Title of Invention

A METHOD OF PRODUCING AN ANIMAL FEED OR ANIMAL FEED SUPPLEMENT

Abstract Transgenic plants that express CIVPS or intein modified proteins, compositions of matter comprising them, products of diverse applications made from the transgenic plants, methods to construct the transgenic plants containing CIVPS or intein modified genes, methods to express CIVPS or intein modified proteins in plants, and methods of using the transgenic plants.
Full Text [0001] ANIMAL FEEDSTOCK COMPRISING A RECOMBINANT
PLANT, METHOD FOR PRODUCING THE SAME AND
COMPOSITIONS THEREOF
[0002] BACKGROUND
[0003] FIELD OF THE INVENTION
[0004] The present invention relates to an animal feedstock comprising a recombinant plant expressing CIVPS or intein modified proteins, methods for producing the same and compositions thereof. The present invention also provides for the production of the recombinant plants, methods for the expression of CIVPS or intein modified proteins in plants, and various uses of and products containing the same.
[0005] DESCRIPTION OF THE BACKGROUND
[0006] Since fossil fuels are non-renewable resources, adequate supplies of energy and organic feedstocks need to be secured for the future. A transition to sustainable resources requires new technologies for the construction of improved feedstocks, the design of efficient processes to convert the feedstocks into valuable products, and/or the design of products that efficiently utilize an altered substrate spectrum. This transformation will create benefits such as decreased pollution from energy production and use, decreased pollution from chemical manufacturing processes, increased sustainability through the utilization of renewable natural resources and organic waste products as substrates, decreased dependence on foreign country's raw materials, and an increase in local economies and markets involved in the production of new substrates. [0007] Plant biomass is one sustainable resource that can help meet future feedstock requirements. The use of plants as substrates for energy, chemical, pharmaceutical and organic feedstock takes advantage of existing large-scale agricultural production, uses energy from the sun to incorporate carbon dioxide into plants via photosynthesis, and has fewer environmentally hazardous byproducts. By using photosynthesis, plants make the carbon dioxide removed from the air available for the production of energy, chemicals, and agricultural products. Finding ways to effectively redistribute this carbon in forms that are readily and economically employable remains a challenge.

