhibit the cytokinin synthesis
activity of the encoded IPT polypeptide.
Thus, many methods may be used to reduce or eliminate the activity of an
IPT polypeptide. More than one method may be used to reduce the activity of a
single IPT polypeptide. In addition, combinations of methods may be employed to
reduce or eliminate the activity of two or more different IPT polypeptides.
Non-limiting examples of methods of reducing or eliminating the expression
of an IPT polypeptide are given below.
1- Polvnucteptide-Based Methods
In some embodiments of the present invention, a plant cell is transformed
with an expression cassette that is capable of expressing a polynucleotide that
inhibits the expression of an IPT sequence. The term "expression" as used herein
refers to the biosynthesis of a gene product, including the transcription and/or
"translation of said gene product. For example, for the purposes of the present
invention, an expression cassette capable of expressing a polynucleotide that
inhibits the expression of at least one IPT sequence is an expression cassette
capable of producing an RNA molecule that inhibits the transcription and/or
translation of at least one IPT polypeptide. The "expression" or "production" of a
protein or polypeptide from a DNA molecule refers to the transcription and
translation of the coding sequence to produce the protein or polypeptide, while the
"expression" or "production" of a protein or polypeptide from an RNA molecule
refers to the translation of the RNA coding sequence to produce the protein or
polypeptide.
Examples of polynucleotides that inhibit the expression of an IPT sequence
are given below.
• Sense SuporBssion/CosuDDression
In some embodiments of the invention, inhibition of the expression of an
IPT polypeptide may be obtained by sense suppression or cosuppression. For
cosuppression, an expression cassette is designed to express an RNA molecule
corresponding to all or part of a messenger RNA encoding an IPT polypeptide in
the "sense" orientation. Over expression of the RNA molecule can result in
reduced expression of the native gene. Accordingly, multiple plant lines
transformed with the cosuppression expression cassette are screened to identify
those that show the greatest inhibition of IPT polypeptide expression.
The polynucleotide used for cosuppression may correspond to all or part of
the sequence encoding the IPT polypeptide, all or part of the 5' and/or 3'
untranslated region of an IPT polypeptide transcript, or all or part of both the
coding sequence and the untranslated regions of a transcript encoding an IPT
polypeptide. In some embodiments where the polynucleotide comprises all or part
of the coding region for the IPT polypeptide, the expression cassette is designed
to eliminate the start codon of the polynucleotide so that no protein product will be
transcribed.
Cosuppression may be used to inhibit the expression of plant genes to
produce plants having undetectable protein levels for the proteins encoded by
these genes. See, for example, Broin at a/. (2002) Plant Cell 14:1417-1432.
Cosuppression may also be used to inhibit the expression of multiple proteins in
the same plant. See, for example, U.S. Patent No. 5,942,657. Methods for using
cosuppression to inhibit the"1"expression of endogenous genes in plants are
described in Flavell et al. (1994) Proc. Natl. Acad. Sci. USA 91:3490-3496;
Jorgensen et al. (1996) Plant Mol. Biol. 31:957-973; Johansen and Carrington
(2001) Plant Physiol. 126:930-938; Broin et al. (2002) Plant Cell 14:1417-1432;
Stoutjesdijk et al (2002) Plant Physiol. 129:1723-1731; Yu et al. (2003)
Phytochemistry 63:753-763; and U.S. Patent Nos. 5,034,323, 5,283,184, and
5,942,657; each of which is herein incorporated by reference. The efficiency of
cosuppression may be increased by including a poly-dT region in the expression
cassette at a position 3' to the sense sequence and 5' of the polyadenylation
signal. See, U.S. Patent. Publication No. 20020048814, herein incorporated by
reference. Typically, such a nucleotide sequence has substantial sequence
identity to the sequence of the transcript of the endogenous gene, optimally
greater than about 65% sequence identity, more optimally greater than about 85%
sequence identity, most optimally greater than about 95% sequence identity. See,
U.S. Patent Nos. 5,283,184 and 5,034,323; herein incorporated by reference.
'• Antisense Suppression
In some embodiments of the invention, inhibition of the expression of the
IPT polypeptide may be obtained by antisense suppression. For antisense
suppression, the expression cassette is designed to express an RNA molecule
complementary to all or part of a messenger RNA encoding the IPT polypeptide.
Over expression of the antisense RNA molecule can result in reduced expression
of the native gene. Accordingly, multiple plant lines transformed with the
antisense suppression expression cassette are screened to identify those that
show the greatest inhibition of IPT polypeptide expression.
The polynucleotide for use in antisense suppression may correspond to all
or part of the complement of the sequence encoding the IPT polypeptide, all or
part of the complement of the 5' and/or 3' untranslated region of the IPT
polypeptide transcript, or all or part of the complement of both the coding
sequence and the untranslated regions of a transcript encoding the IPT
polypeptide. In addition, the antisense polynucleotide may be fully complementary
(i.e.. 100% identical to the complement of the target sequence) or partially
complementary (i.e., less than 100% identical to the complement of the target
sequence) to the target sequence. Antisense suppression may be used to. inhibit
the expression of multiple proteins in the same plant. See, for example, U.S.
Patent No. 5,942,657 FurtrieTmore, portions of the antisense nucleotides may be
used to disrupt the expression of the target gene. Generally, sequences of at
least 50 nucleotides, 100 nucleotides, 200 nucleotides, 300,400,450, 500, 550, or
greater may be used. Methods for using antisense suppression to inhibit the
expression of endogenous genes in plants are described, for example, in Liu at al
(2002) Plant Physiol. 129:1732-1743 and U.S. Patent Nos. 5,759,829 and
5,942,657, each of which is herein incorporated by reference. Efficiency of
antisense suppression may be increased by including a poly-dT region in the
expression cassette at a position 3' to the antisense sequence and 5' of the
polyadenylation signal. See, U.S. Patent Publication No. 20020048814, herein
incorporated by reference.
Hi- Double-Stranded RNA Interference
In some embodiments of the invention, inhibition of the expression of an
IPT polypeptide may be obtained by double-stranded RNA (dsRNA) interference.
For dsRNA interference, a sense RNA molecule like that described above for
cosuppression and an antisense RNA molecule that is fully or partially
complementary to the sense RNA molecule are expressed in the same cell,
resulting in inhibition of the expression of the corresponding endogenous
messenger RNA.
Expression of the sense and antisense molecules can be accomplished by
designing the expression cassette to comprise both a sense sequence and an
antisense sequence. Alternatively, separate expression cassettes may be used
for the sense and antisense sequences. Multiple plant lines transformed with the
dsRNA interference expression cassette or expression cassettes are then
screened to identify plant lines that show the greatest inhibition of IPT polypeptide
expression. Methods for using dsRNA interference to inhibit the expression of
endogenous plant genes are described in Waterhouse et al. (1998) Proc, Natl.
Acad. Sci. USA 95:13959-13964, Liu et al. (2002) Plant Physiol. 129:1732-1743,
and WO 99/49029, WO 99/53050, WO 99/61631, and WO 00/49035; each of
which is herein incorporated by reference.
/V. Hsiimin RNA Interference and Intron-Containina Hairpin
SNA Interference
In some embodiments of the invention, inhibition of the expression of one or
more IPT polypeptides may be obtained by hairpin RNA (hpRNA) interference or
intron-containing hairpin RNA (ihpRNA) interference. These methods are highly
efficient at inhibiting the expression of endogenous genes. See, Waterhouse and
Helliwell (2003) Nat. Rev. Genet. 4:29-38 and the references cited therein.
For hpRNA interference, the expression cassette is designed to express an
RNA molecule that hybridizes with itself to form a hairpin structure that comprises
a single-stranded loop region and a base-paired stem. The base-paired stem
region comprises a sense sequence corresponding to all or part of the
endogenous messenger RNA encoding the gene whose expression is to be
inhibited, and an antisense sequence that is fully or partially complementary to the
sense sequence. Thus, the base-paired stem region of the molecule generally
determines the specificity of the RNA interference. hpRNA molecules are highly
efficient at inhibiting the expression of endogenous genes, and the RNA
interference they induce is inherited by subsequent generations of plants. See, for
example, Chuang and Meyerowitz (2000) Proc. Nail. Acad. Sci. USA 97:4985-
4990; Stoutjesdijk et al. (2002) Plant Physiol. 129:1723-1731; and Waterhouse
and Helliwell (2003) Nat. Rev. Genet. 4:29-38. Methods for using hpRNA
interference to inhibit or silence the expression of genes are described, for
example, in Chuang and Meyerowitz (2000) Proc. Natl. Acad. Sci. USA 97:4985-
4990; Stoutjesdijk et al. (2002) Plant Physiol. 129:1723-1731; Waterhouse and
Helliwell (2003) Nat. Rev. Genet. 4:29-38; Pandolfini et al. BMC Biotechnology
3:7, and U.S. Patent Publication No. 20030175965; each of which is herein
incorporated by reference. A transient assay for the efficiency of hpRNA
constructs to silence gene expression in vivo has been described by Panstruga et
al. (2003) Mol. Biol. Rep. 30:135-140, herein incorporated by reference.
Alternatively, the base-paired stem region may correspond to a portion of a
promoter sequence controlling expression of the gene to be inhibited.
Transcriptional gene silencing (TGS) may be accomplished through use of hpRNA
constructs wherein the inverted repeat of the hairpin shares sequence identity with
the promoter region driving expression of a gene to be silenced. Processing of the
hpRNA into short RNAs which can interact with the homologous promoter, region
may trigger degradation"or methylation to result in silencing (Aufsatz et al. (2002)
PNAS 99 (Suppl. 4): 16499-16506; Matte et al. (2000) EMBO J19(19):5194-5201).
For ihpRNA, the interfering molecules have the same general structure as
for hpRNA, but the RNA molecule additionally comprises an intron that is capable
of being spliced in the cell in which the ihpRNA is expressed. The use of an intron
minimizes the size of the loop in the hairpin RNA molecule following splicing, and
this increases the efficiency of interference. See, for example, Smith et a/. (2000)
Nature 407:319-320. In fact, Smith et al. show 100% suppression of endogenous
gene expression using ihpRNA-mediated interference. Methods for using ihpRNA
interference to inhibit the expression of endogenous plant genes are described, for
example, in Smith et al. (2000) Nature 407:319-320; Wesley et al. (2001) Plant J.
27:581-590; Wang and Waterhouse (2001) Curr. Opin. Plant Biol. 5:146-150;
Waterhouse and Helliwell (2003) Nat. Rev. Genet 4:29-38; Helliwell and
Waterhouse (2003) Methods 30:289-295, and U.S. Patent Publication No.
20030180945, each of which is herein incorporated by reference.
The expression cassette for hpRNA interference may also be designed
such that the sense sequence and the antisense sequence do not correspond to
an endogenous RNA. In this embodiment, the sense and antisense sequence
flank a loop sequence that comprises a nucleotide sequence corresponding to all
or part of the endogenous messenger RNA of the target gene. Thus, it is the loop
region that determines the specificity of the RNA interference. See, for example,
WO 02/00904, herein incorporated by reference.
v- Amolicon-Mediated Interference
Amplicon expression cassettes comprise a plant virus-derived sequence
that contains all or part of the target gene but generally not all of the genes of the
native virus. The viral sequences present in the transcription product of the
expression cassette allow the transcription product to direct its own replication.
The transcripts produced by the amplicon may be either sense or antisense
relative to the target sequence (i.e., the messenger RNA for an IPT polypeptide).
Methods of using amplicons to inhibit the expression of endogenous plant genes
are described, for example, in Angell and Baulcombe (1997) EMBO J. 16:3675-
3684, Angell and Baulcombe (1999) Plant J. 20:357-362, and U.S. Patent No.
6,646,805, each of which is herein incorporated by reference.
vi.
In some embodiments, the polynucleotide" expressed by the expression
cassette of the invention is catalytic RNA or has ribozyme activity specific for the
messenger RNA of an IPT polypeptide. Thus, the polynucleotide causes the
degradation of the endogenous messenger RNA, resulting in reduced expression
of the IPT polypeptide. This method is described, for example, in U.S. Patent No.
4,987,071, herein incorporated by reference.
vii. Small Interfering RNA or Micro RNA
In some embodiments of the invention, inhibition of the expression of one or
more IPT polypeptides may be obtained by RNA interference by expression of a
gene encoding a micro RNA (miRNA). miRNAs are regulatory agents consisting
of about 22 ribonucleotides. miRNA are highly efficient at inhibiting the expression
of endogenous genes. See, for example Javier et al. (2003) Nature 425: 257-263,
herein incorporated by reference.
For miRNA interference, the expression cassette is designed to express an
RNA molecule that is modeled on an endogenous miRNA gene. The miRNA gene
encodes an RNA that forms a hairpin structure containing a 22-nucleotide
sequence that is complementary to another endogenous gene (target sequence).
For suppression of IPT polypeptide expression, the 22-nucleotide sequence is
selected from an IPT polypeptide transcript sequence and contains 22 nucleotides
encoding said IPT polypeptide sequence in sense orientation and 21 nucleotides
of a corresponding antisense sequence that is complementary to the sense
sequence. miRNA molecules are highly efficient at inhibiting the expression of
endogenous genes, and the RNA interference they induce is inherited by
subsequent generations of plants.
2. Polvpeotide-Based Inhibition of Gene Expression
In one embodiment, the polynucleotide encodes a zinc finger protein that
binds to a gene encoding an IPT polypeptide, resulting in reduced expression of
the gene. In particular embodiments, the zinc finger protein binds to a regulatory
region of an IPT polypeptide gene. In other embodiments, the zinc finger protein
binds to a messenger RNA encoding an IPT polypeptide and prevents its
translation. Methods of selecting sites for targeting by zinc finger proteins have
been described, for example, in U.S. Patent No. 6,453,242, and methods for using
zinc finger proteins to inhibit the expression of genes in plants are described, for
example, in U.S. Patent Publication No. 20030037355; each of which is herein
incorporated by reference.
3. Polypeptide-Based Inhibition of Protein Activity
In some embodiments of the invention, the polynucleotide encodes an
antibody that binds to at least one IPT polypeptide, and reduces the cytokinin
synthesis activity of the IPT polypeptide. In another embodiment, the binding of
the antibody results in increased turnover of the antibody-lPT polypeptide complex
by cellular quality control mechanisms. The expression of antibodies in plant cells
and the inhibition of molecular pathways by expression and binding of antibodies
to proteins in plant cells are well known in the art. See, for example, Conrad and
Sonnewald (2003) Nature Biotech, 21:35-36, incorporated herein by reference.
4. Gene Disruption
In some embodiments of the present invention, the activity of an IPT
polypeptide is reduced or eliminated by disrupting the gene encoding the IPT
polypeptide. The gene encoding the IPT polypeptide may be disrupted by any
method known in the art. For example, in one embodiment, the gene is disrupted
by transposon tagging. In another embodiment, the gene is disrupted by
mutagenizing plants using random or targeted mutagenesis, and selecting for
plants that have reduced IPT activity.
'• Transposon Tagging
In one embodiment of the invention, transposon tagging is used to reduce
or eliminate the cytokinin synthesis activity of one or more IPT polypeptides.
Transposon tagging comprises inserting a transposon within an endogenous IPT
gene to reduce or eliminate expression of the IPT polypeptide. "IPT gene" is
intended to mean the gene that encodes an IPT polypeptide according to the
invention.
In this embodiment, the expression of one or more IPT polypeptides is
reduced or eliminated by inserting a transposon within a regulatory region or
coding region of the gene encoding the IPT polypeptide. A transposon that is
within an exon, intron, 5' or 3' untranslated sequence, a promoter, or any other
regulatory sequence of an IPT polypeptide gene may be used to reduce or
eliminate the expression and/or activity of the encoded IPT polypeptide.
Methods for the transposon tagging of specific genes in plants are well
known in the art. See, for example, Maes et al. (1999) Trends Plant Sci. 4:90-96;
Dharmapuri and Sonti (1999) FEMS Microbiol. Lett. 179:53-59; Meissner et al.
(2000) Plant J. 22:265-274; Phogat et al. (2000) J. Biosci. 25:57-63; Walbot (2000)
Curr. Opin. Plant Btol 2:103-107; Gai et al. (2000) Nucleic Acids Res. 28:94-96;
Fitzmaurice et al. (1999) Genetics 153:1919-1928). In addition, theTUSC process
for selecting Mu insertions in selected genes has been described in Bensen et al.
(1995) Plant Cell 7:75-84; Mena et al. (1996) Science 274:1537-1540; and U.S.
Patent No. 5,962,764; each of which is herein incorporated by reference.
//. Mutant Plants with Reduced Activity
Additional methods for decreasing or eliminating the expression of
endogenous genes in plants are also known in the art and can be similarly applied
to the instant invention. These methods include other forms of mutagenesis, such
as ethyl methanesulfonate-induced mutagenesis, deletion mutagenesis, and fast
neutron deletion mutagenesis used in a reverse genetics sense (with PCR) to
identify plant lines in which the endogenous gene has been deleted. For
examples of these methods see Ohshima et al. (1998) Virology 243:472-481;
Okubara et al. (1994) Genetics 137:867-874; and Quesada et al. (2000) Genetics
154:421-436; each of which is herein incorporated by reference. In addition, a fast
and automatable method for screening for chemically induced mutations, TILLING
(Targeting Induced Local Lesions In Genomes), using denaturing HPLC or
selective endonuclease digestion of selected PCR products is also applicable to
the instant invention. See McCallum et al. (2000) Nat Biotechnol. 18:455-457,
herein incorporated by reference.
Mutations that impact gene expression or that interfere with the function
(IPT activity) of the encoded protein are well known in the art. Insertional
mutations in gene exons usually result in null-mutants. Mutations in conserved
residues are particularly effective in inhibiting the cytokinin synthesis activity of the
encoded protein. Conserved residues of plant IPT polypeptides suitable for
mutagenesis with the goal to eliminate IPT activity have been described. See, for
example, Figure 1. Such mutants can be isolated according to well-known
procedures, and mutations In different IPT loci can be stacked by genetic crossing.
See, for example, Gruis ef al. (2002) Plant'Cell 14:2863-2882.
In another embodiment of this invention, dominant mutants can be used to
trigger RNA silencing due to gene inversion and recombination of a duplicated
gene locus. See, for example, Kusaba et al. (2003) Plant Cell 15:1455-1467.
The invention encompasses additional methods for reducing or eliminating
the activity of one or more IPT polypeptides. Examples of other methods for
altering or mutating a genomic nucleotide sequence in a plant are known in the art
and include, but are not limited to, the use of RNA:DNA vectors, RNA:DNA
mutational vectors, RNA:DNA repair vectors, mixed-duplex oligonucleotides, selfcomplementary
RNA:DNA oligonucleotides, and recombinogenic
oligonucleobases. Such vectors and methods of use are known in the art. See,
for example, U.S. Patent Nos. 5,565,350; 5,731,181; 5,756,325; 5,760,012;
5,795,972; and 5,871,984; each of which are herein incorporated by reference.
See also, WO 98/49350, WO 99/07865, WO 99/25821, and Beetham ef al, (1999)
Proc. Natl. Acad. Sci. USA 96:8774-8778; each of which is herein incorporated by
reference.
Ill- Modulating Cvtokinin Level and/or Activity
As used herein, "cytokinin" refers to a class, or member of the class, of
plant-specific hormones that play a central role during the cell cycle and influence
numerous developmental programs. Cytokinins comprise an N8-substituted purine
derivative. Representative cytokinins include isopentenyladenine (N6-(A2-
isopentenyl)adenine (hereinafter, iP), zeatin (6-(4-hydroxy-3methylbut-trans-2-
enylamino) purine) (hereinafter, Z), and dihydrozeatin (DZ). The free bases and
their ribosides (iPR, ZR, and DZR) are believed to be the active compounds.
Additional cytokinins are known. See, for example, U.S. Patent No. 5,211,738 and
Keiber ef al. (2002) Cytokinins, The Arabidopsis Book, American Society of Plant
Biologists, both of which are herein incorporated by reference.
"Modulating the cytokinin level" includes any statistically significant
decrease or increase in cytokinin level and/or activity in the plant when compared
to a control plant. For example, modulating the level and/or activity can comprise
either an increase or a decrease in overall cytokinin content of about 0.1%, 0.5%,
1%, 3% 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,
70%, 75%, 80%, 85%, 90%, 95%, or greater when compared to a control plant or
plant part. Alternatively, the "modulated level and/or activity of the cytokinin can
include about a 0.2 fold, 0.5 fold, 2 fold, 4 fold, 8 fold, 16 fold, 32 fold or greater
overall increase or decrease in cytokinin level/activity in the plant or a plant part
when compared to a control plant or plant part.
It is further recognized that the modulation of the cytokinin level/activity
need not be an overall increase/decrease in cytokinin level and/or activity, but also
includes a change in tissue distribution of the cytokinin. Moreover, the modulation
of the cytokinin level/activity need not be an overall increase/decrease in
cytokinins, but also includes a change in the ratio of various cytokinin derivatives.
For example, the ratio of various cytokinin derivatives such as isopentenyladeninetype,
zeatin-type, or dihydrozeatin-type cytokinins, and the like, could be altered
and thereby modulate the level/activity of the cytokinin of the plant or plant part
when compared to a control plant.
Methods for assaying for a modulation in cytokinin level and/or activity are
known in the art. For example, representative methods for cytokinin extraction,
immunopurification, HPLC separation, and quantification by ELISA methods can
be found, for example, in Faiss et a/. (1997) Plant J. >/2:401-415. See, also,
Werner et al. (2001) PAWS 98:10487-10492) and Dewitte et a/. (1999) Plant
Physiol. 119:111-121. Each of these references are herein incorporated by
reference. As discussed elsewhere herein, modulation in cytokinin level and/or
activity can further be detected by monitoring for particular plant phenotypes.
Such phenotypes are described elsewhere herein.
In specific methods, the level and/or activity of a cytokinin in a plant is
increased by increasing the level or activity of the IPT polypeptide in the plant.
Methods for increasing the level and/or activity of IPT polypeptides in a plant are
discussed elsewhere herein. Briefly, such methods comprise providing an IPT
polypeptide of the invention to a plant and thereby increasing the level and/or
activity of the IPT polypeptide. In other embodiments, an IPT nucleotide sequence
encoding an IPT polypeptide can be provided by introducing into the plant a
polynucleotide comprising an IPT nucleotide sequence of the invention,
expressing the IPT sequence, and thereby increasing the level and/or activity of a
cytokinin in the plant or plant part when compared to a control plant. In some
embodiments, the IPT nucleotide construct introduced into the plant is stably
incorporated into the genome of the plant. -
In otner meinoas, tne level and/or activity of cytokinin in a plant is
decreased by decreasing the level and/or activity of one or more of the IPT
polypeptides in the plant. Such methods are disclosed in detail elsewhere herein.
In one such method, an IPT nucleotide sequence is introduced into the plant and
expression of the IPT nucleotide sequence decreases the activity of the IPT
polypeptide, and thereby decreases the level and/or activity of a cytokinin in the
plant or plant part when compared to a control plant or plant part. In other
embodiments, the IPT nucleotide construct introduced into the plant is stably
incorporated into the genome of the plant.
As discussed above, one of skill will recognize the appropriate promoter to
use to modulate the level/activity of a cytokinin in the plant. Exemplary promoters
for this embodiment have been disclosed elsewhere herein.
Accordingly, the present invention further provides plants having a
modulated level/activity of a cytokinin when compared to the cytokinin level/activity
of a control plant. In one embodiment, the plant of the invention has an increased
level/activity of the iPT polypeptide of the invention, and thus has an increased
level/activity of cytokinin. In other embodiments, the plant of the invention has a
reduced or eliminated level of the IPT polypeptide of the invention, and thus has a
decreased level/activity of a cytokinin. In certain embodiments, such plants have
stably incorporated into their genome a nucleic acid molecule comprising an IPT
nucleotide sequence of the invention operably linked to a promoter that drives
expression in the plant cell.
IV. Modulating Root Development
Methods for modulating root development in a plant are provided. By
"modulating root development" is intended any alteration in the development of the
plant root when compared to a control plant. Such alterations in root development
include, but are not limited to, alterations in the growth rate of the primary root, the
fresh root weight, the extent of lateral and adventitious root formation, the
vasculature system, meristem development, or radial expansion.
Methods for modulating root development in a plant are provided. The
methods comprise modulating the level and/or activity of the IPT polypeptide in the
plant. In one method, an IPT sequence of the invention is provided to the plant.
In another method, the IPT nucleotide sequence is provided by introducing into the
plant a polynucleotide comprising an IPT nucleotide sequence of the invention
(which may be a fragment of a full-length IPT sequence provided), expressing said
IPT sequence, and thereby modifying root development. In still other methods,
the IPT nucleotide construct introduced into the plant is stably incorporated into
the genome of the plant,
In other methods, root development is modulated by decreasing the level or
activity of the IPT polypeptide in the plant. Such methods can comprise
introducing an IPT nucleotide sequence into the plant and decreasing the activity
of the IPT polypeptide. In some methods, the IPT nucleotide construct introduced
into the plant is stably incorporated into the genome of the plant. A decrease in
cytokinin synthesis activity can result in at least one or more of the following
alterations to root development, including, but not limited to, larger root meristems,
increased root growth, enhanced radial expansion, an enhanced vasculature
system, increased root branching, more adventitious roots, and/or an increase in
fresh root weight when compared to a control plant.
As used herein, "root growth" encompasses all aspects of growth of the
different parts that make up the root system at different stages of its development
in both monocotyledonous and dicotyledonous plants. It is to be understood that
enhanced root growth can result from enhanced growth of one or more of its parts
including the primary root, lateral roots, adventitious roots, etc. Methods of
measuring such developmental alterations in the root system are known in the art.
See, for example, U.S. Application No. 2003/0074698 and Werner et a/. (2001)
PA/AS 18:10487-10492, both of which are herein incorporated by reference.
As discussed above, one of skill will recognize the appropriate promoter to
use to modulate root development in the plant. Exemplary promoters for this
embodiment include constitutive promoters and root-preferred promoters.
Exemplary root-preferred promoters have been disclosed elsewhere herein.
Stimulating root growth and increasing root mass by decreasing the activity
and/or level of the IPT polypeptide also finds use in improving the standability of a
plant. The term "resistance to lodging" or "standability" refers to the ability of a
plant to fix itself to the soil. For plants with an erect or semi-erect growth habit,
this term also refers to the ability to maintain an upright position under adverse
environmental conditions. This trait relates to the size, depth and morphology of
the root system. In addition, stimulating root growth and increasing root mass by
decreasing the level and/or activity of the IPT polypeptide at appropriate
developmental stages also finds use in promoting in vitro propagation of explants.
Increased root biomass and/or altered root architecture may also find use in
improving nitrogen-use efficiency of the plant. Such improved efficiency may lead
to, for example, an increase in plant biomass and/or seed yield at an existing level
of available nitrogen, or maintenance of plant biomass and/or seed yield when
available nitrogen is limited. Thus, agronomic and/or environmental benefits may
ensue.
Furthermore, higher root biomass production due to a decreased level
and/or activity of an IPT polypeptide has an indirect effect on production of
compounds produced by root cells or transgenic root cells or cell cultures of said
transgenic root cells. One example of an interesting compound produced in root
cultures is shikonin, the yield of which can be advantageously enhanced by said
methods.
Accordingly, the present invention further provides plants having modulated
root development when compared to the root development of a control plant. In
some embodiments, the plant of the invention has a decreased level/activity of an
IPT polypeptide of the invention and has enhanced root growth and/or root
biomass. In certain embodiments, such plants have stably incorporated into their
genome a nucleic acid molecule comprising an IPT nucleotide sequence of the
invention operably linked to a promoter that drives expression in the plant cell.
V. Modulating Shoot and Leaf Development
Methods are also provided for modulating vegetative tissue growth in
plants. In one embodiment, shoot and leaf development in a plant is modulated.
By "modulating shoot and/or leaf development" is intended any alteration in the
development of the plant shoot and/or leaf when compared to a control plant or
plant part. Such alterations in shoot and/or leaf development include, but are not
limited to, alterations in shoot meristem development, in leaf number, leaf size,
leaf and stem vasculature, internode length, and leaf senescence. As used
herein, "leaf development" and "shoot development" encompasses all aspects of
growth of the different parts that make up the leaf system and the shoot system,
respectively, at different stages of their development, both in monocotyledonous
and dicotyledonous plants. Methods for measuring such developmental
alterations in the shoot and leaf system are known in the art. See, for example,
Werner et at. (2001) PNAS 98:10487-10492 and U.S. Application
No. 2003/0074698, each of which is herein incorporated by reference.
the method tor modulating shoot and/or leaf development in a plant
comprises modulating the activity and/or level of an IPT polypeptide of the
invention. In one embodiment, an IPT sequence of the invention is provided. In
other embodiments, the IPT nucleotide sequence can be provided by introducing
into the plant a poiynucleotide comprising an IPT nucleotide sequence of the
invention, expressing the IPT sequence, and thereby modifying shoot and/or leaf
development. In other embodiments, the IPT nucleotide construct introduced into
the plant is stably incorporated into the genome of the plant.
In specific embodiments, shoot or leaf development is modulated by
decreasing the level and/or activity of the IPT polypeptide in the plant. A decrease
in IPT activity can result in one or more alterations in shoot and/or leaf
development, including, but not limited to, smaller apical meristems, reduced leaf
number, reduced leaf surface, reduced vascular tissues, shorter internodes and
stunted growth, and accelerated leaf senescence, when compared to a control
plant.
As discussed above, one of skill will recognize the appropriate promoter to
use to modulate shoot and leaf development of the plant. Exemplary promoters
for this embodiment include constitutive promoters, shoot-preferred promoters,
shoot meristem-preferred promoters, senescence-activated promoters, stressinduced
promoters, root-preferred promoters, nitrogen-induced promoters and
leaf-preferred promoters. Exemplary promoters have been disclosed elsewhere
herein.
Decreasing cytokinin synthesis activity in a plant generally results in shorter
internodes and stunted growth. Thus, the methods of the invention find use in
producing dwarf plants. In addition, as discussed above, modulation of cytokinin
synthesis activity in the plant modulates both root and shoot growth. Thus, the
present invention further provides methods for altering the root/shoot ratio.
Shoot or leaf development can further be modulated by increasing the level
and/or activity of the IPT polypeptide in the plant. An increase in IPT activity can
result in one or more alterations in shoot and/or leaf development including, but
not limited to, increased leaf number, increased leaf surface, increased vascular
tissue, increased shoot formation, longer intemodes, improved growth, improved
plant yield and vigor, and retarded leaf senescence when compared to a control
plant.
In one embodiment, the tolerance of a plant to flooding is improved.
Flooding is a serious environmental stress that affects plant growth and
productivity. Flooding causes premature senescence which results in leaf
chlorosis, necrosis, defoliation, cessation of growth and reduced yield. Cytokinins
can regulate senescence, and by increasing the level/activity of the IPT
polypeptide in the plant, the present invention improves the tolerance of the plant
to a variety of environmental stresses, including flooding. Delayed senescence
may also advantageously expand the maturity adaptation of crops, improve the
shelf-life of potted plants, and extend the vase-life of cut flowers.
In still other embodiments, methods for modulating shoot regeneration in a
callus are provided. In this method, increasing the level and/or activity of the IPT
polypeptide will increase the level of cytokinins in the plant. Accordingly, lower
concentrations of exogenous growth regulators (i.e., cytokinins) or no exogenous
cytokinins in the culture medium will be needed to enhance shoot regeneration in
callus. Thus, in one embodiment of the invention, the increased level and/or
activity of the IPT sequence can be used to overcome the poor shooting potential
of certain species that has limited the success and speed of transgene technology
for those species. Moreover, multiple shoot induction can be induced for crops
where it is economically desirable to produce as many shoots as possible.
Accordingly, methods are provided to increase the rate of regeneration for
transformation. In specific embodiments, the IPT sequence will be under the
control of an inducible promoter (e.g., heat shock promoter, chemically inducible
promoter). Additional inducible promtors are known in the art and are discussed
elsewhere herein.
Methods for establishing callus from explants are known. For example,
roots, stems, buds, and aseptically germinated seedlings are just a few of the
sources of tissue that can be used to induce callus formation. Generally, young
and actively growing tissues (i.e., young leaves, roots, meristems or other tissues)
are used, but are not required. Callus formation is controlled by growth regulating
substances present in the medium (auxins and cytokinins). The specific
concentrations of plant regulators needed to induce callus formation vary from
species to species and can even depend on the source of explant. In some
instances, it is advised to use different growth substances (e.g. 2, 4-D or NAA) or
a combination of them during tests, since some species may not respond to a
specific growth regulator. In addition, culture conditions (i.e., light, temperature,
etc".) can also influence the establishment of callus. Once established, callus
cultures can be used to initiate shoot regeneration. See, for example, Gurel et a/.
(2001) Turk J. Bat. 25:25-33; Dodds et a/. (1995). Experiments in Plant Tissue
Culture, Cambridge University Press; Gamborg (1995) Plant Cell, Tissue and
Organ Culture, eds. G. Phillips; and, U.S. Application No. 20030180952, all of
which are herein incorporated by reference.
It is further recognized that increasing seed size and/or weight can be
accompanied by an increase in the rate of growth of seedlings or an increase in
vigor. In addition, modulating the plant's tolerance to stress, as discussed below,
along with modulation of root, shoot and leaf development can increase plant yield
and vigor. As used herein, the term "vigor" refers to the relative health,
productivity, and rate of growth of the plant and/or of certain plant parts, and may
be reflected in various developmental attributes, including, but not limited to,
concentration of chlorophyll, photosynthetic rate, total biomass, root biomass,
grain quality, and/or grain yield. In Zee mays in particular, vigor may also be
reflected in ear growth rate, ear size, and/or expansiveness of silk exsertion.
Vigor may relate to the ability of a plant to grow rapidly during early development
and to the successful establishment, after germination, of a well-developed root
system and a well-developed photosynthetic apparatus. Vigor may be determined
with reference to different genotypes under similar environmental conditions, or
with reference to the same or different genotypes under different environmental
conditions.
Accordingly, the present invention further provides plants having modulated
shoot and/or leaf development when compared to a control plant. In some
embodiments, the plant of the invention has an increased level/activity of the IPT
polypeptide of the invention. In other embodiments, the plant of the invention has
a decreased level/activity of the IPT polypeptide of the invention.
VI. Modulating Reproductive Tissue Development
Methods for modulating reproductive tissue development are provided. In
one embodiment, methods are provided to modulate floral development in a plant.
By "modulating floral development" is intended any alteration in a structure of a
plant's reproductive tissue as compared to a control plant or plant part.
"Modulating floral development" further includes any alteration in the timing of the
development of a plant's reproductive tissue (i.e., delayed or accelerated floral
development) when compared to a control plant or plant part. Macroscopic
alterations may include changes in size, shape, number, or location of
reproductive organs, the developmental time period during which these structures
form, or the ability to maintain or proceed through the flowering process in times of
environmental stress. Microscopic alterations may include changes to the types or
shapes of cells that make up the reproductive organs.
The method for modulating floral development in a plant comprises
modulating (either increasing or decreasing) the level and/or activity of the IPT
polypeptide in a plant. In one method, an IPT sequence of the invention is
provided. An IPT nucleotide sequence can be provided by introducing into the
plant a polynucleotide comprising an IPT nucleotide sequence of the invention,
expressing the IPT sequence, and thereby modifying floral development. In some
embodiments, the IPT nucleotide construct introduced into the plant is stably
incorporated into the genome of the plant.
As discussed above, one of skill will recognize the appropriate promoter to
use to modulate floral development in the plant. Exemplary promoters for this
embodiment include constitutive promoters, inducible promoters, shoot-preferred
promoters, and inflorescence-preferred promoters (including developing-femaleinflorescence-
preferred promoters), including those listed elsewhere herein.
In specific methods, floral development is modulated by increasing the level
and/or activity of the IPT sequence of the invention. Such methods can comprise
introducing an IPT nucleotide sequence into the plant and increasing the activity of
the IPT polypeptide. In some methods, the IPT nucleotide construct introduced
into the plant is stably incorporated into the genome of the plant. An increase in
the level and/or activity of the IPT sequences can result in one or more alterations
in floral development including, but not limited to, accelerated flowering, increased
number of flowers, and improved seed set when compared to a control plant. In
addition, an increase in the level or activity of the IPT sequences can result in the
prevention of flower senescence and an alteration in embryo number per kernel.
See, Young et al. (2004) Plant J. 38:910-22. Methods for measuring such
developmental alterations in floral development are known in the art. See, for
example, Mouradov et al. (2002) The Plant Cell S111-S130, herein incorporated
by reference.
In other methods, floral development is modulated by decreasing the level
and/or activity of the IPT sequence of the invention. A decrease in the level and/or
"activity of the IPT sequence""can result in kernel abortion and infertile female
inflorescence, Inducing delayed flowering or inhibiting flowering can be used to
enhance yield in forage crops such as alfalfa.
Accordingly, the present invention further provides plants having modulated
floral development when compared to the floral development of a control plant.
Compositions include plants having a decreased level/activity of the IPT
polypeptide of the invention and having an altered floral development.
Compositions also include plants having an increased level/activity of the IPT
polypeptide of the invention wherein the plant maintains or proceeds through the
flowering process in times of stress.
VII. Modulating the Stress Tolerance of a Plant
Methods are provided for the use of the IPT sequences of the invention to
modify the tolerance of a plant to abiotic stress. Increases in the growth of
seedlings or early vigor is often associated with an increase in stress tolerance.
For example, faster development of seedlings, including the root system of
seedlings upon germination, is critical for survival particularly under adverse
conditions such as drought. Promoters that can be used in this method are
described elsewhere herein, including low-level constitutive, inducible, or rootpreferred
promoters, such as root-preferred promoters derived from ZmlPT4 and
ZmlPTS regulatory sequences. Accordingly, in one method of the invention, a
plant's tolerance to stress is increased or maintained when compared to a control
plant by decreasing the level of IPT activity in the germinating seedling. In other
methods, an IPT nucleotide sequence is provided by introducing into the plant a
polynucleotide comprising a IPT nucleotide sequence of the invention, expressing
the IPT sequence, and thereby increasing the plant's tolerance to stress. In other
embodiments, the IPT nucleotide construct introduced into the plant is stably
incorporated into the genome of the plant.
Methods are also provided to increase or maintain seed set during abiotic
stress episodes. During periods of stress (i.e., drought, salt, heavy metals,
temperature, etc.) embryo development is often aborted. In maize, halted embryo
development results in aborted kernels on the ear (Cheikh and Jones (1994) Plant
Physiol, 106:45-51; Dietrich et al. (1995) Plant Physiol Biochem 33:327-336).
Preventing this kernel loss will maintain yield. Accordingly, methods are provided
to increase the stress resistance in a plant (e.g., during flowering and seed
development). Increasing expression of the IPT sequence of the invention can
also modulate floral development during periods of stress, and thus methods are
provided to maintain or improve the flowering process in plants under stress. The
method comprises increasing the level and/or activity of the IPT sequence of the
invention. In one method, an IPT nucleotide sequence is introduced into the plant
and the level and/or activity of the IPT polypeptide is increased, thereby
maintaining or improving the tolerance of the plant under stress conditions. In
other methods, the IPT nucleotide construct introduced into the plant is stably
incorporated into the genome of the plant. See, for example, WO 00/63401.
Significant yield instability can occur as a result of unfavorable
environments during the lag phase of seed development. During this period,
seeds undergo dramatic changes in ultra structure, biochemistry, and sensitivity to
environmental perturbation, yet demonstrate little change in dry mass
accumulation. Two important events that occur during the lag phase are initiation
and division of endosperm cells and amyloplasts (which are the sites for starch
deposition). It has been demonstrated that during the lag phase (around 10-12
days after pollination (DAP) in maize) a dramatic increase in cytokinin
concentration immediately precedes maximum rates of endosperm cell division
and amyloplast formation, indicating that this hormone plays a central role in these
processes and in what is called the 'sink strength* of the developing seed.
Cytokinins have been demonstrated to play an important role in establishing seed
size, decreasing tip kernel abortion, and increasing seed set during unfavorable
environmental conditions. For example, elevated temperatures affect seed
formation. Elevated temperatures can inhibit the accumulation of cytokinin,
decrease endosperm ceil division and amyloplast number, and as a consequence,
increase kernel abortion.
Kernel sink capacity in maize is principally a function of the number of
endosperm cells and starch granules established during the first 6 to 12 DAP. The
final number of endosperm cells and amyloplasts formed is highly correlated with
final kernel weight. (Capitanio et al., 1983; Reddy and Daynard, 1983; Jones et
al., 1985, 1996; Engelen-Eigles et al., 2000). Hormones, especially cytokinins,
have been shown to stimulate cell division, plastid initiation and other processes
important in the establishment of kernel sink capacity (Davies, 1987). Cytokinin
levels could for example be manipulated using the ZmlPT2 promoter to drive the
expression of the Agrobacterium IPT gene. Similarly, endosperm- and/or pedicel-
preferred promoters could be used to increase the level and/or duration of
expression of ZmlPT2, which would result in an increase of cytokinin levels which
would in turn increase sink strength and kernel yield. Capitano, R., Gentinetta, E.
and Motto, M. (1983). Grain weight and its components in maize inbred lines.
Maydica 23: 365-379. Jones, R. J., Roessler, J. and Ouattar, S. (1985). Thermal
environment during endosperm cell division in maize: effects on number of
endosperm cells and starch granules. Crop Science 25:830-834. Jones, R.J.,
Schreiber, B.M.N. and Roessler, J. (1996). Kernel sink strength capacity in maize:
Genotypic and maternal regulation. Crop Science 36:301-306. Davies, G.C.
(1987).The plant hormones: their nature, occurrences and function. P 1-12. In P.J.
Davies and M. Nijhoff (ed.). Plant hormones and their role in plant growth and
development. Dordrecht, the Netherlands. Engelen-Eigles G., Jones, R. J. and
Phillips R. L. (2000). DNA endoreduplication in maize endosperm cells: the effect
of exposure to short-term high temperature. Plant, Cell and Environment 23: 657-
663.
Methods are therefore provided to increase the activity and/or level of IPT
polypeptides in the developing inflorescence, thereby elevating cytokinin levels
and allowing developing seed to achieve their full genetic potential for size,
minimize seed abortion, and buffer seed set during unfavorable environments.
The methods further allow the plant to maintain and/or improve the flowering
process during unfavorable environments.
In this embodiment, a variety of promoters could be used to direct the
expression of a sequence capable of increasing the level and/or activity of the IPT
polypeptide, including but not limited to, constitutive promoters, seed-preferred
promoters, developing seed or kernel promoters, meristem-preferred promoters,
stress-induced promoters, and inflorescence-preferred (such as developing female
inflorescence promoters). In one method, a promoter that is stress insensitive and
is expressed in a tissue of the developing seed during the lag phase of
development is used. By "insensitive to stress" is intended that the expression
level of a sequence operably linked to the promoter is not altered or only minimally
altered under stress conditions. By "lag phase" promoter is intended a promoter
that is active in the lag phase of seed development. A description of this
developmental phase is found elsewhere herein. By "developing seed-preferred"
is intended a promoter that allows for enhanced IPT expression within a
developing seed. Such promoters that are stress insensitive and are expressed in
a tissue of the developing seecl during the lag phase of development are known in
the art and include Zag2.1 (Theissen et a/. (1995) Gene 156:155-166, Genbank
Accession No. X80206), and mzE40 (Zm40) (U.S. Patent No. 6,403,862 and
WO01/2178).
An expression construct may further comprise nucleotide sequences
encoding peptide signal sequences in order to effect changes in cytokinin level
and/or activity in the mitochondria or chloroplasts. See, for example, Neupert
(1997) Annual Rev, Biochem. 66:863-917; Glaser et al. (1998) Plant Molecular
Biology 38:311-338; Dubyetal. (2001) The Plant J 27(6):539-549.
Methods to assay for an increase in seed set during abiotic stress are
known in the art. For example, plants having the increased IPT activity can be
monitored under various stress conditions and compared to control plants. For
instance, the plant having the increased cytokinin synthesis activity can be
subjected to various degrees of stress during flowering and seed set. Under
identical conditions, the genetically modified plant having the increased cytokinin
synthesis activity will have a higher number of developing kernels than a control
plant.
Accordingly, the present invention further provides plants having increased
yield or a maintained yield and/or an increased or maintained flowering process
during periods of abiotic stress (drought, salt, heavy metals, temperature
extremes, etc.). In some embodiments, the plants having an increased or
maintained yield during abiotic stress have an increased level/activity of the IPT
polypeptide of the invention. In some embodiments, the plant comprises an IPT
nucleotide sequence of the invention operably linked to a promoter that drives
expression in the plant cell. In some embodiments, such plants have stably
incorporated into their genome a nucleic acid molecule comprising an IPT
nucleotide sequence of the invention operably linked to a promoter that drives
expression in the plant cell.
VIII. Methods of Use for IPT promoter Polynucleotides
The polynucleotides compn'sing the IPT promoters disclosed in the present
invention, as well as variants and fragments thereof, are useful in the genetic
manipulation of any host cell, preferably plant cell, when assembled with a DNA
construct such that the promoter sequence is operably linked to a nucleotide
sequence comprising a polynucleotide of interest. In this manner, the IPT
"promoter polynucleoWes" of "the invention are provided in expression cassettes
along with a heterologous polynucleotide sequence of interest for expression in
the host cell of interest. As discussed in Example 2 below, the IPT promoter
sequences of the invention are expressed in a variety of tissues and thus the
promoter sequences can find use in regulating the temporal and/or the spatial
expression of polynucleotides of interest.
Synthetic hybrid promoter regions are known in the art. Such regions
comprise upstream promoter elements of one polynucleotide operably linked to
the promoter element of another polynucleotide. In an embodiment of the
invention, heterologous sequence expression is controlled by a synthetic hybrid
promoter comprising the IPT promoter sequences of the Invention, or a variant or
fragment thereof, operably linked to upstream promoter element(s) from a
heterologous promoter. Upstream promoter elements that are involved in the
plant defense system have been identified and may be used to generate a
synthetic promoter. See, for example, Rushton etal. (1998) Curr. Opin. Plant Biol.
7:311-315. Alternatively, a synthetic IPT promoter sequence may comprise
duplications of the upstream promoter elements found within the IPT promoter
sequences.
It is recognized that a promoter sequence of the invention may be used with
its native IPT coding sequence. A DNA construct comprising an IPT promoter
operably linked with its native IPT gene may be used to transform any plant of
interest to bring about a desired phenotypic change, such as modulating cytokinin
levels, modulating root, shoot, leaf, floral, and embryo development, stress
tolerance, and any other phenotype described elsewhere herein.
The promoter nucleotide sequences and methods disclosed herein are
useful in regulating expression of any heterologous nucleotide sequence in a host
plant in order to vary the phenotype of a plant. Various changes in phenotype are
of interest including modifying the fatty acid composition in a plant, altering the
amino acid content of a plant, altering a plant's pathogen defense mechanism, and
the like. These results can be achieved by providing expression of heterologous
products or increased expression of endogenous products in plants. Alternatively,
the results can be achieved by providing for a reduction of expression of one or
more endogenous products, particularly enzymes or cofactors in the plant. These
changes result in a change in phenotype of the transformed plant.
Genes OT interest are reflective of the commercial markets and interests of
those involved in the development of the crop. Crops and markets of interest"
change, and as developing nations open up world markets, new crops and
technologies will emerge also. In addition, as our understanding of agronomic
traits and characteristics such as yield and heterosis increase, the choice of genes
for transformation will change accordingly. General categories of genes of interest
include, for example, those genes involved in information, such as zinc fingers,
those involved in communication, such as kinases, and those involved in
housekeeping, such as heat shock proteins. More specific categories of
transgenes, for example, include genes encoding important traits for agronomics,
insect resistance, disease resistance, herbicide resistance, sterility, grain
characteristics, and commercial products. Genes of interest include, generally,
those involved in oil, starch, carbohydrate, or nutrient metabolism as well as those
affecting kernel size, sucrose loading, and the like,
In one embodiment, sequences of interest improve plant growth and/or crop
yields. In more specific embodiments, expression of the nucleotide sequence of
interest improves the plant's response to stress induced under high density growth
conditions. For example, sequences of interest include agronomically important
genes that result in improved primary or lateral root systems. Such genes include,
but are not limited to, nutrient/water transporters and growth inducers. Examples
of such genes, include but are not limited to, maize plasma membrane H+-ATPase
(MHA2) (Frias Qt al. (1996) Plant Cell 8:1533-44); AKT1, a component of the
potassium uptake apparatus in Arabidopisis, (Spalding et al. (1999) J Gen Physiol
773:909-18); RML genes which activate cell division cycle in the root apical cells
(Cheng et al. (1995) Plant Physiol 108:881); maize glutamine synthetase genes
(Sukanya et al. (1994) Plant Mol Biol 26:1935-46) and hemoglobin (Duff et al.
(1997) J. Biol. Chem 27:16749-16752, Arredondo-Peter et al. (1997) Plant
Physiol. 115:1259-1266; Arredondo-Peter et al. (1997) Plant Physiol 174:493-500
and references sited therein). The sequence of interest may also be useful in
expressing antisense nucleotide sequences of genes that negatively affect root
development.
Additional, agronomically important traits such as oil, starch, and protein
content can be genetically altered In addition to using traditional breeding
methods. Modifications include increasing content of oleic acid, changing the
proportions of saturated and unsaturated oils, increasing levels of lysine and
sulfur, providing essential amino acids, and also modification of starch.
Hordothionin protein modifications are described in U.S. Patent Nos. 5,703,049,
5,885,801, 5,885,802, and 5,990,389, herein incorporated by reference. Another
example is lysine and/or sulfur rich seed protein encoded by the soybean 2S
albumin described in U.S. Patent No. 5,850,016, and the chymotrypsin inhibitor
from barley, described in Williamson et al. (1987) Eur. J. Biochem. 165:99-106,
the disclosures of which are herein incorporated by reference.
Derivatives of the coding sequences can be made by site-directed
mutagenesis to increase the level of preselected amino acids in the encoded
polypeptide. For example, the gene encoding the barley high lysine polypeptide
(BHL) is derived from barley chymotrypsin inhibitor, U.S. Application Serial No.
08/740,682, filed November 1, 1996, and WO 98/20133, the disclosures of which
are herein incorporated by reference. Other proteins include methionine-rich plant
proteins such as from sunflower seed (Lilley et al. (1989) Proceedings of the
World Congress on Vegetable Protein Utilization in Human Foods and Animal
Feedstuffs, ed. Applewhite (American Oil Chemists Society, Champaign, Illinois),
pp. 497-502; herein incorporated by reference); corn (Pedersen et al. (1986) J.
Blot, Chem. 261:6279; Kirihara et al. (1988) Gene 71:359; both of which are herein
incorporated by reference); and rice (Musumura et al. (1989) Plant Mol. Biol.
12:123, herein incorporated by reference). Other agronomically important genes
encode latex, Floury 2, growth factors, seed storage factors, and transcription
factors.
Insect resistance genes may encode resistance to pests that have great
yield drag such as rootworm, cutworm, European Corn Borer, and the like. Such
genes include, for example, Bacillus thuringiensis toxic protein genes (U.S. Patent
Nos. 5,366,892; 5,747,450; 5,736,514; 5,723,756; 5,593,881; and Geiser et al.
(1986) Gene 48:109); and the like.
Genes encoding disease resistance traits include detoxification genes, such
as against fumonosin (U.S. Patent No. 5,792,931); avirulence (avr) and disease
resistance (R) genes (Jones et al. (1994) Science 266:789; Martin et al. (1993)
Science 262:1432; and Mindrinos et al. (1994) Cell 78:1089); and the like.
Herbicide resistance traits may include genes coding for resistance to
herbicides that act to inhibit the action of acetolactate synthase (ALS), in particular
the sulfonylurea-type herbicides (e.g., the acetolactate synthase (ALS) gene
containing mutations leading to such resistance, in particular the S4 and/or Hra
mufot'ions), genes coding for'resistance to herbicides that act to inhibit action of
glutamine synthase, such as phosphinothricin or basta (e.g., the bar gene), or
other such genes known in the art. The bar gene encodes resistance to the
herbicide basta, the nptll gene encodes resistance to the antibiotics kanamycin
and geneticin, and the ALS-gene mutants encode resistance to the herbicide
chlorsulfuron.
Sterility genes can also be encoded in an expression cassette and provide
an alternative to physical emasculation. Examples of genes used in such ways
include male tissue-preferred genes and genes with male sterility phenotypes
such as DAM, described in U.S. Patent No. 5,750,868; 5,689,051; and 6,281,348.
Other genes include kinases and those encoding compounds toxic to either male
or female gametophytic development.
The quality of grain is reflected in traits such as levels and types of oils,
saturated and unsaturated, quality and quantity of essential amino acids, and
levels of cellulose. In corn, modified hordothionin proteins are described in U.S.
Patent Nos. 5,703,049, 5,885,801, 5,885,802, and 5,990,389.
Commercial traits can also be encoded on a gene or genes that could
increase for example, starch for ethanol production, or provide expression of
proteins. Another important commercial use of transformed plants is the
production of polymers and bioplastics such as described in U.S. Patent No.
5,602,321. Genes such as p-Ketothiolase, PHBase (polyhydroxyburyrate
synthase), and acetoacetyl-CoA reductase (see Schubert et a/. (1988) J. Bacteriol.
170:5837-5847) facilitate expression of polyhyroxyalkanoates (PHAs).
Exogenous products include plant enzymes and products as well as those
from other sources including prokaryotes and other eukaryotes. Such products
include enzymes, cofactors, hormones, and the like. The level of proteins,
particularly modified proteins having improved amino acid distribution to improve
the nutrient value of the plant, can be increased. This is achieved by the
expression of such proteins having enhanced amino acid content.
IX. Antibody Creation and Use
Antibodies can be raised to a protein of the present invention, including
variants and fragments thereof, in both their naturally-occurring and recornbinant
forms. Many methods of making antibodies are known to persons of skill. A
variety of analytic methods are available to generate a hydrophilicity profile of a
protein of the present invention" Such methods can be used to guide the artisan in
the selection of peptides of the present invention for use in the generation or
selection of antibodies which are specifically reactive, under immunogenic
conditions, to a protein of the present invention. See, e.g., J. Janin, Nature,
277(1979) 491-492; Wolfenden, et al., biochemistry 20(1981) 849-855; Kyte and
Doolite, J. MolBiol. 157(1982) 105-132; Rose, era/., Science 229(1985) 834-8S&.
The antibodies can be used to screen expression libraries for particular expression
products such as normal or abnormal protein, or altered levels of the same, which
may be useful for detecting or diagnosing various conditions related to the
presence of the respective antigens. Assays indicating high levels of an IPT
protein of the invention, for example, could be useful in detecting plants, or
specific plant parts, with elevated cytokinin levels. Usually the antibodies in such
a procedure are labeled with a moiety which allows easy detection of presence of
antigen/antibody binding.
The following discussion is presented as a general overview of the
techniques available; however, one of skill will recognize that many variations
upon the following methods are known.
A number of immunogens are used to produce antibodies specifically
reactive with a protein of the present invention. Polypeptides encoded by isolated
recombinant, synthetic, or native polynucleotides of the present invention are the
preferred antigens for the production of monoclonal or polyclonal antibodies.
Polypeptides of the present invention are optionally denatured, and optionally
reduced, prior to injection into an animal capable of producing antibodies. Either
monoclonal or polyclonal antibodies can be generated for subsequent use in
immunoassays to measure the presence and quantity of the protein of the present
invention. Methods of producing polyclonal antibodies are known to those of skill
in the art. In brief, an antigen, preferably a purified protein, a protein coupled to an
appropriate carrier (e.g., GST, keyhole limpet hemanocyanin, etc.), or a protein
incorporated into an immunization vector such as a recombinant vaccinia virus
(see, U.S. Patent No. 4,722,848) is mixed with an adjuvant and animals are
immunized with the mixture. The animal's immune response to the immunogen
preparation is monitored by taking test bleeds and determining the titer of
reactivity to the protein of interest. When appropriately high titers of antibody to
the immunogen are obtained, blood is collected from the animal and antisera are
prepared. Specific monoclonal and polyclonal antibodies will usually have an
antibody binding site with an affinity constant for its cognate monovalent antigen at
least between 106-107, usually at least 108, 109, 1010, and up to about 1011
liters/mole. Further fractionation of the antisera to enrich for antibodies reactive to
