Title of Invention

A PROTEIN FROM STREPTOCOCCUS GROUPS A AND B

Abstract 1. A protein comprising: (a) an amino acid sequence selected from the group consisting of SEQ IDs 3922 and 8780; (b) an amino acid sequence having 50% or greater sequence identity to SEQ IDs 3922 or 8780; or (c) a fragment of n or more consecutive amino acids from amino acid sequence SEQ ID 3922 or SEQ ID 8780 wherein n is 7.
Full Text All documents cited herein are incorporated by reference in their entirety.
TECHNICAL FIELD
This invention relates to nucleic acid and proteins from the bacteria Streptococcus agalactiae (GBS) and
Streptococcus pyogenes (GAS).
BACKGROUND ART
Once thought to infect only cows, the Gram-positive bacterium Streptococcus agalactiae (or "group B
streptococcus", abbreviated to "GBS") is now known to cause serious disease, bacteremia and
meningitis, in immunocompromised individuals and in neonates. There are two types of neonatal
infection. The first (early onset, usually within 5 days of birth) is manifested by bacteremia and
pneumonia. It is contracted vertically as a baby passes through the bird) canal. GBS colonises the vagina
of about 25% of young women, and approximately 1% of infants born via a vaginal birth to colonised
mothers will become infected Mortality is between 50-70%. The second is a meningitis that occurs 10 to
60 days after birth. If pregnant women are vaccinated with type HI capsule so that the infants are
passively immunised, the incidence of the late onset meningitis is reduced but is not entirety eliminated.
The "B" in "GBS" refers to the Lancefield classification, which is based on the antigenicity of a
carbohydrate which is soluble in dilute acid and called the C carbohydrate. Lancefield identified 13 types
of C carbohydrate, designated A to O, that could be serologically differentiated. The organisms that
most commonly infect humans are found in groups A, B, D, and G. Within group B, strains can be
divided into 8 serotypes (Ia, Ib, Ia/c, II, III, IV, V, and VI) based on the structure of their
polysaccharide capsule.
Group A streptococcus ("GAS", S.pyogenes) is a frequent human pathogen, estimated to be present in
between 5-15% of normal individuals without signs of disease. When host defences are compromised,
or when the organism is able to exert its virulence, or when it is introduced to vulnerable tissues or hosts,
however, an acute infection occurs. Diseases include puerperal fever, scarlet fever, erysipelas,
pharyngitis, impetigo, necrotising fasciitis, myositis and streptococcal toxic shock syndrome.
S.pyogenes is typically treated using antibiotics. Although S.agatactiae is inhibited by antibiotics,
however, it is not killed by penicillin as easily as GAS. Prophylactic vaccination is thus preferable.
Current GBS vaccines are based on polysaccharide antigens, although these suffer from poor
immunogenicity. Anti-idiotypic approaches have also been used (e.g. WO99/54457). There remains a
need, however, for effective adult vaccines against S.agalactiae infection. There also remains a need for
vaccines against S.pyogenes infection.
It is an object of the invention to provide proteins which can be used in the development of such
vaccines. The proteins may also be useful for diagnostic purposes, and as targets for antibiotics.
DISCLOSURE OF THE INVENTION
The invention provides proteins comprising the S.agalactiae amino acid sequences disclosed in the
examples, and proteins comprising the S.pyogenes amino acid sequences disclosed in the examples.
These amino acid sequences are the even SEQ IDs between 1 and 10960.
It also provides proteins comprising amino acid sequences having sequence identity to the S.agalactiae
amino acid sequences disclosed in the examples, and proteins comprising amino acid sequences having
sequence identity to the S.pyogenes amino acid sequences disclosed in the examples. Depending on the
particular sequence, the degree of sequence identity is preferably greater than 50% (e.g. 60%, 70%,
80%, 90%, 95%, 99% or more). These proteins include homologs, ormologs, allehc variants and
functional mutants. Typically, 50% identity or more between two proteins is considered to be an
indication of functional equivalence. Identity between proteins is preferably determined by the
Smith-Waterman homology search algorithm as implemented in the MPSRCH program (Oxford
Molecular), using an affine gap search with parameters gap open penalty 12 and gap extension
penalty=1.
Preferred proteins of the invention are GBS1 to GBS689 (see Table IV).
The invention further provides proteins comprising fragments of the S.agalactiae amino acid sequences
disclosed in the examples, and proteins comprising fragments of the S.pyogenes amino acid sequences
disclosed in the examples. The fragments should comprise at least n consecutive amino acids from the
sequences and, depending on the particular sequence, n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 30,
40, 50, 60, 70, 80, 90, 100 or more). Preferably the iragments comprise one or more epitopes from the
sequence. Other preferred fragments are (a) the N-terminal signal pepudes of the proteins disclosed in
the examples, (b) the proteins disclosed in the examples, but without their N-terminal signal peptides, (c)
fragments common to the related GAS and GBS proteins disclosed in the examples, and (d) the proteins
disclosed in the examples, but without their N-terminal amino acid residue.
The proteins of the invention can, of course, be prepared by various means (e.g. recombinant
expression, purification from GAS or GBS, chemical synthesis etc.) and in various forms (e.g. native,
fusions, glycosylated, non-glycosylated etc). They are preferably prepared in substantially pure form
(i.e. substantially free from other streptococcal or host cell proteins) or substantially isolated form.
Proteins of the invention are preferably streptococcal proteins.
According to a further aspect, the invention provides antibodies which bind to these proteins. These
may be polyclonal or monoclonal and may be produced by any suitable means (e.g. by recombinant
expression). To increase compatibility with the human immune system, the antibodies may be chimeric
or humanised (e.g. Breedveld (2000) Lancet 355(9205):735-740:. Gorman & Clark (1990) Semin.
Immunol. 2:457-466), or fully human antibodies may be used. The antibodies may include a detectable
label (e.g. for diagnostic assays).
According to a further aspect, the invention provides nucleic acid composing the S.agalactiae
nucleotide sequences disclosed in the examples, and nucleic acid comprising the S.pyogenes nucleotide
sequences disclosed in the examples. These nucleic acid sequences are the odd SEQ IDs between 1 and
10966.
In addition, the invention provides nucleic acid comprising nucleotide sequences having sequence
identity to the S.agalactiae nucleotide sequences disclosed in the examples, and nucleic acid comprising
nucleotide sequences having sequence identity to the S.pyogenes nucleotide sequences disclosed in the
examples. Identity between sequences is preferably determined by the Smith-Waterman homology
search algorithm as described above.
Furthermore, the invention provides nucleic acid which can hybridise to the S.agalactiae nucleic acid
disclosed in the examples, and nucleic acid which can hybridise to the S.pyogenes nucleic acid disclosed
in the examples preferably under 'high stringency' conditions {e.g. 65°C in 0.1xSSC, 0.5% SDS
solution).
Nucleic acid comprising fragments of these sequences are also provided. These should comprise at least
n consecutive nucleotides from the S.agalactiae or S.pyogenes sequences and, depending on the
particular sequence, n is 10 or more (e.g. 12, 14, 15, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80,90, 100, 150,
200 or more). The fragments may comprise sequences which are common to the related GAS and GBS
sequences disclosed in the examples.
According to a further aspect, the invention provides nucleic acid encoding the proteins and protein
fragments of the invention.
The invention also provides: nucleic acid comprising nucleotide sequence SEQ ID 10967; nucleic acid
comprising nucleotide sequences having sequence identity to SEQ ID 10967; nucleic acid which can
hybridise to SEQ ID 10967 (preferably under 'high stringency' conditions); nucleic acid comprising a
fragment of at least n consecutive nucleotides from SEQ ID 10967, wherein n is 10 or more e.g. 12, 14,
15, 18, 20,25, 30,35,40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350,400, 450,500,600, 700, 800,
900,1000,1500,2000,3000,4000, 5000,10000,100000,1000000 or more
Nucleic acids of the invention can be used in hybridisation reactions (e.g. Northern or Southern blots, or
in nucleic acid microarrays or 'gene chips') and amplification reactions (e.g. PCR, SDA, SSSR, LCR,
TMA, NASBA etc.) and other nucleic acid techniques.
It should also be appreciated that the invention provides nucleic acid comprising sequences
complementary to those described above (e.g. for antisense or probing, or for use as primers).
Nucleic acid according to the invention can, of course, be prepared in many ways (e.g. by chemical
synthesis, from genomic or cDNA libraries, from the organism itself etc.) and can take various forms
(e.g. single stranded, double stranded, vectors, primers, probes, labelled etc.). The nucleic acid is
preferably in substantially isolated form.
Nucleic acid according to the invention may be labelled e.g. with a radioactive or fluorescent label. This
is particularly useful where the nucleic acid is to be used in nucleic acid detection techniques e.g. where
the nucleic acid is a primer or as a probe for use in techniques such as PCR, LCR, TMA, NASBA etc.
In addition, the term "nucleic acid" includes DNA and RNA, and also their analogues, such as those
containing modified backbones, and also peptide nucleic acids (PNA) etc.
According to a further aspect, the invention provides vectors comprising nucleotide sequences of the
invention (e.g. cloning or expression vectors) and host cells transformed with such vectors.
According to a further aspect, the invention provides compositions comprising protein, antibody, and/or
nucleic acid according to the invention. These compositions may be suitable as immunogenic
compositions, for instance, or as diagnostic reagents, or as vaccines.
The invention also provides nucleic acid, protein, or antibody according to the invention for use as
medicaments (e.g. as immunogenic compositions or as vaccines) or as diagnostic reagents. It also
provides the use of nucleic acid, protein, or antibody according to the invention in the manufacture of: (i)
a medicament for treating or preventing disease and/or infection caused by streptococcus; (ii) a
diagnostic reagent for detecting the presence of streptococcus or of antibothes raised against
streptococcus; and/or (iii) a reagent which can raise antibothes against streptococcus. Said
streptococcus may be any species, group or strain, but is preferably S.agalactiae, especially serotype
III or V, or S.pyogenes. Said disease may be bacteremia, meningitis, puerperal fever, scarlet fever,
erysipelas, pharyngitis, impetigo, necrotising fasciitis, myositis or toxic shock syndrome.
The invention also provides a method of treating a patient, comprising administering to the patient a
therapeutically effective amount of nucleic acid, protein, and/or antibody of the invention. The patient
may either be at risk from the disease themselves or may be a pregnant woman ('maternal immunisation'
e.g. Glezen & Alpers (1999) Clin. Infect. Dis. 28:219-224).
Administration of protein antigens is a preferred method of treatment for inducing immunity.
Administration of antibothes of the invention is another preferred method of treatment This method of
passive immunisation is particularly useful for newborn children or for pregnant women. This method
will typically use monoclonal antibothes, which will be humanised or fully human.
The invention also provides a kit comprising primers (e.g. PCR primers) for amplifying a template
sequence contained within a Streptococcus {e.g. S.pyogenes or S.agalactiae) nucleic acid sequence, the
kit comprising a first primer and a second primer, wherein the first primer is substantially complementary
to said template sequence and the second primer is substantially complementary to a complement of said
template sequence, wherein the parts of said primers which have substantial complementarity define the
termini of the template sequence to be amplified. The first primer and/or the second primer may include
a detectable label (e.g. a fluorescent label).