[0008] The production of chemical feedstocks and fuels from plant biomass is st/ill in its infancy. Starch-based raw materials, for example, may be applied to the production of commodity or specialty chemical products. Poor substrate and strain availability hampering byconversion, along with real or perceived safety issues related to containment, and a lack of economic viability, have made progress in this area particularly slow. Non-cellulosic biomass, such as corn starch, compares favorably with fossil resources on a mass basis, but is too costly. Gellulosic biomass, such as short-rotation poplar, pine, switchgrass, corn stover, sugar cane bagasse, waste paper sludge, and municipal solid waste, in contrast, is cost competitive in terms of both mass-and energy. Cellulosic bio.mass, because of its complex structure, is nevertheless difficult to process. Currently, cellulosic biomass requires pretreatment with strong acids, bases, and/or other chemicals for use as a substrate for fuel, e.g. ethanol, or for chemical production, e.g. paper products. This pretreatment efficiently exposes polymeric subuiiits, primarily hexoses, pentoses, and phenolic compounds, which are then cleaved and used as substrates, but is expensive. One alternative to the use of more hazardous chemicals is the use of enzymes, although it is less cost effective.
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[0009] Recombinant DNA technology has been applied to alter microorganisms to perform substrate bioconversion at reduced costs, thus expanding the use of microorganisms, and increasing the number of products that are .produced. For example, plant cells that express lignocellulosic degrading enzymes have been constructed, although they rarely differentiate and regenerate into complete plants due to decomposition of structural components. In cases where they differentiate into complete plants, e.g. with lignin and cellulose substrates, the enzyme activities are low and the plants require further processing. Attempts to combine pretreatment of substrate biomass with fermentation have encountered difficulties as well, in part because of mass transfer limitations and interference with the fermenting organism.
[0010] CIVPS or inteins are in-frame, self-cleaving peptides that generally occur as part of a larger precursor protein molecule. CIVPS or inteins differ from
other proteases or zymogens in several fundamental ways. Unlike proteases that cleave themselves or other proteins into multiple, unligated polypeptides, CIVPS or inteins have the ability to both cleave and ligate in either cis or trans conformations. Thus as opposed to terminal cleavage that would result from the reaction of a protease on a protein, CIVPS or inteins have the ability to cleave at multiple sites, and ligate the resulting protein fragments. This cleavage is induced under specific conditions and can be engineered using molecular biology techniques. CIVPS or inteins have been described in the literature in Sacchromyces cerevisiae (Kane et. al., Science 250: 651; Hirata et al. , J. Bio.Chem. 265: 6726 (1990)), Mycobacterium tuberculosis (Davis et al. , J. Bact.173: 5653 (1991), Davis et al. , Cell 71: 1 (1992)), Thermococcus Htoralis (Perler, et al., PNAS 89 : 5577 (1992)), and in other organisms, but do not occur naturally in plants.
[0011] Accordingly, there is a need for providing novel methods for producing
energy and other pharmaceutical or industrial products from more easily
renewable sources, such as by by modifying plants in a manner such that
they may be used as energy and chemical feedstocks.
[0012] SUMMARY
[0013] The present invention provides for animal feed stock comprising genetically recombinant plants, their parts, plantlets, seeds, seedlings, anc their progeny (collectively referred to as"plants"), which may contain single o] multiple exogenous gene sequences, eaeh being interrupted by, or fused t invention, any modified gene sequence, or set of modified gene sequences, may be expressed in any or all tissues constitutively or at specific times. [0014] The invention also relates to methods of producing transgenlc plants comprising CIVPS or intein modified genes, e. g. by first constructing a piece of DNA comprising the parent CIVPS or intein modified gene, and transforming the plant with the construct.
[0015] The invention also relates to methods of producing an CIVPS or intein modified protein(s) in transgenic plants, e. g. by transforming the plant, or p!ant cells, with a single or multiple modified gene sequence(s), and expressing the CIVPS or intein modified protein(s). In one preferred embodiment the gene sequences may be expressed at any time. In another embodiment, prior to the protein(s) being spliced it preferably is(are) provided with a substantially different activity(ies) and/or structural property(ies). The spliced protein product(s) has(have) its(their) activity(ies) unveiled, unless inhibited by an exogeneously added or endogeneously produced molecule(s) analogous to the non-CIVPS or intein modified protein parent sequence. The CIVPS or intein modified gene products may be expressed in large quantities and recovered from the plant material. Alternatively, the plant or plant material may itself be used as a source of CIVPS or intein modified gene products.
10016] The invention also provides for the use of CIVPS or intein modified gene products expressed in plants, the use of transgenic plants expressing CIVPS or intein modified genes in animal feed, or the use of transgenic plants expressing CIVPS or intein modified genes in batch, semi-batch, and continuous industrial processes for the production of fuels, chemical products, animal food or food additives, Pharmaceuticals, paper, paper products, and for vaccine delivery and the remediation of waste materials.
[0017] Other objects, advantages and features of the present invention will become apparent to those skilled in the art from the following brief description of the drawings and discussion.
[0018] BRIEF DESCRIPTION OF THE DRAWING(S)
[0019] Figure 1 illustrates the construction of an CIVPS or intein modified
protein coding DNA sequence by constructing an CIVPS or intein modified
protein DNA coding sequence constructed by fusion of an CIVPS or intein coding
sequence to the coding sequence of a protein of a purported activity, at either the
3' end of the gene, the 5' end of the gene, or internally, within the protein gene.
Other variants are possible by combining any of the three resulting CIVPS or
intein modified protein coding sequences shown in Figure 1.
[0020] Figure 2 illustrates one configuration of the resulting CIVPS or
intein modified proteins, or components thereof. This figure demonstrates the 'case of a single CIVPS or intein modified protein. Multiple native protein sequences, however, may be combined with single or multiple CIVPS or inteins as well.
[0021] Figure 3 illustrates the cleavage of an CIVPS or intein modified
protein, or components thereof, which may be attained in vitro or in vivo when subjected to an appropriate cleavage stimulus(i). Illustrated here schematically is an example of the cleavage process for a single CIVPS or intein modified protein. Other variants may be constructed as combinations of the CIVPS or intein modified proteins shown in this figure.
[0022] DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT(S)
[0023] This invention arose from a desire by the inventor to provide novel
methods for generating valuable products from renewable resources, e. g. plant materials or biomass, and to do this in a cost effective manner. One way to effectively attain this goal is by modifying plant biomass through the use of CIVPS or intein modified proteins, where the CIVPS or intein is attached to a desired protein. Within the text of this patent the terms CIVPS and intein are intended to refer to similar products, and will be used interchangeably. From the
knowledge that intein modified proteins may be expressed in cells at high titer, yet with substantially decreased activity, he concluded that, if cloned into a plant, this decrease in activity would allow the thus formed transgenic plant cells, plant fragments, or plant tissues, to develop into intein modified protein producing complete plants. Moreover, he thought that such transgenic plants could be provided as several different embodiments, such as those where the recombinant plants are made to express the modified proteins either 1) constitutively or transiently, 2) through chemical induction or biological induction by the plant's growth cycle, (3) throughout the entire plant or specifically in distinct plant tissues, and/or 4) with or without subcellular localization, among others. As envisioned by the inventor, in one embodiment of this invention, the expressed intein modified, protein(s) is(are) comprised of a parent protein sequence(s), whose activity(ies) may be known, inferred through sequence or structure homology and/or produced by mutagenesis or by de novo synthesis; each parent sequence(s) being interrupted by, or fused to, an intein sequence(s) or portions thereof. Once inserted, the intein portion(s) of the modified protein(s) inactivate(s), in vivo, the activity or structural utility of the parent protein. The parent protein's original activity may be, however, substantially recovered, if and when desired, by induction of intein splicing. For example, in one application, following plant harvest and during substrate pretreatment, each CIVPS may be induced to splice itself from its parent protein sequence, which parent protein now has recovered its original activity. Methods for intein splicing with, or without, recombining of the protein to a functioning activity are known to one skilled in the art, and need not be repeated here. These methods include the use of light, temperature, change in pH, and/or the addition of chemical reagents.
[0024] More specifically, this invention is directed to a recombinant plain,
or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendant, comprising an expression construct(s) that encode(s) at least one modified protein comprising a target protein(s) or protein
segment(s), which is(are) fused, either internally or terminally, to a controllable
intervening protein sequence(s) (CIVPS) or intein sequence(s) or segments)
thereof, or to an amino terminus(i) or a carboxyl terminus(i) thereof. In one
embodiment, each expression construct of the plant, or plant part, plantlet,
tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or
descendent comprises, operatively linked to one another, a first nucleic acid
segment(s) encoding a target protein(s), and a second nucleic acid segmenl(s)
encoding a CIVPS or intein sequence(s), and optionally a selectable marker(s) or
reporter gene(s) and/or a prornoterls). It is understood that in a more specific
embodiment the sequences may be fused, either directly or via a linker(s), and
more preferably in reading frame. The modified protein(s) may be expressed by
the plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling,
• prQtoplast, progeny or descendent either constitutively, or inductively. In the
latter ^ase, the expression and/or splicing of the at least one modified protein(s)
may be triggered or induced by a stimulus(i). Examples of suitable stimuli
comprise a pH change, change in osmolality, or temperature, the addition of a
fertilizer, pesticide, or chemical, or a change in light, and/or sound. The plant, or
plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast,
progeny or descendent may express the modified protein(s) either at a pre
determined point of the plant life cycle, in one or more specific tissues or parts
thereof, and/or in at least one specific sub-cellular compartrnent(s). Alternatively
or in conjunction with the latter the modified protein(s) may be expressed and
secreted extracellularly. The plant, or plant part, plantlet, tissue, cell, sub-
cellular fraction, seed, seedling, protoplast, progeny or descendent specific
tissue(s) may be seeds, roots, fruits, stems, tubers and/or leaves, and the specific
subcellular compartments may be a cellular apoplast, cytosol, chloroplast,
plastid, endoplasmic reticulum, inclusion body, vacuole and/or nucleus. Other
variations, however, are also included within the confines of this invention.
[0025] The plant, or plant part, plantlet, tissue, cell, sub-cellular fraction,
seed, seedling, protoplast, progeny or descendent may also carry a selectable
marker that confers it resistance to a chemical. Examples of these are bromoxynil, 2,2-dichloropropionic acid, G418, glyphosphate, haloxyfop, hygromycin, imidazoline, kanamycin, methotrexate, neomycin, phosphinothricin, sethoxydim, 2,2-dichloropropionic acid, glyphosphate, hygromycin, trichothecne, sulfonylurea, s-triazine, and/or triazolopyrimidine. Others, however, may also be employed. The promoter may be included to precede a CIVFS or inte in-modi fled protein polynucleotide. In some cases, the plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent may be tolerant or resistant to normally extremely toxic levels of a selected* chemical(s). In another embodiment, the plant, or plant part, plantlet, tissue, cell, subcellular fraction, seed, seedling, protoplast, progeny or descendent is fertile;' and has 'at least one heritable modified protein encoding polynucleotide sequence(s). However, it may just as well not be fertile. Further,, as indicated above,'also part of this invention are inbred and hybrid genetically recombinant plants, or plant parts, plantlets, tissues, cells, sub-cellular fractions, seeds, seedlings, protoplasts, progeny and descendents, which may or may not be produced by the method of this invention. Of particular interest are plant parts, plant seeds, plant seedlings and plant protoplasts, which have substantial commercial importance. Also of commercial and other interest are plants, plant tissues, plant cells, and sub-cellular fractions. The spliced protein, may have the ability of changing the content or activity of one or more plant component(s). In one example, the content may be altered, e.g. reduced, of a plant component such as glucose, fructose, cellulose, hemicellulose, lignin, glycerol, glycine-betaine, pectin, sucrose, lactose, maltose, galaetose, amino acids, lipids, vitamins and/or starch, and the like. In another, the plant component whose activity is altered, e.g. reduced, may be one or more of proteins, RNA, and/or lipids, among others. In one aspect, the CIVPS or intein sequence and the target protein or protein segment form at least one spike junction with the target protein. In a desirable embodiment, the amino acid residue at the carboxyl terminus(i) of the splice junction(s) is(are) provided with a hydroxyl or a sulfhydryl side chain(s). In
another particularly useful embodiment, the splice junction(s) is placed downstream of the CIVPS or intein sequence(s) or segment(s) thereof, and may comprise(s) an amino acid residue(s) lacking, for example, hydroxyl or sulfliydryl side chains at the amino terminus(i) of the target protein or protein segment(s). In another important variation, the splice junction(s) is(are) placed upstream of the CIVPS or intein sequence(s) or segment(s) thereof, and may comprise an amino acid residue(s) having hydroxyl or sulfhydryl side chains at the amino terminus(i) of the CIVPS or intein sequence(s) or segment(s) thereof. Another important possibility is that where the splice junction(s) is(are) placed upstream of the CIVPS or intein sequence(s) or segments) thereof, and it may comprise(s) a cysteine. Still another important variation is that wherein the splice junction(s) is(are) placed downstream of the CIVPS or intein sequence(s) or segment(s) thereof, and ma'y-be provided with His-Asn at the carboxy terminus(s) comprise(s) Ser, Thr or Cys, among others. As described in
more detail below, the target protein may be expressed in a microorganism, such
as a bacterium, as is known in the art. Examples of microorganisms that may be
employed are Bacillus thuringiensis, or Phytolacca insularis. One preferred
target protein is Bacillus thuringensis endotoxin, which results in a modified
Bacillus thuringiensis endotoxin being expressed. Another embodiment includes
the expression of a target protein from a virus. Although any virus could be
employed, examples are potato virus Y, geminivirus, aspermy virus 2b, and
cucumber mosaic virus, among others. Another embodiment includes the
expression of human target proteins. Although any human protein could be used,
examples of preferred proteins include insulin, erythropoietin, growth hormone,
tumor necrosis factor receptor, leptin, and other proteins of therapeutic value.
[0026] The recombinant plamV or plant part, plantlet, tissue, cell, sub-
cellular fraction, seed, seedling, protoplast, progeny or descendent may be produced by a method comprising
[0027] providing an expression construct that encode(s) at least one
modified protein comprising a target protein, or protein segment(s), which is(arej
fused, either internally or terminally, to a CIVPS or intein sequence(s) or
segment(s) thereof, or to an amino terminus(i) or a carboxyl terminus(i) thereof;
[0028] transforming a plant, or plant part, plantlet, tissue, cell, sub-cellular
fraction, seed, seedling, protoplast, progeny or descendent, with the expression construct; and
[0029] regenerating a genetically recombinant plant, or plant part,
plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent, from the transformed plant, or plant part, plantlet, tissue, cell, sub cellular fraction, seed, seedling, protoplast, progeny or descendent, that encodc(sj at least one modified protein sequence(s).
[0030] It is highly preferred that the transformation be a stable
transformation. However, transformations that have some temporary stability are also desirable. The regeneration step may be conducted by breeding of a
recombinant plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling protoplast, progeny or descendent; crossing of a recombinant plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent and a non-genetically recombinant plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent; and/or back-crossing of two genetically recombinant plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent. The expression construct employed in this method may comprise one or more of promoter, selectable marker, resistance marker, heritable marker, poly-adenylation sequence, represser, enhancer, localization sequence, and/or signaling sequence. These are intended for use in the application of recombinant technologies as is known in the art, and exemplified elsewhere and below in the examples. In an important aspect of the method, the plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent isfare) transformed with the expression construct by either viral transformation, bombardment with DNA-coated microprojectiles, liposomal gene transformation, bacterial gene transfer, electroporation, or chemical gene transformation, or more than one of these. As indicated above, the plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent, may be transformed by means of a bacterium, e, g. Agrobacterium tumefaciens, although other microorganisms may also be employed. In the present method, the transformation may be conducted by chemical gene transformation, and it may be done with the aid of, e.g. calcium phosphate, and/or polyethylene glycol, or other chemicals known in the art as being suitable for this purpose. The selection may be attained with the aid of a selectable marker, or a resistance marker, or of the expression of at least one nucleic acid encoding an CIVPS or intein modified protein. In the method of the invention, the genetically recombinant plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent may be regenerated from a
transformed embryogenic tissue(s); plant protoplasts; cells derived from
immature embryos; or from transformed seeds, among other sources.
[0031] Another method is also provided in this patent, which method is
suitable for producing a modified protein(s) or protein segment(s) from a
recombinant transformed plant, or plant part, plantlet, tissue, cell, sub-cellular
fraction, seed, seedling, protoplast, progeny or descendent expressing the
protein(s) or protein segment(s), that comprises conducting the method described
above, and further harvesting the modified protein(s) or protein segment(s) from
the transformed plant, or plant part, plantlet, tissue, cell, sub-cellular fraction,
seed, seedling, protoplast, progeny or descendent. The method may further
comprise purifying the modified protein, which may be done by one of many
techniques known in the art. As described here, this method may produce a
•modified protein(s) or protein segments) that comprises a CIVPS or intein
modified protein(s) or protein segment(s).
[0032] Still a further method is provided here for producing a modified
protein comprising a target protein(s) or protein segment(s) fused, either
internally or terminally, to a CIVPS or intein sequence(sO or segment(s) thereof,
or to its amino terminus(i) or carboxyl terminus(i), which method comprises
[0033] obtaining an expression construct encoding a target protein having
an in-frame fused CIVPS or intein sequence(s) or segment(s) thereof, or its amino terminus(i) or carboxyl terminus(i);
[0034] transforming a host plant cell(s) with the expression construct; and
[0035] culturing the transformed plant host cell under conditions effective
for expressing the modified protein.
[0036] In one preferred aspect, in the expression construct the at least one
first nucleic acid segment(s) encoding the CIVPS or intein sequence(s) or segment(s) thereof is(are) fused to the 5*-end of the second nucleic acid segment(s) encoding the target protein(s) or protein segment(s). Alternatively, in the expression construct the first nucleic acid segment(s) encoding the CIVPS or intein sequence(s) or segment(s) thereof may be fused to the 3'-end of the second
nucleic acid segment(s) encoding the target protein(s) or protein segment(s). It is particularly suitable to practice the present method to employ a Saccharomyces CIVPS or intein sequence(s) or segment(s) thereof, which is known to effect, either in cis or in trans, excision, cleavage, ligation, excision-ligation, cleavage-ligation, and/or cyclization. When the CIVPS or intein or its(their) segment(s)are employed to induce protein splicing, this event may be induced or triggered by a change of temperature, light or pH, the addition/removal of a chemical reagent that facilitates/inhibits splicing or cleavage, amino acid dephosphorylation or deglycosylation, or by contact with, or removal of, a peptide or peptidomimetic activating or blocking of splicing or of cleavage. Another .manner of inducing protein splicing is either in vitro or in vivo contact with, onremoval of, a peptide or peptidomimetic agent that may either activate or block ^splicing or cleavage. Interesting variations that produce superior results are those where the amino or carboxy terminus(i) of the CIVPS or intein sequence(s) or segnient(s) thereof comprise(s) Ser, Thr or Cys, or where the carboxyl terminus(i) of the CIVPS or intein sequence(s) or segment(s) thereof comprise(s) Asp preceding Ser, Thr or Cys of the target protein(s) or protein segment(s). However, other modifications are also possible, as is known in the art. See, for example, US patent No. 5,834,247 that discloses for the prokaryotic and eukaryotic realms some methodology incorporated in this invention to the production of hybrid plants of useful characteristics. In the present method, the expression construct may further comprise a promoter, a selectable marker, a resistance marker, a heritable marker, a poly-adenylation sequence, a represser, an enhancer, a localization sequence, or a signaling sequence. Moreover, the method presented here may also comprise the transformation of the plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent with the expression construct being implemented by viral transformation, bombardment with DNA-coated microprojectiles, liposomal gene transfer, bacterial gene transfer, electroporation, and/or chemical gene transformation, and/or other methods known in the art, or that will be
subsequently developed. As described above, in the method described here, the
bacterium used to transfer the expression construct may be an Agrobacterium
tumefaciens bacterium; the chemical used for transformation may be calcium
phosphate, or polyethylene glycol; the transformed plant cells, plant parts,
plants, etc. may be selected through their expression of a selectable marker, or
resistance marker; the selection of the transformed plant, or plant part, plantlet,
tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or
descendant may be conducted through their expression of the modified protein
gene sequence; and the regeneration of the genetically recombinant plant, or
plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast,
progeny or descendent may be attained from transformed embryogenic tissue;
from cells derived from immature embryos; or from transformed .seeds, among
others.
[0037] Also disclosed in this patent is a method for producing seed that
express a modified protein(s), this method comprising .-.
[0038] obtaining the genetically recombinant plant, or plant part, plantlet,
tissue,. cell, sub-cellular fraction, seed, seedling, protoplast, progeny or
descendent of the invention;
[0039] culturing or cultivating the genetically recombinant plant, or plant
part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling,; protoplast,
progeny or descendent; and
[0040] obtaining from the cultivated plant seed that expresses a modified
protein(s).
[0041] Still another method provided by this patent is one for using a plant,
or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent expressing a modified protein for producing a
compound the method comprising
[0042] harvesting a recombinant plant, or plant part, plantlet, tissue, cell,
sub-cellular fraction, seed, seedling, protoplast, progeny or descendent in accordance with the teachings of this patent;
[0043] mechanically processing the plant, or plant part, plantlet, tissue,
cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent;
[00441 combining the mechanically processed plant, or plant part, plantlet,
tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent, with a non-genetically recombinant plant in a proportion greater than or equal to zero recombinant:non-recombinant; and
[0045] chemically processing the plant or specific portions of the plant
under conditions effective for obtaining the compound.
[0046] This method may be practiced by mechanical processing of the plant,
or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent by extrusion, grinding, shredding, mulching, chipping, dicing, ^compressing, exploding, and/or tearing. Other processing techniques, however, are also suitable. The chemical processing of the combined components may be attained by various techniques or a combination thereof Some of them are pre-treatment with steam, dilute or concentrated acid, ammonia explosion, sterilization, soaking in water, mixing with a solvent, a change of pH, temperature or osmolality, exposure to or changes in light, inorganic and/or enzyme catalysis, saccharification, bleaching, scouring, fermentation, distillation, chromatography, adsorption, and/or addition of a chemical(s). Others, of course, are also employed successfully. Various steps are of use when practiced as follows: the pre-treatment may include steaming the combined products for sterilization purposes; the chemical processing may be attained by pre-treatment with at least one of sulfuric acid, hydrochloric acid, phosphoric acid, or carbonic acid, or by soaking in water at a temperature greater than or equal to about 20 °C, and/or by mixing the combined products with at least one of water, or an organic or inorganic solvent(s). As already explained, an external stimulus(i) may be applied to induce splicing of the modified protein(s) or protein segment(s). Examples of external stimuli are a change of pH, osmolality, or temperature, exposure to sound, light, or addition of a chemical(s). In some cases the spliced protein(s) or protein segxnent(s) may exhibit altered
activity(ies) with respect to the modified protein(s) or protein segment(s), such as
altered binding, catabolic or anabolic activity(ies) with respect to the original
target protein(s). Examples of spliced protein(s) or protein segment(s)are those
capable of degrading starch, dextrin, pectin, lipids, protein, chitin, lignin,
cellulose, or hemicellulose, or modifying lignin, or having sacchariflcation
activity. Thus, the spliced protein may be capable of producing glucose, fructose,
xylose, phenol, glycerol, mannose, lactic acid, acetic acid, ethylene, propylene,
toluene, ethyl benzene, styrene, xylene, ethylene glycol, butadiene, formaldehyde,
isopropanol, acetone, butanediol, methanol, ethanol, propanol, butanol,
propanediol, vitamins, methane, ethane, propane, butane, pentane, hexane,
heptane, octane, benzene, target proteins, therapeutic proteins, enzymes and/or
biopolymers, among other compounds. In one specific embodiment of the pre-
treatment, sacchariflcation, and fermentation may be conducted in one step, and
the fermentation may be attained by employing a prokaryotic or eukaryotic
microorganism capable of producing lactic acid, acetic acid, ethylene, propylene,
toluene, ethyl benzene, styrene, xylene, ethylene glycol, butadiene, formaldehyde,
isopropanol, acetone, butanediol, methanol, ethanol, propanol, butanol, octanol,
propanediol, vitamins, methane, ethane, propane, butane, pentane, hexane,
heptane, octane, benzene, and/or biopolymers, among other compounds.
[0047] This invention also encompasses the production of animal feedstock
that comprises a nutritious amount of the recombinant plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent of the invention. When the feedstock provided by the inventor is ingested by an animal, the modified prolein(s) or protein segment(s) is(are) spliced by an internal stimulus(i) from the animal. Examples of internal stimuli are the animal's saliva, bile, chymotrypsin, trypsin, bicarbonate, hydrochloric acid, or stomach pH or temperature, among others. The feedstock of the invention may comprise spliced protein(s) such as phytases, endocellulases, exocellulases, amylases, glucanases, hemi-cellulases, pectinases, proteases,
xylanases, or lipases, growth factors or a growth hormone. Other proteins, however, could also be employed as desired.
[0048] Yet another aspect of this invention provides for the use of the