the protein is performed where desired (See, e.g., Coligan, Current Protocols in
Immunology, Wiley/Greene, NY (1991); and Harlow and Lane, Antibodies: A
Laboratory Manual, Cold Spring Harbor Press, NY (1989)).
Antibodies, including binding fragments and single chain recombinant
versions thereof, against predetermined fragments of a protein of the present
invention are raised by immunizing animals, e.g., with conjugates of the fragments
with carrier proteins as described above. Typically, the immunogen of interest is a
protein of at least about 5 amino acids, more typically the protein is 10 amino
acids in length, often 15 to 20 amino acids in length, and may be longer. The
peptides are typically coupled to a carrier protein (e.g., as a fusion protein), or are
recombinantly expressed in an immunization vector. Antigenic determinants on
peptides to which antibodies bind are typically 3 to 10 amino acids in length.
Monoclonal antibodies are prepared from hybrid cells secreting the desired
antibody. Monoclonal antibodies are screened for binding to a protein from which
the antigen was derived. Description of techniques for preparing such monoclonal
antibodies are found in, e.g., Basic and Clinical Immunology, 4th ed., Stites et a/.,
Eds., Lange Medical Publications, Los Altos, CA, and references cited therein;
Harlowand Lane, Supra1, Goding, Monoclonal Antibodies: Principles and Practice,
2nd ed., Academic Press, New York, NY (1986); and Kohler and Milstein, Nature
256: 495-497 (1975). Summarized briefly, this method proceeds by injecting an
animal with an antigen comprising a protein of the present invention. The animal
is then sacrificed and cells taken from its spleen, which are fused with myeloma
cells. The result is a hybrid cell or "hybridoma" that is capable of reproducing in
vitro. The population of hybridomas is then screened to isolate individual clones,
each of which secretes a single antibody species to the antigen. In this manner,
the individual antibody species obtained are the products of immortalized and
cloned single B cells generated by the animal in response to a specific site
recognized on the antigenic substance.
Other suitable techniques involve selection of libraries of recombinant
antibodies in phage or similar vectors (see, e.g., Huse et a/., Science 246: 1275-
1281 (1989); and Ward, et a/., Nature 341: 544-546 (1989); and Vaughan et a/,,
Nature Biotechnology, 14: 309-314 (1996)). Also, recombinant immunoglobulins
may be produced. See, Cabllly, U.S. Patent No. 4,816,567; and Queen et a/.,
Proc. Nat'lAcad. Sci. 86: 10029-10033 (1989).
Antibodies to the polypeptides of the invention are also used for affinity
chromatography in isolating proteins of the present invention. Columns are
prepared, e.g., with the antibodies linked to a solid support, e.g., particles, such as
agarose, SEPHADEX, or the like, where a cell lysate is passed through the
column, washed, and treated with increasing concentrations of a mild denaturant,
whereby purified proteins are released.
Frequently, the proteins and antibodies of the present invention will be
labeled by joining, either covalently or non-covalently, a substance which provides
for a detectable signal. A wide variety of labels and conjugation techniques are
known and are reported extensively in both the scientific and patent literature.
Suitable labels include radionucleotides, enzymes, substrates, cofactors,
inhibitors, fluorescent moieties, chemiluminescent moieties, magnetic particles,
and the like.
Protein Immunoassavs
Means of detecting the proteins of the present invention are not critical
aspects of the present invention. In certain examples, the proteins are detected
and/or quantified using any of a number of well-recognized immunological binding
assays (see, e.g., U.S. Patents 4,366,241; 4,376,110; 4,517,288; and 4,837,168).
For a genera! review of immunoassays, see also Methods in Cell Biology, Vol. 37;
Antibodies in Cell Biology, Asai, Ed., Academic Press, Inc. New York (1993);
Basic and Clinical Immunology 7th Edition, Stites & Terr, Eds. (1991). Moreover,
the immunoassays of the present invention can be performed in any of several
configurations, e.g., those reviewed in Enzyme Immunoassay, Maggio, Ed., CRC
Press, Boca Raton, Florida (1980); Tijan, Practice and Theory of Enzyme
Immunoassays, Laboratory Techniques in Biochemistry and Molecular Biology,
Elsevier Science Publishers B.V., Amsterdam (1985); Harlow and Lane, supra;
Immunoassay: A Practical Guide, Chan, Ed., Academic Press, Orlando, FL
(1987); Principles and Practice of Immunoassaysm, Price and Newman Eds.,
Stockton Press. NY (1991); and Non-isotopic Immunoassays, Ngo, Ed., Plenum
Press, NY (1988).
Immunological binding assays (or immunoassays) typically utilize a
"capture agent" to specifically bind to and often immobilize the analyte (in this
case, a protein of the present invention). The capture agent is a moiety that
specifically binds to the analyte. In certain embodiments, the capture agent is an
antibody that specifically binds a protein of the present invention. The antibody
may be produced by any of a number of means known to those of skill in the art as
described herein.
Immunoassays also often utilize a labeling agent to specifically bind to and
label the binding complex formed by the capture agent and the analyte. The
labeling agent may itself be one of the moieties comprising the antibody/analyte
complex. Thus, the labeling agent may be a labeled protein of the present
invention or a labeled antibody specifically reactive to a protein of the present
invention. Alternatively, the labeling agent may be a third moiety, such as another
antibody, that specifically binds to the antibody/protein complex.
Throughout the assays, incubation and/or washing steps may be required
after each combination of reagents. Incubation steps can vary from about 5
seconds to several hours, often from about 5 minutes to about 24 hours.
However, the incubation time will depend upon the assay format, analyte, volume
of solution, concentrations, and the like. Usually, the assays will be carried out at
ambient temperature, although they can be conducted over a range of
temperatures, such as 10°C to 40°C.
While the details of the immunoassays of the present invention may vary
with the particular format employed, the method of detecting a protein of the
present invention in a biological sample generally comprises the steps of
contacting the biological sample with an antibody which specifically reacts, under
immunologically reactive conditions, to a protein of the present invention. The
antibody is allowed to bind to the protein under immunologically reactive
conditions, and the presence of the bound antibody is detected directly or
indirectly.
A. Non-Competitive Assay Formats
Immunoassays for detecting proteins of the present invention include
competitive and noncompetitive formats. Noncompetitive immunoassays are
assays in which the amount of captured analyte (i.e., a protein of the present
invention) is directly measured. In one example, the "sandwich" assay, the
capture agent (e.g., an antibody specifically reactive, under Immunoreactive
conditions, to a protein of the present invention) can be bound directly to a solid
suosiraie wnere u is immooiiizea. These immobilized antibodies then capture the
protein present in the test sample. The protein thus immobilized is then bound by
a labeling agent, such as a second antibody bearing a label. Alternatively, the
second antibody may lack a label, but it may, in turn, be bound by a labeled third
antibody specific to antibodies of the species from which the second antibody is
derived. The second antibody can be modified with a detectable moiety, such as
biotin, to which a third labeled molecule can specifically bind, such as enzymelabeled
streptavidin
B- Competitive Assay Formats
In competitive assays, the amount of analyte present in the sample is
measured indirectly by measuring the amount of an added (exogenous) analyte
(e.g., a protein of the present invention) displaced (or competed away) from a
capture agent (e.g., an antibody specifically reactive, under immunoreactive
conditions, to the protein) by the analyte present in the sample. In one competitive
assay, a known amount of analyte is added to the sample and the sample is then
contacted with a capture agent that specifically binds a protein of the present
invention. The amount of protein bound to the capture agent is inversely
proportional to the concentration of analyte present in the sample.
In one embodiment, the antibody is immobilized on a solid substrate. The
amount of protein bound to the antibody may be determined either by measuring
the amount of protein present in a protein/antibody complex, or alternatively by
measuring the amount of remaining uncomplexed protein. The amount of protein
may be detected by providing a labeled protein.
A hapten inhibition assay is another competitive assay. In this assay a
known analyte, such as a protein of the present invention, is immobilized on a
solid substrate. A known amount of antibody specifically reactive, under
immunoreactive conditions, to the protein is added to the sample, and the sample
is then contacted with the immobilized protein. In this case, the amount of
antibody bound to the immobilized protein is inversely proportional to the amount
of protein present in the sample. Again, the amount of immobilized antibody may
be determined by detecting either the immobilized fraction of antibody or the
fraction of the antibody that remains in solution. Detection may be direct, where
the antibody is labeled, or indirect, by the subsequent addition of a labeled moiety
that specifically binds to the antibody, as described above.
C. Generation of pooled antisera for use in immunoassavs
A protein that specifically binds to, or that is specifically immunoreactive
with, an antibody generated against a defined antigen is determined in an
immunoassay. The immunoassay uses a polyclonal antiserum which is raised to
a polypeptide of the present invention (i.e., the antigenic polypeptide). This
antiserum is selected to have low cross-reactivity against other proteins, and any
such cross-reactivity is removed by immunoabsorbtion prior to use in the
immunoassay (e.g., by immunosorbtion of the antisera with a protein of different
substrate specificity (e.g., a different enzyme) and/or a protein with the same
substrate specificity but of a different form).
In order to produce antisera for use in an immunoassay, a polypeptide of
the present invention is isolated as described herein. For example, recombinant
protein can be produced in a mammalian or other eukaryotic cell line. An inbred
strain of mice is immunized with the protein using a standard adjuvant, such as
Freund's adjuvant, and a standard mouse immunization protocol (see Harlow and
Lane, supra). Alternatively, a synthetic polypeptide derived from the sequences
disclosed herein and conjugated to a carrier protein is used as an immunogen.
Polyclonal sera are collected and titered against the immunogenic polypeptide in
an immunoassay, for example, a solid phase immunoassay with the immunogen
immobilized on a solid support. Polyclonal antisera with a titer of 104 or greater
are selected and tested for their cross reactivity against polypeptides of different
forms or substrate specificity, using a competitive binding immunoassay such as
the one described in Harlow and Lane, supra, at pages 570-573. Preferably, two
or more distinct forms of polypeptides are used in this determination. These
distinct types of polypeptides are used as competitors to identify antibodies which
are specifically bound by the polypeptide being assayed for. The competitive
polypeptides can be produced as recombinant proteins and isolated using
standard molecular biology and protein chemistry techniques as described herein.
Immunoassays in the competitive binding format are used for crossreactivity
determinations. For example, the immunogenic polypeptide is
immobilized to a solid support. Proteins added to the assay compete with the
binding of the antisera to the immobilized antigen. The ability of the above
proteins to compete with the binding of-the antisera to the immobilized protein is
compared to the immunogenic polypeptide. The percent cross-reactivity for the
above proteins is calculated, using standard methods. Those antisera with less
than 10% cross-reactivity for a distinct form of a poiypeptide are selected and
pooled. The cross-reacting antibodies are then removed from the pooled antisera
by immunoabsorbtion with a distinct form of a poiypeptide.
The immunoabsorbed and pooled antisera are then used in a competitive
binding immunoassay as described herein to compare a second "target"
poiypeptide to the immunogenic poiypeptide. In order to make this comparison,
the two polypeptides are each assayed at a wide range of concentrations and the
amount of each poiypeptide required to inhibit 50% of the binding of the antisera to
the immobilized protein is determined using standard techniques. If the amount of
the target poiypeptide required is less than twice the amount of the immunogenic
poiypeptide that is required, then the target poiypeptide is said to specifically bind
to an antibody generated to the immunogenic protein. As a final determination of
specificity, the pooled antisera is fully immunosorbed with the immunogenic
poiypeptide until no binding to the poiypeptide used in the immunosorbtion is
detectable. The fully immunosorbed antisera is then tested for reactivity with the
test poiypeptide. If no reactivity is observed, then the test poiypeptide is
specifically bound by the antisera elicited by the immunogenic protein.
D- Other Assay Formats
In certain embodiments, Western blot (immunoblot) analysis is used to
detect and quantify the presence of protein of the present invention in the sample.
The technique generally comprises separating sample proteins by gel
electrophoresis on the basis of molecular weight, transferring the separated
proteins to a suitable solid support, (such as a nitrocellulose filter, a nylon filter, or
derivatized nylon filter), and incubating the sample with the antibodies that
specifically bind a protein of the present invention. The antibodies specifically bind
to the protein on the solid support. These antibodies may be directly labeled, or
may be subsequently detected using labeled antibodies (e.g., labeled sheep antimouse
antibodies) that specifically bind to the antibodies.
£• Quantification of Proteins.
The proteins of the present invention may be detected and quantified by
any of a number of means well known to those of skill in the art. These include
analytic biochemical methods such as electrophoresis, capillary electrophoresis,
high'" performance liquid chromatography (HPLC), thin layer chromatography
(TLC), hyperdiffusion chromatography, and the like, and various immunological
methods such as fluid or gel precipitin reactions, immunodiffusion (single or
double), immunoelectrophoresis, radioimmunoassays (RIAs), enzyme-linked
5 immunosorbent assays (ELISAs), immunofluorescent assays, and the like.
F. Reduction pf Non-specific Binding
One of skill will appreciate that It is often desirable to reduce non-specific
binding in immunoassays and during analyte purification. Where the assay
10 involves an antigen, antibody, or other capture agent immobilized on a solid
substrate, it is desirable to minimize the amount of non-specific binding to the
substrate. Means of reducing such non-specific binding are well known to those of
skill in the art. Typically, this involves coating the substrate with a proteinaceous
composition. In particular, protein compositions such as bovine serum albumin
15 (BSA), nonfat powdered milk, and gelatin are widely used.
G. Imiyiunoassav Labels
The labeling agent can be, e.g., a monoclonal antibody, a polyclonal
antibody, a binding protein or complex, or a polymer such as an affinity matrix,
20 carbohydrate or lipid. Detectable labels suitable for use in the present invention
include any composition detectable by spectroscopic, radioisotopic,
photochemical, biochemical, immunochemical, electrical, optical or chemical
means. Detection may proceed by any known method, such as immunoblotting,
Western analysis, gel-mobility shift assays, fluorescent in situ hybridization
25 analysis (FISH), tracking of radioactive or bioluminescent markers, nuclear
magnetic resonance, electron paramagnetic resonance, stopped-flow
spectroscopy, column chromatography, capillary electrophoresis, or other
methods which track a molecule based upon an alteration in size and/or charge.
The particular label or detectable group used in the assay is not a critical aspect of
30 the invention. The detectable group can be any material having a detectable
physical or chemical property, including magnetic beads, fluorescent dyes,
radiolabels, enzymes, and colorimetric labels or colored glass or plastic beads, as
discussed for nucleic acid labels, supra. The label may be coupled directly or
indirectly to the desired component of the assay according to methods well known
35 in the art. As indicated above, a wide variety of labels may be used, with the
choice of label depending onlhe sensitivity required, ease of conjugation of the
compound, stability requirements, available instrumentation, and disposal
provisions. Means of detecting labels are well known to those of skill in the art.
Non-radioactive labels are often attached by indirect means. Generally, a
5 ligand molecule (e.g., biotin) is covalently bound to the molecule. The ligarid then
binds to an anti-ligand (e.g., streptavidin) molecule which is either inherently
detectable or covalently bound to a signal system, such as a detectable enzyme, a
fluorescent compound, or a chemiluminescent compound. A number of ligands
and anti-ligands can be used.
10 The molecules can also be conjugated directly to signal-generating
compounds, e.g., by conjugation with an enzyme or fluorophore. Enzymes of
interest as labels will primarily be hydrolases, particularly phosphatases, esterases
and glycosidases, or oxidoreductases, particularly peroxidases. Fluorescent
compounds include fluorescein and its derivatives, rhodamine and its derivatives,
15 dansyl, umbelliferone, etc. Chemiluminescent compounds include luciferin, and
2,3-dihydrophthalazinediones, e.g., luminol. For a review of various labeling or
signal-producing systems which may be used, see, U.S. Patent No. 4,391,904,
which is incorporated herein by reference.
Some assay formats do not require the use of labeled components. For
20 instance, agglutination assays can be used to detect the presence of the target
antibodies. In this case, antigen-coated particles are agglutinated by samples
comprising the target antibodies. In this format, none of the components need be
labeled and the presence of the target antibody is detected by simple visual
inspection.
25
Assays for Compounds that Modulate Enzymatic Activity or Expression
A catalytically active polypeptide of the present invention may be contacted
with a compound in order to determine whether said compound binds to and/or
modulates the enzymatic activity of such polypeptide. The polypeptide employed
30 will have at least 20%, 30%, 40%, 50% 60%, 70% or 80% of the specific activity of
the native, full-length enzyme of the present invention. Generally, the polypeptide
will be present in a range sufficient to determine the effect of the compound,
typically about 1 nM to 10 |*M. Likewise, the compound being tested will be
present in a concentration of from about 1 nM to 10 jaM. Those of "skill will
35 understand that such factors as enzyme concentration, ligand concentrations (i.e.,
substrates, products, inhibitors, activators), pH, ionic strength, and temperature
will be controlled so as to obtain useful kinetic data and determine the presence or
absence of a compound that binds or modulates polypeptide activity. Methods of
measuring enzyme kinetics are well known in the art. See, e.g., Segel,
Biochemical Calculations, 2nd ed., John Wiley and Sons, New York (1976).
Embodiments of the invention include the following:
1. An isolated polypeptide comprising an amino acid sequence selected from
the group consisting of:
(a) an amino acid sequence comprising SEQ ID N0:2, 6, 9, 12, 15, 18,
23, 27, 41, 43,46,49, 52, 54, 57, 59, 61, 63, 66, or 77;
(b) an amino acid sequence comprising at least 85% sequence identity
to SEQ ID NO: 2, 6, 9, 12, 15, 18, 23, 27, 41, 43, 46, 49, 52, 54, 57,
59, 61, 63, 66, or 77, wherein said polypeptide has cytokinin
synthesis activity;
(c) an amino acid sequence encoded by a nucleotide sequence that
hybridizes under stringent conditions to the complement of SEQ ID
NO:1, 3, 4, 5, 7, 8, 10, 11, 13, 14, 16, 17, 19, 20, 21, 22, 24, 26, 28,
40, 42, 44, 45, 47, 48, 50, 51, 53, 55, 56, 58, 60, 62, 64, 65, 69, 70,
71, 72, 73, 74, or 76, wherein said stringent conditions comprise
hybridization in 50% formamide, 1 M NaCI, 1% SDS at 37°C, and a
wash in 0.1X SSC at 60°C to 65°C, wherein said polypeptide retains
cytokinin synthesis activity; and,
(d) an amino acid sequence comprising at least 50 consecutive amino
acids of SEQ ID NO: 2, 6, 9, 12, 15, 18, 23, 27, 41, 43, 46, 49, 52,
54, 57, 59, 61, 63, 66, or 77, wherein said polypeptide retains
cytokinin synthesis activity.
2. An isolated polynucleotide comprising a nucleotide sequence selected from
the group consisting of:
(a) a nucleotide sequence comprising SEQ ID N0:1, 3, 4, 5, 7, 8, 10,
11,13, 14, 16, 17, 19, 20, 21, 22, 24, 26, 28, 40, 42, 44, 45, 47, 48,
50, 51, 53, 55, 56, 58, 60, 62, 64, 65, 69, 70, 71, 72, 7.3, 74, or 76;
(b) a nucleotide sequence encoding an amino acid sequence
comprising SEQ ID NO: 2, 6, 9, 12, 15, 18, 23, 27, 41, 43, 46, 49,
52, 54, 57, 59,61,63, 66, or 77;
(c) a nuclebtide sequence comprising at least 85% sequence identity to
SEQ ID NO: 1, 3, 4, 5, 7, 8, 10,11, 13,14, 16,17, 19, 20, 21, 22, 24,
26, 28, 40, 42, 44, 45, 47, 48, 50, 51, 53, 55, 56, 58, 60, 62, 64, 65,
69, 70, 71, 72, 73, 74, or 76, wherein said polynucleotide encodes a
polypeptide having cytokinin synthesis activity;
(d) a nucleotide sequence comprising at least 50 consecutive
nucleotides of SEQ ID NO: 1, 3, 4, 5, 7, 8, 10, 11, 13,14, 16, 17, 19,
20, 21, 22, 24, 26, 28, 40, 42, 44, 45, 47, 48, 50, 51, 53, 55, 56, 58,
60, 62, 64, 65, 69, 70, 71, 72, 73, 74, or 76, or a complement
thereof; and,
(e) a nucleotide sequence that hybridizes under stringent conditions to
the complement of a nucleotide sequence of a), wherein said
stringent conditions comprise hybridization in 50% formamide, 1 M
NaCI, 1% SDS at 37°G, and a wash in 0.1X SSC at 60°C to 65°C.
An expression cassette comprising a polynucleotide of embodiment 2.
The expression cassette of embodiment 3, wherein said polynucleotide is
operably linked to a promoter that drives expression in a plant.
A plant comprising a polynucleotide operably linked to a promoter that
drives expression in the plant, wherein said polynucleotide comprises a
nucleotide sequence selected from the group consisting of:
(a) a nucleotide sequence comprising SEQ ID NO: 1, 3, 4, 5, 7, 8, 10,
11, 13, 14, 16, 17, 19, 20, 21, 22, 24, 26, 28, 40, 42, 44, 45, 47, 48,
50, 51, 53, 55, 56, 58, 60, 62, 64, 65, 69, 70, 71, 72, 73,74, or 76;
(b) a nucieotide sequence encoding an amino acid sequence
comprising SEQ ID NO: 2, 6, 9, 12, 15, 18, 23, 27, 41, 43, 46, 49,
52, 54, 57, 59, 61,63,66, or 77;
(c) a nucleotide sequence comprising at least 85% sequence identity to
SEQ ID N0:1, 3, 4, 5, 7, 8, 10, 11, 13, 14, 16, 17, 19, 20, 21, 22, 24,
26, 28, 40, 42, 44, 45, 47, 48, 50, 51, 53, 55, 56, 58, 60, 62, 64, 65,
69, 70, 71, 72, 73, 74, or 76, wherein said polynucleotide encodes a
polypeptide having cytokinin synthesis activity;
(d) a nucleotide sequence that hybridizes under stringent conditions to
the complement of a nucleotide sequence of a), wherein said
stringent conditions comprise hybridization in 50% formamide, 1 M
NaCI, 1% SDS at 37°C, and a wash in 0.1X SSC at 60°C to 65°C,
wherein said pblynucleotide encodes a polypeptide having cytokinin
synthesis activity; and,
(e) a nucleotide sequence comprising at least 50 consecutive
nucleotidesofSEQIDNO:1,3, 4,5, 7,8, 10, 11, 13, 14, 16,17, 19,
20, 21, 22, 24, 26, 28, 40, 42, 44, 45, 47, 48, 50, 51, 53, 55, 56, 58,
60, 62,64, 65, 69, 70, 71,72, 73, or 74 or a complement thereof.
6. The plant of embodiment 5, wherein said plant has a modulated cytokinin
level.
7. The plant of embodiment 6, wherein said cytokinin level is modulated in a
vegetative tissue, a reproductive tissue, or vegetative tissue and
reproductive tissue.
8. The plant of embodiment 6, wherein said cytokinin level is increased.
9. The plant of embodiment 6, wherein said cytokinin level is decreased.
10. The plant of embodiment 5, 6, 7, 8, or 9, wherein said promoter is a tissuepreferred
promoter, a constitutive promoter, or an inducible promoter.
11. The plant of embodiment 10, wherein said promoter is a root-preferred
promoter, a leaf-preferred promoter, a shoot-preferred promoter, or an
inflorescence-preferred promoter.
12. The plant of embodiment 5, wherein said plant has modulated floral
development.
13. The plant of embodiment 5, wherein said plant has modulated root
development.
14. The plant of embodiment 13, wherein the modulated root development
comprises at least one of an increase in root growth or an increase in the
formation of lateral or adventitious roots.
15. The plant of embodiment 5, wherein the plant has an altered shoot-to-root
ratio.
16. The plant of embodiment 5, wherein said plant has an increased seed size
or an increased seed weight.
17. The plant of embodiment 16, wherein the increase in seed size or seed
weight comprises an increase in at least one of embryo size, embryo
weight, cotyledon size, or cotyledon weight.
18. The plant of embodiment 5, wherein vigor or biomass yield of said plant is
increased.
'19. The plant of emBoBimeht 5, wherein the stress tolerance of said plant is
maintained or improved.
20. The plant of embodiment 19, wherein the size of the plant is increased or
maintained.
21. The plant of embodiment 19, wherein tip kernel abortion is minimized.
22. The plant of embodiment 19, wherein the seed set of said plant is increased
or maintained.
23. The plant of embodiment 19, 20, 21, or 22, wherein said promoter is stressinsensitive
and is expressed in a tissue of the developing seed or related
maternal tissue, at least during the lag phase of seed development.
24. The plant of embodiment 5, wherein said plant has a decrease in shoot
growth.
25. The plant of embodiment 5, wherein said plant has a delayed senescence
or an enhanced vegetative growth.
26. The plant of any one of embodiments 5 to 9, 12 to 22, 24, and 25 wherein
said polynucleotide is stably incorporated into the genome of the plant.
27. A transformed seed of the plant of claim 26.
28. A plant that is genetically modified at a native genomic locus, said genomic
locus encoding a polypeptide selected from the group consisting of:
(a) an amino acid sequence comprising SEQ ID NO: 2, 6, 9, 12,15, 18,
23, 27, 41, 43, 46, 49, 52, 54, 57, 59, 61, 63, 66, or 77;
(b) an amino acid sequence comprising at least 85% sequence identity
to SEQ ID NO: SEQ ID NO: 2, 6, 9, 12, 15, 18, 23, 27, 41, 43, 46,
49, 52, 54, 57, 59, 61, 63, 66, or 77, wherein said polypeptide has
cytokinin synthesis activity;
wherein said plant is genetically modified to increase, reduce, or eliminate
the activity of said polypeptide.
29. The plant of any one of embodiments 5 to 9, 12 to 22, and 24 to 28,
wherein said plant is a monocot.
30. The plant of embodiment 29, wherein said monocot is maize, wheat, rice,
barley, sorghum, or rye.
31. The plant of any one of embodiment 5 to 9,12 to 22, and 24 to 28, wherein
said plant is a dicot.
32. A method for reducing or eliminating the activity of a polypeptide in a plant
comprising Introducing into said plant a polynucleotide comprising a
nucleotide sequence comprising a fragment of SEQ ID NO: 1, 3, 4, 5, 7, 8,
10, 11, 13, 14, 16, 17, 19, 20, 21, 22, 24, 26, 28, 40, 42, 44, 45, 47, 48, 50,
51, 53, 55, 56, 58, 60, 62, 64, 65, 69, 70, 71, 72, 73, 74, or 76, or
comprising a sequence complementary to said fragment.
33. The method of embodiment 32, wherein providing said polynucleotide
decreases the level of cytokinin in said plant.
34. The method of embodiment 32, wherein the activity of said polypeptide is
reduced or eliminated in a vegetative tissue, a reproductive tissue, or the
vegetative tissue and the reproductive tissue.
35. The method of embodiment 32, wherein said introduced polynucleotide is
operably linked to a tissue-preferred promoter, a constitutive promoter, or
an inducible promoter.
36. The method of embodiment 35, wherein said promoter is a root-preferred
promoter.
37. The method of embodiment 32, wherein reducing or eliminating the activity
of said polypeptide modulates root development of the plant.
38. The method of embodiment 37, wherein the modulated root development
comprises at least one of an increase in root growth or an increase in the
formation of lateral or adventitious roots.
39. A method for increasing the level of a polypeptide in a plant comprising
introducing into said plant a polynucleotide comprising a nucleotide
sequence selected from the group consisting of:
(a) a nucleotide sequence comprising SEQ ID NO: 1, 3,4, 5, 7, 8, 10,
11,13, 14,16, 17, 19, 20, 21, 22, 24, 26, 28, 40, 42, 44,45, 47, 48,
50, 51, 53, 55, 56, 58, 60, 62, 64, 65, 69, 70, 71, 72, 73, 74, or 76;
(b) a nucleotide sequence encoding an amino acid sequence
comprising SEQ ID NO: 2, 6, 9, 12, 15, 18, 23, 27, 41, 43, 46, 49,
52, 54, 57, 59, 61,63, 66, or 77;
(c) a nucleotide sequence comprising at least 85% sequence identity to
SEQ ID NO: 1, 3,4, 5, 7, 8, 10, 11, 13,14, 16,17, 19, 20, 21, 22, 24,
26, 28, 40, 42, 44, 45, 47, 48, 50, 51, 53, 55, 56, 58, 60, 62, 64, 65,
69, 70, 71, 72, 73, 74, or 76, wherein said polynucleotide encodes a
polypeptide having cytokinin synthesis activity;
(d)' a nucleotide" sequence comprising at least 40 consecutive
nucleotides of SEQ ID NO: 1, 3, 4, 5, 7, 8, 10, 11, 13, 14,16,17,19,
20, 21, 22, 24, 26, 28, 40, 42, 44, 45, 47, 48, 50, 51, 53, 55, 56, 58,
60, 62, 64, 65, 69, 70, 71, 72, 73, 74, or 76, or a complement
thereof, wherein said polynucleotide encodes a polypeptide having
cytokinin synthesis activity; and,
(e) a nucleotide sequence that hybridizes under stringent conditions to
the complement of the nucleotide sequence of a), wherein said
stringent conditions comprise hybridization In 50% formamide, 1 M
NaCI, 1% SDS at 37°C, and a wash in 0.1X SSC at 60°C to 65°C,
wherein said polynucleotide encodes a polypeptide having cytokinin
synthesis activity.
40. The method of embodiment 39, wherein expressing said polynucleotide
increases the level of a cytokinin in the plant.
41. The method of embodiment 39 or 40, wherein the level of the polypeptide is
increased in a vegetative tissue, a reproductive tissue, or the vegetative
tissue and the reproductive tissue.
42. The method of embodiment 39 or 40, wherein said promoter is a tissuepreferred
promoter, a constitutive promoter, or an inducible promoter.
43. The method of embodiment 42, wherein said promoter is a root-preferred
promoter, a leaf-preferred promoter, a shoot-preferred promoter, a seedpreferred
promoter, a kernel-preferred promoter, or an inflorescencepreferred
promoter.
44. The method of embodiment 39 or 40, wherein the stress tolerance of said
plant is maintained or improved.
45. The method of embodiment 44, wherein the size of the plant is increased or
maintained.
46. The method of embodiment 44, wherein seed abortion is minimized.
47. The method of embodiment 44, wherein the seed set of said plant is
increased or maintained.
48. The method of embodiment 44, wherein said promoter is stress-insensitive
and is expressed in a tissue of the developing seed during the lag phase of
development.
49. The method of embodiment 39 or 40, wherein increasing the level -of the
polypeptide increases the shoot growth of the plant.
50".' The method oFem'BbS'iment 39 or 40, wherein increasing the activity of the
polypeptide increases seed size or seed weight of the plant.
51. The method of embodiment 50, wherein the increased seed size or seed
weight comprises an increase in at least one of embryo size, embryo
weight, cotyledon size, or cotyledon weight.
52. The method of embodiment 39 or 40, wherein increasing the activity of the
polypeptide increases plant yield or plant vigor of said plant.
53. The method of embodiment 39 or 40, wherein increasing the activity of the
poiypeptide modulates floral development.
54. The method of embodiment 39 or 40, wherein increasing the level of the
polypeptide delays senescence or increases leaf growth.
55. The method of any one of embodiments 32-40, wherein said plant is a
dicot.
56. The method of any one of embodiments 32-40, wherein said plant is a
monocot.
57. The method of embodiment 56, wherein said monocot is maize, wheat, rice,
barley, sorghum, or rye.
58. An isolated polynucleotide comprising a nucleotide sequence comprising
SEQ ID NO: 25 or 75.
59. A DNA construct comprising a promoter operably linked to a nucleotide
sequence of interest, wherein said promoter comprises the polynucleotide
of embodiment 58.
60. An expression vector comprising the DNA construct of embodiment 59.
61. A plant having at least one DNA construct comprising a heterologous
nucleotide sequence of interest operably linked to a promoter, wherein said
promoter comprises SEQ ID NO: 25 or 75.
62. The plant of claim 61, wherein said DNA construct is stably incorporated
into the genome of the plant.
63. The plant of embodiment 61 or 62, wherein said plant is a dicot.
64. The plant of embodiment 61 or 62, wherein said plant is a monocot.
65. The plant of embodiment 63, wherein said monocot is maize, wheat, rice,
barley, sorghum, or rye.
66. The plant of embodiment 61 or 62, wherein said DNA sequence of interest
encodes a polypeptide.
67. A method of regulating the expression of a nucleotide sequence of interest,
said method comprising introducing into' a plant a DNA construct
comprising a heterologous nucleotide sequence of interest operably linked
to a promoter comprising the nucleotide sequence of embodiment 58.
68. The method of claim 67, wherein said DNA construct is stably integrated
into the genome of the plant.
69. The method of embodiment 67 or 68, wherein said plant is a dicot.
70. The method of embodiment 67 or 68, wherein said plant is a monocot.
71. The method of embodiment 70, wherein said monocot is maize, wheat, rice,
barley, sorghum, or rye.
72. The method of embodiment 67 or 68, wherein said DNA sequence of
interest encodes a polypeptide.
The following examples are offered by way of illustration and not by way of
limitation.
EXPERIMENTAL
Example 1. Cloning and Gene Characterization of ZmlPTI
Below we describe the identification and characterization of an IPT
polypeptide from maize designated ZmlPTI.
Material and methods: A Mo17 BAG library was screened using a 3'-end
fragment of the ZmlPTI cDNA from B73, identified by sequence similarity to
Agrobacterium ipt. One of the positive clones was digested by H/ndlll, and
subcloned into pBluescript. Recombinant plasmids were screened using colony
screening and a 3'-end fragment as a probe. One positive clone was sequenced.
Samples used for RT-PCR were harvested in the field from three individual plants.
Five jig of total RNA was used for RT-PCR using ThermoScript RT-PCR System
from invitrogen. The reverse transcribed mixture for PCR used primers designed
across an intron-exon-intron junction in order to avoid amplification of genomic
DNA.
Results:
A. . Deduced protein sequence:
Two putative maize ipt ESTs were identified whose deduced amino acid
sequences show similarity to the Agrobacterium (data not shown), Arabidopsis
and Petunia IPT proteins (Figure 1). Full-insert sequencing of these two ESTs
revealed that they were identical and the corresponding cDNA sequence was
called ZmlPTI (SEQ ID NO: 22).
Figure 1 provides an amino acid alignment of the ZmlPTI, Arabidopsis, and
Petunia cytokinin biosynthetic enzymes. Asterisks indicate amino acids conserved
in many cytokinin biosynthetic enzymes. The amino acids designated by the
underline indicate a putative ATP/GTP binding site (at about amino acids 84-90).
As shown in Figure 1, the deduced protein sequence of ZmlPTI contains the
exact consensus sequence
GxTxxGKtST]xxxxx[VLI]xxxxxxx[VLI)[VLI]xxDxxQx{57,60}[VLI][VLI]xGG[ST] (SEQ
ID NO: 32) (where x denotes any amino acid residue, [ ] any one of the amino
acids shown in [ ], and x{m,n} m to n amino acid residues in number) that was
used by Take! et a/. (2001) J. Biol. Chem. 276:26405-26410 to isolate the
Arabidopsis genes. Note that ZmlPTI also has a putative ATP/GTP binding site
at about amino acids 51-58. In addition, the length of ZmlPTI is very similar to the
AtlPT4 and Sho genes. In addition, the specific zinc-finger like motif
(CxxCx{12,18}HxxxxxH) (SEQ ID NO:33) found in all tRNA IPTs of eukaryotes
(which is necessary to bind tRNA molecules) is absent from ZmlPTI.
The ZmlPTI sequence shares 21.9% amino acid sequence identity (34.1%
similarity) across the full length to Sho (cytokinin biosynthetic protein from
Petunia); 10.8% identity (21.2% similarity) across its full length to ipt
(Agrobacterium); 24.7% identity (34.8% similarity) across its full length to AtlPTI
(Arabidopsis); 35.6% identity (45.3% similarity) across its full length to AtlPT2
(Arabidopsis); 22.4% identity (34.6% similarity) across its full length to AtlPT3
(Arabidopsis); 20.7% identity (31.6% similarity) across its full length to AtlPT4
(Arabidopsis); 22.7% identity (35.7% similarity) across its full length to AtlPT5
(Arabidopsis); 21.8% identity (36.4% similarity) across its full length to AtlPT6
(Arabidopsis); 23.4% identity (33.1% similarity) across its full length to AtlPT7
(Arabidopsis); 26.3% identity (35.9% similarity) across its full length to AtlPTS
(Arabidopsis); and, 18.9% identity (31.2% similarity) across its full length to AtlPT9
(Arabidopsis).
A variant of the ZmlPTI sequence is also provided. SEQ ID NOS: 22, 23,
and 24 correspond to the nucleotide and amino acid sequence of ZmlPTI derived
from the spliced sequence of the Mo17 genomic clone. SEQ ID NOS: 26, 27, and
28 are variants of the ZmlPTI sequence derived from sequencing the full-length
EST from B73. An alignment of ZmlPTI and its variant is shown in Figure 3.
These sequences share 98% overall amino acid sequence identity.
B. Gene structure:
A Mo17 BAG library was screened using probes corresponding to the two
ESTs and four identical clones were identified. An 11kb Hind\\\ fragment from one
of the clones was subcloned in pBluescript and sequenced. Alignment with the
full-insert sequence of the EST clone revealed the presence of six introns.
Interestingly neither the AtlPT4 gene from Arabidopsis nor the Sho gene from
Petunia contain introns. The genomic sequence of ZmlPTI is set forth in SEQ ID
NO: 21.
Example 2. Gene expression of ZmlPTI
One of the identified ZrnlPTI ESTs was from a B73 embryo library, the
other one was from a developing root library. In order to gain an impression of the
level of expression of ZmlPTI, a search of the Lynx database was performed. A
perfect tag was found in the 3'-end of the gene, 231 bp from the poly A tail start.
Tissue types, number of library hits, and average pprn are presented in Table 1.
Expression was found to be very low in most organs, but higher in seedling and
embryo libraries. In embryo libraries, expression was higher at 10 DAP than at
later development stages (Figure 4),
(Table Removed)
Using RT-PCR, the expression pattern of ZmlPT in various maize organs
and on a kernel developmental series was tested. No amplification product could
be detected after 20 cycles, confirming the very low expression of the gene.
However, after 30 cycles, bands of the appropriate size were amplified (Figure 5).
Figure 5A shows ZmlPTI transcripts are present in ovaries of mature plants and
leaf, mesocotyl, ana roots or seedlings. This distribution indicates a bias in
expression of this gene to meristematic-iike and rapidly developing tissues. In
developing B73 kernels (Figure 5B), ZmlPTI transcript is strongly present from 0
to 10 DAP, then decreases beyond 15 DAP. This pattern of expression of ZmlPTI
correlates with the known profile of cytokinin accumulation in developing kernels,
which peaks during the lag phase. This accumulation of cytokinin is thought to
drive early cell division in endosperm and embryo development.
In a similar manner, the ZmlPTI tag could only be detected in the cell
division zone of leaves, and in leaf discs treated with BA. This distribution of
transcripts indicates a bias in expression of ZmlPTI to meristematic-like and
rapidly developing tissues, indicating that maize roots and developing kernels are
strong sites for cytokinin synthesis.
Examples. Isolation and Gene Characterization of ZmlPT2. ZmlPT4.
ZrnlPTS. ZmlPT6. ZmlPTT. ZmlPTS and ZmlPT9
The AtlPTI and AtlPT3 to AtlPT8 protein sequences were blasted against
the six possible frames generated by the maize genomic sequences and searched
for some degree of similarity. Because rice and maize genomes show a significant
degree of synteny, the same method was used against rice genomic database to
optimize this search. The rice sequences with an E-score of at least 200 were then
used for an additional screen of the GSS maize database. Since at that time, the
GSS database had not been assembled into contigs, the sequences obtained
which had an E-score of at least 150 were pooled and aligned using Sequencher.
Using this method, eight maize contigs encoding putative CK biosynthetic
enzymes were identified (ZmlPT2 to ZmlPT9), six of them showing an open
reading frame without introns. The translated proteins corresponding to these
putative genes contained 320 to 380 amino acids, which correlates with the
expected size for plant IPT proteins. An alignment of the corresponding proteins is
presented in Figure 1. The deduced protein sequences of the new ZmlPT genes
(except for ZmlPTS) contain the exact consensus sequence found in IPT proteins
from different species. This sequence,
GxTxxGK[ST]xxxxx[VLI]xxxxx)0([VLI][VLI]xxDxxQx{57,60}[VLI][VLI]xGG[ST3
(where x denotes any amino acid residue, [ ] anyone of the amino acids shown in [
], and x{m,n} m to n amino acid residues in number) (SEQ ID NO:32) is also found
in ZmlPTI and was previously used by Kakimoto and Takei to isolate the
Arabidopsis IPi genes. Homoiogy with other plant IPT proteins was found to be
around 40%.
The amino acid sequence identity and similarity to top BLAST hits across
the full length of ZmlPT2, ZmlPT4, ZmlPTS, ZmlPTS, ZmlPT7, ZmlPTS and
ZmlPT9 are provided below in Table 2.
(Table Removed)
The maize IPT sequences also have putative ATP/GTP binding sites at
about arnino acids 17-24 for ZmlPT2, about amino acids 72-79 for ZmlPT4, about
amino acids 57-64 for ZrnlPTS, about amino acids 55-62 for ZmlPT6, about amino
acids 23-30 for ZmlPT7, and about amino acids 83-90 for ZmlPTS.
The polypeptides encoded by ZmlPT polynucleotides share sequence
similarity to known proteins. For example, a polypeptide encoded by nucleotides
821 to 3 of ZmlPT9 shares 55% amino acid sequence identity to amino acids 48 to
327 of a tRNA isopentenyltransferase from Arabidopsis thaliana (GenBank
Accession No. BAB59048.1). A polypeptide encoded by nucleotides 821 to 3 of
ZmlPT9 shares 55% arnino acid sequence identity to amino acids 48 to 327 of a
putative IPP transferase from Arabidopsis thaliana (GenBank Accession No.
AAK64114.1). A polypeptide encoded by nucleotides 821 to 3 of ZmlPT9 shares
55% amino acid sequence identity to amino acids 48 to 327 of a IPP transferaselike
protein from Arabidopsis thaliana (GenBank Accession No. AAM63091.1). A
polypeptide encoded by nucleotides 839 to 3 of ZmlPT9 shares 36% amino acid
sequence identity to amino acids 28 to 278 of a putative tRNA delta-2-
isopentenylpyrophosphate transferase from Arabidopsis thaliana (GenBank
Accession No. YP_008242.1). A polypeptide encoded by nucleotides 824 to 3 of
ZmiPTG shares 35% aininu add sequence identity to amino acids 17 to 248 of a
tRNA isopentenylpyrophosphate transferase from Streptococcus pneumoniae R6
(GenBank Accession No. NP_358182.1). A polypeptide encoded by nucleotides
818 to 3 of ^.miPT9 shares 34% amino acid sequence identity to amino acids 2 to
231 of a tRNA delta(2)-isopentenylpyrophosphate transferase (GenBank
Accession No. Q8CWS7). A polypeptide encoded by nucleotides 818 to 3 of
ZmlPT9 shares 34% amino acid sequence identity to amino acids 2 to 231 of a
tRNA isopentenylpyrophosphate transferase from Streptococcus pneumoniae R6
(GenBank Accession No. NP_345176.1). A polypeptide encoded by nucleotides
818 to 3 of ZmlPT9 shares 34% amino acid sequence identity to amino acids 31 to
275 of a tRNA delta(2)-isopentenylpyrophosphate transferase from Chlamydophila
caviae (GenBank Accession No. AAP05599.1). A polypeptide encoded by
nucleotides 818 to 435 of ZmlPT9 shares 48% amino acid sequence identity to
amino acids 6 to 133 of a tRNA delta(2)-isopentenylpyrophosphate transferase
from Xylella fastidiosa 9a5c (GenBank Accession No. NP_297383.1). A
polypeptide encoded by nucleotides 818 to 435 of ZmlPT9 shares 48% amino acid
sequence identity to amino acids 6 to 133 of a tRNA delta(2)-
isopentenylpyrophosphate transferase from Xylella fastidiosa Dixon (GenBank
Accession No. Xylella fastidiosa Dixon).
Example 4. Isolation of ZmlPT2 from Mo17 and B73 maize lines and
molecular characterization of the ZmlPT2 gene
Material and Methods:
Plant materials: Maize (Zee mays) varieties B73 and Mo 17 were used in
this study. Samples were harvested from field-grown plants at different stages of
development and stored at -80°C. Kernel samples were harvested every five days
from 0 to 25 DAP and dissected by isolating whole kernels (0 DAP), pedicel,
nucellus and pericarp (5 DAP), pedicel, nucellus, endosperm/embryo sac arid
pericarp (10 DAP), or pedicel, embryo, endosperm and pericarp (15, 20 and 25
DAP). Tissues corresponding to 2 to 4 different ears were pooled. The series of
sample harvested every DAP from 0 to 5 (whole kernels), from 6 to 15 and then
20, 27 and 34 DAP (seeds without pedicel) or 20, 25, 30 and 35 DAP (pedicels)
were previously used to study the expression pattern of the cytokinin oxidase 1
gene (Ckx1) from corn (Brugiere et a/., 2003, supra).
Arabidopsis thaliana ecotype Columbia was used for Arabidopsis
transformation studies.
PCR: ZmlPT2 coding sequence was PCR amplified from B73 and Mo 17
genomic DNA. Primers ZmlPT2-5' f5'-ATCATCAAGACAATGGAGCACGGTG-3')
'(SEQ" ID NO: 78) and Zm/PT2-3' (5'-CGTCCGCTAGCTACTTATGCATCAG-3"i
(SEQ ID NO: 79) were designed based on the GSS contig sequence (coding
sequence is underlined). As part of the Gateway cloning procedure, aft-flanked
ZmlPT2 fragment was amplified using primers ZmlPT2-5-Gateway (5'-
GGGGACAAGTTTGTACAAAAAAGCAGGCTCAATGGAGCACGGTGCCGTCGCCG-
31) (SEQ ID NO: 80) and ZmlPT2-3-Gateway (51-
GGGGACCACTTTGTACAAGAAAGCTGGGTCTTATGCATCAGCCACGGCGGTG-
3') (SEQ ID NO: 81).
In each case, a touchdown PCR was performed (GeneAmp PCR System
9700), using the following cycling parameters: 94°C for 2 min (one cycle), 94°C for
30 s, 65°C for 45 s and 72°C for 1 min 30 s (5 cycles, annealing temperature
reduced by 1°C per cycle), 94°C for 30 s, 60°C for 45 s and 72°C for 1 min 30 s
(30 cycles), 72°C for 7 min, and termination at 4°C. Pfu Ultra Hotstart DNA
polymerase (Stratagene) for its very low average error rate (less than 0.5 % per
500-bp fragment amplified) was used.
PCR products were loaded on an agarose gel containing ethidium bromide
(1:10000, v/v). Bands corresponding to ZmlPT2 gene and aft-flanked ZmlPT2
gene were gel extracted using QIAquick PCR purification kit (QIAgen).
DNA and RNA extraction: Genomic DNA was extracted from B73 and
Mo17 plant samples at V3-4 stage according to Dellaporta et a/. (1983) Plant Mol
Biol 1:19-21 and stored at -20°C. Total RNA was prepared using a hot phenol
extraction procedure according to Verwoerd et a/. (1989) Nucleic Acid Res
17:2362 and stored at -80°C. The kernel developmental series samples were
purified using RNeasy Mini Protocol for RNA Cleanup (QIAgen) and eluted in 50 ul
DEPC water. Optical Density (DO) at 260 and 280 nm was used to assess the
purity of RNA preps and measure RNA and DNA concentrations.
Southern blots. Northern blots, and hybridization: For Southern blots,
digested genomic or BAG clones DNA were run on 0.8% agarose gel at 110V,
stained after migration in a 1:10000 (v/v) ethidium bromide solution in TAE buffer,
and transferred as indicated below. For Northern blots, ethidium bromide was
added to denatured RNA samples and run at 80 V on 1.5% denaturing agarose
gel (Brugiere et al. (2003) Plant Physiol. 732:1228-1240). Blotting was performed
using Turbo-blotter (Schleicher & Schuell) according to the manufacturer
guidelines. After transfer, nylon membranes (Nytran plus, Schleicher & Schuell)
were cross-linked with a Stratalinker (Stratagene) and baked at 80°C for 30 min.
Probes were labeled with" [a-32P]-dCTP using random priming (Red/prime //
RandomPrime Labelling System, Amersham Biosciences) and purified with Quick
Spin Columns (Roche). Hybridizations were carried out at 65°C for 16h using
ExpressHyb hybridization solution (BD Biosciences) and membranes were
washed under stringent conditions (O.lxSSC, 0.1% SDS) as previously described
(Brugiere et a/. (2003) Plant Physiol. 132:1228-1240). Relative transcript
abundance was quantified using a phosphor imager (MD860, Molecular Dynamic)
with imaging software (ImageQuant, Molecular Dynamics).
BAG subclonina: BAG clones were digested and subcloned in pBluescript
SK+. This plasmid includes a multiple cloning site between the /acZgene and its
promoter. The lacZ gene is often used as a reporter gene because it encodes a pgalactosidase,
which produces a dark blue precipitate on X-gal1 enzymatic
hydrolysis. The bacteria containing a plasmid in which the BAG fragment is
inserted in the multiple cloning site and therefore do not synthesize this enzyme
will appear white. This allows the selection of colonies containing BAG subclones
that can be further screened by PCR or Southern blot.
Results:
Isolation of the ZmlPT2 gene from corn aenomlc DNA: Genornic DNA from
two different varieties of corn, B73 and Mo17, was extracted and ZmlPT2 coding
sequence was amplified by touch-down PCR. The ZmlPT2 gene amplification
product was used as a probe for Southern and Northern blot experiments. The
Z/77/PT2 CDS was cloned in pDONR221 (Invitrogen) and sequenced. The Mo17
sequence was 100% homologous to the GSS contig sequence. The B73 and
Mo17 genes were found to be 98.8% homologous at the nucleotide level. The
differences between the two genes at the nucleotide level resulted in the
modification of 3 amino acids at the protein level (96.1% identity). The nucleotide
and amino acid sequences of ZmlPT2 are set forth in SEQ ID N0:3 and 2, and the
nucleotide and amino acid sequences of a variant of ZmlPT2 are set forth in SEQ
ID N0:76 and 77. An alignment of ZmlPT 2 and the variant of ZmlPT2 shows that
the differences in the polypeptides ocurr at amino acid 125 (A-»L), amino acid 138
(O-*R): and amino acid 193 R-»H.
Mapping of the gene on the maize genome: To determine if ZmlPT2 was a
single- or multi-copy gene in maize, B73 and Mo17 genomic DNA were digested
with" H/ndlll, EcoRI, and"'£=coW and run on a gel, which was blotted as described
in the Materials and Methods section. The membrane was hybridized with the
previously extracted ZmlPT2 genomic fragment as a probe. The picture of the
membrane autoradiography is presented in Figure 6.
The single bands observed for each of these digestions show that ZmlPT2
is most likely a single-copy gene. The size of the corresponding H/ndlll fragment
was later confirmed using BAG clones. To obtain additional information regarding
the physical location of the ZmlPT2 gene in the maize genome, the Oat-Maize
chromosome addition lines were used (Ananiev ef a/, (1997) Proc. A/a//. Acad. Sci.
94:3524-3529). A PCR was performed with the ZmlPT2-5' and ZmlPT2-3' primers
as described in the Materials and Methods section (data not shown). The
expected size of the amplification fragment was 995 bp. B73 genomic DNA
samples were used as positive controls, while oat genomic DNA and water were
used as negative ones.
The data shows that the amplification of the ZmlPT2 sequence could only
be seen with the chromosome 2 oat-maize addition line. This finding was verified
and the position on chromosome 2 refined using a bioinformatics approach. The
ZmlPT2 sequence was first used to screen the B73 and Mo17 public and
proprietary Bacterial Artificial Chromosomes (BAG) libraries. Positive clones were
identified and used to identify a BAG contig using FPC Contig Viewer. Using this
strategy, markers were identified including several MZA markers that were
physically mapped on maize chromosome 2, bin 4 (data not shown), which
confirmed the experimental mapping of ZmlPT2 gene using the OMA lines.
Example 5. Gene Expression of ZmlPTZ. ZmlPT4. ZmlPTS. ZmlPTS and
ZmlPTS
In order to gain an impression of the level of expression of the various
ZmlPT sequences, a search of the Lynx database was performed. Tissue types,
number of library hits, and average ppm are presented in Tables 3-7.
As shown in table 3, expression of ZmlPT2 was found to be restricted to
kernel tissue and to correlate with the start of cytokinin biosynthesis in the kernel
as described in Bruqiere et al. (2003) Plant Physiol. 132(3): 1228-1240. Figure 9
provides a graphical illustration of the ppm values for ZmlPT2 in the Lynx embryo
libraries. Other ZmlPT genes have low expression, consistent with their possible
function as cytokinin synthases in other tissues such as root, meristem and
endosperm. See table 4-7 below.
(Table Removed)
Example 6. Expression of the ZmlPT2 Gene in Corn Tissues
The expression pattern of ZmlPT2 in different organs at different stages of
development was studied in order to provide information regarding its putative
function in cytokinin biosynthesis. Based on Lynx data (discussed in Example 5),
the expression of ZmlPT2 seemed to be restricted to developing kernels (Figure
9), To get an overall view of ZmlPT2 expression in corn and verify Lynx data,
RNA was extracted from different B73 tissues: leaf, stalk, roots, and whole kernels
at 0, 5, 10, 15, 20 and 25 DAP. Forty ug of total RNA from each sample were
stained with ethidiurn bromide and loaded on an agarose gel. The blot obtained
was hybridized with a [a-32P]-dCTP labeled ZmlPT2 probe. In a second
hybridisation, a nyclophilin probe was used as a loading control. After
quantification via a phosphor-imager, the ratio of the expression of ZrnlPT2
compared to cyclophilin was calculated. Cyclophilin is considered to be
constitutively expressed across different organs (Marivet et a/. (1995) Mol Genet
•Den"247:222-228. Results are shown in Figure 7. ZmlPT2 transcripts are
detected at low levels in the leaf, stalk and roots, but at higher levels in kernels,
where expression is low at 0 DAP, increases from 5 to 10 DAP and decreases
from 15 to 25 DAP, This expression profile not only confirms the Lynx data but
coincides with the appearance and disappearance of CK in the kernels (See,
Example 5).
To obtain a more precise view of the expression pattern of ZmlPT2 in
kernels, levels of ZmlPT2 transcripts were measured in 0- to 5-DAP kernels with
pedicels; 6- to 34-DAP kernels without pedicels; and pedicels alone, 6 to 42 DAP.
See Figure 8. As previously done, the gel was loaded with 40 ug of total RNA,
stained with ethidium bromide, and blotted on a nylon membrane. Membranes
were hybridized with a 32P-dCTP labeled ZmlPT2 probe. The results of the
Northern experiment with "seed without pedicel" samples indicate that low levels
of ZmlPT2 expression are detected between 0 and 4 DAP. The expression
increases from 5 to 8 DAP, peaks at 8 DAP, and decreases until 14 DAP. At later
stages (15 to 34 DAP), transcript levels seem to increase again. However, it is not
clear whether this is the result of diminution of cyclophilin expression. This
phenomenon was also observed for Ckx1 expression (Brugiere etal. (2003) Plant
Physiol ?32:1228-1240). In the Northern experiment with pedicel samples,
transcript levels drastically increase from 6 to 10 DAP, peak at 10 DAP, and slowly
decrease until 15 DAP. In this experiment again, transcript levels seem to rise at
later stages, but it is unclear whether this is due to the diminution of cyclophilin
expression. In this experiment, the sample corresponding to "seed without pedicel
at 9 DAP" was used as a control to allow the comparison with the other blot. The
relative expression at 9 DAP is four times as high as in the control, showing that
Zm/P72 expression in the pedicel is much higher than in the rest of the seed. This
difference is consistent with the fact that CK levels are nearly twice as abundant in
the pedicel as in the rest of the seed (Brugiere et at. (2003) Plant Physiol
732:1228-1240).
The relative transcript levels were compared to ZR concentrations
measured in the same samples (solid line in Figure 8). Interestingly, ZmlPT2
expression nicely overlaid ZR accumulation in the pedicel, whereas in the rest of
the seed, it slightly preceded the peak in ZR, including at later stages.
Taken together, these results indicate that ZmlPT2 is expressed transiently
during kernel development both in the pedicel and the rest of the seed, and that its
pattern of expression, which parallels ZR levels in the kernel, is consistent witn
ZmlPT2 role as a CK biosynthetic gene.
The expression of ZmlPT2 in different kernel tissue was also studied in
different kernel tissues. In this study, dissected kernel samples from 0 to 25 DAP
were used. Samples were collected from the field in Johnston, Iowa, USA. Kernels
were dissected into different parts (pedicel, nucelius, endosperm/embryo sac,
endosperm, embryo and pericarp) depending on the stage considered. The gel
was loaded with 30ug of purified total RNA, stained with ethidium bromide, and
blotted onto a nylon membrane.
The results shown in Figure 11 confirm that ZmlPT2 transcripts levels in
pedicel are more abundant than in the rest of the seed. This is especially true at
15, 20 and 25 DAP where some expression is also seen in the embryo samples.
At 10 DAP however, ZmlPT2 transcripts are found in similar amounts in
developing endosperm/embryo sac and pedicel. Together with the fact that 1)
cytokinins are more abundant in the pedicel than the rest of the seed and that 2)
transcript and activity of cytokinin oxidase in this organ is also more abundant than
the rest of the seed (Brugiere et at. (2003) Plant Physiol. 732:1228-1240), these
results indicate that the pedicel is most likely a major site for CK biosynthesis.
Recent data presented on the expression of Arabidopsis IPT genes allows us to
hypothesize that the expression of ZmlPT2 could occur in phloem cells where it
could be responsible for the synthesis of CK, which would be targeted to the
vascular bundles for transport to developing kernels. The presence of ZmlPT2
transcripts in both developing endosperm and embryo is observed at times when
cell division is the most active in these tissues. This again supports a role for
ZmlPT2 as a CK biosynthetic protein, which catalyzes CK formation in fast
dividing/developing tissues such as endosperm at 10 DAP and growing embryo,
and could drive sink strength in the pedicel to support kernel growth.
Example 7. Expression and Purlfiatlon of the 2mlPT2 Polvpeptide
From E co//'
Materials and Methods:
Recombinant protein purification, gel electrophoresis and Western blot:
BL21-AI (Invitrogen) £ col! harboring the pDEST17-ZmlPT2 (Mo17) plasmid was
grown overnight. A 1/200 dilution of this culture was used to inoculate fresh LB
medium and bacteria were grown at 37°C for 2h before induction with 0.2% L-
arablriose arid then growni for 2"' to 4h. Bacterial protein extracts were prepared as
described by the supplier and run on a 12.5% polyacrylamide gel in denaturing
condition. The His-tagged protein was purified from crude protein extracts using a
Ni-NTA agarose solution according to the provider's recommendations (Qiagen).
After electrophoresis, proteins were either revealed by gel staining with GelCode
(Pierce) or blotted onto a polyvinylidene difluoride (PVDF) membrane using an
electro-transfer procedure. Western blot was carried out as described previously
(Brugiere et al. (1999) Plant Cell 77:1995-2012) using an anti-poly histidine
monoclonal antibody developed in mice (Sigma-AIdrich) and an anti-mice IgG
antibody conjugated to alkaline phosphatase developed in goat.
Results:
Cloning of the ZmlPT2 coding sequence in a vector compatible with the
Gateway system: In an effort to characterize the function of the ZmlPT2 protein
both in vitro and in vivo, two approaches were used. The first aimed at expressing
and purifying a tagged ZmlPT2 protein in E. coll, and the second at transforming
Arabidopsis calli with a construct driving the over-expression of the ZmlPT2 gene
under the control of the 35S promoter of the cauliflower mosaic virus. For this
purpose the Gateway system for molecular cloning was used.
The Gateway technology was used to build both the protein expression
vector (£. colt Expression System with Gateway Technology kit, Invitrogen) and
Arabidopsis transformation vector (Multisite Gateway Three-Fragment Vector
Construction Kit, Invitrogen). The.first step was the addition of specific att
sequences to the previously extracted ZmlPT2 fragment. This was achieved by
amplifying this fragment by PCR with a pair of primers specially designed to flank
the gene with the proper att sites.
Once flanked with these specific sites, the new gel-extracted fragment was
inserted by recombination into a donor vector (pDONR221). Recombination was
catalyzed in vitro by the BP clonase. The vector generated was checked by
digestion with multiple restriction enzymes and migration on agarose gel
electrophoresis, The sizes of digested fragments matched with the expected
length of digestion products for each enzyme. Both Mo17 and B73 ZmlPT2 genes
were cloned in individual donor vectors and the inserts sequenced using M13
forward and reverse primers. The Mo17 clone showed a homology of 100% with
the GSS contig sequence and was therefore used to build the expression and
transformation constructs.
in vitro study: expression of the ZmlPT2 protein in £ coli: A tagged
recombinant ZmlPT2 protein was expressed in £ coli. Besides allowing the
ZmlPT2 gene to be transcrlptionally activated in £ coli via induction of the 77
promoter, this approach also permitted addition of a six-histidine-tag to the Nterminal
end of the recombinant ZmlPT2 protein, which could be used for its
purification. The expression vector was generated by recombination of the
ZmlPT2 coding sequence between pDONR221-ZmlPT2 and pDEST17
(Invitrogen).
The transcriptional fusjon of the 6xHis-tag with ZmlPT2 was sequenced and
the expression vector was used to transform the BL21-A1 strain of £ coli. These
cells contain an expression system modulated by L-arabinose, which Induces the
expression of 77 RNA polymerase. Protein extracts collected at different times
(2h and 4h) after 77 RNA polymerase induction were tested on denaturing
polyacrylamide gel electrophoresis (SDS-PAGE). Samples that had not been
induced were collected and used as negative controls, as well as GUS protein
expression with and without induction. The gel was stained with Coomassie blue,
which reveals the presence of proteins.
After electrophoresis, induced and non-induced samples were blotted onto
a PVDF membrane, A Western blot was performed to confirm that the induced
protein contained a His-tag. For this purpose, we used mice antibodies raised
against a poly histidine peptide. These antibodies would only recognize the
tagged protein and would be in turn recognized by anti-mice IgG antibodies
carrying alkaline phosphatase. The presence of the recombinant protein could
therefore be characterized by a reaction transforming a colorless substrate in a
purple product that precipitates on the membrane.
Two bands could be observed, one of expected size (approximately 37kDa)
and one of a slightly bigger size (approximately 40kDa), both of which were
induced by L-arabinose. The two bands could be due to the addition of extrabasic
residues that would increase the positive charge of the protein therefore
altering its migration. It could also be due to the presence of a covalently bound
co-factor on the E.coli expressed protein. In order to decipher between these two
possibilities trypsic digestions of each purified bands could be analyzed by mass
spectrometry. In order to further characterize the two bands it was necessary to
partially purify the protein.
Purification of the His-taaqed ZrnlPT2 protein: The presence of a 6xHis tag
allowed affinity purification of this protein using a Ni-NTA resin column. The crude
extract was loaded on the column and the effluent collected. After several washes
of the column, the protein was eluted using a solution containing imidazol that,
because of its higher affinity to the column, Is able to release the protein from the
column. Samples were collected at each step of the purification and run on a gel,
which was stained as previously.
The experiment indicated that the protein is expressed in a soluble form
since it was shown to be present in both the supernatant and the effluent, but in
smaller amounts in the pellet. The protein was eluted in the second and third
elution fractions. The amount of ZmlPT2 protein in the fraction corresponding to
the second volume of elution was visually estimated to represent 70 to 80% of the