The invention also provides a kit comprising first and second single-stranded ohgonucleotides which
allow amplification of a Streptococcus template nucleic acid sequence contained in. a single- or double-
stranded nucleic acid (or mixture thereof), wherein: (a) the first oligonucleotide comprises a primer
sequence which is substantially complementary to said template nucleic acid sequence; (b) the second
oligonucleotide comprises a primer sequence which is substantially complementary to the complement
of said template nucleic acid sequence; (c) the first oligonucleotide and/or the second oligonucleotide
comprises) sequence which is not compementary to said template nucleic acid; and (d) said primer
sequences define the termini of the template sequence to be amplified. The non-complementary
sequence(s) of feature (c) are preferably upstream of (i.e. 5' to) the primer sequences. One or both of
these (c) sequences may comprise a restriction site (e.g. EP-B-0509612) or a promoter sequence (e.g.
EP-B-0505012). The first oligonucleotide and/or the second oligonucleotide may include a detectable
label (e.g. a fluorescent label).
The template sequence may be any part of a genome sequence (e.g. SEQ ED 10967). For example, it
could be a rRNA gene (e.g. Turenne et al. (2000) J. Clin. Microbiol. 38:513-520; SEQ IDs 12018-12024
herein) or a protein-coding gene. The template sequence is preferably specific to GBS.
The invention also provides a computer-readable medium (e.g. a floppy disk, a hard: disk, a CD-ROM, a
DVD etc.) and/or a computer database containing one or more of the sequences in the sequence listing.
The medium preferably contains SEQ ID 10967.
The invention also provides a hybrid protein represented by the formula NH2-A-[-X-L-]-B-COOH,
wherein X is a protein of the invention, L is an optional linker ammo acid sequence, A is an optional
N-terminal amino acid sequence, B is an optional C-terminal amino acid sequence, and n is an integer
greater than 1. The value of n is between 2 and x, and the value of x is typically 3, 4, 5, 6, 7, 8, 9 or 10.
Preferably n is 2, 3 or 4; it is more preferabry 2 or 3; most preferably, n - 2. For each n instances, -X-
may be the same or different For each n instances of [-X-L-], linker amino acid sequence -L- may be
present or absent. For instance, when n=2 the hybrid may be NH2-X1-L1-X2-L2-COOH, NH2-X1-X2-
COOH, NH2-X1L1-X2-COOH, NH2-X1-X1-L2-COOH, etc. Linker amino acid sequence(s) -L- will
typically be short (eg. 20 or fewer amino acids i.e. 19, 18, 17, 16, 15,14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4,
3,2,1). Examples include short peptide sequences which facilitate cloning, poly-glycine linkers (i.e. Glyn
where n = 2,3, 4, 5, 6, 7, 8, 9, 10 or more), and histidine tags (i.e. Hisn where n = 3, 4, 5, 6, 7, 8, 9, 10
or more). Other suitable linker amino acid sequences will be apparent to those skilled in the art -A- and -
B- are optional sequences which will typically be short (e.g. 40 or fewer ammo acids i.e. 39, 38, 37, 36,
35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8,
7, 6, 5, 4, 3, 2, 1). Examples include leader sequences to direct protein trafficking, or short peptide
sequences which facilitate cloning or purification (e.g. histidine tags i.e. His, where n = 3, 4, 5, 6, 7, 8, 9,
10 or more). Other suitable N-terminal and Gterminal amino acid sequences will be apparent to those
skilled in the art in some embodiments, each X will be a GBS sequence; in others, mixtures of GAS and
GBS will be used.
According to further aspects, the invention provides various processes.
A process for producing proteins of the invention is provided, comprising the step of culturing a host
cell of to fee invention under conditions which induce protein expression.
A process for producing protein or nucleic acid of the invention is provided, wherein the protein or
nucleic acid is synthesised in part or in whole using chemical means.
A process for detecting polynucleotides of the invention is provided, comprising the steps of: (a)
contacting a nucleic probe according to the invention with a biological sample under hybridising
conditions to form duplexes; and (b) detecting said duplexes.
A process for detecting Streptococcus in a biological sample (e.g. blood) is also provided, comprising
the step of contacting nucleic acid according to the invention with the biological sample under
hybridising conditions. The process may involve nucleic acid amplification ie.g. PCR, SDA, SSSR,
LCR, TMA, NASBA etc.) or hybridisation (e.g. microarrays, blots, hybridisation with a probe in
solution etc.). PCR detection of Streptococcus in clinical samples, in particular S.pyogenes, has been
reported [see e.g. Louie et al. (2000) CMAJ 163:301-309; Louie et al. (1998) J. Clin. Microbiol.
36:1769-1771]. Clinical assays based on nucleic acid are described in general in Tang et al. (1997) Clin.
Chem. 432021-2038.
A process for detecting proteins of the invention is provided, comprising the steps of: (a) contacting an
antibody of the invention with a biological sample under conditions suitable for the formation of an
antibody-antigen complexes; and (b) detecting said complexes.
A process for identifying an amino acid sequence is provided, comprising the step of searching for
putative open reading frames or protein-coding regions within a genome sequence of S.agalactiae. This
will typically involve in silico searching the sequence for an initiation codon and for an in-frame
termination codon in the downstream sequence. The region between these initiation and termination
codons is a putative protein-coding sequence. Typically, all six possible reading frames will be searched.
Suitable software for such analysis includes ORFFINDER (NCBI), GENEMARK [Borodovsky &
McIninch (1993) Computers Chem. 17:122-133), GLIMMER [Salzberg et al. (1998) Nucleic Acids Res.
26:544-548; Salzberg et al. (1999) Genomics 59-24-31; Delcher et al. (1999) Nucleic Acids Res. 27:4636-
4641], or other software which uses Markov models [e.g. Shmarkov et al. (1999) Bioinformatics
15:874-876]. The invention also provides a protein comprising the identified amino acid sequence. These
proteins can then expressed using conventional techniques.
The invention also provides a process for determining whether a test compound binds to a protein bf the
invention. If a test compound binds to a protein of the invention and this binding inhibits the life cycle of
the GBS bacterium, men the test compound can be used as an antibiotic or as a lead compound for the
design of antibiotics. The process will typically comprise the steps of contacting a test compound with a
protein of the invention, and determining whether the test compound binds to said protein. Preferred
proteins of the invention for use in these processes are enzymes(e.g. tRNA synthetases), membrane
transporters and ribosomal proteins. Suitable test compounds include proteins, polypeptides,
carbohydrates, lipids, nucleic acids (e.g. DNA, RNA, and modified forms thereof), as well as small
organic compounds (e.g. MW between 200 and 2000 Da). The test compounds may be provided
indrvidually, but will typically be port of a library (e.g. a combinatorial library). Methods for detecting a
binding interaction include NMR, filter-binding assays, gel-retardation assays, displacement assays,
surface plasmon resonance, reverse two-hybrid etc. A compound which binds to a protein of the
invention can be tested for antibiotic activity by contacting the compound with GBS bacteria and then
monitoring for inhibition of growth. The invention also provides a compound identified using these
methods.
The invention also provides a composition comprising a protein or the invention and one or more of the
following antigens:
- a protein antigen from Helicobacter pylori such as VacA, CagA, NAP, HopX, HopY [e.g.
WO98/04702] and/or urease.
- a protein antigen from N.meningitidis serogroup B, such as those in WO99/24578, WO99/36544,
WO99/57280, WOOO/22430, Tettelin et al. (2000) Science 287:1809-1815, Pizza et al. (2000)
Science 287:1816-1820 and WO96/29412, with protein '287' and derivatives being particularly
preferred.
- an outer-membrane vesicle (OMV) preparation from N.meningitidis serogroup B, such as those
disclosed in WO01/52885; Bjune et al. (1991) Lancet 338(8775):1093-1096; Fukasawa et al. (1999)
Vaccine 17:2951-2958; Rosenqvist et al. (1998) Dev. Biol. Stand. 92:323-333 etc
- a saccharide antigen from N.meningitidis serogroup A, C, W135 and/or Y, such as the
oligosaccharide disclosed in Costantino et al. (1992) Vaccine 10:691-698from serogroup C [see
also Costantino et al. (1999) Vaccine 17:1251-1263].
- a saccharide antigen from Streptococcus pneumoniae [e.g. Watson (2000) Pediatr Infect Dis J
19:331-332; Rubin (2000) Pediatr Clin North Am 47:269-285, v; Jedrzejas (2001) Microbiol Mol
Biol Rev 65:187-207].
- an antigen from hepatitis A virus, such as inactivated virus (e.g. Bell (2000) Pediatr Infect Dis J
19:1187-1188; Iwarson (1995) APM1S 103:321-326].
- an antigen from hepatitis B virus, such as the surface and/or core antigens [e.g. Gerlich et al. (1990)
Vaccine 8 Suppl:S63-68 & 79-80].
- an antigen from hepatitis C virus [e.g. Hsu et al. (1999) Clin Liver Dis 3:901-915].
- an antigen from Bordetella pertussis, such as pertussis holotoxin (PT) and filamentous
haemagglutinin (FHA) from B.pertussis, optionally also in combination with pertactin and/or
agglutinogens 2 and 3 [e.g Gustafsson et al. (1996) N. Engl. J. Med. 334:349-355; Rappuoli et al.
(1991) TIBTECH 9:232-238].
- a diphtheria antigen, such as a diphtheria toxoid [e.g chapter 3 of Vaccines (1988) eds. Plotkin &
Mortimer. ISBN 0-7216-1946-0] e.g. the CRM197 mutant [e.g Del Guidice et al. (1998) Molecular
Aspects of Medicine 19:1-70].
- a tetanus antigen, such as a tetanus toxoid [e.g chapter 4 of Plotkin & Mortimer],
- a saccharide antigen from Haemophilus influenzae B.
- an antigen from N.gonorrhoeae [e.g WO99/24578, WO99/36544, WO99/57280].
- an antigen from Chlamydia pneumoniae [e.g PCT/IB01/01445; Kabnan et al. (1999) Nature
Genetics 21:385-389; Read et al. (2000) Nucleic Acids Res 28:1397-406; Shirai et al. (2000) J.
Infect Dis. 181(Suppl 3):S524-S527; WO99/27105; WO00/27994; WOOO/37494]
- an antigen from Chlamydia trachomatis [e.g WO99/28475].
- an antigen from Porphyromonas gingivalis [e.g Ross et al. (2001) Vaccine 19:4135-4142].
- polio antigen(s) [e.g Sutter et al. (2000) Pediatr Clin North Am 47:287-308; Zimmerman & Spann
(1999) Am Font Physician 59:113-118, 125-126] such as IPV or OPV.
- rabies antigen(s) [e.g Dreesen (1997) Vaccine 15 Suppl:S2-6] such as lyophilised inactivated virus
[e.g MMWR Morb Mortal Wkly Rep 1998 Jan 16;47(1):12,19; RabAvert™].
- measles, mumps and/or rubella antigens [e.g chapters 9,10 & 11 of Plotkin & Mortimer].
- influenza antigens) [e.g chapter 19 of Plotkin & Mortimer], such as the haemagglutinin and/or
neuraminidase surface proteins.
- an antigen from Moraxella catarrhalis [e.g McMichael (2000) Vaccine 19 Suppl l:S101-107].