feedstock described above in the manufacture of an immune response enhancing

composition, wherein the spliced protein(s) or protein segment(s) comprise(s) at
least one recombinant immunogen(s). The immunogen may included one or more
viral or bacterial immunogens, and it may be formulated in various suitable
forms. Preferred are an oral formulation, a trans-mucosal formulation, a
gastrointestinal (G.I.) tract absorbed formulation. However, this composition of
matter may" be formulated in any systemic or topical form suitable for
administration to an animal, including its addition to animal feed.
[0049] The animal feedstock of the invention may be produced by first
conducting the steps indicated above to obtain agenetically recombinant plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent, and then processing the genetically modified plant, or a portion of the resulting product under conditions effective to obtain an animal digestible feedstock.
[00501 The product of this invention may also be employed for promoting
animal growth, for example by producing feedstock that comprises a growth
promoting product, and allowing an animal access to the modified feedstock. The
product of this invention may also be employed for enhancing an animals
immune response. This may be done by administering to an animal in need of the
treatment, an immune enhancing amount of the composition of the invention.
[0051] A further aspect of this invention involves a method for producing a
target protein(s) or protein segments), the method comprising
[0052] producing a first modified protein(s) or protein segment(s), wherein
the amino terminus of a CIVPS or intein sequence(s) or segment(s) thereof is(are) fused to the carboxyl terminus(i) of a target protein(s) or protein segment(s) by the method described above;
[0053] producing a second modified protein(s) comprising a segment(s) of
the CIVPS or intein sequence(s); and
[0054] contacting first and second modified proteins under conditions
effective for trans cleavage of the CIVPS or intein sequence(s) or segment(s) thereof by the second modified protein(s).
[0055] Yet another variation of the above method for producing a target
protein(s), comprises
[0056] producing a first modified protein(s), wherein the carboxyl terminus
of a CIVPS or intein sequence(s) or protein segment(s) thereof is(are) fused to the amino terminus(i) of the target protein(s) or protean segment(s) by the already described method;
[0057] similarly producing a second modified protein(s) or protein
-segment(s) comprising a segment(s) of the CIVPS or intein sequence(s); and
•[0058] contacting first and second modified: proteins under conditions
effective for trans cleaving the CIVPS or intein sequence(s) or segment(s) thereof from the first modified protein(s) or protein segment(s). The cleavage may be induced in this procedure by a change in temperature, light, or pH, addition/removal of chemical that facilitates/inhibits splicing or blocking of cleavage, amino acid dephosphorylation or deglycosylation, and/or contact/removal of peptide or peptidomimetic that activates/blocks splicing/cleavage, among others.
[0059] Thus, the invention is directed towards transgenic plants, which
term is intended in this patent to be synonymous with genetically recombinant plants, their seeds and progeny plants, or any plant portion, tissue or cell, containing a gene(s) for an CIVPS or intein modified protein(s). The invention is further directed towards methods for the production of the transgenic plants that produce CIVPS or intein modified proteins, methods for the production of CIVPS or intein modified proteins in plants, and uses of the plants as substrates for fuels, chemicals, animal food or food additives, paper, and pharmaceutical production. The invention allows for the production of transgenic plants that can
be used as a source of binding, structural or catalytic components, or can have their intein modified proteins purified and used separately as binding, structural or catalytic proteins. Transgenic plants are multi-cellular plants that express single or multiple exogenous genes and their associated protein (or ribonucleic acid) activities. Within the context of this invention, gene or enzyme classes may be specifically referred to, however this is not a limiting aspect of the invention. When specific classes are stated, this is understood to identify any gene or enzyme within the specific classification. CIVPS or inteins are protein sequences internal or adjacent to a parent protein sequence, that may spontaneously cleave themselves at either, or both, the carboxyl or amino terminal ends and are capable of selectively ligatingthe resulting extein protein fragments when appropriate, under specific conditions. See, for example, Perler, et al., Nucl. Acids Res., 22:1125-1127 (1994); Wallace, C. J.; Protein'Sci., 2:697-705 (1993); Xu, et al., Cell, 75: 1371-1377 (1993); Pietrokovski, S.,Protein Sci., 2:697-705 (1994). Thus, CIVPSs may be said to be in-frame, self-cleaving peptides that generally occur as part of a larger precursor protein molecule. CIVPS or inteins differ from other proteases or zymogens in several fundamental ways. Unlike proteases that cleave themselves or other proteins into multiple, unligated polypeptides, inteins have the ability to both cleave and ligate in either cis or trans conformations. Thus as opposed to terminal cleavage that would result from the reaction of a protease on a protein, inteins have the ability to cleave at multiple sites, and ligate the resulting protein fragments. This cleavage is induced under specific conditions and may be brought about implementing techniques that are known in molecular biology. Inteins from various sources, their sequences, characteristics and functions have been described fully in the literature. See, for example, Kane et. al., Science 250:651 (1990); Hirata et al., J. Bio. Chem. 265:6726 (1990) (Sacchromy-ces cerevisiae); Davis et al., J. Bact. 173:5653 (1991), Davis et al., Cell 71:1 (1992) (Mycobacterium tuberculosis); Perler, et al., PNAS 89:5577 (1992) (Thermococcus litoralis). As shown in Figure 1, the combination of an CIVPS with a protein of
purported activity or structural role yields an intein modified protein, whose
purported activity or structural role may be substantially altered. Transgenic
plants that express CIVPS modified proteins (from their associated intein
modified genes) are an improvement upon previous transgenic plants, because
the parent intein modified protein can have two substantially different states
that are controllably mediated by intein cleavage. This cleavagemay or may not
be associated with recombination of the purported protein sequence. The
invention may be formed from any plant species, combined with any combination
of single or multiple proteins and CIVPS Plant species may include; but are not
limited to: poplar, birch, cedar, pine, hardwoods, softwoods, soybeans,
switchgrass, corn, tobacco, alfalfa, sugar cane, cauliflowers, artichokes, bananas,
apples, cherries, cranberries, cucumbers, lettuce, grapes, lemons, melons, nuts,
tangerines; rice, oranges, peaches,, pears, blueberries, strawberries, tomatoes,
carrots, cabbages, potatoes, endive, leeks, spinach, weeds, arrowroot, beets,
carrots, cassava, turnips, yams, radishes, sweet potatoes, wheat, barley, soya,
beans, rapeseed, millet, sunflower, oats, peas, tubers, bamboo, seaweed, algae, or
any other plant species. Proteins may include any known, putative, modified, or
de novo created proteins. Although the selection of the native protein is not
restricted,' preferred proteins include lignocellulosic degrading .proteins
(cellulases', lignases, amylases), starch degrading enzymes (amylases,
glucanases), enzymes in the biosynthetic pathways required for fuel or chemical
production, bacterial or viral antigens, enzymes in the biosynthetic pathways for
vitamins or other food additives (phytases, cellulases, amylases, glucanases,
hemi-cellulase, pectinase, protease, xylanase, lipase, growth hormone), proteins
that impart pest or insect resistance, proteins that impart herbicide resistance,
and therapeutic proteins (insulin, erythropoietin, growth hormone, leptin, tissue
plasminogen activator, tumor necrosis factor receptor, Her2 receptor) implicated
in disease pathogenesis. The choice of CIVPS or intein used to modify the
protein, the fusion of which is expressed in the desired plant, is also not limited,
Any single or multiple CIVPS or intein may be used in any configuration with
respect to the desired protein or proteins. The CIVPS or inteins should have the capability to be spliced at one or both ends in response to some stimuli, and may or may not permit ligation of the proteins to which single or multiple CIVPS or inteins are fused.
[0060] Transgenic plants expressing CIVPS or intein modified proteins,
and the production of CIVPS or intein modified proteins in transgenic plants can be accomplished by combining methods (Ausubel, et al.) known in the art. Generally, these methods include construction of a DNA containing the CIVPS or intein modified protein of interest and the necessary regulatory elements required for its expression, amplification and selection-of the constructed DNA, transformation of the desired plant species, regeneration and selection of the appropriately transformed plant species, and if necessary, purification of the CIVPS or intein modified protein in its native form or the cleaved form. Both the production of transgenic plants expressing CIVPS or intein modified proteins, and the production of CIVPS or intein modified proteins in transgenic plants form part of this invention. For the production of the transgenic plants, or CIVPS or intein modified proteins in transgenic plants, the CIVPS or intein modified protein DNA sequence must be constructed. This is easily accomplished by cloning the gene sequence of the desired activity and the desired intein sequence into E. colt or any other suitable host (e.g., yeast may be beneficial in some cases, or expression in mammalian or plant cells with or without the use of viral or non-viral vectors). Once the gene and intein coding sequences have been cloned, they must be joined in the desired configuration. The chosen intein sequence should be able to perform the desired functions such as splicing in response to an imposed stimuli (for example, light, pH change, temperature, pressure, or changes in the local chemical composition surrounding the intein modified protein), and if necessary permitting ligation of the. fused protein, Joining of the CIVPS or intein's DNA sequence and the protein's DNA sequence is easily accomplished by methods known in the art, resulting in CIVPS or intein modified protein DNA coding sequences, or combinations thereof, as shown in
Figure 1. As already indicated, an CIVPS or intein modified protein is one which fuses the CIVPS or intein to one of either the carboxy terminal, amino terminal, or internal portions of the native protein or proteins. Although many alternative methods exist, one way of creating the fusion between the CIVPS or intein and desired protein coding sequences would be to purify the DNA encoding the desired protein sequence, use a restriction enzyme to cut the protein coding sequence at the desired point of intein insertion, and then ligate the intein coding sequence into the restricted site. The polynucleotide, or either of the nucleic acid segments may be cloned directly to appropriate regulatory and/or selection sequences, or via a vector them. Examples of regulatory segments are promoters to control the temporal expression of the CIVPS or intein-modified protein, origins of replication, and/or signaling sequences to control the spatial distribution of CIVPS or intein-modified proteins in vivo in specific plant tissues and/or specific subcellular cornpartments,;and/examples of selection elements are herbicidal or antibacterial genes, fluorescent makers, dye markers, and other suitable selective markers. The resulting polynucleotide or vector comprising the CIVPS or intein modified protein(s) encoding polynucleotide(s), and optionally any desired regulatory, and selection elements, then may be amplified to obtain larger amounts of product, which may be used for subsequent transformation of a desired plant species. Modification of any and all of these steps is possible to facilitate specific orientation and fusion between any desired CIVPS or intein(s) and protein(s) polynucleotides, and it is conducted employing methods that are known in the art. Alteration of either the coding sequences and/or the CIVPS or intein coding sequence and the ligation of either or both of these sequences may also be easily accomplished by techniques known in the a'rt, such as site-directed mutagenesis, codon optimization, random mutagenesis, polymerase chain reaction (PCR), error-prone PCR, and/or any other suitable method that would be considered routine by an artisan. These techniques facilitate the placement of a number of joining sequences, and any desirable and suitable combination may be used. Likewise, any combination or orientation of regulatory and selective
elements may also be implemented in accordance with this invention. Gene
regulatory elements, such as promoters (Guilley et al., Higgins, T.J.V., Coruzzi et
al., Tingey et al., Ryan et al., Rocha-Sosa et al., Wenzler et al., Bird et al.),
enhancers (Brederode, et al.), RNA splicing sites, ribosomal binding sites,
glycosylation sites, protein splicing sites, subcellular signalling sequences
(Smeekens et aU van den Broeck et al, Schreier et al., Tague et al.), secretory
signal sequences (Von Heijne, G., Symons, et al.), or others may be advantageous
in controlling either the temporal or spatial distribution of the CIVPS or intein
modified protein concentration and activity in vivo in the transformed plant. Use
of these elements may be desired to facilitate the production and processing of
intein modified proteins in transgenic plants.. The expression of the intein-
modified protein(s) may be conducted either in a constitutive or induced manner.
In order to attain either of these modes? any ,of the methods that are either
described in this patent or known in the art, or later made available, may be
implemented. The induction of protein expression may be attained with the aid
of a foreign stimulus(i). Examples of these-are the exposure to a pesticide(s), to
light, a temperature change(s), and/or sound(s). Other foreign stimuli, however,
may also be employed. In addition, the'recombinant plant may also express any
one or more of the selectable marker gene or reporter gene(s) mentioned above.
[0061] Once the CIVPS or intein modified protein DNA sequence has been
constructed, optionally codon optimized, combined with the desired regulatory and selection DNA sequences, successfully cloned and selected, then transformation of the desired plant species and generation of full plants is required. Methods for transformation of a desired plant species, and the generation of full plants can be accomplished by techniques known in the art (Draper, et al., Potrykus, et al-). Transformation techniques include, but are not limited to: Agrobacterium tumefactens mediated gene transfer Agrobacterium rhizogenes mediated gene transfer, direct gene transfer to plant protoplasts, Ti plasmid mediated gene transfer (with or without a helper plasmid), biolistic or particle bombardment plant tranformation (Gordon-Kamm et al.), microinjection
and fiber-mediated transformation, and tissue electroploration (Shimamoto et al.). Gene transfer may occur in whole plants, plant explants (such as, but not limited to root explants), any plant portion (such as, but not limited to plant leaf segments, seeds, or seed segments), plant protoplasts or apoplasts, or single or multiple plant cells. Each different method has been substantially described in detail by the prior art. Methods of selection of properly transformed plants are known in the art. Selection methods may be facilitated by including a selectable marker in the transformed DNA containing the GIVPS or intein modified protein (such as a resistance gene, gene coding the production of a colored compound, gene coding the production of a fluorescent compound, or any other suitable method). Additionally, DNA from transformed plants may be isolated and sequenced to confirm the presence of the desired • CIVPS or intein modified protein coding sequence. Other techniques are also suitable for confirmation of the selection process, such as polymerase chain reaction, restriction digest analysis and southern analysis. Any method, of selection that allows identification of the desired transgenic plant may be used. Once the plant is transformed with the CIVPS or intein modified protein and desired regulatory and selection sequences, whole plants can be regenerated by methods know to the art (Horsch et al.). Most methods consist of culturing the transformed plant cells, explants, tissues, parts, or whole plants in the proper medium and under appropriate conditions of light and temperature. The method used to regenerate the plant should not limit the invention and any effective method may be used. The resulting transgenic plant should produce CIVPS or intern-modified proteins that are substantially described as, or a combination of, those shown schematically in Figure 2. Once the whole, transgenic plant has been selected, it can be monitored for CIVPS or intein modified protein expression. This is not required for the production of transgenic plants expressing CIVPS or intein modified proteins, but is prudent to confirm that the desired transgenic plant expressing the desired CIVPS or intein modified protein has been obtained and expression is properly controlled by the desired control elements used.
Monitoring of CIVPS or intern modified protein expression is necessary for the purification of the CIVPS or intein modified proteins in the cleaved or uncleaved state, as described schematically in Figure 3 for either whole intein modified proteins, or components of intein modified proteins that are composed of combinations of elements shown in Figure 3. Protein expression of the intein modified protein can be monitored 'by western analysis, 2-dimensional gel electrophoresis (and staining), or mass spectrometry, conducted on plant extracts or protein fractions purified from the transgenic plant. In addition, either some of the purified proteins, or the transgenic plant itself, should be exposed to the intein cleavage stimulus. After exposure, both the CIVPS or intein modified protein and the resulting protein that appears as a consequence of CIVPS or intein cleavage can both be analyzed by western analysis, and other .assays, to verify the presence of the appropriate proteins, and the difference in- activity between the intein modified protein and the resulting cleaved protein. The activity assays must be designed so as to monitor the desired protein activity and should be specific to that activity and not vulnerable to competing interferences. A control can be used as a standard to compare the native activity with both the intein modified activity and the activity following intein cleavage. Methods and processes using transgenic plants expressing CIVPS or intein modified proteins include the use of the plants as substrates for fuel production (including, but not limited to: burnable biornass, ethanol, methanol, propanol, propane, methane, or octane production), the use of the plants as substrates for commodity chemical production (including, but not limited to: lactic acid, ethanol, glucose or other hexoses, pentoses, propane diols, ethene, ethane, ethylene, phenolic compounds, amino acids, paper pulp, pesticides, insecticides, other alcohols, other ethers, other esters), the use of the plants as substrates for food production and or food additive production (including but not limited to: amino acids, sugars, vitamins, fiber, or cattle feed), the use of the plants for vaccine delivery, the use of the plants for the production of therapeutic proteins (including but not limited to: insulin, erythropoietin, growth hormone, leptin, tumor necrosis factor receptor,