total protein.
A Western blot was carried out using the same samples. The result
confirmed that although the protein is present in small amount in the pellet, most
of it remains in solution (effluent). The strong signal with the effluent indicates that
the amount of ZmlPT2 protein in the crude extract exceeded the column capacity.
In addition, the ZmlPT2 protein was expressed using a C-terminal tag
which allowed the purification of ZmlPT2 as one single band on SDS-PAGE. The
purity of the fractions was close to 100%. Fractions were found to provide
DMAPP:ADP and DMAPP:ATP isopentenyltransferase activity.
Example 8. In vivo Study of the Over-Expression of the ZmlPT2 Gene in
Arabidopsis Calli
Materials and Methods:
In vitro culture: Different media were used for Arabidopsis germination,
callus culture and regeneration (Kakimoto (1998) J. Plant Res. 111:261-265). The
media used were as follows:
• 5000X CIM (callus-inducing medium) hormone mix: 2.5 mg/ml 2,4
dichlorophenoxyacetic acid (2,4-D), 0.25 mg/ml kinetin and 5 mg/ml biotin
dissolved in dimethyl sulfoxide (DMSO).
• 500X vitamin mix: 50 mg/ml myo-inositol, 10 mg/ml thiamine-HCI,
0.5 mg/ml pyridoxine-HCI, and 0.5 mg/ml nicotinic acid.
• GM (germination medium): 1L of mixture comprising 4.3 g Murashige
and Skoog's medium salt base (Sigma), 10 g sucrose, 2 ml 500X vitamin
mix, "10 ml 5% 2-(N-m6rpholino)-ethanesulfonic acid (MES, adjusted to pH
5.7 with KOH), and 3 g Phytagel (Sigma), autoclaved".
• CIM (callus-inducing medium): 1L of mixture comprising 3.08 g
Gamborg's B5 medium salt base (Sigma), 20 g glucose, 2 ml 500X vitamin
mix, 10 ml 5% MES (adjusted to pH 5.7 with KOH), and 3 g Phytagel,
autoclaved and 200 Ml 5000X CIM hormone mix added to it.
• AIM (Agrobacterium infection medium): CIM from which Phytagel is
omitted.
• WASHM (washing medium): GM from which Phytagel is omitted,
plus 100 mg/l sodium cefotaxime.
Selection media for transformed calli:
• GM+IBA (GIBA): GM plus 100 mg/l cefotaxime, 50 mg/l carbenicilin,
3 mg/l Bialaphos and 0.3 mg/l indolebutyric acid (IBA).
• GM+IBA+Z (GIBAZ): GM plus 100 mg/l cefotaxime, 50 mg/l
carbenicilin, 3 mg/l Bialaphos, 0.3 mg/l indolebutyric acid (IBA), and 1 mg/l
frans-zeatin (tZ).
In the experiment aimed at testing the effect of auxin to cytokinin ratio on
root and shoot regeneration, GM was prepared and different amounts of
hormones were added. Twenty-five media containing different combinations of tZ
and IBA concentrations, which were set at 0, 100, 300, 1000 and 3000 ng/ml for
each hormone, were prepared.
Sterilized Arabidopsis thallana seeds were germinated on GM medium and
grown on continuous light at 23°C. For the above experiment, hypocotyls from 15
day-old seedlings were cut with a scalpel and grown on each of the 25 media for 3
weeks at 23°C under continuous light. For experiments requiring the use of callus
tissue, hypocotyls were grown on CIM for 10 to 12 days in the same conditions.
Arabidopsis calli transformation: Induced call! were soaked in a suspension
of Agrobacterium (0.2 ODeoo) in AIM for 5 minutes. Most of the liquid was removed
on filter paper, and calli were placed on CIM culture medium and grown in
continuous light at 23°C for 2 days. Calli were then washed thoroughly in WASHM
medium and placed on GIBA or GIBAZ medium and cultured for about 3 weeks.
Cloning: In order to constitutively express ZmlPT2 in Arabidopsis using the
Gateway system, a construct was built in which the gene was placed under the
control of the 35S promoter of the cauliflower mosaic virus. A Gateway clone
'b'ri'ta'ihing the 35S promoter was constructed using the pDONR-P4-P1R plasmid.
Once these 3 elements were available, a multisite recombination was performed
using the three donor vectors and a fourth vector called destination vector.
The LR cionase allows an organized "three-site" recombination to occur
between the plasmids carrying the promoter, gene of interest and terminator, and
a binary vector containing the left and right border of the Ti plasmid and the BAR
resistance gene. The resulting construct was verified by digestion with restriction
enzymes, migration on agarose gel, and comparison of digested fragment sizes
with expected digestion products.
The final construct contained the 35S-ZmlPT2-PINII sequence and included
the BAR gene. This gene is used as a selection marker for the herbicide
resistance it confers to transformed plant cells.
Transformation in Aarobacterium: The next step was the transformation of
a plasmid containing the 35S-ZmlPT2-PINII construct in Agrobacterium
tumefaciens (LBA4044). This plasmid contains the genes required for infection
and delivery of the T-DNA to A. thaliana cells (vir genes). After electroporation in
the bacteria (Suzuki (1999) Plant Cell Physiol 39:1258-1268), the two plasmids
are able to recombine at their respective COS sites. The result of this
recombination is a 48 kb plasmid called "co-integrate".
Agrobacteria containing this co-integrate were checked using a quality
control process. This procedure consists of extracting the co-integrate plasmid
and transforming it into E. coli in order to verify it by restriction digestions. This
step is necessary to screen for "mis-recombinations" of the two plasmids at the
COS sites, which would result in a non-functional construct.
Although many trials were attempted to transform Agrobacterium cells with
the 35S-ZmlPT2-PINII construct, no colonies containing the right co-integrate
plasmid could be identified. Since the 35S promoter is leaky in Agrobacterium, it
was assumed that ZmlPT2 expression could be lethal for Agrobacterium. The
lethality of the construct could be the result of an active degradation of an
essential compound for Agrobacterium. Such a metabolite could for example be
from the isoprenoid biosynthetic pathway, which includes potential substrates of
CK biosynthesis, such as 4-hydroxy-3methyl-2-(E)-butenyl diphosphate (HMBPP).
Analysis of microbial genomes combined with biochemical experiments
established the existence of two pathways for isoprenoid synthesis, the
mevalonate (MVA) and non-mevalonate (1-deoxyxylulose 5-phosphate, DXP or 2-
u-methyl-u-erythritol- 4-phosphate, MEP) pathways. The DXP pathway has been
found to be present in some bacteria and the chloroplasts of plants. The genes
encoding the non-mevalonate pathway are present mostly in Gram-positive
bacteria, HMBPP is a precursor of the non-mevalonate (MEP) pathway of
isoprenoid biosynthesis and was shown to be a possible substrate for AtlPT7
(Take! et al. (2003) J Plant RQS 116:265-9). Analysis of the genomic sequence of
A. tumefaciens C58 showed that it encodes the enzymes of the MEP pathway but
that those of the MVA pathway are absent (Wood et al. (2001) Science 294:2317-
2323; Qoodner ef al. (2001) Science 294:232-2328). Based on these results we
believe that HMBPP could be the substrate of the ZmlPT2 protein and that
utilization of this compound by the enzyme could prevent the formation of
isoprenoid, which would result in the incapacity of the bacteria to grow.
To elude this problem, the same construct was built but this time using the
35S promoter with the ADH1 intron to prevent the expression of ZmlPT2 gene in
Agrobacterium. Using this construct, Agrobacteria carrying the right co-integrate
were obtained,
Results:
Arabidopsis calli in culture regenerate roots or shoots depending on auxin
and cytokinin levels present in the medium. As a proof of concept, Arabidopsis
hypocotyls were cultured on media containing increasing levels of auxin and
cytokinin. Twenty-five different combinations of tZ and IBA concentrations, at 0,
100, 300, 1000 and 3000 ng/ml for each hormone, were prepared and hypocotyls
transferred to the media as described above. After 3 weeks in the culture room,
pictures of 2 representative calli were taken for each hormone combination.
Results indicated that a higher auxin:cytokinin ratio favored root formation, while a
higher cytokinin:auxin ratio favored shoot formation.
This experiment confirmed that root or shoot formation is influenced by the
auxin/cytokinin ratio. Auxins have a root-inducing effect whereas cytokinins
induce shoot formation. Based on these results, Arabidopsis calli over-expressing
a cytokinin biosynthetic gene should not be able to develop roots on a medium
containing only auxin. The functionality of this assay to characterize putative
cvtokinin biosynthetic genes by using the Agrobacterium tumefaciens IPT (tmr)
gene has been tested. Specifically, using the Gateway cloning system, two
constructs were developed aimed at over-expressing either IPT as a cytokinin
biosynthetic enzyme or GUS as a control. Three weeks after transformation of
•A/£fc/S6jbs7s"cal]li™'"roots could"be observed on calli transformed with the 35S-GUSPINII
construct but not on calli transformed with the 35S-IPT-PINII construct. In
order to demonstrate that calli were efficiently transformed, in situ GUS staining
was performed. Tissue transformed with 35S-GUS-PINII contained the GUS
protein as revealed by the blue color observed after incubation in a solution
containing the GUS substrate. These experiments validated the use of a highthroughput
assay to test the putative com CK biosynthetic genes.
The 35$-ADHI-ZmlPT2-Pinll construct was transformed into 10 day-old
Arabidopsis calli which were transferred onto GM medium containing either auxin
or both auxin and cytokinin. Bialaphos was added to select for transformed calli.
Clear phenotypes could be observed 3 weeks after transformation. Control and
35S-ADHI-ZmlPT2-PINII calli grew identically on medium containing both auxin
and cytokinin. As expected, control calli transformed with the 35S-GUS-PINII
construct were able to regenerate roots on medium containing only auxin. On the
contrary, calli transformed with the 35S-ADH1-ZmlPT2-PINII construct, like calli
transformed with the 35S-IPT-PINII construct, could not form any roots on this
medium and some calli were even able to regenerate shoots. Given results of the
preliminary experiment described above, this implies that these calli are
synthesizing CK due to the expression of the ZmlPT2 gene. In turn this decreases
the auxin:cytokinin ratio, which prevents root formation. These results support the
conclusion that ZmlPT2 is a cytokinin biosynthetic gene.
Example 9. isolation and Sequencing of the ZmlPT2 Promoter
To isolate the promoter of the ZmlPT2 gene, a high-throughput Bacterial
Artificial Chromosomes (BAG) screening process was used. Five positive clones
were isolated by PCR screening based on the ZmlPT2 sequence. To confirm that
the gene of interest was present in the bacterial chromosome, the BAC clones
were cultured and propped. The BACs obtained were digested with H/ndlll and
run on an agarose gel, which was used for a Southern blot. The blot was
hybridized with a [a-32P]-dCTP labeled ZmlPT2 probe. Methods for the Southern
blot are described above in Example 4.
The Southern blot confirmed the presence of the ZmlPT2 sequence on all
BAC clones isolated. Once checked, the BACs were subcloned in pBluescript
after digestion with BamHI and H/ndlll. After ligation, chemically competent E. coli
were transformed and grown on ampiciliin LB medium. Positive clones were then
screened by a colony hybridization method. Colonies were transferred onto a
nylon membrane, which was hybridized with a [a-32P]-dCTP ZmlPT2 probe to
detect the clones containing the ZmlPT2 region on their plasmid. Finally, the
colonies selected were prepped and the plasmid was sent for sequencing using
5'OH-oriented primers. This allowed the upstream region of ZmlPT2 up to 1354
bp to be sequenced. A BAG walking strategy was employed which gave 3280 bp
of promoter sequence for this gene. The sequence for the ZmlPT2 promoter is set
forth in SEQ ID NO: 75. A similar strategy was followed to identify the ZmlPTI
promoter set forth in SEQ ID NO: 25.
Promoter sequences for ZmlPT4 through ZmlPTS, and OslPT 1 through
OslPT11, may be isolated in a similar manner. Sequences provided herein for
ZmlPT4 (SEQ ID NO: 5), ZmlPTS (SEQ ID NO: 8), ZmlPT6 (SEQ ID NO: 11),
ZmlPT? (SEQ ID NO: 14), ZmlPTS (SEQ ID NO: 17), and ZmlPTQ (SEQ ID NO:
20), OslPTI (SEQ ID NO: 47), OslPT2 (SEQ ID NO: 44), OslPTS (SEQ ID NO:
62), OslPT4 (SEQ ID NO: 64), OslPT5 (SEQ ID NO: 50), OslPT6 (SEQ ID NO:
55), OslPT7 (SEQ ID NO: 53), OslPTS (SEQ ID NO: 40), OslPT9 (SEQ ID NO:
60), OslPTI 0 (SEQ ID NO: 58), and OslPT11 (SEQ ID NO: 42) include
appropriate upstream regions useful for characterization of functional promoter
sequence.
Example 10. Assayingfor IPT Activity
A. Synthesis of Cvtokinin bv maize or rice IPT Sequences in Bacterial
Culture Medium
The ability of an IPT sequence of the invention to synthesize cytokinin is
assayed in a bacterial culture medium in which cytokinin is known to be secreted.
Enzyme activity in E. coll is measured.
£ co// strain BL21-AI (Invitrogen) containing a T7 promoter::IPT sequence
(IPT cloned in pDEST17 (Invitrogen)) is cultured for 4 h at 37°C and the
accumulation of the protein is induced for 12 hours at 20°C in the presence of
0.2% arabinose. The microorganisms are collected by centrifugation, and after
Buffer A (25 mM Tris-HCI, 50 mM KCI, 5 mM (3-mercaptoethanol, 1 mM PMSF
and 20 pg/ml of leupeptin) is added to an OD600 of 100, the E. co// are disrupted
by freezing and thawing. The disrupted £ co// are then centrifuged for 10 minutes
at 300,000 g followed by recovery of the supernatants. 10 ul of these
supernatants are mixed with Buffer A containing 60 uM DMAPP, 5 uM [3H]AMP
(7±2"(3Bq7mmbl)"'ariiaTO'"'MM''MgCl2 followed by incubation for 30 minutes at
25°C. Subsequently, 50 mM of Tris-HCI (pH 9) is added to this reaction liquid
followed by the addition of calf intestine alkaline phosphatase to a concentration of
2 units/30 pi and incubating for 30 minutes at 37°C to carry out a
dephosphatization reaction. As a result of developing the reaction liquid by C18
reversed-phase thin layer chromatography (mobile phase: 50% rnethanol) and
detecting the reaction products by autoradiography, formation of isopentenyl
adenosine is confirmed in the reaction liquids containing extracts of £ coli having
T7::IPT sequence.
It is further recognized that 3H-HMBPP (4-hydroxyl-3-methyl-2-(E)-butenyl
diphosphate) could also be used as a substrate in the assay described above.
See, for example, Krall et a/. (2002) FEBS Letters 527:318-8, herein incorporated
by reference.
B. Assay for DMAPP:ATP or APR or AMP isooentenvl
Transferase activity
DMAPP:ATP (or ADP or AMP) isopentenyl transferase activity is measured
by the method described by Blackwell and Morgan (1991) FEBS Lett 76:10-12,
with some modifications. The samples to be assayed are crude extracts and
purified proteins of £ coll harboring the T7 promoter.:IPT sequence. Purified
proteins are diluted to appropriate concentrations with dilution buffer (25 mM
Tris-HC1, pH 7.5; 5 mM 2-mercaptoethanol; 0.2 mg ml"1 bovine serum albumin).
Isopentenylation reactions are started by mixing samples with an equal volume of
2x assay mixture containing 25 mM Tris-HC1 (pH 7.5), 10 mM MgCb, 5 mM 2-
mercaptoethanol, 60 uM DMAPP, and 2 uM [2,8-3H]ATP (120 GBq mmol-1), [2,8-
3H]ADP (118 GBq mmol-1), [2-3H]AMP (72 GBq mmol-1), or [2,8-3H]adenosine
(143 GBq mmol-1). After incubation for an appropriate time, 1/2 volume of calf
intestine alkaline phosphatase (CIAP) mix [0.5 Tris-HC1 (pH 9.0), 10 mM MgCI2,
and 1,000 units ml-1 of CIAP (Takara Shuzo Co. Ltd., Otsu, Shiga, Japan)] is
added and the mixtures are incubated at 37°C for 30 min. Then, 700 ul of ethyl
acetate is added and the mixtures are vortexed. After centrifugation at 17,000xg
for 2 min, the organic phase is recovered and washed twice with water. The
organic phase is mixed with ten volumes of scintillant, ACSII (Amersham
Pharmacia Biotech, Tokyo, Japan), and radioactivity levels are measured with a
liquid scintillation counter. Recovery of [2,8-3H]isopentenyladenosine (iPA) is
measured and is used to calculate the amounts of the products formed. The
[2,8-3H]iPA is synthesized through isopentenylation of ATP by using purified IPT
sequences, followed by CIAP treatment as described above. All assays are
performed in duplicate and mean values are used for calculation.
To determine the Km for ATP, purified protein (2 ng ml"1 in dilution buffer) is
mixed with the same volume of a 2x assay mixture containing 25 mM Tris-HC1
(pH 7.5), 10 mM MgCI2, 5 mM 2-mercaptoethanol, 0.4 mM DMAPP, and ATP (2-
502 uM [2,8-3H]ATP, 1.22 MBq ml-1). To determine the Km for DMAPP, purified
protein (2 ng ml-1) is mixed with the same volume of a 2x assay mixture containing
25 mM Tris-HC1 (pH 7.5), 10 mM MgCI2, 5 mM 2-mercaptoethanol, 0.25-200 uM
DMAPP, and 200 |jM [2,8-3]ATP (7.07 GBq mmol-1). After the mixture is
incubated at 24°C for 0 min or 4 min, the reaction mixtures are treated with CIAP,
and then extracted with ethyl acetate as described above. Values obtained at 0
min are subtracted from those at 4 min, and the resulting differences are taken as
enzyme activity.
To confirm that the IPT sequences catalyzed the transfer of the isopenteny!
moiety to ATP, ADP, or AMP, the reaction products are analyzed by HPLC and
mass spectrometry. Briefly, crude extract prepared from IPTG-induced E. coli
harboring the pDEST17-IPT plasmid is incubated with Ni-NTA agarose beads.
After the beads have been washed thoroughly, they are re-suspended in a
solution containing 25 mM Tris-HC1 (pH 7.5), 100 mM KC1, and 5 mM 2-
mercaptoethanol. The bead pellets are mixed with an equal volume of a 2x assay
mixture that contains I mM unlabeled ATP and 1 mM DMAPP, and incubated at
25°C for 1 h with shaking. After a brief spin, the supernatant is recovered and
separated into two portions, and one portion is treated with CIAP as described
before. The supernatant with or without treatment with CIAP is mixed with three
volumes of acetone. The mixture is incubated at -80°C for 30 min and centrifuged
at 17,000xg for 30 min to remove the proteins. The supernatants are dried under
vacuum, and the residues are dissolved in methanol. Aliquots are separated by
HPLC with a Chemcobond ODS-W column (Chemco, Osaka, Japan), by using the
following program: 20 mM KHaPC^t for 15 min, followed by linear gradient of 0%
acetonitrile and 20 mM KHaP04 to 80% acetonitrile and 4 mM KHaPCvt over 30
min. The fractions are collected and dried under vacuum, and the residues are
resuspended in ethanol. After centrifugation to remove any possible salt
precipitates, the solutions" are subjected to fast atom bombardment mass
spectrornetry (JMS-SX102 or JEOL MStation, JEOL DATUM LTD., Tokyo, Japan).
C. Assaying for Shoot and Root Regeneration
Transformation of Arabidopsis callus is performed as follows. Selection for
transformants is made using 3mg/L of bialaphos. Arabidopsis seeds are sterilized
according to Koncz et a/. (1992) Methods in Arabidopsis Research, Sinapore,
River Edge, N.J., World Scientific. Seeds are placed on GM medium and grown in
continuous light at 23°C for 11 days. Hypocotyl segments are cut and placed on
CIM for 8 days. Calli are soaked in a suspension of Agrobacterium (0.2 ODeoo) in
AIM for 5 minutes. Most of the liquid is removed on the filter paper, and the
Arabidopsis is placed on CIM culture medium and grown in continuous light at
23°C for 2 days. The calli are washed thoroughly in WASHM medium and placed
on GM+IBA or GM+Z+IBA medium and cultured for about 3 weeks. Selection for
transformants is made on 3 mg/L of bialaphos.
Media recipes for the transformation protocol discussed above are as
follows. SOOOxCIM hormone mix comprises 2.5 mg/ml 2,4-D (Sigma Cat. No. D
6679); 0.25 mg/ml kinetin (Sigma Cat no. K 0753); and, 5 mg/ml biotin dissolved in
DMSO (Sigma Cat. No. B 3399. 500x vitamin mix comprises 50 g/l myo-inositol
(Sigma Cat. No. I 3011); 10 g/l thiamine-HCI (Sigma Cat. No. T 3902); 0.5 g/l
pyridoxine-HCl (Sigma Cat. No. P 8666); and, 0.5 g/l nicotinic acid (Sigma Cat.
No. N0765). GM (germination medium) (for 1 liter) comprises 4.3 g MS medium
salt base (Sigma Cat. No. M 5524); 10 g sucrose (Sigma Cat. No. S 8501); 2 ml
500x vitamin mix; 10 ml 5% MES (adjusted to pH 5.7 with KOH) (Sigma Cat. No.
M 2933); and, 3 g Phytagel (Sigma Cat. No. P 8169). The mixture is autoclaved
and poured in Petri dishes. CIM (callus inducing medium) comprises 3.08 g
Gamborg's B5 medium salt base (Sigma Cat. No. G 5768); 20 g glucose (Sigma
Cat. No. G7528); 2 ml 500x vitamin mix; 10 ml 5% MES (adjusted to pH 5.7 with
KOH); and, 3 g Phytagel. The mixture is autoclaved, cooled and 200 ul of CIM
hormone mix is added. The mixture is then poured into Petri dishes. AIM
(Agrobacterium infection medium) comprises CIM without Phytagel. WASHM
(washing medium) comprises GM from which Phytagel has been omitted, plus
100mg/l of sodium cefotaxime. GM+ (selection of transformed calli) comprises
GM medium that was autoclaved with the following components add via filter: 1
ml of 100 mg/ml cefotaxime (Sigma Cat. No. C 7039); 1 ml of 50 mg/ml of
Ca"t7NoTC!"3416); and, 3 ml of 1 mg/ml Bialaphos. GM-HBA
comprises the addition of 300 M' of 1 mg/ml indolebutyric acid (IBA) (Sigma Cat.
No. I 7512) to the GM media described above. GM+IBA+Z comprises the addition
of 300 Ml of 1 mg/ml IBA and 1 ml of 1 mg/ml trans-Zeatin (Z) (Sigma Cat. No. Z
2753) to the GM media described above.
In order to examine the function of IPT, the maize IPT sequences are first
selected and introduced in Arabidopsis calli under the control of the 35S promoter.
Call! transformed with a control vector will exhibit normal hormone responses:
root formation in the presence of only an auxin and shoot formation in the
presence of a cytokinin and an auxin. By contrast, calli transformed with 35S::IPT
will regenerate shoots even in the absence of exogenously applied cytokinins or in
the presence of a reduced concentration of exogenously applied cytokinins. In
addition, modulation in cytokinin synthesis could be assayed for changes in either
direction. Representative methods include cytokinin extraction,
immunopurification, HPLC separation, and quantification by ELISA methods can
be found, for example, in Faiss et a/. (1997) Plant J. 72:401-415. See, also,
Werner et a/. (2001) PNAS 98:10487-10492) and Dewitte ef a/. (1999) Plant
Physiol. 119:111-121.
D, Assaying for DMAPP:tRNA isopentenvltransferase activity
Undermodified tRNA is prepared by permanganate-treatment of yeast tRNA
(type X, Sigma-Aldrich Japan, Tokyo, Japan) according to the method of Kline et
a/. (1969) Biochemistry 8:4361-4371. Twenty microliters of purified protein
samples (20ng (protein ml"1) in dilution buffer is mixed with the same volume of 2X
tRNA isopentenyltransferase assay mixture (25 mM Tris-HCI, pH 7.5; 10mM
MgCIa; 5 mM 2-mercaptoethanol; 0.67 uM [1-3H]DMAPP, 555 GBq mmor1; and
567 A aeo units ml"1 undermodified tRNA), and incubated at 25°C for 30 min. After
160 u of 0.4 M sodium acetate and 500 pi of ethanol is added and allowed to
settle on ice for 10 minutes, the tRNA precipitates are recovered by centrifugation
(17,000xg for 20 minutes), washed with 80% ETOH, and dissolved in 30 ul of
distilled water. These are mixed with ten volumes of ACSII, and radioactivity
levels are measured.
'E)(arnple11. Maintaining or Increasing Seed Set During Stress
Targeted overexpression of the IPT sequences of the invention to the
developing female inflorescence will elevate cytokinin levels and allow developing
maize seed to achieve their full genetic potential for size, minimize tip kernel
abortion, and buffer seed set during unfavorable environments. Abiotic stress that
occurs during kernel development in maize has been shown to cause reduction in
cytokinin levels. Under stress conditions, it is likely that cytokinin biosynthesis
activity is decreased and cytokinin degradation is increased (Brugiere et al, (2003)
Plant Physiol. 132(3):1228-40). Consequently, in one non-limiting method, to
maintain cytokinin levels in lag phase kernels, IPT genes could be ligated to
control elements that: 1) are stress insensitive; 2) direct expression of structural
genes predominantly to the developing kernels; and 3) preferentially drive
expression of structural genes during the lag phase of kernel development.
Promoters which target expression to related maternal tissues at or around
anthesis may also be employed. Alternatively, a constitutive promoter could be
employed.
For example, immature maize embryos from greenhouse donor plants are
bombarded with a plasmid containing a sequence, chosen from ZmlPT1-9 or
OslPT1-11, operably linked to the Zag2.1 promoter (Schmidt et al. (1993) Plant
Cell 5:729-737) and containing the selectable marker gene BAR (Wohlleben et al.
(1988) Gene 70:25-37), which confers resistance to the herbicide Bialaphos.
Alternatively, the selectable marker gene is provided on a separate plasmid.
Transformation is performed as follows. Media recipes follow below.
The ears are husked and surface-sterilized in 30% Clorox bleach plus 0.5%
Micro detergent for 20 minutes, and rinsed two times with sterile water. The
immature embryos are excised and placed embryo axis side down (scutellum side
up), 25 embryos per plate, on 560Y medium for 4 hours and then aligned within
the 2.5cm target zone in preparation for bombardment.
A plasmid vector comprising the IPT sequence operably linked to a Zag2.1
promoter is made. This plasmid DNA plus plasmid DNA containing a BAR
selectable marker is precipitated onto 1.1 Mm (average diameter) tungsten pellets
using a CaCI2 precipitation procedure as follows: 100ul prepared tungsten
particles in water; 10 |j| (1 pg) DNA in Tris EDTA buffer (1 ug total DNA); 100 \J2.5 M CaC12; and, 10 (Jl 0.1 M spermidine.
Ea"6H'""r'§a§e'nt"1§""a'cldea" sequentially to the tungsten particle suspension,
while maintained on the multitube vortexer. The final mixture is sonicated briefly
and allowed to incubate under constant vortexing for 10 minutes. After the
precipitation period, the tubes are centrifuged briefly, liquid removed, washed with
500 ml 100% ethanol, and centrifuged for 30 seconds. Again the liquid is
removed, and 105 ul 100% ethanol is added to the final tungsten particle pellet.
For particle gun bombardment, the tungsten/DNA particles are briefly sonicated
and 10 pi spotted onto the center of each macrocarrier and allowed to dry about 2
minutes before bombardment.
The sample plates are bombarded at level #4 in particle gun #HE34-1 or
#HE34-2. All samples receive a single shot at 650 PSI, with a total often aliquots
taken from each tube of prepared particles/DNA.
Following bombardment, the embryos are kept on 560Y medium for 2 days,
then transferred to 560R selection medium containing 3 mg/liter Bialaphos, and
subcultured every 2 weeks. After approximately 10 weeks of selection, selectionresistant
callus clones are transferred to 288J medium to initiate plant
regeneration. Following somatic embryo maturation (2-4 weeks), well-developed
somatic embryos are transferred to medium for germination and transferred to the
lighted culture room. Approximately 7-10 days later, developing plantlets are
transferred to 272V hormone-free medium in tubes for 7-10 days until plantlets are
well established. Plants are then transferred to inserts in flats (equivalent to 2.5"
pot) containing potting soil and grown for 1 week in a growth chamber,
subsequently grown an additional 1-2 weeks in the greenhouse, then transferred
to classic 600 pots (1.6 gallon) and grown to maturity. Plants are monitored and
scored for the maintenance or increase of seed set during an abiotic stress
episode. In addition, transformants under stress will be monitored for cytokinin
levels (as described in Example 5c) and maintenance of kernel growth.
Bombardment medium (560Y) comprises 4.0 g/l N6 basal salts (SIGMA C-
1416), 1.0 ml/I Eriksson's Vitamin Mix (1000X SIGMA-1511), 0.5 mg/l thiamine
HCI, 120.0 g/l sucrose, 1.0 mg/l 2,4-D, and 2.88 g/l L-proline (brought to volume
with D-l H2O following adjustment to pH 5.8 with KOH); 2.0 g/l Gelrite (added after
bringing to volume with D-l HaO); and 8.5 mg/l silver nitrate (added after sterilizing
the medium and cooling to room temperature). Selection medium (560R)
comprises 4.0 g/l N6 basal salts (SIGMA C-1416), 1.0 ml/l Eriksson's Vitamin Mix
(1000X SIGMA-1511), 0.5 mg/l thiamine HCI, 30.0 g/l sucrose, and 2.0 mg/l 2,4-D
"(brought toWlume flftrTDtfftjb following adjustment to pH 5.8 with KOH); 3.0 g/l
Gelrite (added after bringing to volume with D-l H2O); and 0.85 mg/l silver nitrate
and 3.0 mg/l bialaphos(both added after sterilizing the medium and cooling to
room temperature).
Plant regeneration medium (288J) comprises 4.3 g/l MS salts (GIBCO
11117-074), 5.0 ml/I MS vitamins stock solution (0.100 g nicotinic acid, 0.02 g/l
thiamine HCL, 0.10 g/l pyridoxine HCL, and 0.40 g/l glycine brought to volume with
polished D-l H2O) (Murashige and Skoog (1962) Physiol. Plant 15:473), 100 mg/l
myo-inositof, 0.5 mg/l zeatin, 60 g/I sucrose, and 1.0 ml/I of 0.1 mM abscisic acid
(brought to volume with polished D-l H2O after adjusting to pH 5.6); 3.0 g/l Gelrite
(added after bringing to volume with D-l H2O); and 1.0 mg/l indoleacetic acid and
3.0 mg/l bialaphos (added after sterilizing the medium and cooling to 60°C).
Hormone-free medium (272V) comprises 4.3 g/l MS salts (GIBCO 11117-074), 5.0
ml/l MS vitamins stock solution (0.100 g/l nicotinic acid, 0.02 g/l thiamine HCL,
0.10 g/l pyridoxine HCL, and 0.40 g/! glycine brought to volume with polished D-l
H2O), 0.1 g/l myo-inositol, and 40.0 g/l sucrose (brought to volume with polished
D-l H2O after adjusting pH to 5.6); and 6 g/l bacto-agar (added after bringing to
volume with polished D-l H2O), sterilized and cooled to 60°C.
Example 12: Modulating Root Development
For Agrobacterium-mediated transformation of maize with a plasmid
designed to achieve post-transcriptional gene silencing (PTGS) with an
appropriate promoter, the method of Zhao may be employed (U.S. Patent No.
5,981,840, and PCT patent publication WO98/32326, the contents of which are
hereby incorporated by reference). Briefly, immature embryos are isolated from
maize and the embryos contacted with a suspension of Agrobacterium capable of
transferring a DNA construct. Said construct may comprise the CRWAQ81 rootpreferred
promoter::ADH intron promoter operably linked to a hairpin structure
made from the coding sequence of any one of the ZmlPT1-9 or OsfPT1-11
polynucleotides of the invention. Other useful constructs may comprise a hairpin
construct targeting the promoter of any one of the ZmlPT1-9 or OslPT1-11
polynucleotides of the invention. (Aufsatz et al. (2002) PNAS 99 (Suppl. 4):16499-
16506; Mette et al. (2000) EMBO J 19(19):5194-5201) The construct is
ransferred to at least one cell of at least one of the immature embryos (step 1: the
nfection step). In this step the immature embryos are immersed in an
•Mgrooacra/70/W fO^p^rfslon toT the initiation of inoculation. The embryos are cocultured
for a time with the Agrobacterium (step 2: the co-cultivation step); this
may take place on solid medium. Following this co-cultivation period an optional
"resting" step is contemplated. In this resting step, the embryos are incubated in
the presence of at (east one antibiotic known to inhibit the growth of
Agrobacterium without the addition of a selective agent for plant transformants
(step 3: resting step). Next, inoculated embryos are cultured on medium
containing a selective agent; growing, transformed callus is recovered (step 4: the
selection step). The callus is then regenerated into plants (step 5: the
regeneration step).
Plants are monitored and scored for a modulation in root development. The
modulation in root development includes monitoring for enhanced root growth of
one or more root parts including the primary root, lateral roots, adventitious roots,
etc. Methods of measuring such developmental alterations in the root system are
known in the art. See, for example, U.S. Application No. 2003/0074698 and
Werner et al. (2001) PNAS 18:10487-10492, both of which are herein incorporated
by reference.
Example 13. Modulating Senescence of a Plant
A DNA construct comprising any of the ZmlPT1-9 or OslPT1-11
polynudeotides operably linked to a constitutive promoter, a root-preferred
promoter, or a senescence-activated promoter, such as SAG12 (Gan et al. (1995)
Science 270:5244, Genbank Ace. No. U37336) is introduced into maize plants as
outlined in Zhao et al. (1998) Maize Genetics Corporation Newsletter 72:34-37,
herein incorporated by reference.
For example, maize plants comprising the IPT sequence operably linked to
the SAG12 promoter are obtained. As a control, a non-cytokinin-related construct
is also introduced into maize plants using the transformation method outlined
above. The phenotypes of transgenic maize plants having an elevated level of the
IPT polypeptide are studied. For example, plants can be monitored for an
improved vitality, shelf and vase life, and improved tolerance against infection.
Plants could also be monitored for delayed senescence under various
environmental1 stresses including, for example, flooding which normally results in
leaf chlorosis, necrosis, defoliation, cessation of growth and reduction in yield.
"fcxamdltm: saymitrEmtfrtto Transformation
Soybean embryos are bombarded with a plasmid containing the IPT
sequence operably linked to a ubiquitin promoter as follows. To induce somatic
embryos, cotyledons, 3-5 mm in length dissected from surface-sterilized, immature
seeds of the soybean cultivar A2872, are cultured in the light or dark at 26°C on
an appropriate agar medium for six to ten weeks. Somatic embryos producing
secondary embryos are then excised and placed into a suitable liquid medium.
After repeated selection for clusters of somatic embryos that multiplied as early,
globular-staged embryos, the suspensions are maintained as described below.
Soybean embryogenic suspension cultures can be maintained in 35 ml
liquid media on a rotary shaker, 150 rpm, at |26°C with florescent lights on a
16:8 hour day/night schedule. Cultures are subcultured every two weeks by
inoculating approximately 35 mg of tissue into 35 ml of liquid medium.
Soybean embryogenic suspension cultures may then be transformed by the
method of particle gun bombardment (Klein et al. (1987) Nature (London)
327:70-73, U.S. Patent No. 4,945,050). A Du Pont Biolistic PDS1000/HE
instrument (helium retrofit) can be used for these transformations.
A selectable marker gene that can be used to facilitate soybean
transformation is a transgene composed of the 35S promoter from Cauliflower
Mosaic Virus (Odelf et al. (1985) Nature 313:810-812), the hygromycin
phosphotransferase gene from plasmid pJR225 (from E. coir, Gritz et al. (1983)
Gene 25:179-188), and the 3' region of the nopaline synthase gene from the
T-DNA of the Ti plasmid of Agrobacterium tumefaciens. The expression cassette
comprising the IPT sequence operably linked to the ubiquitin can be isolated as a
restriction fragment This fragment can then be inserted into a unique restriction
site of the vector carrying the marker gene.
To 50 ul of a 60 mg/ml 1 urn gold particle suspension is added (in order):
5 Ml DNA (1 ug/pl), 20 ul spermidine (0.1 M), and 50 ul CaCl2 (2.5 M). The
particle preparation js then agitated for three minutes, spun in a microfuge for
10 seconds and the supernatant removed. The ONA-coated particles are then
washed once in 400 ul 70% ethartol and resuspended in 40 pi of anhydrous
ethanol. The DNA/particle suspension can be sonicated three times for
one second each. Five microliters of the DNA-coated gold particles are then
loaded on each macro carrier disk.
of a two-week-old suspension culture is placed
in an empty 60x15 mm petri dish and the residual liquid removed from the tissue
with a pipette. For each transformation experiment, approximately 5-10 plates of
tissue are normally bombarded. Membrane rupture pressure is set at 1100psi,
and the chamber is evacuated to a vacuum of 28 inches mercury. The tissue is
placed approximately 3.5 inches away from the retaining screen and bombarded
three times. Following bombardment, the tissue can be divided in half and placed
back into liquid and cultured as described above.
Five to seven days post bombardment, the liquid media may be exchanged
with fresh media, and eleven to twelve days post-bombardment with fresh media
containing 50 mg/ml hygromycin. This selective media can be refreshed weekly.
Seven to eight weeks post-bombardment, green, transformed tissue may be
observed growing from untransformed, necrotic embryogenic clusters. Isolated
green tissue is removed and inoculated into individual flasks to generate new,
clonally propagated, transformed embryogenic suspension cultures. Each new
line may be treated as an independent transformation event. These suspensions
can then be subcultured and maintained as clusters of immature embryos or
regenerated into whole plants by maturation and germination of individual somatic
embryos.
Example 15. Sunflower Meristem Tissue Transformation
Sunflower meristem tissues are transformed with an expression cassette
containing the IPT sequence operably linked to a ubiquitin promoter as follows
(see also European Patent Number EP 0 486233, herein incorporated by
reference, and Malone-Schoneberg ef a/. (1994) Plant Science 103:199-207).
Mature sunflower seed (Hetianthus annuus L) are dehulled using a single wheathead
thresher. Seeds are surface sterilized for 30 minutes in a 20% Clorox bleach
solution with the addition of two drops of Tween 20 per 50 ml of solution. The
seeds are rinsed twice with sterile distilled water.
Split embryonic axis expiants are prepared by a modification of procedures
described by Schrammeijer et al. (Schrammeijer ef a/.(1990) Plant Cell Rep. 9:55-
60). Seeds are imbibed in distilled water for 60 minutes following the surface
sterilization procedure. The cotyledons of each seed are then broken off,
producing a clean fracture at the plane of the embryonic axis. Following excision
of the root tip, the expiants are bisected longitudinally between the primordial
placed, cut surface up, on GBA medium consisting of
Murashige and Skoog mineral elements (Murashige et al. (1962) Physiol. Plant,
15: 473-497), Shepard's vitamin additions (Shepard (1980) in Emergent
Techniques for the Genetic Improvement of Crops (University of Minnesota Press,
St. Paul, Minnesota), 40 mg/l adenine sulfate, 30 g/l sucrose, 0.5 mg/l 6-benzylaminopurine
(BAP), 0.25 mg/l indole-3-acetic acid (IAA), 0.1 rng/l gibberellic acid
(GAa), pH 5.6, and 8 g/l Phytagar.
The explants are subjected to microprojectile bombardment prior to
Agrobacterium treatment (Sidney et al (1992) Plant Mol. Biol. 18:301-313). Thirty
to forty explants are placed in a circle at the center of a 60 X 20 mm plate for this
treatment. Approximately 4.7 mg of 1.8 mm tungsten microprojectiles are
resuspended in 25 ml of sterile TE buffer (10 mM Tris HCI, 1 mM EDTA, pH 8.0)
and 1.5 ml aliquots are used per bombardment. Each plate is bombarded twice
through a 150 mrn nytex screen placed 2 cm above the samples in a PDS 1000®
particle acceleration device.
Disarmed Agrobacterium tumefaciens strain EHA105 is used in all
transformation experiments. A binary plasmid vector comprising the expression
cassette that contains the IPT gene operably linked to the ubiquitin promoter is
introduced into Agrobacterium strain EHA105 via freeze-thawing as described by
Holsters et al. (1978) Mol. Gen. Genet. 163:181-187. This plasmid further
comprises a kanamycin selectable marker gene (i.e., nptfl). Bacteria for plant
transformation experiments are grown overnight (28°C and 100 RPM continuous
agitation) in liquid YEP medium (10 gm/1 yeast extract, 10 gm/l Bactopeptone, and
5 gm/l NaCI, pH 7.0) with the appropriate antibiotics required for bacterial strain
and binary plasmid maintenance. The suspension is used when it reaches an
ODeoo of about 0.4 to 0.8. The Agrobacterium cells are pelleted and
resuspended at a final ODgoo of 0.5 in an inoculation medium comprised of 12.5
mM MES pH 5.7, 1 gm/l NH4CI, and 0.3 gm/l MgSO4-
Freshly bombarded explants are placed in an Agrobacterium suspension,
mixed, and left undisturbed for 30 minutes. The explants are then transferred to
GBA medium and co-cultivated, cut surface down, at 26°C and 18-hour days.
After three days of co-cultivation, the explants are transferred to 374B (GBA
medium lacking growth regulators and a reduced sucrose level of 1%)
supplemented with 250 mg/l cefotaxime and 50 mg/l kanamycin sutfate. The
explants are cultured for two to five weeks on selection and then transferred to
fresh 374B medium lacking kanamycin for one to two weeks of continued
development. Explants with differentiating, antibiotic-resistant areas of growth that
have not produced shoots suitable for excision are transferred to GBA medium
containing 250 mg/l cefotaxime for a second 3-day phytohormone treatment. Leaf
samples from green, kanamycin-resistant shoots are assayed for the presence of
NPTII by ELISA and for the presence of transgene expression by assaying for
cytokinin synthesis activity. Such assays are described elsewhere herein.
NPTII-positive shoots are grafted to Pioneer® hybrid 6440 in vitro-grown
sunflower seedling rootstock. Surface sterilized seeds are germinated in 48-0
medium (half-strength Murashige and Skoog salts, 0.5% sucrose, 0.3% geJrite, pH
5.6) and grown under conditions described for explant culture. The upper portion
of the seedling is removed, a 1 cm vertical slice is made in the hypocotyl, and the
transformed shoot inserted into the cut. The entire area is wrapped with parafilm
to secure the shoot. Grafted plants can be transferred to soil following one week
of in vitro culture. Grafts in soil are maintained under high humidity conditions
followed by a slow acclimatization to the greenhouse environment. Transformed
sectors of TO plants (parental generation) maturing in the greenhouse are
identified by NPTII ELISA and/or by cytokinin synthesis activity analysis of leaf
extracts while transgenic seeds harvested from NPTII-positive TO plants are
identified by cytokinin synthesis activity analysis of small portions of dry seed
cotyledon.
Example 16. Variants of IPT
A. Variant Nucleotide Sequences ofZmlPT1-9 and OslPT1-11 (SEQ ID
NO: 1, 3, 4, 5, 7, 8, 10, 11, 13, 14, 16, 17, 19, 20, 21, 22, 24, 26, 28, 40, 42, 44,
45, 47, 48, 50, 51, 53, 55, 56, 58, 60, 62, 64, 65, 69, 70, 71, 72, 73, 74, or 76)
That Do Not Alter the Encoded Amino Acid Sequence
The ZmlPT1-9 or OslPT1-11 nucleotide sequences set forth in SEQ ID NO:
1, 3, 4, 5, 7, 8, 10, 11,13,14,16, 17,19, 20, 21, 22, 24, 26, 28, 40,42, 44,45, 47,
48, 50, 51, 53, 55, 56, 58, 60, 62, 64, 65, 69, 70, 71, 72, 73, 74, or 76 are used to
generate variant nucleotide sequences having the nucleotide sequence of the
open reading frame with about 70%, 75%, 80%, 85%, 90%, and 95% nucleotide
sequence identity when compared to the corresponding starting unaltered ORF
nucleotide sequence. These functional variants are generated using a standard
"coddn table. While the nucleotide sequence of the variant is altered, the amino
acid sequence encoded by the open reading frame does not change.
8. Variant Amino Acid Sequences of ZmlPTI-9 and OslPT1-11
Variant amino acid sequences of ZmlPT1-9 and Os!PT1-11 are generated,
tn this example, one or more amino acids are altered. Specifically, the open
reading frame set forth in SEQ ID NO: 1, 3, 4, 5, 7, 8, 10, 11, 13, 14, 16, 17, 19,
20, 21, 22, 24, 26, 28, 40, 42, 44, 45, 47, 48, 50, 51, 53, 55. 56, 58, 60, 62, 64, 65,
69, 70, 71, 72, 73, 74, or 76 is reviewed to determine the appropriate amino acid
alteration. The selection of an amino acid to change is made by consulting a
protein alignment with orthologs and other gene family members from various
species. See Figure 1 and/or Figure 10. An amino acid is selected that is
deemed not to be under high selection pressure (not highly conserved) and which
is rather easily substituted by an amino acid with similar chemical characteristics
(i.e., similar functional side-chain). Assays as outlined in Example 10 may be
followed to confirm functionality. Variants having about 70%, 75%, 80%, 85%,
90%, or 95% nucleic acid sequence identity to each of SEQ ID NO: 1, 3,4, 5, 7, 8,
10, 11, 13,14, 16,17,19, 20, 21, 22, 24, 26, 28, 40, 42, 44, 45,47, 48, 50, 51, 53,
55, 56, 58, 60, 62, 64, 65, 69, 70, 71, 72, 73, 74, and 76 are generated using this
method.
B. Additional Variant Amino Acid Sequences of ZmlPTI-9
andOslPT1-11
In this example, artificial protein sequences are created having 80%, 85%,
90%, and 95% identity relative to the reference protein sequence. This latter effort
requires identifying conserved and variable regions from the alignment set forth in
Figure 1 and/or Figure 10 and then the judicious application of an amino acid
substitutions table. These parts will be discussed in more detail below.
Largely, the determination of which amino acid sequences are altered is
made based on the conserved regions among the IPT proteins or among the other
IPT polypeptides. See Figures 1 and 10. Based on tine sequence alignment, the
various regions of the IPT polypeptides that can likely be altered can be
determined. It is recognized that conservative substitutions can be made in the
conserved regions without altering function, in addition, one of skill will
understand that functional variants of the IPT sequence of the invention can have
minor non-conserved amino acid alterations in the conserved domain.
Artificial protein sequences are then created that are different from the
original in the intervals of 80-85%, 85-90%, 90-95%, and 95-100% identity.
Midpoints of these intervals are targeted, with liberal latitude of plus or minus 1%,
for example. The amino acids substitutions will be effected by a custom Perl
script. The substitution table is provided below in Table 8.
(Table Removed)
First, any conserved amino acids in the protein that should not be changed
are identified and "marked off' for insulation from the substitution. The start
methionine will of course be added to this list automatically. Next, the changes
are made.
H, C, and P are not changed. The changes will occur with isoleucine first,
sweeping N-terminal to C-terminal. Then leucine, and so on down the list until the
desired target is reached. Interim number substitutions can be made so as not to
cause reversal of changes. The list is ordered 1-17, so start with as many
isoleucine changes as needed before leucine, and so on down to methionine.
Clearly many amino acids will in this manner not need to be changed. L, I and V
will involve a 50:50 substitution of the two alternate optimal substitutions.
The variant amino acid sequences are written as output. Perl script is used
to calculate the percent identities. Using this procedure, variants of ZmlPT1-9 and
OslPT1-11 are generating having about 82%, 87%, 92%, and 97% amino acid
identity to the starting unaltered ORF nucleotide sequence of SEQ ID NO: 1, 3, 4,
5, 7, 8, 10. 11,13, 14,16, 17, 19,20,21,22,24,26,28,40,42,44,45,47,48,50,
51, 53, 55, 56, 58, 60, 62, 64, 65, 69, 70, 71, 72, 73, 74, or 76.
Example 17. Characterization of Rice IPT Sequences
Eleven putative rice ipt sequences were identified which comprise deduced
amino acid sequences showing similarity to the Arabidopsis and Petunia IPT
proteins. Figure 10 provides an alignment of the amino acid sequences
corresponding to Arabidopsis IPT proteins (AtlPT), the petunia IPT protein (Sho)
and rice putative IPT proteins (OslPT). Asterisks indicate the positions of amino
acids conserved in most IPT proteins and following the consensus sequence
GxTxxGK[ST]xxxxxIVLI]xxx)c ID NO: 32) (where x denotes any amino acid residue, [ ] any one of the amino
acids shown in [ ], and x{m,n} m to n amino acid residues in number) (Takei et at.
(2001) J. Biol. Chem. 276:26405-26410).
The presence of putative ATP/GTP-binding site (P-loop) motif (prosite
PS00017: consensus [AGJ-x(4)-G-K-[STj), (SEQ ID NO: 69) is underlined. This
domain is found at about amino acids 128-135 of SEQ ID NO: 54; at about amino
acids 59-66 of SEQ ID NO: 66: at about amino acids 59-66 of SEQ ID NO: 63; at
about amino acids 40-47 of SEQ ID NO: 61; at about amino acids 320-327 of SEQ
ID NO: 43; at about amino acids 22-29 of SEQ ID NO: 49; at about amino acids
315-322 of SEQ ID NO: 59; at about amino acids 32-39 of SEQ ID NO: 57; at
about amino acids 41-48 of SEQ ID NO: 41; at about amino acids 25-32 of SEQ
ID NO: 46; and, at about amino acids 37-44 of SEQ ID NO: 52. The presence of a
putative tRNA isopentenyltransferase domain (PF01715) was found at about
amino acids 59-348 of SEQ ID NO: 57 and about amino acids 69-352 of SEQ ID
NO: 41.
The Align X program was used on default settings to determine the overall
amino acid sequence identity for the various rice IPT sequences compared with
known Arabidopsis IPT sequences. Table 9 summarizes these results. Table 10
provides polypeptides that share homology to the rice IPT sequences. Such
(Table Removed)
Example 18. IPT Activity Assay
Assays were conducted to test the ability of a protein encoded by a
sequence of the invention to synthesize cytokinin in a bacterial culture medium.
The results confirmed that sequences of the invention encode proteins with
128
"isopentenyltransferase activity. The reaction catalyzed by Agrobacterium ipt is
shown in Akiyoshi et al. (1984) PNAS 81(19):5994-5998.
The IPT assay protocol was adapted from the following references:
Kakimoto, T. (2001) Identification of plant biosynthetic enzymes as dimethylallyl
diphosphate: ATP/ADP isopentenyltransferases, Plant Cell Physio! 42: 677-685.
Sakakibara, H., and Takei, K. (2002) Identification of Cytokinin Biosynthesis
Genes in Arabidopsis: A Breakthrough for Understanding the Metabolic Pathway
and the Regulation in Higher Plants, J. Plant Growth Reguf. 21:17-23. Sakano, Y.,
Okada, Y., Matsunaga, A., Suwama, T., Kaneko, T., Ito, K., Noguchi, H., and Abe,
I. (2004) Molecular cloning, expression, and characterization of adenylate
isopentenyltransferase from hop (Humulus lupulus L), Phytochemistry 65:2439-
2446.
The ZmlPT2 gene was amplified using gene-specific primers with
appropriate Ndel and Notl restriction site extensions and cloned into pET28a (Nterminal
tag) or pETSOb (C-terminal tag) digested by Ndel and Notl. The sequence
of the resulting plasmid was verified by sequencing of the His-tag translational
fusion with ZmlPT2, and BL21-Star™ E. coll competent cells (Invitrogen™) were
transformed with pET28a-ZmlPT2 and pET30b-Zm(PT2. Similarly, The tzs IPT
gene from Agrobacterium tumefaciens was cloned into pET28a to yield a plasmid
for transformation of Rosetta2(DE3)pLysS.
Recombinant his-tagged proteins were purified using a TALON™ column (BD
Biosciences) according to the instructions provided by the manufacturer. Purified
protein samples were used to determine Dimethylallyl diphosphate
(DMAPP)::AMP and DMAPP::ATP isopentenyl transferase activities using the
following protocol:
« Each purified protein extract was incubated in a reaction mixture containing
12.5 mM Tris-HCI (pH 7.5), 37.5 mM KCI, 5 mM MgCI2, 1 mM DMAPP and
1mM AMP or ATP for 2 hours at 30°C. The reaction was stopped by boiling
the samples for 5 minutes.
• Half of the reaction mixture was treated with calf intestine alkaline
phosphatase (CAIP) by adding one volume of 2 x CAIP reaction buffer
(0.45M Tris-HCI pH 9, 10 mM MgC!2, 1000 unit of CAlP7ml) and incubating
for 1 hour at 37°C.
• The reaction products were separated using reversed phase HPLC (Agilent
1100 system with diode-array-detector) using a C18-ODS2 column
(Phenomenex) ana a separation protocol using 0.1 M acetic acid pH 3.3
(Buffer A) and acetonitrile (Buffer B) as follows:
o 100% buffer A for 15 minutes,
o linear gradient from 100% buffer A and 0% buffer B to 20% buffer A
and 80% buffer B over 35 minutes.
UV absorbance was monitored at 280nm. Product retention times were
compared to standards obtained from Sigma or OlChemlm.
The recombinant Tzs and ZmlPT2 proteins were first used to determine
DMAPP::AMP isopentenyl transferase activity. Figure 12A and Figure 12B show
HPLC chromatograms obtained for one of the substrates of the reaction, 5'-AMP
(Sigma), and the expected product isopentenyladenosine S'-monophosphate
(iPMP) (OlChemlm). The chromatogram obtained with the IPT (tzs) protein shows
that almost all 5'-AMP substrate has been converted to iPMP (Figure 12C).
Similarly, the chromatogram obtained with ZmlPT2 purified protein shows that the
enzyme is able to convert 5'-AMP to iPMP but with a lower efficiency than does
Agrobacterium IPT since not all the 5'-AMP has been converted (Figure 12D).
Treatment of reaction products with calf intestine alkaline phosphatase
(CAIP) and chromatography using HPLC confirmed the identity of the reaction
product iPMP. Figure 13A and 13B show chromatograms obtained with Adenosine
(Ado) (Sigma) and isopentenyladenosine (iPAR) (Sigma). As expected, after
dephosphorylation of the product of each reaction, iPMP was transformed to
isopentenyladenosine (iPAR) (Figure 13C and 13D) whereas remaining 5'-AMP
was transformed to Ado (Figure 13D). This confirms that ZmlPT2 can metabolize
5'-AMP and DMAPP into iPMP.
Determination of DMAPP::ATP activity was carried out using the same
reaction buffer but replacing S'-AMP by 5-ATP in the reaction mixture. Figure 14A
shows the chromatogram obtained with 5-ATP. If ZmlPT2 is able to catalyze the
transfer of DMAPP onto 5'ATP, the resulting product should create iPTP. The
chromatogram of Figure 14B shows that all 5'-ATP was metabolized into iPTP by
ZmlPT2, suggesting that ZmlPT2 uses 5'-ATP with higher efficiency than 5'-AMP.
The reaction product was treated with CAIP to ascertain its identity. Such
treatment should yield iPAR. After separation by HPLC, the chromatogram was
compared to the chromatogram of an iPAR standard (Figure 14C). After treatment,
the reaction product was transformed to iPAR (Figure 14D) therefore confirming
that ZmlPT2 can metabolize 5-ATP and DMAPP into iPTP. Altogether these
results prove that ZmlPT2 is a cytokinin biosynthetic enzyme preferentially using
5'-ATP as a substrate.
Similar experiments established that 5'-ADP is also a suitable substrate for
the encoded enzyme. Taken together, these results prove that ZmlPT2 is a
cytokinin biosynthetic enzyme preferentially using 5'-ATP as a substrate. Future
experiments will determine the kinetic properties for each substrate using a
purified ZmlPT2 protein.
Example 19. Detection of the ZmlPT2 protein in developing kernels.
In order to study further the expression pattern of the ZmlPT2 protein,
polyclonal antibodies were used for a Western blot experiment. Poiyclonal
antibodies were raised in rabbit against purified N-terminal His-tagged
recombinant ZmlPT2 protein. Fifteen micrograms of proteins extracted from whole
kernels harvested at different days after pollination (DAP) were run using SDSPAGE
and blotted on a PVDF membrane. ZmlPT2 proteins were detected using
the method of Laemmli (Nature 227:680-685, 1970) with anti-ZmlPT2 polyclonal
antibodies as primary antibodies and anti-rabbit IgG antibodies raised in goat
conjugated to an alkaline phosphatase as secondary antibodies.
Figure 15 shows that ZmlPT2 protein levels increase from 0 to 10 DAP,
peak at 10 DAP, then decrease from 10 DAP to 15 DAP and stay approximately
constant thereafter. This is in agreement with Northern blot results showing that
expression of the gene peaks around 10 DAP where it is strong in the pedicel and
the endosperm. Although total expression of the gene decreases thereafter,
expression levels remain high in the pedicel at later stages. ZmlPT2 protein levels
in kernels were very high compared to other organs. Results suggest that the
cytokinin activity of ZmlPT2 protein in kernels is most likely controlled at the
transcriptional level. The Western blot analysis of protein levels in kernels
suggests that the antibodies are very specific to ZmlPT2. Antibodies, together with
in situ hybridization, will be very useful in determining the precise site of
expression of the gene during kernel development.
Example 20. Ectopic overexpression of ZmlPT2 in transgenic Arabidopsis.
Previous examples describe the overexpression of ZmiPT2 in Arabidopsis
calli. In order to study the effects of the overexpression of ZmlPT2 at the whole
plant level, Arabidopsis plants were transformed with an Agmbacterium
tumeraciens strain containing a plasmid comprising the construct 35S-Adhl-
ZmlPT2-Pinll with the bar herbicide resistance gene as a marker. (Tho'mpson et
al. (1987) EMBO J 6(9):2519-2523; White et al. (1990) Nucleic Acids Res.
18(4): 1062) The simplified Abrabidopsis transformation protocol (Clough and Bent
(1998) Plant J. 16:735-743) was used. Seeds were sown in flats containing soil
and incubated for 2 days at 4°C to optimize germination. After 10 days in the
greenhouse, transformants were selected by spraying the seedlings daily for 5
days with a 1/1000 dilution of Finale™ herbicide.
After selection, several plants resistant to the herbicide treatment were
identified. Some plants appeared small and dark green compared to others. Leaf
greenness is linked to cytokinin levels, suggesting that the dark green transformed
plants have elevated levels of cytokinin. Some transgenic plants appeared more
affected than others, possibly linked to the level of expression of the transgene
which is known to be variable depending on position effects related to insertion in
the genome.
At an early stage of development, some transgenic plants showed signs of
anthocyanin accumulation in leaves compared to non transgenic plants. Some
transgenics had highly serrated leaves compared to wild-type Arabidopsis. This
phenotype has previously been reported in Arabidopsis plants over-expressing the
Agrobacterium ipt gene (van der Graaff et al. (2001) Plant Growth Regul.
34(3):305-315). High levels of cytokinin are often detrimental to plant growth (van
der Graaff et al., 2001) and some transgenic plants appeared to struggle in their
development compared to control plants. Some transgenics appeared to have a
decreased apical dominance in inflorescence stems compared to controls, which
was previously reported in Arabidopsis and tobacco plants with high levels of
cytokinins (van der Graaff et al., 2001; Crozier et al. (2000) Biosynthesis of
hormones and ellicitor molecules. In Biochemistry and molecular biology of plants,
B. Buchanan. W. Gruissem, and R.L. Jones, eds (Rockville, Maryland: American
Society of Plant Biologists), pp. 850-929)
Some transgenics appeared to have a "bushy" phenotype, most likely due
to a larger number of leaves resulting from decreased apical dominance. Some
plants also had a poor seed set due to the absence of siliques or smaller siliques
with few seeds. They also displayed anthocyanin accumulation in leaves and
along inflorescence stems. Plants often displayed serrated cauline leaves. The
most extreme phenotype was a transgenic plant with a rosette of approximately 5
mm in diameter with very small curly leaves showing signs of anthocyanin
accumulation. The plant was able to flower but never yielded seeds, it also
displayed an unusual abundance of large trichomes. Curly leaf phenotype was
previously described in tobacco with higher cytokinin levels (Crozier et al., 2000).
Thus, over-expression of the protein in Arabidopsis further confirmed the
protein's function by creating a range of phenotypes in agreement with previous
attempts to over-express the IPT gene in Arabidopsis and tobacco (Van der Graaff
at al., 2001; Crozier et al., 2000). The phenotypes observed in several
independent transgenic plants are consistent with a phenotype of cytokinin
accumulation, confirming that ZmlPT2 is a cytokinin biosynthetic enzyme.
Example 21. Determining gene function through Mu tagging.
Gene function can be further confirmed and described by the study of
mutants in which transcription and/or translation of the sequence of interest is
disrupted. In certain embodiments this is accomplished through use of methods
disclosed in US 5,962,764. The Trait Utility Sytstem for Corn (TUSC) is a
proprietary resource for selecting gene-specific transposon insertions from a
saturated collection of maize mutants created using the Mutator transposable
element system. For example, effect of the ZmlPT sequences of the invention on
traits such as plant sink strength may be investigated. The following methods
were applied to identify and characterize a TUSC mutant for ZmlPT2.
A 1495bp genomic sequence was supplied for TUSC screening to identify
germinal Mutator insertions in the maize IPT2 gene (ZmlPT2). This working
annotation of the gene contained a 966bp open reading frame (ORF; nt83-1048)
that is uninterrupted by introns.
Primary screening against TUSC DNA Pools was initiated with two
ZmlPT2-specific primers (PHN79087 and PHN79088), each in combination with
the Mutator terminal inverted repeat (TIR) primer as described in US 5,962,764.
Primer sequences are listed below and provided as SEQ ID Nos: 82-84,
respectively.
PHN79087 zmIPT2-F 5'> TGTTGTGTGCACAGAATCGAGCGG PHN79088 zmIPT2-R 5'> CGTCCGCTAGCTACTTATGCATCAG PHNS242 MuTIR 5'> AGAGAAGCCAACGCCAWCGCCTCYATTTCGTC Primers were validated prior to use by performing gene-specific
amplification of ZmlPT2 using B73 genomic DNA and the PHN79087+79088
primer combination. The control amplification product was excised from an
agarose gel and used as a ^P-labeled hybridization probe for the TUSC
screening.
Primer Pair
79087 + 79088
expected (re. reference seq) (bp)
1033
observed B73 gDNA (bp)
-1050
Following successive rounds of screening the TUSC DNA template Pools
and Individual samples by PCR and ZmlPT2 hybridization, prospective
zmlPT2::Mu alleles were tested for their heritability through the germline. This
was achieved by repeating the ZmlPT2::Mu PCR assays against DNA template
prepared from 5 kernels of selfed (F2) seed from selected Individual TUSC plants.
One TUSC family, PV03_13 H-07 (from Pool 26), showed strong positive results in
the F2 template assay for both 79087+9242 and 79088+9242 primer
combinations. These PCR products were cloned into Topo-TA vector (Invitrogen)
for DNA sequence confirmation of the Mu insertion allele of zmlPT2 harbored by
family PV03 13 H-07. Each PCR fragment was expected to be homologous to the
ZmlPT2 locus, and also share ~71bp of Mutator TIR homology. An expected 9bp
host site duplication, which is created upon insertion of Mu elements into maize
genomic DNA, was also an expected outcome of the PV03 13 H-07 ZmlPT2::Mu
allele.
As shown in Figure 16, DNA sequence characterization of each TUSC PCR
product exhibits these expected features. The 79087+9242 PCR product contains
600bp of direct homology to ZmlPT2 from the left flank of the PV03 13 H-07 Mu
insertion site. This product contains the PHN79087 PCR primer site. The
79088+9242 PCR product contains 442bp of DNA sequence identity with ZmlPT2,
representing the right flank of the Mu insertion site, and contains the PHN79088
primer site. When trimmed of Mutator TIR sequences and aligned to the zmlPT2
referennce sequence, these PCR fragments overlap by 9bp (nt 624-632 of the
1495bp ZmlPT2 reference sequence), representing the expected 9bp host site
duplication created upon insertion of Mutator into ZmlPT2.
Thus, TUSC family PV03 13 H-07 contains a heritable Mutator insertion into
the coding sequence (ORF) of the ZmlPT2 gene. This allele is expected to
produce a null mutation or "knockout" of the ZmlPT2 locus. F2 progeny seed from
PV03 13 H-07, which genetically segregates for the ZmlPT2::Mu mutation, known
as zmlPT2-H07, was withdrawn from the TUSC seed bank and propagated for
phenotypic and biomolecular analyses.
Figure 16 graphically summarizes this TUSC result, and the corresponding
sequence is provided as SEQ ID NO: 85.
As added characterization, BLAST searches of the MuTIR portions of each
zmlPT2::Mu PCR product were conducted to ascribe an identity for the Mu
element residing at the ZmlPT2 locus. TUSC PCR products amplified with the
Mutator PHN9242 primer contain 39bp of flanking TIR sequence that are specific
to the resident element being amplified. BLAST results are consistent with the
zmlPT2::Mu element being either a Mu4 or a Mu3 element.
>IPT2_TIR_L (SEQ ID NO: 86}
GAGATAATTGCCATTATAGAAGAAGAGAGAAGGGGATTCGACGAAATAGAGGCGATGGCGTTGGCTTCTCT
>IPT2_TIR_R (SEQ ID NO: 87)
AAGCCAACGCCUUiCGCCTCTATTTCGTCGAATCCCCITCTCTCTTCTTCTATAATGGCAATTATCTC
In certain embodiments the nucleic acid constructs of the present invention
can be used in combination ("stacked") with other polynucleotide sequences of
interest in order to create plants with a desired phenotype. The polynucleotides of
the present invention may be stacked with any gene or combination of genes, and
the combinations generated can include multiple copies of any one or more of the
polynucleotides of interest. The desired combination may affect one or more
traits; that is, certain combinations may be created for modulation of gene
expression affecting cytokinin activity. For example, up-regulation of cytokinin
synthesis may be combined with down-regulation of cytokinin degradation. Other
combinations may be designed to produce plants with a variety of desired traits,
such as those previously described.
All publications and patent applications mentioned in the specification are
indicative of the level of those skilled in the art to which this invention pertains. All
publications and patent applications are herein incorporated by reference to the
same extent as if each individual publication or patent application was specifically
and individually indicated to be incorporated by reference.
Although the foregoing invention has been described in some detail by way
of illustration and example for purposes of clarity of understanding, it will be
obvious that certain changes and modifications may be practiced within the scope
of the appended claims.