- an antigen from Staphylococcus aureus [e.g Kuroda et al. (2001) Lancet 357(9264): 1225-1240;
see also pages 1218-1219].
Where a saccharide or carbohydrate antigen is included, it is preferably conjugated to a carrier protein in
order to enhance immunogencity [e.g Ramsay et al. (2001) Lancet 357(9251):195-196; Lindberg (1999)
Vaccine 17 Suppl 2:S28-36; Conjugate Vaccines (eds. Cruse et al.) ISBN 3805549326, particularly vol.
10:48-114 etc.]. Preferred carrier proteins are bacterial toxins or toxoids, such as diphtheria or tetanus
toxoids. The CRM197 diphtheria toxoid is particularly preferred Other suitable carrier proteins include
the N.meningitidis outer membrane protein [e.g EP-0372501], synthetic peptides [e.g EP-0378881, EP-
0427347], heat shock proteins [e.g WO93/17712], pertussis proteins [e.g. WO98/58668; EP-0471177],
protein D from H.influenzae [e.g WO00/56360], toxin A or B from C.difficile [e.g WO00/61761], etc
Any suitable conjugation reaction can be used, with any suitable linker where necessary.
Toxic protein antigens may be detoxified where necessary (e.g. detoxification of pertussis toxin by
chemical and/or genetic means).
Where a diphtheria antigen is included in the composition it is preferred also to include tetanus antigen
and pertussis antigens. Similarly, where a tetanus antigen is included it is preferred also to include
diphtheria and pertussis antigens. Similarly, where a pertussis antigen is included it is preferred also to
include diphtheria and tetanus antigens.
Antigens are preferably adsorbed to an aluminium salt.
Antigens in the composition will typically be present at a concentration of at least 1µg/ml each. In
general, the concentration of any given antigen will be sufficient to elicit an immune response against that
antigen.
The invention also provides compositions comprising two or more proteins of the present invention.
The two or more proteins may comprise GBS sequences or may comprise GAS and GBS sequences.
A summary of standard techniques and procedures which may be employed to perform the invention
(e.g. to utilise the disclosed sequences for vaccination or diagnostic purposes) follows. This summary is
not a limitation on the invention but, rather, gives examples that may be used, but are not required.
General
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of
molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the
art Such techniques are explained fully in the literature eg. Sambrook Molecular Cloning; A Laboratory
Manual, Second Edition (1989); DNA Cloning, Volumes I and II (D.N Glover ed. 1985);
Oligonucleotide Synthesis (M.J. Gait ed, 1984); Nucleic Acid Hybridization (B.D. Hames & S.J.
Higgins eds. 1984); Transcription and Translation (B.D. Hames & S.J. Higgins eds. 1984); Animal
Cell Culture (R.I. Freshney ed 1986); Immobilized Cells and Enzymes (IRL Press, 1986); B. Perbal, A
Practical Guide to Molecular Cloning (1984); the Methods in Enzymology series (Academic Press,
Inc.), especially volumes 154& 155; Gene Transfer Vectors for Mammalian Cells (J.H Miller and M.P.
Calos eds. 1987, Cold Spring Harbor Laboratory); Mayer and Walker, eds. (1987), Immunochemical
Methods in Cell and Molecular Biology (Academic Press, London); Scopes, (1987) Protein
Purification: Principles and Practice, Second Edition (Springer-Verlag, N.Y.), and Handbook of
Experimental Immunology, Volumes I-IV (D.M. Weir and C. C. Blackwell eds 1986).
Standard abbreviations for nucleotides and amino acids are used in this specification.
Definitions
A composition containing X is "substantially free of Y when at least 85% by weight of the total X+Y in the composition is X.
Preferably, X comprises at least about 90% by weight of the total of X+Y in the composition, more preferable at least about 95%
or even 99% by weight
The tarn "comprising" means "including" as well as "consisting" e.g. a composition "comprising" X may consist exclusively of
X or may include something additional e.g. X+Y.
The term "heterologous" refers to two biological components that are not found together in nature. The components may be host
cells, genes, or regulatory regions, such as promoters. Although the beterologous components are not found together in nature,
they can function together, as when a promoter heterologous to a gene is operably linked to the gene. Another example is where a
streptococcus sequence is heterologous to a mouse host cell. A further examples would be two epitopes from the same or
differ proteins which have been assembled in a single protein in an arrangement not found in nature.
An "origin of replication" is a polynucleotide sequence that initiates and regulates replication of polynucleotides, such as an
expression vector. The origin of replication behaves as an autonomous unit of polynucleotide replication within a cell, capable of
replication under its own control. An origin of replication may be needed for a vector to replicate in a particular host cell. With
certain origins of replication, an expression vector can be reproduced at a high copy number in the presence of the qppropriate
protein within the cell. Examples of origins are the autonomously replicating sequences, which are effective in yeast; and the viral
T-antigen, effective in OOS-7 cells.
A "mutant" sequence is defined as DNA, RNA or amino acid sequence differing from but having sequence identify with the
native or disclosed sequence. Depending on the particular sequence, the degree of sequence identity between the native or
disclosed sequence and the mutant sequence is preferably greater than 50% (e.g. 60%, 70%, 80%, 90%, or more,
calculated using the Smith-Watarman algorithm as described above). As used herein, an "allelic variant" of a nucleic acid
molecule, or region, for which nucleic acid sequence is provided herein is a nucleic acid molecule, or region, that occurs essentially
at the same locus in the genome of another or second isolate, and that, due to natural variation caused by, for example, mutation
or recombination, has a similar but not identical nucleic acid sequence. A coding region allelic variant typically ensodes a protein
having similar activity to that of the protein encoded by the gene to which it is being compared. An allelic variant can also
comprise an alteration in the 5' or 3' untranslated region of the gene, such as in regulatory control regions (e.g. see US patent
5,753,235).
Expression system
The streptococcus nucleotide sequences can be expressed in a variety of different expression systems; for example those used
with mammalian cells, beculoviruses, plants, bacteria, and yeast.
Mammalian expression systems are known in the art. A mammalian promoter is any DNA sequence capable of binding
mammalian RNA polymerase and initiating the downstream (3') transcription of a coding sequence (e.g. structural gene) into
mRNA. A promoter will have a transcription initiating region, which is usually placed proximal to the 5' end of the coding
sequence, and a TATA box, usually located 25-30 base pairs (bp) upstream of the transcription initiation site. The TATA box is
thought to direct RNA polymerase II to begin RNA synthesis at the correcsst site. A mammalian promoter will also contain an
upstream promoter element, usually located within 100 to 200 bp upstream of the TATA box. An upstream promoter element
determines the rate at which transcription is initiated and can act in either orientation [Sambrook et al. (1989) "Expression of
Cloned Genes in Mammalian Cells." In Molecular Cloning: A Laboratory Manual, 2nd ed.]
Mammalian viral genes ate often highly expressed and have a broad host range; therefore sequences encoding mammalian viral
genes provide particularly useful promoter sequences. Examples include the SV40 early promoter, mouse mammary tumor virus
LTR promoter, adenovirus major late promoter (Ad MLP), and herpes simplex virus promoter. In addition, sequences derived
from non-viral genes, such as the munite metallotheionein gene, also provide useful promoter sequences. Expression may be either
constitutive or regulated (inducible), depending on the promoter can be induced with glucocorticoid in hormone-responsive cells.
The presence of an enbancer element (enhancer), combined with the promoter elements described above, will usually increase
expression levels. An enhancer is a regulatory DNA sequence that can stimulate transcription up to 1000-fold when linked to
homologous or heterotogous promoters, with synthesis beginning at the normal RNA start site. Enhancers are also active when
they are placed upstream or downstream from the transcription initiation site, in either normal or flipped orientation or at a
distance of more than 1000 nucleotides from the promoter [Maniatis et al. (1987) Science 236:1237; Alberts et al. (1989)
Molecular Biology of the Cell, 2nd ed]. Enhancer elements derived fiom viruses may be particularly useful, because they
usually have a broader host range. Examples include the SV40 early gene enhancer [Dijkema et al (1985) EMBO J. 4:761] and
the enhancer/promoters derived from the long terminal repeat (LTR) of the Rous Sarcoma Vine [Gorman et al. (1982b) Proa
Natl. Acad. Sci. 79:6777] and fiom human cytomegalovirus (Boshart et al. (1985) Cell 41:521]. Additioally, some enhancers
are regulatable and become active only in the presence of an inducer, such as a hormaone or metal ion [Sassone-Corsi an Borelli
(1986) Trends Genet. 2:215; Maniatis etal. (1987) Science 236:1237].
A DNA molecule may be expressed intracelllularly in mammalian cells. A promoter sequence may be ditectly linked with the
DNA molecule, in which case the first amino acid at the N-terminus of the recombinant protein will always be a methionine, which
is encoded by the ATG start codon. If desired, the N-tenninus may be cleaved from the protein by in vitro incubation with
cyanogen bromide.
Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating chimeric DNA molecules that
encode a fusion protein comprised of a leader sequence fiagment that provides for secretion of the foreign protein in mammalian
cells. Preferably, there are processing sites encoded between the leader fragment and the foreign gene that can be cleaved either
in vivo or in vitro. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which
direct the secretion of the protein from the cell. The adenovirus triparite leader is an example of a leader sequence that provides
for secretion of a foreign protein in mammalian cells.
Usually, translation termination and polyadenylation sequences recongnized by mammalian cells are regulatory regions located 3'
to the translation stop codon and thus, together with the promoter elements, flank the coding sequence. The 3' terminus of the
mature mRNA is formed by site specific post transcriptional cleavage and polydenylation [Binstiel et al. (1985) cekk 41:349;
Proudfoot and Whitelaw (1988) "Termination and 3' end processing of eukaryotic RNA. In Transcription and splicing (ed.
B.D. Hames and D.M. Glover); Proudfoot (1989) Trends Biochem. Sci. 14:105]. These sequences direct the transcription of an
mRNA which can be translated into the polypeptide encoded by the DNA. Examples of transcription terminater/polyadenylation
signals include those derived from SV40 [Sambrook et al (1989) "Exprission of cloned genes in cultured mammalian cells." In
Molecular Cloning: A Laboratory Manual].
Usually, the above described components, comprising a promoter, polyadenylation signal, and transcription termination sequence
are put together into expression constructs. Enhancers, introns with funcional splice donor and acceptor sites, and leader
sequences may also be included in an expression construct, if desired. Expression constructs are often maintained in a replicon,
such as an extrachromosomal element (e.g. plasmids) capable of stable maintenance in a host, such as mammalian cells or
bacteria. Mammalian replication systems incllude those derived from animal viruses, which require trans acting factors to replicate.
For example, plasmids containing the replication systems of papovaviruses, such as SV40 [Gluzman (1981) Cell 25:175] or
polyomavirus, replication systems, thus allowing it to be maintained, for example, in mammalian cells for expression and in a
mammalian replicas include those derived from bovine papillomavirus and Epstsin-Barr virus. Additionally, the replicon may
have two replicaton systems, thus allowing it to be mainted, for example, in mammalian cells for expression and in a
prokaryotic host far cloning and amplification. Examples of such mammalian-bacteria shuttle vectors include pMT2 [Kaufman et
al. (1989) Mol. Cell. Biol. 9.946] and pHEBO [Shimizu et al. (1986) Mol. Cell Biol. 6:1074].