glucagon, gamma interferon, or Her2 receptor), the use of the plants for paper
production, and the use of the plants for remediation of waste materials. Any
batch, semi-batch, or continuous process in which transgenic plants that express
intern modified proteins are used as substrates for one of the purposes described
above is claimed. These processes may include, but are not limited in scope to,
processes in which the transgenic plants expressing intein modified proteins are
harvested, exerted to the intein cleavage stimuli, mixed with other substrates in
a transgenic plant to substrate ratio greater than or equal to zero, and then
converted either chemically, enzymatically, or biologically to one of the products
detailed above.
[0062] The examples provided below illustrate the process of the invention, as well as the manufacture of transgenic plants expressing CIVPS or intein modified celhilase enzymes, and the thus produced plants. In these plants the cellulase enzymes are expressed as dictated by the regulatory elements controlling 'the CIVPS or intein modified genes. The cellulase activity is substantially reduced in vivo by interruption of the native cellulase enzyme by the fused intein. This allows the plant to grow, uninhibited or with little inhibition by cellulase activity. The plants may be harvested and exerted to the intein cleavage stimuli, such as exposure to a certain wavelength of light, mixed with a soilfurous or pH altering chemical, mixed with a salt, mixed with any other chemical, or exerted to a change in temperature. In this case, the CIVPSs or intein is be cleaved and the cellulase activity recovered, which then catalyzes the cleavage of cellulose and/or lignin. At this point the cleaved protein plant mash may be mixed in any proportion, preferably greater than or equal to zero, with other plant substrates, chemical substrates, municipal waste, manufacturing by-products, enzymes, and/or prokaryotic or eukaryotic cells, among others, to aid in the conversion of the plant substrate to the desired product, e.g. a fuel, commodity chemical, food for human or animal consumption, food additive, paper pulp, or vaccine antigen, among others. It should also be noted that the use of the present invention is not limited to manufacturing
processes or mechanical processes. Non-limiting examples of applications of this invention are in the delivery of vaccines, hormones, or therapeutic proteins, in which case the intein modified protein may comprise a combination of therapeutic protein(s) and/or protein antigen(s), potentially protective protein sequences, and CIVPSs or intein(s) that may be expressed by the transgenic plant, e.g. a banana plant. The delivery process may occur, for example, by ingestion of the plant product by a human or non-human animal. The plant is then masticated in the mouth and exposed to a stimulus(i) in vivo in the stomach, which in turn triggers or induces cleavage by the CIVPS or intein. In the case of humans the stimulus may be the reduced pH of the stomach, which induces the cleavage of the CIVPS or intein from the antigen or therapeutic protein, and provides for appropriate ligation, if necessary. The therapeutic protein or antigen would then flow into the duodenum, or small intestine, where the pH would be neutralized and protein products are now ready to be absorbed into the blood stream.
[0063] Background For Exemplary Information Provided Below
[0064] Many different variations in the protocol presented in Example 1
below are suitable for practicing the present invention, as an artisan would know. In general, a DNA sequence encoding a CIVPS or intein modified protein is constructed and packaged into an appropriate vector, plant material, whether it is single cells grown in suspension, protoplasts, plant segments or parts, whole plants, or other forms suitably described here are transformed with the vector, and complete plants, seeds, or other plant forms described here are regenerated. Example 1 shows one embodiment of the inventive method, variations of which are possible that may be used to generate a transgenic tree, e.g. a poplar species expressing an intein modified cellulase. The choice of desired protein, however, depends upon the application the transgenic plant species is intended for. In this regard native proteins, de novo synthetic proteins, or evolved proteins, e.g., by gene shuffling, error prone PCR, or any other analogous method, may be used. Cellulases catalyze a cleavage reaction in breaking down cellulose, a chemical
component of the plant. While other plants have been constructed expressing
cellulases the enzymes typically have to be transiently expressed, or sequestered
in parts of the cell so as not to disrupt plant tissue differentiation and
development. See, for example, Ziegler et al. (2000); Dai et al, (a), (2000); Dai et
al. (b) (2000); Montalvo-Rodriguez et a\ (2000). Hence, in the case where the
cellulase activity is not controlled by localization or transient expression, whole
plants are often very difficult to regenerate, or the cellulase activity is often too
low to be useful. By using an intern modified cellulase, the whole plant can be
regenerated while the less activate intein modified cellulase is produced
throughout the plant and at higbtiter See, Aspergen et al., Molecular Breeding
1:91-99 (1995). The enzyme can be subsequently activated by the self-splicing
ability of the intein to yield a cellulase of increased activity relative to the intein
modified cellulase. It is noteworthy that, any native protein will meet the
requirement for this invention, and selection of the protein is dependent upon the
plant's intended purpose. In this Case, a poplar species that could be induced to
de-polymerize its own cellulose would be beneficial for ethanol production from
biomass, or as a substrate for fermentation of other chemicals.
[0065] Contraction of CIVPS or Intein Modified Proteins
[0066] Various recombinant DNA techniques may be used in combination
to construct the vector carrying the DNA encoding the modified protein. One of the easiest and most direct utilizes the polymerase chain reaction (PCR) to assemble the nucleic acid sequence encoding the intern-modified protein with appropriate complementary ends that facilitates ligation into the desired vector. The PCR method is illustrated here. Other methods may be used to accomplish this same goal, and some rely on specific restriction and ligation of the desired protein and intein encoding sequences, but may still include PCR steps. PCR Kits for conducting the reaction are readily available (Epicentre, Madison, WI). The only requirements on the primers is that one should match the 5J end of the sense strain to be amplified, and the other should match the 5' end of the corresponding antisense strain; relative sequence uniqueness is beneficial.
[0067] Clean-up and Purification from a Gel
[0068] The purification of DNA from a gel may be accomplished using
electroelution, phenol extraction, agarase digestion, glass bead extraction, or from a number of commercially available kits. The commercially available QIAquick Gel Extraction Kit (Qiagen, Valencia, CA) and associated method is one example.
[0069] Selection of Intein According to Intended Use
[0070] Two features are of importance in this step: the property the CIVPC
or intein possesses to induce splicing that will facilitate optimization of the transgenic plantibr its intended purpose, and where to place the intein within the nucleic acid sequence encoding the target protein,-Any coding sequence for a self-splicing protein, i.e. an intein, may be used in this invention. A compilation of some known inteins is given on • the. following website http://blocks.fhcrc.org/~pietro/intems/. Other inteins remain to be discovered and new inteins may be created through sequence analysis, recombinant DNA methods, and mutation of known sequences. This intein of Example 1 is advantageous for the intended transgenic poplar species because upon splicing it yields predominantly ligated, native protein (>75%), and is temperature sensitive so that intein splicing is inhibited at temperatures less than 30°C, and is not substantial until 50 °C, at which temperature the half-life of the uncleaved protein is less than 2 hours.
[0071] Construction of Intein Modified Protein
[0072] In order to ensure proper intein splicing, the intein is inserted in
Example 1 in frame next to a serine, cysteine, or threonine residue of the native target protein. This leaves the native target protein's serine, cysteine, or threonine on the carboxylic acid side, of this intein's histidine - asparagine, conserved residues at the terminal 536 and 537 intein amino acid positions, respectively. Other terminal residues may be used, depending upon the desired stimulus and mechanism for intein splicing. If desired, the codons at the extein-intein junction may be altered to facilitate these requirements. Care is advised
when altering the junction codons, so that the intein modified protein may cleave as desired, and allow the resulting products to perform the appropriate activity. The intein position within the native target protein such is to substantially change the activity of the resulting intein modified protein. In most circumstances virtually any interruption within or near the active site of the molecule meets this criterion. The combination of the amplified intein sequence and the amplified native protein sequence is easily accomplished if a serine residue resides close to a unique restriction site of-the native protein's coding sequence. Conversely, the intein coding sequence is readily incorporated at any desired position in the native protein sequence by using several polymerase chain reactions. A preferred PCR method is set forth 'here. Preferrably 50 oligonucleotide primers are used. Shorter primers may be used, however it is beneficial, although not necessary, to use primers of the.same.length. The sense primer of the C-extein may hybridize to both the C-extein and intein sequence at the junction to facilitate the fusion of the amplified sequences in subsequent PCR amplifications. For intein amplification, both primers preferably overlap with their respective desired adjacent extein sequences to facilitate fusion of the intein sequence and extein sequences in subsequent PCR amplifications. The polymerase chain reaction is preferably carried out using the standard protocol outlined above, but may have some optimization. Typical optimization parameters are the amount of template and primer DNA added to the mixture (generally the primer DNA is added in great excess relative to the template DNA), the temperatures and times for the reaction cycles, the number of cycles, and the MgCh concentration. The length and composition of the primers used may also be varied to yield an effective intein modified protein, so long as the constraints on placement are observed. Kits are commercially available which include all necessary reagents: Tag DNA polymerase, MgCU, 25 mM dNTP mixture (containing equamolar amounts of dATP, dCTP, dGTP, and dTTP), reaction buffer, and water.
[0073] At this point the next round of PCR is started to fuse the extein and
intein sequences. In this case the intein fragment is preferably mixed with an equimolar portion of the C-extein cellulase fragment. Combination of these fragments represents both the template and primers (overlapping regions) to be used. Addition of reaction buffer, 25 mM dNTPs, MgCh, and Taq DNA . polymerase is still required, as are the changing temperature cycles. This reaction is preferably augmented by addition of the following sense and anti-sense primers, respectively, along with E. coll DNA ligase (New England Biolabs, Beverly, MA), however this addition is not necessary and depending upon the exact reaction conditions employed may not lead to an increase in the yield. 5'-ACAGAATGGGGAACGAGH3GATGCTAGCATTTTACCGGAAGAATGGGTTC-3' [SEQIDNO: 1]
5VCGTGTCTGCTCCGTTTACCGCTTTTTTTAATTGGACGAATTTGTGCGTC [SEQIDNO: 2]
[0074] Once completed, the PCR products are preferably again run on an
agarose gel, and the appropriate band, 2665 nucleotides long, purified from the gel and analyzed according to the methods described above. A small amount of the purified reaction product is preferably used for quantitation by measuring the absorbance at 260 nm and 280 nm wavelengths on a UV spectrophotometer. To complete assembly a PCR reaction of the intein modified cellulase coding sequence is carried out combining equimolar amounts of the fused C-extein and intein fragments just constructed, with the N-extein fragment purified previously. The PCR reaction is preferably conducted using the same temperature cycles as in the previous reaction after addition of reaction buffer, 25 mM dNTPs, MgCb, and Taq DNA polymerase. This reaction is preferably augmented by addition of the following sense and anti-sense primers, and E, colt DNA ligase (New England Biolabs, Beverly, MA); however this addition is not necessary and depending upon the exact reaction conditions employed may not lead to an increase in the yield.
5'-AGCATTCAGACCTCCCATTTCATACGAAAAGAGGAAATAGATAGATTTTC-
3' [SEQIDNO: 3]
5'-CGTGTCTGCTCCGTTTACCGCTTTTTTTAATTGGACGAATTTGTGCGT [SEQIDNO: 4]
[0075] Vector Construction
[0076] • Other elements may be included in the expression cassette prepared in Example 1, e.g. extracellular secretion signaling sequences, intracellular localization signaling sequences, other inducible promoters, etc. As the vector is now contained within the recombinant strain A. tumefaciens, the gene transfer to the poplar plant relies on the bacteria's specialized delivery system. Other gene transfer methods-are available, and selection of a suitable transformation method depends upon the source of the plant material. For example, protoplasts or individual plant cells may be transformed directly with the recombinant pTiBo542 plasmid using electroploration, calcium chloride, or Biolistic particle bombardment (Bio-Rad, Hercules, CA). Conversely plant callus, plant segments, or in some cases, whole plants may be used as starting material, when appropriate. For efficient gene transfer to occur, the time of incubation and cell density of the culture is preferably optimized.
[00771 Advantages and Uses for Transgenic Poplar of Example 1
[0078] The resulting transgenic poplar species may be grown and passaged
indefinitely while producing the intern modified cellulase in high titer. The cellulase may be subsequently activated by harvesting the plant, mechanically chipping or grinding it to increase the exposed surface area, and then incubating the resulting mash in a vat or tank at an elevated temperature (preferably 30^0 to 50°C) and/or lower pH (6.5 or below). Exposure to the elevated temperature, and lower pH, if used, will induce the intein splicing and yield the native cellulase at a substantially increased activity. Under these conditions the cellulase may now catalyze the cleavage reaction of cellulose to economically produce substrates that may be subsequently fermented into ethanol or other chemical entities. In addition, this plant may be used as a source of either the
intein modified cellulase, or the recovered native cellulase, post splicing. In
either case, the protein is preferably purified from the plant using methods well
known in the prior art, such as precipitation, membrane filtration,
chromatography including affinity chromatography, extraction, etc.
[0079] The use of transgenic plants producing intein modified proteins has
two advantages over previously reported transgenic plants. Because the intein
modified protein has substantially less activity than the native protein, it may be
expressed at higher titer and localized anywhere in the plant species. Previous
reports of transgenic plants expressing cellulase enzymes have taught
elimination of the secretion signals to contain the cellulase enzymes in the
cytosol of cells. This is not necessary with the use of intein modified proteins and
is a substantial improvement as the modified protein may be placed in close
proximity with its substrate, but not catalyze the reaction until desired. In
addition, these plants have a higher degree of environmental safety. Because the
genes transferred encode proteins of substantially less activity under
physiological conditions, horizontal gene transfer between species is less likely to
impart any selective advantage. For this reason it is unlikely that either the
transgenic plants would outperform native plants in the wild, or that gene
transfer would yield a selective advantage favoring a transformed population.
[0080] Example 2 demonstrates the broad applications of this invention.
Example 2 shows a variation of the method of Example 1 to generate a transgenic Douglas-fir species expressing an intein modified Hgnin peroxidase. The choice of a specific target protein depends upon the application intended for the transgenic plant species. For this example, a lignin peroxidase gene that facilitates the catalytic breakdown of lignin, a chemical component of wood was selected. By using an intein modified lignin peroxidase, the whole plant may be regenerated while the inactivated intein modified lignin peroxidase is produced throughout the plant, at high titer if desirable. The enzyme may be subsequently activated by the self-splicing ability of the intein to yield the native lignin peroxidase at increased activity than the intein modified lignin peroxidase. This allows
improved control of the lignin peroxidase activity that is not currently available.
Such a transgenic plant species is valuable for the production of pulp, animal
feeds, substrates for other processes, improvements on mechanical pulping,
biobleaching of pulp, improvement from decreased pulp processing wastes, and
the production of biopolymers with unique properties,
[0081] Construction of Gene & Intein Modified Protein
{0082] As indicated above, any native protein is suitable as the target
protein, and its selection is dependent upon the plant's intended purpose. For
this example, a Douglas-fir species that may modify its own lignin is beneficial as
a substrate for different pulping processes. The protein encoding nucleic acid of
interest may be isolated from Phanerochaete chrysosporium (GenBank Accession
# M37701). One primer preferably matches the 5' end of the sense strain to be
amplified, and the other the 5' end of the complementing DNA strand at the end
of the gene.lt is beneficial to have relative sequence uniqueness.
[0083] Purification of PCR Fragments from Gel
[0084] The purification of the nucleic acid from the gel is accomplished
using electroelution, phenol extraction, agarase digestion, glass bead extraction, or from a number of commercially available kits. Preferably the commercially available QIAquick Gel Extraction Kit, available from Qiagen (Valencia, CA) is used.
[0085] Intein Selection
[0086] The choice of intern is very dependent upon both the intended
purpose of the plant and the intein modified protein. Many different inteins exist and may be used. For this example an intein with the same properties as in Example 1 is beneficial for the intended use of a transgenic Douglas-fir species. Hence, a variant of the Psp pol intein (GenBank Accession # PSU00707) from Pyrrococcus spp. is preferably used. The advantage of this intein is that upon splicing it yields predominantly ligated, native protein (>75%), and is temperature sensitive so that intein splicing is inhibited at temperatures less than 30°C, and is not substantial until 50°C, where the half-life of the uncleaved