THAT WHICH IS CLAIMED:
1. An isolated polypeptide comprising an amino acid sequence of SEQ ID NO:
2, 6, 9, 12, 15, 18, 23, 27, or 77.
2. An isolated polypeptide comprising an amino acid sequence of SEQ ID NO:
41, 43, 46, 49, 52, 54, 57, 59, 61, 63, or 66.
3. An isolated polypeptide comprising an amino acid sequence selected from
the group consisting of:

(a) an amino acid sequence comprising at least 85% sequence identity
to SEQ ID NO: 2, 6, 9, 12, 15, 18, 23, 27, 41, 43, 46, 49, 52, 54, 57,
59, 61, 63, 66, or 77, wherein said polypeptide has cytokinin
synthesis activity;
(b) an amino acid sequence encoded by a polynudeotide that hybridizes
under stringent conditions to the complement of a polynudeotide
represented by SEQ ID NO: 1, 3, 4, 5, 7, 8, 10, 11, 13, 14, 16, 17,
19, 20. 21, 22, 24, 26, 28, 40, 42, 44, 45, 47, 48, 50, 51, 53, 55, 56,
58, 60, 62, 64, 65, 69, 70, 71, 72, 73, 74, or 76, wherein said
stringent conditions comprise hybridization in 50% formamide, 1 M
NaCI, 1% SDS at 37°C, and a wash in 0.1 X SSC at 60°C to 65°C,
wherein said polypeptide retains cytokinin synthesis activity; and,
(d) an amino add sequence comprising at least 50 consecutive amino adds of SEQ ID NO: 2, 6, 9, 12, 15, 18, 23, 27, 41, 43, 46, 49, 52, 54, 57, 59, 61, 63, 66, or 77, wherein said polypeptide retains cytokinin synthesis activity.
4 An isolated polynudeotide comprising a nucleotide sequence of SEQ ID
NO: 1, 3, 5, 7, 8,10, 11,13,14, 16, 17,19, 20, 21, 22, 24, 26, 28, or 76.
5 An isolated polynudeotide comprising a nucleotide sequence of SEQ ID
NO: 40, 42, 44, 45, 47, 48, 50, 51, 53, 55, 56, 58, 60, 62, 64, 65, 69, 70, 71,
72, 73, or 74.
6. An isolated polynudeotide comprising a nudeotide sequence selected from the group consisting of:
(a) a nudeotide sequence encoding an amino acid sequence comprising SEQ ID NO: 2, 6, 9, 12, 15, 18, 23, 27, 41, 43, 46, 49, 52, 54, 57, 59, 61, 63, 66, or 77;