The transformation procedure used depends upon the host to be transformed Methods for introduction of heterologous
polynucleotides into mammalian cells are known in the art and include dextran-mediated transfection, calcium phosphate
precipitation, polybrene mediated transtection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in
liposomes, and direct microinjection of the DNA into nuclei.
Mammalian cell lines available as hosts for expression are known in the art include many immortallized cell lines available from
the American Type Culture Collection (ATCC), including but not limited to, Chinese hermater ovary (CHO) cells, Hela cells,
baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cell (e.g. Hep G2), and a
number of other cell lines.
ii Baculovirus Systems
The polynucleotide encoding the protein can also be inserted into a suitable insect expression vector, and is operably linked to the
control elements within that vector. Vector construction employs techniques which are known in fee art. Generally, the
components of the expression system include a transfer vector, usually a bacterial plasmid, which contains both a fragment of the
baculovirus genome, and a convenient restriction site for insertion of the heterologous gene or genes to be expressed; a wild type
baculovirus with a sequence homologous to the baculovirus specific fragment in the transfer vector (this allows for the
homologous recombination of the heterologous gene in to the baculovirus genome); and appropriate insect host cells and growth
media.
After inserting the DNA sequence encoding the protein into the transfer vector, the vector and the wild type viral genome are
transfected into an insect host cell where the vector and viral genome are allowed to recombine. The packaged recombinent virus
is expressed and recombinant plaques are identified and purified. Materials and methods for baculovirus/insect cell expression
systems are commercially available in kit form from, inter alia, Invitrogen, San Diego CA("MaxBac" kit). These techniques are
generally known to those skilled in the art and fully described in Summers and Smith, Texas Agricultural Experiment Station
Bulletin No. 1555 (1987) (hereinafter "Summers and Smith").
Prior to inserting the DMA sequence encoding the protein into the baculovirus genome, the above described components,
comprising a promoter, leader (if desired), coding sequence, and transcription termination sequence, are usually assembled into an
intermediate transplacement construct (transfer vector). This may contain a single gene and operably linked regulatory elements;
multiple genes, each with its owned set of operably linked regulatory elements; or multiple genes, regulated by the same set of
regulatory elements. Intermediate transplacement constructs are often maintained in a replicon, such as an extra-chromosomal
element (e.g. plasmids) capable of stable maintenance in a host, such as a bacterium. The replicon will have a replication system,
thus allowing it to be maintained in a suitable host for cloning and amplification.
Currently, the most commonly used transfer vector for introducing foreign genes into AcNPV is pAc373. Many other vectors,
known to those of skill in the art, have also been designed. These include, for example, pVL985 (which alters the polyhedrin start
codon form ATG to ATT, and which introduces a BamHI cloning site 32 basepairs downstream from the ATT; see Luckow and
summers, Virology (1989) 17:31.
The plasmid usually also contains the polyhedrin polyadenylation signal (Miller et al. (1988) Ann. Rev. Microbiol., 42:177) and a
prokaryotic ampicillin-resistance (amp) gene and origin of replication for selection and propagation in E. coli.
Baculovirus transfer vectors usually contain a baculovirus promoter. A baculovirus promoter is any DNA sequence capable of
binding a baculovirus RNA polymerase and initiating the downstream (5' to 3) transcription of a coding sequence (e.g. structural
gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to fee 5' end of fee
coding sequence. This transcription initiation region usually include an RNA polymerase binding site and a transcription initiation
site. A baculovirus transfer vector may also have a second domain called an enhancer, which, if present, is usually disital to the
structural gene. Expression may be either regulated or constitutive.
Structural genes, abundantly transcribed at late times in a viral infection cycle, provide particularly useful promoter sequences.
Examples include sequences derived from the gene encoding the viral polyhedron protein, Friesen et al. (1986) The Regulation
of Baculovirus Gene Expression," in: The Molecular Biology of Baculoviruses (ed. Walter Doerfler); EPO Publ. Nos. 127 839
and 155 476; and the gene encoding the p10 protein, Vlak et al., (1988),J. Gen. Virol. 69:165.
DNA encoding suitable signal sequences can be derived from genes for secreted insect or baculovinjs proteins, such as the
baculovirus polyhedrin gene (Carbonell et al. (1988) Gene, 75:409). Alternatively, since the signals for mammalian cell
posttranslational modifications (such as signal peptide cleavage, proteolytic cleavage, and phospborylation) appear to be
recognized by insect cells, and the signals required for secretion and nuclear accumulation also appear to be conserved between
the invertebrate cells and vertebate cells, leaders of non-insect origin, such as those derived from genes encoding human a-
interferon, Maeda et al., (1985), Nature 375:592; human gastrin-releasing peptide, Lebacq-Verheyden et al., (1988), Molec.
Cell. Biol. 8:3129; human IL-2, Smith et al., (1985) Proc. Nat'l Acad. Sci. USA, 82:8404; mouse IL-3, (miyajima et al.,
(1987) Gene 58:273; and human glucocerebrosidase, Martin et aL (1988) DNA, 7:99, can also be used to provide for secretion
in insects.
A recombinant polypeptide or polyprotein may be expressed intracellularly or, if it is expressed with the proper regulatory
sequences, it can be secreted. Good intracellular expression of nonfused foreign protein usually requires heterologous genes that
ideally have a short leader sequence containing suitable translation initiation signals preceding an ATG start signal. If desired,
methionine at the N-terminus may be cleaved from the mature protein by in vitro incubation with cyanogen bromide.
Alternatively, recombinant polyproteins or proteins which are not naturally secreted can be secreted from the insect cell by
creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provides for
secretion of the foreign protein in insects. The leader sequence fragment usually encodes a signal peptide comprised of
hydrophobic amino acids which direct the translocation of the protein into the endoplasmic reticulum.
After insertion of the DNA sequence and/or the gene encoding the expression product precursor of the protein, an insect cell host
is co-transformed with the heterologous DNA of the transfer vector and the genomic DNA of wild type baculovirus-usually by
co-transfection. The promoter and transcription termination sequence of the construct will usually comprise a 2-5kb section of the
baculovirus genome. Methods for introducing heterologous DNA into the desired site in the baculovirus virus are known in the art.
(See Summers and Smith supra: Ju et al. (1987); Smith et al., Mol. Cell Biol. (1983) 3:2156; and Luckow and Summers
(1989)). For example, the insertion can be into a gene such as the polyhedrin gene, by homologous double crossover
recombination; insertion can also be into a restriction enzyme site engineered into the desired baculovirus gene. Miller et al.,
(1989), Bioessays 4:91. The DNA sequence, when cloned in place of the polyhedrin gene in the expression vector, is flanked
both 5' and 3' by polyhedrin-specific sequences and is positioned downstream of the polyhedrin promoter.
The newly formed baculovirus expression vector is subsequently packaged into an infectious recombinant baculovirus.
Homologous recombination occurs at low frequency (between about 1% and abort 5%); thus, the majority of the virus produced
after cotransfection is still wild-type virus Therefore, a method is necessary to identify recombinant viruses. An advantage of the
expression system is a visual screen allowing recombinant viruses to be distinguised. The polyhedrin protein, which is produced
by the native virus, is produced at very high levels in the nuclei of infected cells at late times after viral infection, Accumulated
polyhedrin protein forms occlusion bodies that also contain embedded particles. These occlusion bodies, up to 15µm in size, are
highly retractile, giving them a bright shiny appearance that is readily visualized under the light microscope. Cells infected with
recombinant viruses lack occlusion bodies. To distinguish recombinant virus from wild-type virus, the transfection supernatant is
plaqued onto a monolayer of insect cells by techniques known to those skilled in the art. Namely, the plaques are screened under
the light miaoscope for the presence (indicative of wild-type virus) or absence (indicative of recombinant virus) of occlusion
bodies. "Current Protocols in Microbiology" Vol. 2 (Ausubel et al. eds) at 16.8 (Supp. 10, 1990); Summers and Smith, supra;
Miller et al. (1989).
Recombinant baculovirus expression vectors have been developed for infection into several insect cells. For example,
recombinant baculoviruses have been developed for, inter alia: Aedes aegypti, Autographa californica, Bombyx mori,
Drosophila melanogaster, spodoptera frugiperda, and Trichoplusia ni (WO 89/046699; Carbonell et al., (1985) J. Virol
56:153; Wright (1986) Nature 527:718; Smith et al, (1983) Mol. Cell Biol 3:2156; and see generally, Fraser, et al. (1989) In
Vitro Cett.Dev.Biol 25:225).
Cells and cell culture media are commercially available for both direct and fusion expression of heterologous polypeptides in a
baculovirus/expression system; cell culture technology is generally known to those skilled in the art. See, e.g. Summers and Smith
supra.
The modified insect cells may then be grown in an appropriate nutrient medium, which allows for stable maintenance of the
plasmid(s) present in the modified insect host Where the expression product gene is tinder inducible control, the host may be
grown to high density, and expression induced. Alternatively, wine expression is constitutive, the product will be continuously
expressed into the medium and the nutrient medium must be continuously circulated, while removing the product of interest and
augmenting depleted nutrients. The product may be purified by such techniques as chromatography, eg. HPLC, affinity
chromatography, ion exchange chromatography, etc.; electrophoresis; density gradient centrifugation; solvent extraction, etc. As
appropriate, the product may be further purified, as required, so as to remove substantially any insect proteins which are also
present in the medium, so as to provide a product which is at least substantially free of host debris, eg. proteins, lipib and
polysaccharides.
In order to obtain protein expression, recombinant host cells derived from the transformants are incubated under conditions which
allow expression of the recombinant protein encoding sequence. These conditions will vary, dependent upon the host cell
selected However, the conditions are readily ascertainable to those of ordinary skill in the art, based upon what is known in the
art.
iii. Plant Systems
There are many plant cell culture and whole plant genetic expression systems known in the art. Exemplary plant cellular genetic
expression systems include those described in patents, such as: US 5,693,506; US 5,659,122; and US 5,608,143. Additional
examples of genetic expression in plant cell culture has been described by Zenk, Phytochemistry 30:3861-3863 (1991).
Descriptions of plant protein signal peptides may be found in addition to the references described above in Vaulcombe et al., Mol.
Gen. Genet. 2O9:33-40 (1987); Chandler et al., Plant Molecular Biology 3:407-418 (1984); Rogers, J. Biol Chem.
260:3731-3738 (1985); Rothstein et al., Gene 55:353-356 (1987); Whittier et al., Nucleic Acids Research 15:2515-2535
(1987); Wirsel et al., Molecular Microbiology 33-14 (1989); Yu et al. Gene 122:247-253 (1992). A description of the
regulation of plant gene expression by the phytohormone, gibberellic acid and secreted enzymes induced by gibberellic acid can
be found in R.L. Jones and J. MacMillin, Gibberellins: in Advanced Plant Physiology, Malcolm B. Wilkms, ed, 1984 Pitman
Publishing limited, London, pp. 21-51 References that describe other metabolically-regulated genes: Sheen, Plant Cell,
2:1027-1038(1990); Maas et al., EMBO J. 9-3447-3452 (1990); Benkel and Hickey, Proc Natl. Acad. Sci. 84:1337-1339
(1987).