protein is less than 2 hours. This intein induces splicing in vitro by a pH shift,
thus adding increased flexibility to subsequent processing of the transgenic plant.
[0087] Vector Transformation
[0088] With the vector contained within the recombinant strain of A.
tumefaciens, gene transfer to Douglas-fir relies on the bacteria's specialized
delivery system. Other gene transfer methods are available, and selection of a
suitable transformation method depends upon the source of the plant material
and ease with which the method can be applied. Some modification and
optimization of the transformation parameters is usually necessary.
[0089] Uses of the Recombinant Trees
[0090] The tree of Example 2 may be used as a source material for the
purification of lignin peroxidase or in tern-modified ' lignin peroxidase. Alternatively, it may be used also by itself as a substrate for producing wood pulp in any number of applications, e.g. paper production, animal feed, composite materials, etc. Both Example 1 and Example 2 have illustrated the use of trees, certainly other plants are useful options and depend upon the intended use of the invention. In many areas these types of trees do not grow well and grasses, vines, seaweed, or other plant species do, and may be used equally well. In addition, many fruits and vegetables may benefit from intein modified protein technology, such as for example to induce ripening, pesticide resistance, or any number of other applications. Hence the choice of host plant is not limiting. The use of plants as sources for recombinant proteins is facilitated by use of the CIVPS or intein technology of this invention. Plants are made to express any number effusion proteins where the fuuon point is comprised of an intein that does not facilitate recombination effused protein exteins, but instead links the desired protein to a binding protein for purification via affinity chromatography. In this case the desired protein may or may not have full activity in vivo. Once expressed in the plant, the fusion protein is eluted onto an affinity column where the binding portion of the fusion protein binds the column. The column is then treated to induce intein splicing and the desired protein is washed away and
recovered. Another variation of the invention that is of medical interest is a
fusion protein comprising a therapeutic protein or vaccine fused by inteins to
protect protein groups or relying on inteins to distrupt their natural activities
when in the plant. Such a therapeutic protein can be expressed in a plant and
purified and injected, or simply eaten by a human and non-human animal, e. g.
in the case of animal vaccination or hormonal treatment. Intein splicing then
occurs either in vitro in a process tank or inside the patient, or animal, relying on
the change of pH within the stomach, or a thiol gradient induced by ingestion of a
third chemical. Splicing removes the protective protein groups, yielding the
native therapeutic protein or vaccine, which is then absorbed in the gut.
[0091] ' Either of the transgenic trees expressing intein modified proteins
from Examples 1 and 2 may be effectively used in an industrial scale process as is
shown in Example 3. The pulping itself may be enhanced by a- modification
similar to that used in Example 2 for the Douglas-fir species.
. [0092] Tree Processing
[0093] Typical pretreatment processes for the degradation of lignocellulosic
substrates include concentrated acid pretreatment (usually Sulfuric Acid), dilute acid pretreatment, ammonia explosion pretreatment, and hot water pretreatment. Other pretreatment processes are possible, and design of the transgenic tree expressing an intein modified protein should be optimized to take full advantage of a pretreatment process when necessary. Intein splicing may occur in a vessel via any known method, such as, but not limited to: pH shift, temperature change, light exposure, acoustic stimulation, or any exogeneous chemical addition.
[0094] Intended Uses and Process Variations
[0095] Preferred variations of the process of Examples include combining
the pretreatment, splicing, digestion, and fermentation steps. This preferred processing consolidation may occur between any of the steps, however a preferred manifestation incorporates all steps simultaneously in a single unit operation. This preferred combination may realize cost savings through a decrease in capital
expenditure and depreciation, decrease in the cost of substrates, and a process
dependent decrease in the cost of energy and chemicals input to the process. In
addition, as opposed to competing chemical processes making the same products,
environmental benefits may be realized through decreased emissions and
hazardous waste generation. In Example 3 the choice of product is dependent
upon the organism used in the fermentation for the desired bioconversion. Any
organism that may adequately utilize the degraded cellulose as a substrate may
be used to effectively produce a desired product. For this reason the spectrum of
end products that may be made is very large. Applications that will benefit from
substrates with preferred processing traits facilitated by the intein. modified
proteins carrying plant of this invention include, but are not limited to, fuel
production, chemicals production, textiles production, biopolymer production,
* food production, a;nd saccharification. Although Example 3 is mostly focused on
the fermentation of the degraded transgenic plants, intein modified plants may
also be used as substrates for traditional chemical processes. For example, the
plants of Example 2 may be preferentially used in paper pulping. In such a
process, benefits are derived from a decrease in the harsh chemicals used to
bleach the wood. This will likely result in a decrease in the costs of chemical
input, hazardous material generation and containment, and potentially some
consolidation in processing. Another use is that of pectinase for cotton scouring,
or cellulases for other textile production processes. In these instances, the end
products are derived from more traditional chemical processes, although benefits
accrue through the use of intein modified protein plant substrates, as opposed to
the normally harsh chemical processing environment generally employed
[0096] Animal feed is commonly supplemented with a variety of enzymesi
used to increase the nutritional value of the feed, as well as decrease the environmental burden experienced in proximities where animal manure accumulation is substantial. Nutritional value is increased through the putative enzyme action on plant polymers, which assist the animal in digesting the feed and thereby utilizing more of the beneficial feed components. The environmental
burden may be decreased by limiting the amounts of added minerals, such as
inorganic phosphate, which may be obtained from the plants themselves in the
presence of the active enzyme. The benefits associated with using intein
modified proteins, as opposed to unmodified proteins, result in multi-protein
expression, at high levels, which do not interfere with plant regeneration yet
impart a desired enzyme activity upon splicing within the animals stomach. This
decreases the cost of feed by delivering the enzymes within the meal itself, as
opposed to their being produced exogenously and added to the meal. In addition,
the added benefit of using genes that code for nearly inactive proteins in vivo in
plants, provides a technology platform that is less likely to be associated with
environmental risks associated with horizontal gene transfer to native plant
species. This advantageous environmental affect, whether real or perceived,
holds for all intein modified protein plant products. Example 4 illustrates the
construction an intein modified phytase in rapeseed, for use as animal feed.
(0097] Uses and Variations
[00981 Phytase is an enzyme that assists in the evolution of inorganic
phosphorous from myoinositol phosphates contained inherently in animal food. An economic impact is brought about through a decrease in the amount of phosphate supplementation required for the production of animal feed, and a decrease in the phosphate content of the animal's manure, which contributes to the contamination of local waters. Although Example 4 below illustrates the construction and use of an intein modified phytase expressed in rapeseed for animal feed, a number of other valuable native proteins may be used as well. For example, phytase may be substituted with, or used in addition to any number of cellulases, amylases, glucanases, hemi-cellulases, pectinases, proteases, xylanases, lipases, growth hormones, or immunogenic antigens, among others. Each of these other proteins has a potential economic value in the use of animal feed supplementation.
[00991 Example 5 illustrates one of the preferred embodiments of the
invention. A transgenic corn is constructed and used as a substrate for ethanol
processing. In this case the intein modified gene sequence of Example 1 is again
used for demonstration purposes only. In a preferred embodiment, however,
several intein modified proteins may be expressed simultaneously to optimize the
desired plant degradation processing trait for use in the fermentation process.
The target enzymes may be selected from enzymes commonly known as cellulases
(E.G. 3.2.1.4), exocellobiohydrolases (E.G. 3.2.1.91), glucosidases (E.G. 3.2.1.21),
and may be expressed optimally with other enzymes selected from the Enzyme
Classification heading 3.2.1.x, or any other classification group necessary. In
addition to the simultaneous expression of multiple intein modified proteins, the
preferred composition of matter embodiment is a fertile plant capable of
reproduction and stable gene inheritance.
[00100] Transformation Information
[00101] The macroprojectiles are used to accelerate the microprojectiles,
which enter the plant cells.
[00102] Having now generally described this invention, the same will be
better understood by reference to certain specific examples, which are included herein for purposes of illustration only, and are not intended to be limiting of the invention or any embodiment thereof, unless and where it is so specified. [00103] EXAMPLES
[00104] Examnle 1: Production of Transgenic Poplar Expressing an Intein-
Modified Cellulase
[00105] For this example a cellulase enzyme is used. A vector is first
assembled containing the DNA coding sequence for the intein modified protein. In order to construct such a vector, an intein modified protein DNA sequence is first prepared, and then packaged into the desired vector. The desired protein for this plant is a cellulase (GenBank Accession # AY039744) isolated from Bacillus sp. NBL420. The gene corresponding to this protein is amplified using PCR from a genomic DNA template isolated from the Bacillus sp. NBL420. The PCR reaction is performed by mixing the template DNA, two primers complimentary to the 3'ends of the template DNA to be amplified, Taq DNA polyermase, reaction
buffer (500 mM KC1, 100 mM Tris-Cl pH 9.0, 0.1% Triton X-100), and MgCl2 in a thin-walled 250 uL PCR tube. Once mixed, each reaction tube is placed in a thermocycler, and the thermocylcer is set for 35 cycles comprised of three segments: 94 °C for 30 seconds, 60 °C for 60 seconds, 72 °C for 120 seconds. Following amplification, the resulting PCR product is analyzed by electrophoresis on a 1% agarose gel, along with molecular weight standards (Invitrogen, Carlsbad, CA), with the aid of IX TAE (or TBE) running buffer, and stained with ethidium bromide (0.5 ug/ mL). Care should be taken to ensure that the appropriately sized band, of approximately 3200 base pairs (bp), has been obtained. This band is then cut out from the gel with a scalpel, and purified (separated from the gel material) using a commerically available gel purification kit (Qiagen). Once the fragment has,been purified from the gel, the band is analyzed using restriction digestion or sequencing as described by Ausubelet. al., Current Protocols in Molecular Biology, Wiley, New York (1998). After gene amplification, the gene is modified by insertion of the intein sequence segment. In this case, a variant of the Psp pol intein (GenBank Accession # PSU00707) from Pyrrococcus spp. is used This variant, described in the literature , contains a mutation at the tyrosine 534 residue which converts that tyrosine to methionine. See, Xu, M, Perler, F, (1996), The mechanism of protein splicing and its modulation by mutation, The EMBO Journal 15:5146-5153. This intein may be cleaved in vitro by a pH shift. The coding sequence of this intein is then amplified by PCR using genomic DNA from Pyrrococcus spp, as a template. The PCR reaction is conducted using a standard protocol (e.g., 30 cycles comprised of a 94 °C for 30 seconds, 50 °C for 60 seconds, 72 °C for 120 seconds) and the following primers.
[00106] 5'-ATTATGTGCATAGAGGAATCCAAAG-3' [SEQ ID NO: 5]
[00107] 5'-AGCATTTTACCGGAAGAATGGGTTC-3' [SEQ ID NO: 6]
[001081 Once the amplification is complete, the PCR product is transferred to and elecrophoresed on a 1% agarose gel in IX TAE or TBE buffer. The resulting band is then purified and analyzed as described above for the native
cellulase coding sequence. At this point the two PCR fragments shown in Figure 1, one encoding the cellulase protein and one encoding the intein polypeptide sequence, are joined. Here, the intein is inserted in frame into the native protein, such that a serine residue of the native protein becomes the terminal C-extein amino acid at the junction point between the native intein and C-extein of the native protein. This intein modified protein segment is produced using PCR by first amplifying the C-extein coding sequence of the cellulase gene. Primers that overlap both the C-extein, and the intein end containing the histidine and asparagine codons immediately adjacent to the C-extein are used to amplify the C-extein sequence:
'5'-CTTTGGATTCCTCTATGCACATAATTCCGGAAACGGCGGTGTCTACCTCG-3' ISEQIDNO: 7]
.5'-CGTGTCTGCTCCGTTTACCGCTTTTTTTAATTGGACGAATTTGTGCGTG [SEQ ID NO; 8]
[00109] The resulting sequence is 604 nucleotides long. The intein is then
amplified using a sense primer that contains both the intein end containing the
terminal serine codon, and the N-extein end of the cellulase gene, along with an
antisense primer that contains specific nucleotides of the intein and C-extein. For
this PCR reaction the following primers are used to obtain a sequence 1661
nucleotides long: .
5'-ACAGAATGGGGAACGAGCGATGCTAGCATTTTACCGGAAGAATGGGTTC-3' [SEQ ID NO: 9]
5'-CGAGGTAGACACCGCCGTTTCCGGAATTATGTGCATAGAGGAATCCAAAG-3' [SEQ ID NO: 101
[00110J The N-extein is then amplified using PCR and one primer that
contains specific nucleotides of the sense N-extein strand, and another primer that contains specific nucleotides of the N-extein and adjacent intein sequence. The N-extein portion of the cellulase gene is amplified with the following primers resulting in a sequence 1541 nucleotides long.
5'-AGCATTCAGACCTCCCATTTCATACGAAAAGAGGAAATAGATAGATTTTC-3' [SEQIDNO: 11]
5'-GAACCCATTCTTCCGGTAAAATGCTAGCATCGCTCGTTCCCCATTCTGTG-3' [SEQIDNO: 12]
[00111] Once these three reactions are complete, each PCR fragment is cleaned to remove residual primers, and the C-extein, intein, and N-extein PCR fragments are joined by conducting two more polymerase chain reactions. The intein and one of the cellulase extein regions, either the C-extein or the N-extein, are amplified in a single reaction by mixing equimolar portions of the two PCR fragments generated above and performing PCR as described earlier. This reaction requires no extra external primers and results in the first intein-extein fusion. This reaction mixture is cleaned, and then equimolar portions of the : cleaned fusion product are mixed with the remaining extein portion, and PCR is conducted once again without adding additional primers. No exogeneous primer is required in either of the last two PCR reactions, and annealing occurs at the mtein-extein junctions. The annealed regions are extended by Taq polymerase resulting in the final fusion products. This sequence of reactions results in the coding sequence of the intein modified protein with the intein inserted at the exact position desired. The product of the final reaction is cleaned again, and amplified using PCR one last time with primers specific to the cellulase extein termini with specific ends to facilitate ligation into the cloning vector. Once this reaction is complete, the PCR products are run on an agarose gel, and the appropriate band, 3806 nucleotides long, is purified from the gel and analyzed according to the methods described above. The resulting intein modified protein coding sequence (nucleic acid segment) contains a ribosome binding site, a start codon at the beginning of the N-extein, the complete sequence of the intein modified cellulase with the intein inserted in frame in the proper orientation, and a stop codon at the end of the C-extein coding sequence. The intein modified cellulase coding sequence is then cloned into pTiBo542, replacing the tms and *mr genes in the T DNA, using the methods described in Ausubel, et. al., Current
Protocols in Molecular Biology (1998). See, Parsons TJ, Sinkar, VP, Stettler, RF, Nester, EW, Gordon, MP, "Transformation of Poplar by Agrobacterium tumefaciens," Biotechnology 4:533 536, 1986. Here the expression cassette includes a "MAC" promoter, a mannopine synthetase terminator, and a kanamycin resistance marker. This vector is transformed into A. tumefaciens A281 using any suitable method known in the art (e.g., electroploration, or the calcium chloride method). Various transformation methods are also described by Ausubel, et. al. (1998), above. ,
[00112] To transform the desired Populas trichocarpa x deltoides, H11 plant species, with the recombinant A. tumefaciens,.a variation of the leaf disk method is employed. The recombinant A. tumefaciens is cultured in selective medium containing 50% MG medium (10 g/ L marmitol, 2.32 g/L sodium glutamate, 0.5 g/ L KH2P04) 0.2 g/ L NaCl, 0.2 g/ L MgSO4-7H20, 0.002 g/ L biotin, pH 7.0), 50% luria broth (20 g/ L tryptone, 10 g/ L yeast extract, and 10 g/ L NaCl), and appropriate antibiotic, at 30 °C in an incubator-shaker. For plant transformation, small greenwood stem sections, approximately 7 mm in length and 2 - 3 mm in diameter, are sterilized with a 20% bleach, 0.1% Tween 20, and 30 mg/ L Benomyl systemic fungicide (Chas. H. Lilly Co., Portland, OR) solution. After washing with sterile water, the stem sections are aseptically transferred to a culture of A. tumefaciens at a cell concentration of approximately 5 x 10s cells per mL, and the sections allowed to incubate for 16 hours. After exposure to the recombinant A. tumefaciens culture, the plant stems are transferred to solid Murashige-Skoog medium supplemented with zeatin riboside and kanamycin in a vertical position. See, Murashige T, Skoog F, "A revised medium for rapid growth and bioassays with tobacco tissue cultures," Physiol. Plant, 15:473-497, 1962. Once roots have begun to grow, shoots will develop. The regenerating plants are transferred to fresh plates every two to three weeks, and a normal light cycle is maintained during plant growth and at elevated humidity in the incubator. Once roots form, the explants are transferred to a solid medium lacking zeatin riboside, but containing kanamycin for another two to three weeks,