(b) a nucleotide sequence comprising at least 85% sequence identity to
SEQ ID NO: 1, 3, 5, 7, 8, 10, 11, 13, 14, 16, 17, 19, 20, 21, 22, 24,
26, 28, 40, 42, 44, 45, 47, 48, 50, 51, 53, 55, 56, 58, 60, 62, 64, 65,
69, 70, 71, 72, 73, 74, or 76, wherein said polynucleotide encodes a
polypeptide having cytokinin synthesis activity;
(c) a nucleotide sequence comprising at least 50 consecutive
nucleotides of SEQ ID NO: 1, 3, 5, 7, 8, 10, 11, 13, 14, 16, 17, 19,
20, 21, 22, 24, 26, 28, 40, 42, 44, 45, 47, 48, 50, 51, 53, 55, 56, 58,
60, 62, 64, 65, 69, 70, 71, 72, 73, 74, or 76, wherein said
polynudeotide encodes a polypeptide having cytokinin synthesis
activity; and,
(d) a nudeotide sequence which represents a polynucleotide that
hybridizes under stringent conditions to the complement of a
polynudeotide represented by the nucleotide sequence of a),
wherein said stringent conditions comprise hybridization in 50%
formamide, 1 M NaCI, 1% SDS at 37°C, and a wash in 0.1 X SSC at
60°C to 65°C.