Typically, using techniques known in the art, a desired polynucleotide sequence is inserted into an expression cassette comprising
genetic regulatory elements designed for operation in plants. The expression cassette is inserted into a desired expression vector
with companion sequences upstream and downstream from the expression cassette suitable for expression in a plant host. The
companion sequences will be of plasmid or viral origin and provide necessary characteristics to the vector to permit the vectors to
move DNA from an original cloning host, such as bacteria, to the desired plant chromosomes. Where the heterologous gene is
preferably provide a broad host range prokaryote replication origin; a prokaryote selectable marker; and, for Agrobacterium
transformations, T DNA sequences for Agrobacterium-mediated transfer to plant chromosomes. Where the heterologous gene is
not readily amenable to detection, the construct will preferably also have a selectable marker gene suitable for determining if a
plant cell has been transformed. A general review of suitable makers, for example for the members of the grass family, is found in
Wilmink and Dons, 1993, Plant Mol Biol. Reptr, 11(2):165-185.
Sequences suitable for permitting integration of the heterologous sequence into the plant genome are also recommended. These
might include transposon sequences and the like for homologous recombination as well as Ti sequences which permit random
insertion of a heterologous expression cassette into a plant genome. Suitable prokaryote selectable markers include resistance
toward antibiotics such as ampicillin or tetracycline. Other DNA sequences encoding additional functions may also be present in
the vector, as is known in the art.
The nucleic acid molecules of the subject invention may be included into an expression cassette for expression of the protein(s) of
interest. Usually, line will be only one expression cassette, although two or more are feasible. The reoombinant expression
cassatte will contain in addition to the heterologous protein encoding sequence the following elements, a promoter region, plant 5'
untranslated sequences, initiation codon depending upon whether or not the structural gene comes equipped with one, and a
transcription and translation termination sequence. Unique restriction enzyme sites at the 5' and 3' ends of the cassette allow for
easy insertion into a pre-existing vector.
A heterologous coding sequence may be for any protein relating to the present invention. The sequence encoding the protein of
interest will encode a signal peptide which allows processing and translocation of the protein, as appropriate, and will usually lack
any sequence which might result in the binding of the desired protein of the invention to a membrane. Since, for the most part, the
transcriptional initiation region will be for a gene which is expressed and translocated during germination, by employing the signal
peptide which provides for translocation, one may also provide for translocation of the protein of interest. In this way, the
protein(s) of interest will be translocated from fee cells in which they are expressed and may be efficiency harvested. Typically
secretion in seeds are across the aleurone or scutellar epithelium layer into the endosperm of the seed. While it is not required that
the protein be secreted from the cells in which the protein is produced, this facilitates the isolation and purification of the
recombinant protein.
Since the ultimate expression of the desired gene product will be in a eucaryotic cell it is desirable to determine whether any
portion of the cloned gene contains sequences which wffl be processed out as introns by the hosts splicosome machinery. If so,
site-directed mutagenesis of the "intron" region may be conducted to prevent losing a portion of the genetic message as a false
intran code, Reed and Maniatis,Cell 41:95-105, 1985.
The vector can be microinjected directly into plant cells by use of micropipetes to mechanically transfer the recombinant DNA
Crossway, Mol. Gen. Genet, 202:179-185, 1985. The genetic material may also be transferred into the plant cell by using
polyethylene glycol, Krens, et al., Nature, 296, 72-74, 1982. Another method of introduction of nucleic acid segments is high
velocity balistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the
surface, Klein, et al., Nature, 327, 70-73, 1987 and Knudsen and Muller, 1991, Planta, 185-330-336 teaching paricle
bombaardment of barley endosperm to create transgenic barley. Yet another method of introduction would be fusion of protoplasts
with other entities, either minicells, cells, lysosomes or other fusible lipid-surfaced bodies, Fraley, et al., Proc. Natl. Acad. Sci.
USA, 79,1859-1863, 1982.
The vector may also be introduced into the plant cells by electroporation. (From et al., Proc. Natl. Acad. Sci. USA 82:5824,
1985). In this technique, plant protoplasts re electroporated in the presence of plasmids containing the gene construct. Electrical
impulses of high field strength reversibly permeabilize biomembranes allowing the introduction of the plasmids. Electropoated
plant protoplasts feform the cell wall, divide, and form plant cellus.
All plants from which protoplasts can be isolated and cultured to give whole regenerated plants can be transformed by the present
invention so flat whole plants are recovered which contain the transferred gene. It is known that practically all phots can be
regenerated from cultured cells or tissues, including but not limited to all major species of sugarcane, sugar beet, cotton, fruit and
other trees, legumes and vegetables. Some suitable plants include, for example, species from the genera Frugaria, Lotus,
Medicago, Onobrychis, Trifotium, Trigonella, Vigna, Citrus, Linum, Geranium, Mamhot, Dauaa, Arabidopsis, Brassica,
Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoseyamus, Lycopersion, Nicotiana, Solanum, Petunia, Digitalis,
Majorana, Cichorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Hererocallis, Nemesia, Pelargonium,
Panicum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Glycine, Lolium, Zea, Triticum, Sorghum,
and Datura.
Means for regeneration vary from species to species of plants, but generally a suspension of transformed protoplasts containing
copies of the heterologous gene is first provided Callus tissue is formed and shoots may be induced from callus and subsequently
rooted. Alternatively, embryo formation can be induced from the protoplast suspension. These embryos gemmate as natural
embryos to form plants. The culture media will generally contain various amino acids and hormones, such as sixom and cytokinins
It is also advantageous to add glutamic acid and proline to the medium, especially for such species as corn and alfalfa. Shoots and
roots normally develop simultaneously. Efficient regeneration will depend on the medium, on the genotype, and on the history of
the culture. If these three variables are controlled, then regeneration is fully reproducible and repeatable.
In some plant cell culture systems, the desired protein of the invention may be excreted or alternatively, the protein may be
extracted from the whole plant. Where the desired protein of the invention is secreted into the medium, it may be collected.
Alternatively, the embryos and embryoless-half seeds or other plant tissue may be mechanically distrupted to release any secreted
protein between cells and tissues. The mixture may be suspended in a buffer solution to retrieve soluble proteins. Conventional
protein isolation and purification methods will be then used to purify the recombinant protein. Paarameters of time, temperature pH
oxygen, and volumes will be adjusted through routine methods to optimize expression and recovery of heterologous protein.
iv. Bacterial System
Bacterial expression techniques are known in the art. A bacterial promoter is any DNA sequence capable of binding bacterial
RNA polymerase and initiating the downstream (3') transcription of a coding sequence (e.g. structural gene) into mRNA. A
promoter will have a transcription initiation region which is usually placed proximal to the 5' end of the coding sequence. This
transcription initiation region usually includes an RNA polymerase binding site and a transcription initiation site. A bacterial
promoter may also have a second domain called an operator, that may overlap an adjacent RNA polymerase binding site at
which RNA synthesis begins. The operator permits negative regulated (inclucible) transcription, as a gene represser protein may
bind the operator and thereby inhibit transcription of a specific gene. Constitutive expression may occur in the absence of negative
regulatory elements, such as the operator. In addition, positive regulation may be achieved by a gene activator protein binding
sequence, which, if present is usually proximal (5') to the RNA polymerase binding sequence. An example of a gene activator
protein is the catabolite activator protein (CAP), which helps initiate transcription of the lac operon in Escherichia coli (E.coli)
[Raibaud et al. (1984) Annu. Rev. Genet. 18:173]. Regulated expression may therefore be either positive or negative, thereby
either enhancing or reducing transcription.
Sequences encoding metabolic pathway enzymes provide particularly useful promoter sequences. Examples include promoter
sequences derived from sugar metabolizing enzymes, such as galaciose, lactose (lac) [Chang et al. (1977) Nature 198:1056],
and maltose. Additional examples include promoter sequences derived from biosynthetic enzymes such as tryptophan (trp)
[Goeddel et al. (1980) Nuc Acids Res. 8:4057; Yelvorton et al. (1981) Nucl. Acids Res. 9:731; US patent 4,738,921; EP-A-
0036776 and EP-A-0121775]. The g-lactamase (bla) promoter system [Weissmann (1981) "The ctoning of interferon and other
mistakes." In Interferon 3 (ed. I. Gresser)], bacteriophage lambda PL [Shimatake et al. (1981) Nature 292:128] and T5 [US
patent 4,689,406] promoter systems also provide useful promoter sequences.
In addition, synthetic promoters which do not occur in nature also function as bacterial promoters. For example, transcription
activation sequences of one bacterial or bacteriophage promoter may be joined with the operon sequnces of another bacterial or
bacteriophage promoter, creating a synthetic hybrid promotor [US patent 4,551,433]. Furthermore, a bacterial promoter can include
trp-lac promoter comprised of both trp promoter and lac operon sequence that is regulated by the lac repressor [Amam et al.
(1983) Gene 25:167; de Boer et al. (1983) Proc Natl. Acad. Sci. 8021]. Furthermore, a bacterial promoter can include
naturally occurring promoters of non-bacterial origin that have the ability to bind bacterial RNA polymerase and initiate
transcription. A naturally occurring promoter of non-bacterial origin can also be coupied with a compatible RNA polymenanse to
produce high levels of expression of some genes in prokaryotes. The bacteriophage T7 RNA polymerase/promoter system is an
example of a coupled promoter system [Studier et al. (1986) J. Mol. Biol. 189:113; Tabor et al. (1985) Proc Natl. Acad. Sci.
82:1074]. In addition, a hybrid promoter can also be comprised of a bacteriophage promoter and an E.coli operator region
(EPO-A-0267851).
In addition to a functioning promoter sequence, an efficient ribosame binding site is also useful for the expression of foreign genes
in prokaryotes. In E.coli, the ribosome binding site is called the Shine-Dalgamo (SD) sequence and includes an initiation codon
(ATG) and a sequence 3-9 nucleotides in length located 3-11 nucleotides upstream of the initiation codon [Shine et al. (1975)
Nature 254:34]. The SD sequence is thought to promote binding of mRNA to the ribosome by the pairing of bases between the
SD sequence and the 3' and of E.coli 16S rRNA [Strifz et al. (1979) "Genetic signals and nucleotide sequences in messenger
RNA." In Biological Regulation and Development: Gene Expression (ed. R.F. Goldberger)]. To express eukaryotic genes
and prokaryotic genes with weak ribosome-binding site [Sambrook et al. (1989) "Expression of cloned genes in Escherichia
coli." In Molecular Cloning: A Laboratory Manual].
A DNA molecule may be expressed intracellularly. A promoter sequence may be directly linked with the DNA molecule, in which
case the first ammo acid at the N-teminns will always be a methionine, which is encoded by the ATG start codon. If desired,
methionine at the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide or by either in vivo
on in vitro incubation with a bacterial methionine N-terminal peptidase (EP-A-0 219 237).
Fusion proteins provide an alternative to direct expression. Usually, a DNA sequence encoding the N-terminal potion of an
endogenous bacterial protein, or other stable protein, is fused to the 5' end of heterologous coding sequences. Upon expression,
das construct will provide a fusion of the two ammo acid sequences. For example, the bacteriophage lambda cell gene can be
linked at the 5' terminus of a foreign gene and expressed in bacteria The resulting fusion protein preferably retains a site for a
processing enzyme (factor Xa) to cleave the bacteriophage protein from the foreign gene [Nagai et al. (1984) Nature 309:810].