after which period the plants are transferred to boxes containing soil for four to five days prior to replanting in soil and full growth in a greenhouse or controlled plot of soil. Initial plants are screened by several methods to ensure the intein modified cellulase DNA sequence has been transferred to the genome and protein expression is active. Genetic screening is conducted by southern analysis on genomic DNA -isolated from the transgenic plant using the intein modified cellulase coding sequence as a probe, as described by Ausubel, et. al. (1998), above. PCR is conducted using probes specific to the intein modified cellulase coding sequence and the transgenic plant's genomic DNA as a template, as described above. Appearance of the appropriately sized band on an ethidium bromide stained gel verifies the presence of the intein modified cellulase coding sequence. Direct sequencing of the plant's genomic DNA may also be performed.
Protein production is monitored by western analysis using antibodies specific to both the intein modified cellulase and the native cellulase. In addition, enzymatic assays for cellulase activity are known in the art and may be used to quantify the activity of the unspliced intein modified cellulase and the spliced cellulase.
(00113] Example 2: Production of Transgenic Douglase Fir
[00114] Expressing Intein Modified Lignin Peroxidase
[00115] This example uses the same method for constructing the vector
containing the intein modified lignin peroxidase coding sequence as used in example one. The primary differences are in the A. tumefaciens plasmid employed, the native protein sequence that is modified, and the primers selected to amplify the new intein modified lignin peroxidase coding sequence. [001161 The lignin peroxidase gene (GenBank Accession # M37701) is amplified by PCR using genomic DNA from P. chrysosporium as a template. The primers
5'-ATGGCCTTCAAGCAGCTCGTCGCAG-3' [SEQ ID NO: 13] 5'-TTAAGCACCCGGCGGCGGGGGGCTG-3' [SEQ ID NO: 141
are are used in the PCR reaction as described in example one. Following amplification, the resulting PCR product is analyzed using gel electrophoresis on an agarose gel, along with molecular weight standards as described in example one. After staining the gel with ethidium bromide, the 1567 base pair (bp) band is cut from the gel with a scalpel, and purified from the gel as described above. After purifying the fragment from the gel, the fragment is analyzed using restriction digestion or sequencing for direct verification as described by Ausubel, etal., 1998.
[00117] After the gene is amplified, it is modified by insertion of the intein sequence into the gene sequence. For this example, the same intein -is used as in example one. The coding sequence of this intein is amplified in the same manner as described in example one. The resulting, intein DNA sequence is purified by gel electrophoresis and analyzed as described previously..
[00118] The two PCR fragments, one encoding the lignin peroxidase and one
encoding the intein polypeptide sequence, are joined. To ensure proper intein splicing, the intein is inserted in frame next to a serine residue of the lignin peroxidase such that this serine is on the carboxylic acid side, of this intern's histidine - asparagine conserved residues at the terminal 536 and 537 intein amino acid positions, respectively. The intein is inserted into the native protein, such that the serine residue of the native protein becomes the terminal C-extein amino acid at the junction point between the native intein and C-extein of the native protein. The intein is positioned within the native protein such that its presence substantially reduces the activity of the resulting intein modified protein. In most circumstances virtually any serine residue within or near the active site of the molecule will meet this criterion, however some optimization may be necessary.
[00119] The intein modified protein sequence is produced using PCR the
same as described in example one, with the only difference being the choice of primers. The C-extein portion of the lignin peroxidase gene is amplified using
the cleaned gene product from the PCR reaction above, and the following primers resulting in a 445 nucleotide sequence:
5'-CTTTGGATTCCTCTATGCACATAATTCTCGCCCGCGACTCCCGCACCGCT-3' [SEQIDNO: 15]
5'-TAAGCACCCGGCGGCGGGGGGCTGGAAGAGGAATATGTCAGCTGGGGGC-3' [SEQIDNO: 16]
[00120] The N-extein portion of the lignin peroxidase gene is amplified using
the same template, by PCR using the following primers.
S^ATGGCCTTCAAGCAGCTCGTCGCAG^GATTTCCCTCGCACTCTCGCTCAC-3' [SEQIDNO: 17]
5'-GAACCCATTCTTCCGGTAAAATGCTGTGTGGTCGGTCTGGATGCGGATCT-3' [SEQIDNO: 18]
[00121] .- The resulting sequence is 1196 nucleotides long. The intein coding
sequence to be placed into the lignin peroxidase gene is .amplified using PCR as
described in example one. In this reaction use a Pyrrococcus spp genomic DNA
template and the following primers. ;
5'-AGATCCGCATCCAGACCGACCACAOAGCATTTTACCGGAAGAATGGGTTC-3' [SEQIDNO: 19]
5'-GCGGTGCGGGAGTCGCGGGCGAGAATTATGTGCATAGAGGAATCCAAAG-3' [SEQIDNO: 20]
[00122] The resulting sequence is 1661 nucleotides long. Once these
reactions are complete, the reaction products are electrophoresed on an agarose gel, purified from the gel, and analyzed as described above. The extein and intein portions are joined as described in example one. In this case the intein fragment is mixed with an equamolar portion of the C-extein lignin peroxidase fragment. Combination of these fragments represents both the template and primers required for the PCR reaction. PCR is performed using the same reaction conditions as in example one. Once complete, the PCR products are electrophoresed on a 1% agarose gel, and the appropriate band, 2106 nucleotides long, is purified from the gel. The purified band is analyzed as described in
example one. A small amount of the purified reaction product is then quantified
by measuring the absorbance at 260 nm and 280 nm on a UV spectrophotometer.
[00123] The intein modified protein DNA coding sequence is completed with
one more PCR reaction. Equamolar amounts of the fused C-extein and intein
fragment just constructed are combined with the N-extein fragment purified
previously. The PCR reaction is conducted using the same conditions in the
previous reactions. The reaction products are electrophoresed on a 1% agarose
gel, the appropriate hand, 3302 nucleotides long, is purified from the gel, and
analyzed according to the methods described in example one. The final intein
modified protein coding sequence has the complete intein sequence in frame, in
the proper orientation, within the lignin peroxidase coding sequence.
[00124.] The intein modified lignin peroxidase coding sequence is cloned into
a plant expression cassette. In this case, the pTiA6 plasmid .is used with
kanamycin resistance and lacking the octupine synthetase genes, but containing
the octupine transcription control sequences. The intein modified lignin
peroxidase is ligated into a restricted pTiA6 under the octupine transcription
control sequences (promoter and 3J polyadenylation site). A. tumefaciens
K12X562 is transformed using the resulting ligated vector, and any suitable
method known in the art (e.g., electroploration, or the calcium chloride method).
Transformation methods are described by Ausubel, et. al. (1998).
[00125] Douglas-fir is transformed, with the recombinant A. tumefaciens,
and nodal segments or seeds sampled from these trees. The shoot multiplication and elongation is conducted as previously described (Gupta PK, Durzan, DJ, "Shoot multiplication from mature trees of Douglas-fir, and sugar pine,"Plant Cell Reports, 9:177-179,1985) in culture on DCR basal medium plates. A culture of the recombinant A. tumefaciens is grown according to the method described in example one. For plant transformation, the regenerated shoots from culture, approximately 50 mm. in length, or seeds are surface sterilized by treatment with a 10% bleach and 0.1% Tween 20. Once sterilized, the shoots or seeds are aseptically rinsed with sterile, distilled, and deionized water. The seeds or the
shoots are transformed by first wounding the epidermal tissue with a sterile
needle or by cutting the surface with a sterile scalpel. The wounded shoots or
seeds are soaked in a culture of the recombinant A. tumefaciens at a cell
concentration of approximately 5 x 108 cells per mL. After a 12 hour exposure to
the recombinant A. tumefaciens culture, the shoots and seeds are cultured in
DCR basal medium with 2.2% sucrose and 0.8% Bacto (Difco) agar. The culture
conditions include a 16 hour light cycle at 25 °C, followed by and 8 hour dark
.cycle at 20°C in a green house or growth chamber. The regenerating plants are
transferred to fresh plates every two to three weeks. Once roots form, the
explants are transferred to boxes containing soil for four to five days prior to
• replanting in soil and full growth in a greenhouse or controlled plot of soil. The
first year of ^growth is conducted within a green house under controlled
temperature conditions, not exceeding 30 °C, .
[00126] The plants are screened using methods similar to those of example
one;:except specific to the lignin peroxidase protein or intein modified lignin peroxidase protein in the case of western analysis.
[00127] The resulting transgenic Douglas-fir species is grown indefinitely
while producing the intein modified lignin peroxidase in high titer. The lignin peroxidase is subsequently activated using the same methods described in example one because the same intein was employed for modification in this example.
100128] Example 3: Fermentation Substrate Preparation Process
[00129] Using Plants Expressing Intein Modified Protein
100 3 30] In the case of example one, the transgenic poplar species can be used
as substrate for ethanol production via fermentation. For this process the transgenic tree is harvested using a suitable tool, such as a chain saw or ax. The tree is subsequently pulped using a mechanical pulper. The pulp is then placed it in a tank. After any necessary pretreatraent has been conducted, intein splicing is induced by raising the temperature of the tank and reducing the pH to a value of 4. Depending on the pretreatment used, intein splicing may be stimulated by
the pretreatment and thereby occur in parallel with that process operation. Once spliced the native enzyme activity begins digesting the cellulose of the pulp, increasing the concentration of monosaccharides.
[00131] Following the induction of splicing, the contents of the saccharification vessel are mixed in any proportion with native poplar pulp or other substrates, to facilitate cellulose degradation of those substrates. The proportion of the mixing depends upon the cellulase activity of the transgenic poplar which is a function of the amount of intein modified cellulase expressed in the plant, the efficiency of splicing, the efficiency of recombination, and the activity of the recombined, native cellulase on the substrate. Each one of those parameters has a broad spectrum of possible values and can be optimized to facilitate process economics.
[00132] The resulting glucose is then filter sterilized from the degraded
cellulose through a 0.22 (or less) um filter, or heat sterilized in batch or
continuous mode through a heat exchanger. The sterilized glucose is fed to a
fermentation process, where it can be used as a substrate for ethanol production
as described in the literature. See, H.K. Sreenath and T. W. Jeffries, "Production
of ethanol from wood hydrolysate by yeasts," Bioresource Technology, 72(3): 253-
260, 2000; Lisbeth Olsson and Barbel Hahn-Hagerdal, "Fermentation of
lignocellulosic hydrolysates for ethanol production," Enzyme and Microbial
Technology, 18(5):312-331, 1996; Kutluo O. Ulgen, et. al., "Byconversion of
starch into ethanol by a recombinant Saccharomyces cerevisiae strain YPG-AB",
Process Biochemistry, 37(10):1157-1168, 2002; M. Mete Altintas, et al,
"Improvement of ethanol production from starch by recombinant yeast through
manipulation of environmental factors," Enzyme and Microbial Technology,
31(5):640-647, 2002; Farooq Latif, et al,, "Production of ethanol and xylitol from
corn cobs by yeasts," Bioresource Technology, 77(l):57-63, 2001.
[00133] The fermentation process is conducted in batch, fed-batch, or
continuous modes.
[001341 Example 4: Plants Expressing an Intein Modified Protein used for Animal Feed
[00135] A transgenic rapeseed is constructed following essentially the same
methods described in Examples 1 and 2 above, with the following modifications.
In constructing the CIVPS or intern modified gene sequence, the same intein
coding sequence can be used, however in this case it is fused within the phytase
expressed by Aspergillus ficuum. In this example the selected intein modified
protein relies upon the acidity of the animal's stomach to induce protein splicing.
The selected phytase was chosen because of its high level of activity at low pH
(van Ooijen et al. (2000), United States Patent Publication No. 6,022,846). The
C-extehr portion of the please is amplified using the following primers under the
same conditions as previously described.
5'-CTTTGGATTCCTCTATGCACATAATTTCCTTCGACACCATCTCCACCAGCA-3' [SEQIDNO: 21]
5'-CTAAG€AAAACACTCCGCCCAATCACCGCCAGATCTGGCAAAGCTCAACC-3' [SEQIDNO: 22]
[00136] The resulting sequence is 627 nucleotides long. The intein sequence
is amplified using primers under the same conditions as previously described. 5'- AGTGACCTACCTCATGGACATGTGCAGCATTTTACCGOAAGAATGGGTTC 3' [SEQIDNO: 23] 5'-GCTGGTGGAGATGGTGTCGAAGGAATTATGTGCATAGAGGAATCCAAAG
3' [SEQIDNO: 24]
[00137] Finally the N-extein is amplified using primers resulting in a PCR
fragment 928 nucleotides long.
5'-ATGGGTGTCTCTGCCGTTCTACTTCCTTTGTACCTCCTGTCCGGAGTATG-
3' [SEQIDNO: 25] 5'-GAACCCATTCTTCCGGTAAAATGCTG€ACATGTCCATGAGGTAGGTCACT-
3' [SEQIDNO: 26]
[00138] The resulting DNA fragments are cleaned and analyzed, then
combined using PCR and the associated methods described in Examples 1 and 2.
This procedure results in the intein modified phytase coding sequence. The final composite intein modified phytase sequence is then amplified, cleaned and analyzed as described in Examples 1 and 2. The intein modified phytase DNA coding sequence is cloned into the same expression cassette, and used to transform A. tumefaciens as described in Example 2. Rapeseed stem segments are transformed using the resulting recombinant A. tumefaciens. Transformation occurs substantially as described in Examples 1 and 2 with the following modifications. The rapeseed stem segments are surface sterilized from five to six week-old plants using a 20% bleach solution for 25 minutes at room temperature. Following sterilization, the stem segments are aseptically rinsed with sterile, distilled, and deionized water. The segments are preconditioned by incubation for 24 hours on Murashige-Skoog medium supplemented with 1 mg/L of BAP. Once the 24 hours has transpired, the stem segments are incubated for 48 hours with the newly transformed strain of A. tumefaciens containing the intein modified phytase. Following this incubation step, regenerate transgenic plants and select them using the kanamycin resistance marker, following substantially the same procedures described in Examples 1 and 2. Confirmation of incorporation of the intein modified phytase can also be conducted as described in Examples 1 and 2.
[00139] The resulting transgenic rapeseed is grown in an approved area
according to local legislation. The rapeseed is harvested when it's mature and
used to supplement animal feed. Conversely, the rapeseed can be grown on
grazing land for the animals since intein splicing should occur spontaneously in
the animal's stomach, allowing for activation of the phytase activity.
(001401 Example 5: Production of Transgenic Maize Expressing an Intein
Modified
[00141] Cellulase and Utilization in the Production of Ethanol
[00142] This example illustrates one way in which the invention may be
practiced. Here, transgenic corn is constructed and used as a substrate for ethanol processing, or as a substrate in other fermentations. In this example the