7. A transgenic plant comprising a polynucleotide operably linked to a
promoter that drives expression in the plant, wherein said polynucleotide
comprises a nudeotide sequence of daim 6, and wherein cytokinin level in
said plant is modulated relative to a control plant.
8. The plant of claim 7, wherein said cytokinin level is increased.
9. The plant of daim 7, wherein said cytokinin level is decreased.
10. The plant of daim 7, wherein said polynucleotide is operably linked to a a
tissue-preferred promoter, a constitutive promoter, or an inducible
promoter.
11. The plant of daim 10, wherein said promoter is a root-preferred promoter, a
leaf-preferred promoter, a shoot-preferred promoter, or an inflorescence-
preferred promoter.
12. The plant of daim 7, wherein said cytokinin level modulation affects floral
development.
13. The plant of daim 7, wherein said cytokinin level modulation affects root
development,
14. The plant of daim 7, wherein the plant has an altered shoot-to-root ratio.
15. The plant of daim 7, wherein seed size or seed weight is increased.

16. The plant of daim 7, wherein vigor or biomass yield of said plant is
increased.
17. The plant of claim 7, wherein the stress tolerance of said plant is increased.
18. The plant of claim 7, wherein said plant is maize, and tip kernel abortion is
reduced.
19. The plant of claim 7, wherein said promoter is stress-insensitive and is
expressed in a tissue of the developing seed or related maternal tissue at
or about the time of anthesis.
20. A transformed seed of the plant of claim 7.
21. The plant of claim 7, wherein said plant is maize, wheat, rice, barley,
sorghum, or rye.
22. A plant that is genetically modified at a native genomic locus, said genomic
locus comprising a polynucleotide of claim 6, wherein the cytokinin level of
said plant is modulated.
23. A. method of modulating cytokinin level in a plant, comprising transforming
said plant with a polynucleotide of claim 6 operably linked to a promoter.
24. The method of daim 23 wherein said modulation of cytokinin level affects
root growth or the shoot-to-root ratio.
25. The method of daim 23 wherein said modulation of cytokinin level affects
floral development.
26. The method of claim 23 wherein said modulation of cytokinin level
increases seed size or seed weight.
27. The method of claim 23 wherein said modulation of cytokinin level
increases plant stress tolerance.
28. The method of daim 23 wherein said modulation of cytokinin level affects
vigor or biomass yield.
29. The method of daim 23 wherein said operably-linked promoter is a tissue-
preferred and/or inducible promoter.
30. The method of daim 23 wherein said promoter is stress-insensitive and is
expressed in a tissue of the developing seed or related maternal tissue at
or about the time of anthesis.
31 The method of daim 23, wherein senescence is delayed. 32. The method of claim 23 wherein sink strength of the seed of the plant is modulated.