Fusion proteins can also be made with sequences from the lacZ [lia et al. (1987) Gene 60:197], trpE [Allen et aL (1987) J.
Biotechnol. 5:93; Makoff et al. (1989) J. Gen. Microbiol. 135:11], and Chey [EP-A-0 324 647] genes. The DNA sequence at
the junction of the two amino acid sequences may or may not encode a cleavable site. Another example is a ubiquitin fusion
protein. Such a fusion protein is made with the ubiquitin region that preferably retains a site for a processing enzyme (e.g. ubiquin
specific processing-protease) to cleave the ubiquitin from the foreign protein. Through this method, native foreign protein can be
isolated [Miller et al. (1989) Bio/Technology 7:698].
Alternatively, foreign proteins can also be secreted from the cell by creating chimeric DNA molecules that encode a fusion protein
comprised of a signal peptide sequence fragment that provides for secretion of the foreign protein in bacteria [US patent
4336336]. The signal sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct
the secretion of the protein from the cell. The protein is either secreted into the growth media (gram-positive bacteria) or into the
periplasmic space, located between the inner and outer membrane of the cell (gram-negative bacteria). Preferably there are
processing sites, which can be cleaved either in vivo or in vitro encoded between the signal peptide fragment and the foreign
gene.
DNA encoding suitable signal sequences can be derived from genes for secreted bacterial proteins, such as the E.coli outer
membrane protein gene (ompA) [Masui et al. (1983), in: Experimental Manipulation of Gene Expression; Ghrayeb et al.
(1984) EMBO J. 3:2437] and the E.coli alkatine phosphatase signal sequence (phoA) [Oka ei al. (1985) Proc. Natl. Acad.
Sci. 82:7212]. As an additional example, the signal sequence of the alpha-amylase gene from various Bacillus strains can be used
to secrete heterologous proteins from B. subtilis [Palva et al. (1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 244 042].
Usually, transcription termination sequences recognized by bacteria are regulatory regions located 3' to the translation stop codon,
and thus together with the promoter flank the coding sequence. These sequences direct the transcription of an mRNA which can
be translated into the polypeptide encoded by the DNA. Transcription termination sequences frequently include DNA sequences
of about 50 nucleotides capable of forming stem loop structures that aid in terminating transcription. Examples include
transcription termination sequences derived from genes with strong promoters, such as the trp gene in E.coli as well as other
biosynthetic genes.
Usually, fee above described components, comprising a promoter, signal sequence (if desired), coding sequence of interest, and
transcription termination sequence, are put together into expression constructs. Expression constructs arc often maintained in a
replicon, such as an extrachromosomal element (e.g. plasmids) capable of stable maintenance in a host, such as bacteria. The
replicon will have a replication system, thus allowing it to be maintained in a prokaryotic host either for expression or for cloning
and amplification. In addition, a replicon may be cither a high or low copy number plasmid. A high copy number plasmid will
generally have a copy number ranging from about 5 to about 200, and usually about 10 to about 150. A host contianing a high
copy number plasmid will preferably contain at least about 10, and more preferably at least about 20 plasmids. Either a high or
low copy member vector may be selected, depending upon the effect of the vector and the foreign protein on the host.
Alternatively, the expression constructs can be integrated into the bacterial genome with an integrating vector. Integrating vectors
usually contain at least one sequence homologous to the bacterial chromosome that allows the vector to integrate, Integrations
appear to result from recombinations between homologous DNA m in the vector and the bacterial chromosome. For example, inte-
grating vectors constructed with DNA from various Bacillus strains integrate into the Bacillus chromosome (EP-A- 0 127 328).
Integrating vectors may also be comprised of bacteriophage or transposon sequences.
Usually, extrachromosomal and integrating expression constructs may contain selectable markers to allow for the selection of
bacterial strains that have been transformed Selectable markers can be expressed in the bacterial host and may include genes
which render bacteria resistant to drags such as ampicillin, chloramphenicol, erythromycin, kanarnycin (neomycin), and
tetracycline [Davies et al. (1978) Annu. Rev. Microbiol. 32:469]. Selectable markers may also include biosynthetic genes, such
as those in the bistidine, tryptophan, and leucine biosynthetic pathways.
Alternatively, some of the above described components can be put together in transtomation vectors. Transformation vectors are
usually comprised of a selectable market that is either maintained in a replicon or developed into an integrating vector, as
described above.
Expression and transformation vectors, either extra-chromosomal replicons or integrating vectors, have been developed for
transformation into many bacteria. For example, expression vectors have been developed for, inter alia, the following bacteria:
Bacillus subtilis [Palva et al. (1982) Proc Nad. Acad. Sci. USA 79:5582; EP-A-0 036 259 and EP-A-0 063 953; WO
84/04541], Escherichia coli [Shimatake et al. (1981) Nature 292:128, Amaun et al. (1985) Gene 40:183; Studier et al. (1986)
J. Mol. Biol. 189:113; EP-A-0 036 776.EP-A-0 136 829 and EP-A-0136 907], Streptococcus cremoris (Powell et al. (1988)
Appl. Environ. Microbiol. 54:655]; Streptococcus lividans [Powell et al. (1988) Appl. Environ. Microbiol. 54:655],
Streptomyces lividans [US patent 4,745,056].
Methods of introducing exogenous DNA into bacterial hosts are well-known in the art, and usually include either the
transformation of bacteria treated with CaCl2 or other agents, such as divalent cations and DMSO. DNA can also be introduced
into bacterial cells by electroporation. Transformation procedures usually vary with the bacterial species to be transformed. See
eg. [Masson et al. (1989) FEMS Microbiol. l.ett. (50:273; Palva et al. (1982) Proc Nad. Acad. Sci. USA 79:5582; EP-A-0
036 259 and EP-A-0 063 953; WO 84/04541, Bacillus], [Miller et al. (1988) Proc. Nail. Acad. Sci. 55:856; Wang et al.
(1990)/ Bacterial. 172549, Campylobacter], [Cohen et al. (1973) Proc. Natl. Acad. Sci. 69:2110; Dower et al. (1988)
Nucleic Acids Res. 76:6127; Kushner (1978) "An improved method for transformation of Escherichia coli with ColEl-derived
plasmids. In Genetic Engineering: Proceedings of the International Symposium on Genetic Engineering (eds. H.W. Boyer
and S. Nicosia); Mandel et al. (1970) J. Mol. Biol. 53:159; Taketo (1988) Biochim. Biophys. Acta 949:318; Escherichia],
[Chassy et al. (1987) FEMS Microbiol. l.ett. 44:173 l.actobacillus]; [Fiedler et al. (1988) Anal. Biochem 770:38,
Pseudomonas]; [Auguslin et al. (1990) FEMS Microbiol. l.ett. 56:203, Staphylococcus], [Barany et al. (1980) J. Bacteriol.
744:698; Harlander (1987) Transformation of Streptococcus lactis by electroporation, in: Streptococcal Genetics (ed. J.
Ferretti and R. Curtiss III); Perry et al. (1981) Infect Immun. 52:1295; Powell et al. (1988) Appl. Environ. Microbiol
54:655; Somkuti et al. (1987) Proc 4th Evr. Cong. Biotechnology 7:412, Streptococcus].
v. Yeast Expression
Yeast expression systems are also known to one of ordinary skill in the art A yeast promoter is any DNA sequence capable of
binding yeast RNA polymerase and initiating the downstream (3) transcription of a coding sequence (eg. structural gene) into
mRNA A promoter will have a transcription initiation region which is usually placed proximal to the 5' end of the coding
sequence. This transcription initiation region usually includes an RNA polymerase binding site (the "TATA Box") and a
transcription initiation site. A yeast promoter may also have a second domain called an upstream activator sequence (UAS),
which, if present, is usually distal to the structural gene. The UAS permits regulated (inducible) expression. Constitutive expression
occurs in the absence of a UAS. Regulated expression may be either positive or negative, thereby either enhancing or reducing
transcription.
Yeast is a fermenting organism with an active metabolic pathway, therefore sequences encoding enzymes in the metabolic
pathway provide particularly useful promoter sequences. Examples include alcohol dehydrogenase (ADH) (EP-A-0 284 044),
enolase, glucokinaae, glucose-6-phosphate isomerase, glyceraldehyde-3-phosphate-dehydrogenase (GAP or GAPDH),
hexokinase, phosphofructokinase, 3-phosphoglycerate mutase, and pyruvate kinase (PyK) (EPO-A-0 329 203). The yeast
PHO5 gene, encoding acid phosphatase, also provides useful promoter sequences [Myanobara et al. (1983) Proc. Nad. Acad
Sci USA 80:1].
In addition, synthetic promoters which do not occur in nature also function as yeast promoters. For example, USA sequences of
one yeast promoter may be joined with the transcription activation region of another yeast promoter, creating a synthetic hybrid
promoter. Examples of such hybrid promoters include the ADH regulatory sequence linked to the GAP transcription activation
region (US Patent Nos. 4,876,197 and 4,880,734). Other examples of hybrid promoters include promoters which consist of the
regulatory sequences of either the ADH2, GAL4, GAL10, OR PH05 genes, combined with the transcriptional activation region
of a glycorytic enzyme gene such as GAP or PyK (EP-A-0 164 556). Furthermore, a yeast promoter can include naturally
occurring promotes of non-yeast origin that have the ability to bind yeast RNA polymerase and initiate transcription. Examples of
such, promoters include, inter alia, [Cohen et al. (1980) Proc. Nail. Acad. Sci. USA 77:1078; Henikoff et al. (1981) Nature
283:835;Hollenberg et al. (1981) Curr. Topics Microbiol. Immunol. 96:119; Hollenberg et al. (1979) "The Expression of
Bacterial Antibiotic Resistance Genes in the Yeast Saccharomyces cerevisiae," in: Plasmids of Medical, Environmental and
Commercial Importance (eds. K.N. Timmis and A. Publer); Mercerau-Puigalon et al. (1980) Gene 77:163; Panther et al.
(1980) Curr. Genet 2:109;].
A DNA molecule may be expressed intracellularly in yeast. A promoter sequence may be directly linked with the DNA molecule,
in which case the first amino acid at the N-teminus of the recombinant protein will always be a methionine, which is encoded by
the ATG start codon. If desired, methionine at the N-terminus may be cleaved from the protein by in vitro incubation with
cyanogen bromide.
Fusion proteins provide an alternative far yeast expression systems, as well as in mammalian, baculovirus, and bacterial
expression systems. Usually, a DMA sequence encoding the N-terminal portion of an endogenous; yeast protein, or other stable
protein, is fused to the 5' end of heterologous coding sequences. Upon expression, this construct will provide a fussion of the two
amino acid sequences. For example, the yeast or human superoxide dismutase (SOD) gene, can be linked at the 5' terminus of a
foreign gene and expressed in yeast The DNA sequence at the junction of the two amino acid sequences may or may not encode
a cleavable site. See eg. EP-A-0 196 056. Another example is a ubiquitin fusion protein Such a fusion protein is made with the
ubiquitin region bat preferably retains a site for a processing enzyme (e.g. ubiquitin-specific processing protease) to cleave the
ubiquitin from the foreign protein. Through this method, Therefore, native foreign protein can be isolated (eg. WO88/024066).
Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating chimeric DNA molecules that
encode a fusion protein comprised of a leader sequence fragment that provide for secretion in yeast of the foreign protein.
Preferably, there are processing sites encoded between the leader fragment and the foreign gene that can be cleaved either in vivo
or in vitro. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic atnino acids which direct
the secretion of the protein from the cell.
DNA encoding suitable signal sequences can be derived from genes for secreted yeast proteins, such as the yeast invertase gene
(EP-A-0 012 873; JPO. 62,096,086) and the A-foctor gene (US patent 4,588,684). Alternatively, leaders of non-yeast origin,
such as an interferon leader, exist that also provide for secretion in yeast (EP-A-0 060 057).
A preferred class of secretion leaders are those that employ a fragment of the yeast alpha-factor gene, which contains both a "pie"
signal sequence, and a "pro" region. The types of alpha-factor fragments that can be employed include the full-length pre-pro
alpha factor leader (about 83 ammo acid residues) as well as truncated alpha-factor leaders (usually about 25 to about 50 amino
acid residues) (US Patents 4,546,083 and 4,870,008; EP-A-0 324 274). Additional leaders employing an alpha-factor leader
fragment that provides for secretion include hybrid alpha-factor leadets made with a presequence of a first yeast, but a pro-region
from a second yeast alphafactor. (eg. see WO 89/02463.)
Usually, transcription termination sequences recognized by yeast arc regulatory regions located 3' to the translation stop codon,
and thus together with the promoter flank the coding sequence. These sequences direct the transcription of an mRNA which can
be translated into the polypeptide encoded by the DNA. Examples of transcription terminator sequence and other yeast-
recognized termination sequences, such as those coding for glycolytic enzymes.
Usually, the above described components, comprising a promoter, leader (if desired), coding sequence of interest, and
transcription termination sequence, are put together into expression constructs. Expression constructs are often maintained in a
replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as yeast or bacteria
The replicon may have two replication systems, thus allowing it to be maintained, for example, in yeast for expression and in a
prokaryotic host for cloning and amplification Examples of such yeast-bacteria shuttle vectors include YEp24 [Botstein et al.
(1979) Gene 5:17-24], pCl/1 [Brake et al. (1984) Proc Natl. Acad. Sci USA 81:4642-4646], and YRpl7 [Stinchcomb et al.
(1982) J. Mol. Biol. 158:157]. In addition, a replicon may be either a high or low copy number plasmid. A high copy number
plasmid will generally have a copy number ranging from about 5 to about 200, and usually about 10 to about 150. A host
containing a high copy number plasmid will preferably have at least about 10, and more preferably at least abort 20. Enter a high
or low copy number vector may be selected, depending upon the effect of the vector and the foreign protein on the host. See eg.
Brake et al, supra.
Alternatively, the expression constructs can be integrated into the yeast genome with an integrating vector. Integrating vectors
usually contain at least one sequence homologous to a yeast chromosome that allows the vector to integrate, and preferably
contain two homologous sequences flanking the expression construct Integrations appear to result from recombinations between
homologous DNA in the vector and the yeast chromosome [Orr-Weaver et al.(1983) Methods in Enzymol. 101:228-245]. An
integrating vector may be directed to a specific locus in yeast by selecting the appropriate homologous sequence for inclusion in
the vector. See Orr-Weavcr et al., supra. One or more expression constmct may integrate, possibly affecting levels of
recombinant protein produced [Rine et al. (1983) Proc. Natl. Acad. Sci. USA 80:6750]. The chromosomal sequences included
in the vector can occur either as a single segment in the vector, which results in the integration of the entire vector, or two
segments homologous to adjacent segments in. the chromosome and flanking the expression construct in the vector, which can
result in the stable integration of only the expression construct.
Usually, extrachromosomal and integrating expression constructs may contain selectable markers to allow for the selection of
yeast strains that have been transformed Selectable markers may include biosynthetic genes that can be expressed in the yeast
host, such as ADE2, HIS4, LEU2, TRPl, and ALG7, and the G418 resistance gene, which confer resistance in yeast cells to
tunicamycin and G418, respectively. In addition, a suitable selectable marker may also provide yeast with the ability to grow in the
presence of toxic compounds, such as metal. For example, the presence of CUP1 allows yeast to grow in the presence of copper
ions [Butt et. al. (1987) Microbiol. Rev. 51:351]:
Alternatively, some of the above described components can be put together into transformation vectors. Transformation vectors
are usually comprised of a selectable marker that is either maintained in a replicon or developed into an integrating vector, as
described above.
Expression and transformation vectors, either extrachromosomal replicons or integrating vectors, have been developed for
transformation into many yeasts. For example, expression vectors have been developed for, inter alia, the following
yeasts:Candida albkans [Kurtz, et al. (1986) Mol. Cell. Biol. 6:142], Candida maltosa [Kunze, et al. (1985) J. Basic
Microbiol. 25:141]. Hansenula polymorpha [Geeson, et al. (1986) J. Gen. Microbiol. 7323459; Roggenkamp et al. (1986)
Mol. Gen. Genet 202-302], Kluyveromyces fragilis [Das, et al. (1984) J. Bacteriol. 755:1165], Kluyveromyces lactis [De
Louvencourt et al. (1983) J. Bacteriol. 754:737; Van den Berg et al. (1990) Bio/Technology 8:135], Pichia guillerimondii
[Kunze et al. (1985) J. Basic Microbiol. 25:141], Pichia pastoris [Cregg, et al. (1985) Mol. Cell. Biol. 5:3376; US Patent
Nos. 4,837,148 and 4,929,555], Saccharomyces cerevisiae et al. (1978) Proc Natl. Acad. Sci. USA 75:1929; Bo et
al. (1983) J. Bacteriol. 755:163], Schizosacharomyces pombe [Beach and Nurse (1981) Nature 500:706], and Yarrowia
lipolytica [Davidow, et al. (1985) Curr. Genet 7ft380471 Gaillardin, et al. (1985) Curr. Genet. 10:49].
Methods of introducing exogenous DNA into yeast hosts are well-known in the ait, and usually include either the transformation
of spheroplasts or of intact yeast cells treated with alkali cations. Transformation procedures usually vary with the yeast species to
be transformed See eg. {Kurtz et al. (1986) Mol. Cell. Biol. 6:142; Kunze et al. (1985) J. Basic Microbiol. 25:141; Candida];
[Geeson et al. (1986) J. Gen. Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet. 202302; Hansenula]; [Das
et al. (1984) J. Bacteriol. 158:1165; De l.ouvencourt et al. (1983) J. Bacteriol. 154:1165; Van den Berg et al. (1990)
Bio/Technology 8:135; Kluyveromyces]; [Cregg et al. (1985) Mol. Cell. Biol. 5:3376; Kunze et al. (1985) J. Basic Microbiol.
25:141; US Patent Nos. 4,837,148 and 4,929,555; Pichia]; [Hinnen et al. (1978) Proa Natl. Acad. Sci. USA 75;1929; Ito et
al. (1983) J. Bacteriol. 755:163 Saccharomyces]; [Beach and Nurse (1981) Nature 300:106; Schizosaccharomyces];
[Davidow et al. (1985) Curr. Genet 1059; Gaillardin et al. (1985) Curr. Genet 70:49; Yarrowia|.
Antibothes
As used herein, the term "antibody" refers to a polypeptide or group of polypeptides composed of at least one antibody
combining site. An "antibody combining site" is the three-dimensional binding space with an internal surface shape and charge
distribution complementary to the features of an epitope of an antigen, which allows a binding of the antibody with the antigen.
"Antibody" includes, for example, vertebrate antibothes, hybrid antibothes, chimeric antibothes, humanised antibothes, altered
antibodies, univalent antibothes, Fab proteins, and single domain antibothes.
Antibothes against the proteins of the invention are useful for affinity chrornatography, immunoassays, and distinguishing/identigying
streptococcus proteins.
Antibothes to the proteins of the invention, both polyclonal and monoclonal, may be prepared by conventional methods. In
general, the protein is first used to immunize a suitable animal, preferably a mouse, rat, rabbit or goat Rabbits and goats are
preferred for the preparation of palyclonal sera due to the volume of serum obtainable, and availability of labeled antirabbit
and anti-goat antibothes. Immumzation is generally performed by mixing or emulsifying the protein in saline, preferably in an
adjuvant such as Flood's complete adjuvant, and injecting the mixture or emulsion parenterally (generally subcutaneously or
intramuscularly). A dose of 50-200 µg/injection is typically sufficient Immunization is generally boosted 26 weeks later with one
or more injections of the protein in saline, preferably using Freund's incomplete adjuvant One may alternatively generate
antibothes by in vitro immunization using methods known in the art, which for the purposes of tins invention is considered
equivalent to in vivo immunization. Poryclonal antisera is obtained by bleeding the immunized animal into a glass or plastic
container, incubating the blood at 25°C for one hour, followed by incubating at 4°C for 2-18 hours. The serum is recovered by
centriiugation(eg. 1,000g for 10 minutes). About 20-50 ml per bleed may be obtained from rabbits.
Monoclonal antibothes are prepared using the standard method of Kohler & Milstein [Nature (1975) 256:495-96], or a
modification thereof. Typically, a mouse or rat is immunized as described above. However, rather than bleeding the animal to
extract serum, the spleen (and optionally several large lymph nodes) is removed and dissociated into single cells. If desired, the
spleen cells may be screened (after removal of nonspecifically adherent cells) by applying a cell suspension to a plate or well
coated with the protein antigen. B-cells expressing membrane-bound immunoglobulin specific for the antigen bind to the plate, and
are not rinsed away with the rest of the suspension. Resulting B-cells, or all dissociated spleen cells, are then induced to fuse with
myeloma cells to form hybridomas, and ate cultured in a selective medium (eg. hypoxanthine, aminopterin, thymidine medium,
"HAT"). The resulting hybridomas ate plated by limiting dilution, and are assayed for production of antibothes which bind
specifically to the immunizing antigen (and which do not bind to unrelated antigens). The selected MAb-secreting hybridomas are
then cultured either in vitro (eg. in tissue culture bottles or hollow fibre reactors), or in vivo (as ascites in mice).
If desired, the antibothes (whether polyclonal or monoclonal) may be labeled using conventional techniques. Suitable labels
include fluorophores, chromophores, radioactive atoms (particularly 32P and 125I), electron-dense reagents, enzymes, and ligands
having specific binding partners. Enzymes ate typically detected by their activity. For example, horseradish peroxidase is usually
detected by its ability to convert 3,3',5,5'-tetramethylbenzidine (TMB) to a blue pigment, quantifiable with a spectrophotometer.