intein modified gene sequence of Example 1 is again used for demonstration. The
growth of Zea mays friable, embryogenic type II callus cultures is initiated from
immature embryos, approximately 1.6 mm to 1.8 mm in length, from greenhouse
grown A188 (University of Minnesota, Crop Improvement Association) x B73
(Iowa State University) plants. After harvest, fragments are surface sterilized
using 50% bleach, for 25 minutes at room temperature, and then washed with
sterile, distilled, deionized water. New cultures are aspetically initiated from the
harvested fragments and maintained under no more than 10 pE nv2 s-1 light, at
24 °C, on modified N6 medium (Chu, et al., (1975), "Establishment of an Efficient
Medium for Anther Culture of Rice through Comparative Experiments on
Nitrogen Sources," Sci. Sin., 18:659-668) at pH 5.8, with 2 mg/ L glycine, 2.9 g/ L
L-proline, 1 mg/ L 2,4-dichiorophenoxyacetic acid (2,4-D), 100 mg/ L casein
hydrolysate, 20 g/ L sucrose, and solidified with 2 g/ L Gelgro (ICN Biochemicals).
[00143] After approximately two weeks of incubation, the cultures are
manually evaluated for proper morphology. This entails visual observation for friable consistency in the presence of well-characterized somatic embryos. Proliferations demonstrating proper morphology are transferred to fresh modified N6 medium (described above). Tissues resulting with the proper morphology are routinely subcultured every two to three weeks, until the microprojectile bombardment is prepared. The desired intein modified gene sequence and expression vector can be constructed as described in Example 1. In this example, the preferred expression vector also has the following alterations. Replace the kanamycin resistance marker with a hygromycin resistance marker using methods known in the art (for example, PCR of the hygromycin resistance marker from a suitable template, DNA endonuclease restriction of the vector, followed by purification, and Hgation of the hygromycin resistance marker) as described by Ausubel, et. al., 1998. Once constructed, the vector is precipitated in a 1:1 molar ratio onto either tungsten (average diameter 1.2 um, GTE Sylvania), or gold, particles. As with other steps in this procedure, the precipitation parameters may require some minor optimization. The precipitation is
performed by combining 1.25 mg of the tungsten particles, and 25 pg of the vector
DNA in solution with 1.1 M CaCb and 8.7 mM spermidine at a total volume of
575 uL. The precipitate is vortexed for 10 minutes at 0 °C. Once vortexed, the
mixture is centrifuged at 500xg for five minutes. After centrifugation, the
supernatant, approximately 550 pL, is removed and the remaining 25 pL of
precipitate is dispensed in 1 uL aliquots onto macroprojectiles (Biolistics, Inc,
Ithaca, NY) for bombardment as described by Klein et al. (1987), except for the
changes noted above. AH manipulations are performed aseptically and on ice.
[001441 Once the biolistic projectiles are ready, the desired plant tissues are
prepared for'the bombardment procedure. Any number of callus clumps are
aseptically arranged, each weighing 50 mg (wet weight), in an x-pattern near the
center of a sterile 60 x 15 mm petri dish (Falcon 1007). Several dishes should be
prepared for each bombardment procedure. These dishes are each paced in turn,
5 cm below the stopping plate of the microprojectile instrument. The dishes are
centered below the device, with the lids removed, and a 3 x 3 mm mesh screen
covering the top of the plate. The mesh screen helps contain bombarded tissue
within the dish during the procedure. The tissue bombardment is performed
with the microprojectile instrument as described by the manufacturer's
instructions; commercial microprojectile instruments are available through Bio-
Rad (Hercules, CA). Following bombardment, the callus are transferred to fresh
modified N6 medium plates and cultured under the same conditions used above.
[00145] The selection of transformed cells for subsequent regeneration is
began after two days of culture. The callus plates subjected to the bombardment procedure are aseptically transferred to fresh, sterile, modified N6 medium plates formulated to a final concentration of lOmg/ L hygromycin B (Calbiochem). After two weeks of exposure, all callus are asepticaliy transferred from the selective plates to fresh, sterile, modified N6 medium plates formulated to a final concentration of 50 mg/ L hygromycin B. This transfer is conducted so that only five 30 mg pieces of callus are contained on a single plate, resulting in an expansion of the number of plates used. Following three weeks on the 50 mg/ L
hygromycin B plates, all callus are aseptically transferred to fresh, sterile,
modified N6 medium plates formulated to a final concentration of 60 mg/ L
hygromycin B. Ailer two weeks of incubation, the callus are inspected for
proliferating clumps. Selected proliferating clumps are transferred to a modified
Murashige-Skoog medium supplemented with 0.5 mg/ L thiamine-HCl, 0.75 mg/
L 2,4-E>, 50 g/ L sucrose, 150 mg/ L asparagines, and 2.0 g/ L Gelgro.
[00146] At this point it is prudent to ensure transformation of the selected
plants. The presence of the intein modified cellulase is verified using the methods described in Examples 1 and 2. In this case, either or both of the intein modified cellulase coding sequence, and the hygromycin resistance marker can be used as the subject of the transformation validation, using methods known in the art, as described by Ausubel, et ah, 1998. After two weeks on the modified Murashige-Skoog medium, the plates are exposed to a light cycle incubation regimen composed of 14 hours of light, followed by 10 hours of dark, at 24 °C. Plantlets that form are aseptically transferred to 1 L, wide mouthed Erlenmeyer flasks containing 100 mL of the modified Murashige-Skoog medium. The resulting plants are transferred to vermiculite for one to two weeks prior to plantation in soil and growth to maturity. The mature plants are analyzed substantially as described in Example 1 to ensure stable transformation of the intein modified protein sequence, and preferentially, expression of the intein modified cellulase.
[00147] The resulting mature plants may be cross-pollinated using standard techniques. This can be done either between transformed plants, or between a single transformed plant and an untransformed plant. The progeny resulting from the breeding are screened for containment of the intein modified cellulase, as well as the hygromycin resistance marker. Note, at this point the hygromycin resistance marker used in the selection is no longer an essential element for the use and application of the constructed transgenic corn plants. So long as the intein modified cellulase sequence is contained, retention of the hygromycin resistance marker is not an essential component of the transgenic corn. Seed can
be harvested from the fertile transgenic plants and used for plant expansion. The
resulting transgenic plants can be grown for use in processes similar to those
described in Example 3. The process using a transgenic corn species expressing
multiple intein modified proteins, would have the economic advantages of
utilizing both the starch and cellulosic portions of the corn plant, consolidating
the pretreatment, saccharification, and fermentation steps, and decreased energy
and raw material input costs. Effective use of this process for the production of
ethanol would be enabled by the inclusion of the intein modified proteins in the
transgenic plant.
[00148] The enclosed examples do not in any way limit the scope of this
patent, as they solely provided to help illustrate applications of the invention
disclosed in this patent. Other variations>are possible as an artisan would know,
and are included within the four corners of this invention.
[00149] BIBLIOGRAPHY
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[00198] The invention now being fully described, it will be apparent to one of
ordinary skill in the art that many changes and modifications can be made
thereto without departing from the spirit or scope of the invention as set forth
herein.