33. The method of claim 32 wherein cytokinin level is increased in one or more
of the embryo, the endosperm, and tissues proximal thereto.
34. The method of Claim 33 wherein said proximal tissue comprises the
pedicel.
35. A method for modulating the rate or incidence of shoot regeneration in
callus tissue, comprising expressing in said callus tissue a polynucleotide of
Claim 6 operably linked to a heterologous promoter.
36. The method of Claim 35, wherein said promoter is inducible.
37. An isolated polynucleotide comprising a nucleotide sequence of SEQ ID
NO: 25 or 75 or a functional fragment or variant thereof.
38. A DNA construct comprising a promoter operably linked to a nucleotide
sequence of interest, wherein said promoter comprises the polynucleotide
of claim 37.
39. An expression vector comprising the DNA construct of claim 38.
40. A plant comprising at least one DNA construct of claim 38.
41. Amethod of regulating the expression of a nucleotide sequence of interest,
said method comprising introducing into a plant a DNA construct of claim
38.
42. The method of Claim 41 wherein said nucleotide sequence of interest is
transcribed to form an RNA molecule which interferes with expression of a
homologous native nucleotide sequence.
43. A method of downregulating expression of ZmlPTI or ZmlPT2 in a plant,
comprising transforming said plant with a construct comprising a promoter
operably linked to a polynucleotide which comprises a portion of the
polynucleotide of claim 37, such that a hairpin molecule is formed which
corresponds to the ZmlPTI promoter or ZmlPT2 promoter.
44. The method of claim 43 wherein said promoter is tissue-preferred.