We Claim:
t
1. A method of producing an animal feed or animal feed supplement, the method
consisting:
preparing an expression construct that encode(s) one or multiple modified protein(s) such as herein described comprising a target protein, or protein segment(s), which is(are) fused to a CIVPS or intein sequence(s) or segment(s) thereof, wherein the CIVPS or intein sequence(s) or segment(s) thereof is(are) capable of effecting cis splicing of the modified protein when exposed to an internal stimulus from the animal;
transforming a plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent, with the expression construct,
producing a genetically recombinant plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent, from the transformed plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent, that encode(s) a modified protein sequence(s);
harvesting genetically recombinant plant, or plant part, plantlet, tissue, cell, sub-cellular fraction, seed, seedling, protoplast, progeny or descendent;
pulping the harvested resultant using a mechanical pulper;
inducing intein splicing by raising the temperature of the pulp to 40°C and reducing the pH to a value of 5.5 to 7 to express the desired protein, for use as an animal feed or to supplement an animal feed.
2. The method as claimed in claim 1, wherein the target protein(s) or protein segment(s) is(are) internally fused to the controllable intervening protein sequence(s) (CIVPS) or intein sequence(s) or segment(s) thereof.
3. The method as claimed in claim 1 wherein the target protein(s) or protein segment(s) is(are) terminally fused to the controllable intervening protein sequence(s) (CIVPS) or intein sequence(s) or segment(s) thereof.
4. The method as claimed in claim 1, wherein the target protein(s) consist(s) phytase, endocellulase, exocellulase, amylase, glucanase, hemi-cellulase, pectinase, protease, xylanase, lipase enzyme, or a growth hormone.
5. The method as claimed in claim 1, wherein the animal's internal stimulus(i) consist(s) saliva, bile, chymotrypsin, trypsin, bicarbonate, hydrochloric acid, stomach pH or stomach temperature.
6. The method as claimed in claim 1, wherein the spliced protein(s) consist(s) phytase, endocellulase, exocellulase, amylase, glucanase, hemi-cellulase, pectinase, protease, xylanase, lipase enzyme, exocellobiohydrase, immunogenic antigen, recombinant antigen, or a growth hormone.
7. An animal feed or animal feed supplement prepared by the method as claimed
in claim 1.
8. An animal growth promoting composition consisting the feedstock as claimed
in claim 7.

Documents:

1758-DELNP-2005-Abstract.pdf

1758-DELNP-2005-Claims-(17-05-2010).pdf

1758-DELNP-2005-Claims-cancelled.pdf

1758-DELNP-2005-Claims.pdf

1758-delnp-2005-complete specification (granted).pdf

1758-DELNP-2005-Correspondence-Others-(17-05-2010).pdf

1758-delnp-2005-correspondence-others.pdf

1758-delnp-2005-correspondence-po.pdf

1758-DELNP-2005-Description (Complete).pdf

1758-DELNP-2005-Drawings.pdf

1758-DELNP-2005-Form-1.pdf

1758-delnp-2005-form-18.pdf

1758-DELNP-2005-Form-2.pdf

1758-delnp-2005-form-26.pdf

1758-delnp-2005-form-3.pdf

1758-delnp-2005-form-5.pdf

1758-delnp-2005-pct-101.pdf

1758-delnp-2005-pct-210.pdf

1758-delnp-2005-pct-401.pdf

1758-delnp-2005-pct-405.pdf

1758-delnp-2005-pct-408.pdf

1758-delnp-2005-pct-409.pdf


Patent Number 242116
Indian Patent Application Number 1758/DELNP/2005
PG Journal Number 33/2010
Publication Date 13-Aug-2010
Grant Date 12-Aug-2010
Date of Filing 29-Apr-2005
Name of Patentee RAAB, R. MICHAEL
Applicant Address 1 FIFTH STREET, CAMBRIDGE,MA 02141, UNITED STATE OF AMERICA.
Inventors:
# Inventor's Name Inventor's Address
1 RAAB, R. MICHAEL 1 FIFTH STREET, CAMBRIDGE,MA 02141, UNITED STATE OF AMERICA.
PCT International Classification Number C12N 15/82
PCT International Application Number PCT/US03/000432
PCT International Filing date 2003-01-07
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/346,541 2002-01-08 U.S.A.