Documents:

2159-delnp-2007-Abstract-(12-09-2013).pdf

2159-delnp-2007-abstract.pdf

2159-delnp-2007-Claims-(05-02-2014).pdf

2159-delnp-2007-Claims-(12-09-2013).pdf

2159-delnp-2007-claims.pdf

2159-delnp-2007-Correspondence Others-(05-02-2014).pdf

2159-delnp-2007-Correspondence Others-(12-09-2013).pdf

2159-delnp-2007-Correspondence Others-(21-01-2014).pdf

2159-DELNP-2007-Correspondence-Others-(16-05-2007).pdf

2159-delnp-2007-correspondence-others.pdf

2159-delnp-2007-description (complete).pdf

2159-delnp-2007-drawings.pdf

2159-DELNP-2007-Form-1-(16-05-2007).pdf

2159-delnp-2007-form-1.pdf

2159-delnp-2007-Form-13-(05-02-2014).pdf

2159-DELNP-2007-Form-18-(16-09-2008).pdf

2159-delnp-2007-Form-2-(12-09-2013).pdf

2159-delnp-2007-form-2.pdf

2159-delnp-2007-Form-3-(12-09-2013).pdf

2159-delnp-2007-Form-3-(21-01-2014).pdf

2159-delnp-2007-form-3.pdf

2159-delnp-2007-form-5.pdf

2159-delnp-2007-GPA-(12-09-2013).pdf

2159-DELNP-2007-GPA-(16-05-2007).pdf

2159-delnp-2007-pct-237.pdf

2159-delnp-2007-pct-304.pdf

2159-delnp-2007-Petition-137-(12-09-2013).pdf


Patent Number 258986
Indian Patent Application Number 2159/DELNP/2007
PG Journal Number 08/2014
Publication Date 21-Feb-2014
Grant Date 19-Feb-2014
Date of Filing 20-Mar-2007
Name of Patentee PIONEER HI-BRED INTERNATIONAL, INC.
Applicant Address 7100 N.W 62ND AVENUE, JOHNSTON, IA 50131-1014 USA
Inventors:
# Inventor's Name Inventor's Address
1 BRUGIERE NORBERT 6321 N.W. 96TH STREET, JOHNSTON, IA 50131 USA
PCT International Classification Number C12N15/82; A01H5/00; A01H5/10
PCT International Application Number PCT/US2005/033693
PCT International Filing date 2005-09-19
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/610,656 2004-09-17 U.S.A.
2 60/637,230 2004-12-17 U.S.A.
3 60/696,405 2005-07-01 U.S.A.