"Specific binding partner" refers to a protein capable of binding a ligand molecule with high specificity, as for example in 'the case
of an antigen and a monoclonal antibody specific therefor. Other specific binding partners include biotin and avidin or streptavidin,
IgG and protein A, and the numerous receptor-ligand couples known in the art ft should be understood that the above
description is not meant to categorize the various labels into distinct classes, as the same label may serve in several different
modes. For example, 125I may serve as a radioactive label or as an electron-dense reagent HRP may serve as enzyme or as
antigen for a MAb. Further, one may combine various labels for desired effect For example;, MAbs and avidin also require labels
in the practice of this invention: thus, one might label a MAb with biotin, and detect its presence with avidin labeled with 125I, or
with an anti-biotin MAb labeled with HRP. Other permutations and possibilities will be readily apparent to those of ordinary skill
in the art, and are considered as equivalents within the scope of the instant invention.
Pharmaceutical Compositions
Pharmaceutical compositions can comprise either polypeptides, antibothes, or nucleic acid of the invention. The pharmaceutical
compositions will comprise a therapeutically effective amount of either polypeptides, antibothes, or polynucleotides of the claimed
invention.
The term "therapeutically effective amount" as used herein refers to an amount of a therapeutic agent to treat, ameliorate, or
prevent a desired disease or condition, or to exhibit a detectable therapeutic or preventative effect The effect can be detected by,
for example, chemical markers or antigen levels. Therapeutic effects also include reduction in physical symptoms, such as
decreased body temperature. The precise effective amount for a subject will depend upon the subjects size and health, the nature
and extent of the condition, and the therapeutics or combination of therapeutics selected for administration. Thus, it is not useful to
specify an exact effective amount in advance. However, the effective amount for a given situation am be determined by routine
experimentation and is within the judgement of the clinician.
For purposes of the present invention, an effective dose will be from about 0.01 mg/ kg to 50 mg/kg or 0.05 mg/kg to about 10
mg/kg of the molecule of the invention in the individual to which it is administered.
A pharmaceutical composition can also contain a pharmaceutically acceptable carrier. The term "pharmaceutically acceptable
carrier" refers to a carrier for administration of a therapeutic agent, such as antibothes or a polypeptide, genes, and other
therapeutic agents. The term refers to any pharmaceutical carrier that does not itself induce the production of antibothes harmful to
the individual receiving the composition, and which may be administered without undue toxicity. Suitable carriers may be large,
slowly metabolized macromolecules such as proteins, polysaccharides, polyiactic acids, polyglycolic acids, polymeric ammo acids,
amino acid copolymers, and inactive virus particles. Such carriers are well known to those of ordinary skill in the art
Pharmaceutically acceptable salts can be used therein, for example, mineral acid salts such as hydrochlorides, hydrobromides,
phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like.
A thorough discussion of pharmaceutically acceptable excipients is available in Remington's Pharmaceutical Sciences (Mack Pub.
Ca.NJ.1991).
Pharmaceutically acceptable carriers in therapeutic compositions may contain liquids such as water, saline, glycerol and ethanol.
Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in
such vehicles. Typically, the therapeutic compositions are prepared as injectables, either as liquid solutions or suspensions; solid
forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. l.iposomes are included
within the definition of a pharmaceutically acceptable carrier.
Delivery Methods
Once formulated, the compositions of the invention can be administered directly to the subject The subjects to be treated can be
animals; in particular, human subjects can be treated.
Direct delivery of the compositions will generally be accomplished by injection, either subcutaneously, intraperitoneally,
intravenously or intramuscularly or delivered to the interstitial space of a tissue. The compositions can also be administered into a
lesion. Other modes of administration include oral and pulmonary administration, suppositories, and transdermal or transcutaneous
applications (eg. see WO98/20734), needles, and gene guns or hyposprays. Dosage treatment may be a single dose schedule or
a multiple dose schedule.
Vaccines
Vaccines according to the invention may either be prophylactic (ie. to prevent infection) or therapeutic (ie. to treat disease after
infection).
Such vaccmes comprise immunising antigen(s), immunogen(s), polypeptide(s), protein(s) or nucleic acid, usually in combination
with "pharmaceutically acceptable carriers," which include any carrier that does not itself induce the production of antibothes
harmful to the individual receiving the composition. Suitable carriers are typically large, slowly metabolized macromolecules such
as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, lipid aggregates
(such as oil droplets or liposomes), and inactive virus particles. Such carriers are well known to those of ordinary skill in the art
Additionally, these carriers may function as lmmunostimulatmg agents ("adjuvants") Furthermore, the antigen or immunogen may
be conjugated to a bacterial toxoid, such as a toxoid from diphtheria, tetanus, cholera,.H. pylori, etc. pathogens.
Preferred adjuvants to enhance effectiveness of the composition include, but are not limited to: (1) oil-in-water emulsion
formulations (with or without other specific immunostimulating agents such as muramyl peptides (see below) or bacterial cell wall
components), such as for example (a) MF59™ (WO90/14837; Chapter 10 in Vaccine Design - the subunit and adjuvant
approach (1995) ed. Powell & Newman), containing 5% Squalene, 0.5% Tween 80, and 05% Span 85 (optionally containing
MTP-PE) formulated into submicron particles using a rnicrofluidizer, (b) SAF, containing 10% Squalane, 0.4% Tween 80, 5%
pluronic-blocked polymer l.121, and thr-MDP either microfluidized into a submicron emulsion or vortexed to generate a larger
particle size emulsion, and (c) Ribi™ adjuvant system (RAS), (Ribi Immunocnem, Hamilton, MT) containing 2% Squalene, 02%
Tween 80, and one or more bacterial cell wall components from the group consisting of monopbosphorylipid A (MPL), trehalose
dimycolate (TDM), and cell wall skeleton (CWS), preferably MPl. + CWS (Detox"'); (2) saponin adjuvants, such as QS21 or
Stimulon™ (Cambridge Bioscience, Worcester, MA) may be used or paracles generated therefrom such as ISCOMs
(immunostirrulating complexes), which ISCOMS may be devoid of additional detergent e.g. WO00/07621; (3) Complete
Freund's Adjuvant (CFA) and Incomplete Freund's Adjuvant (IFA); (4) cytokines, such as interleukins (e.g. IL-1,IL-2, IL-4,
IL-5, IL-6, IL-7, IL-12 (WO99/44636), etc.), interferons (e.g. gamma interferon), macrophage colony stimulating iactor (M-
CSF), tumor necrosis factor (TNF), etc.; (5) monophosphoryl lipid A (MPl.) or 3-O-deacylated MPl. (3dMPl.) eg. GB-
2220221, EP-A-0689454; (6) combinations of 3dMPl. with, for example, QS21 and/or oil-in-water emulsions e.g. EP-A-
0835318, EP-A-0735898, EP-A-0761231; (7) oligonucleotides comprising CpG motifs [Krieg Vaccine 2000, 19, 618-622;
Krieg Curr opin Mol Ther 2001 3:15-24; Roman et al, Nat. Med, 1997, 3, 849-854; Weiner et al, PNAS USA, 1997, 94,
10833-10837; Davis et al, J. Immunol, 1998, 160, 870-876; Chu et al., J. Exp. Med., 1997, 186,1623-1631; Lipford et
al., Eur.J. Immunol, 1997,27,2340-2344; Moldoveanu et al., Vaccine, 1988, 16,1216-1224, Krieg et al., Nature, 1995,
374, 546-549; Klinman et al, PNAS USA, 1996, 93, 2879-2883; Ballas et al, J. Immunol, 1996, 157, 1840-1845;
Cowdery et al, J. Immunol, 1996, 156,45704575; Halpern et al, Cell. Immunol, 19%, 167, 72-78; Yamamoto et al,
Jpn. J. Cancer Res., 1988, 79, 866-873; Stacey et al., J. Immunol., 1996, 157, 2116-2122, Messina et al, J. Immunol.,
1991,147,1759-1764; Yi et al., J. Immunol, 1996,157,4918-4925; Yi et al, J. Immunol, 1996,157, 5394-5402; Yi et
al, J. Immunol, 1998, 160,4755-4761; and Yi et al., J. Immunol, 1998. 160, 5898-5906; International patent applications
WO96/02555, WO98/16247, WO98/18810, WO98/40100, WO98/55495, WO98/37919 and WO98/52581] l.e. containing
at least one CG dinucleotide, with 5-methylcytosine optionally being used in place of cytosine; (8) a polyoxyethylene ether or a
polyoxyethylene ester e.g. WO99/52549; (9) a polyoxyethylene sorbitan ester surfactant in commbination with an octoxynol (e.g.
WO01/21207) or a polyoxyethylene alkyl ether or ester surfactant in combination with at least one additional non-ionic surfactant
such as an octoxynol (e.g. WO01/21152); (10) an irnrnunostimulatory oligonudeotide (e.g. a CpG oliganucleotide) and a saponin
e.g. WO00/62800; (11) an immunostimulant and a particle of metal salt e.g. WO00/23105; (12) a saponin and an oil-in-water
emulsion eg. WO99/11241; (13) a saponin (e.g. QS21) + 3dMPl. + IL-12 (optionally - a sterol) e.g. WO98/57659; (14)
aluminium salts, preferably hydroxide or phosphate, but any other suitable salt may also be used (eg. hydroxyphosphate,
oxyhydroxide, orthophosphate, sulphate etc. [e.g see chapters 8 & 9 of Powell & Newman]). Mixtures of different aluminium
salts may also be used. The salt may take any suitable form (e.g. gel, crystalline, amorphous etc.); (15) other substances that act
as immunostimulating agents to enhance the efficacy of the composition. Aluminium salts and/or MF59TM are preferred.
As mentioned above, muramyl peptides include, but are not limited to N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP),
N-acetyl-muramyl-L-threonyl-D-isoglutamine (nor-MDP), N-acetyl-muramyl-L-threonyl-D-isoglutaminyl-L-alanine-2-(1'-2'-
dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (MTP-PE), etc.
The immunogeric compositions (eg. the immunising antigen/immunogen/polypeptide/protein/nucleic acid, pharmaceutically
acceptable carrier, and adjuvant) typically will contain diluents, such as water, saline, glycerol, ethanol, etc. Additionally, auxiliary
substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles..
Typically, the irnmunogenic compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable
for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. The preparation also may be emulsified or
encapsulated in liposomes for enhanced adjuvant effect, as discussed above under pharmaceuotically acceptable carriers.
Immunogenic compositions used as vaccines comprise an immunologically effective amount of the antigenic or immunogenic
polypeptides, as well as any other of the above-mentioned components, as needed By "immumologically effective amount", it is
meant that the administration of that amount to an individual, either in a single dose or as part of a series, is effective for treatment
or prevention. This amount varies depending upon the health and physical condition of the indrvidual to be treated, the taxonomic
group of individual to be treated (eg. nonhuman primate, primate, etc.), the capacity of the individual's immune system to
synthesize antibodies, the degree of protection desired, the formulation of the vaccine, the treating doctor's assessment of the
medical situation, and other relevant factors. It is expected that the amount will fell in a relatively broad range that can be
determined through routine trials.
The immunogenic compositions are conventionally administered parenterally, eg. by injection, either subcutaneously,
intramuscularly, or transdennally/transcutaneously (eg. WO98/20734). Additional formulations; suitable for other modes of
administration include oral and pulmonary formulations, suppositories, and transdermal applications. Dosage treatment may be a
single dose schedule or a multiple dose schedule. The vaccine may be administered in conjunction wife other immunoregulatory
agents.
As an alternative to protein-based vaccines, DMA vaccination may be used (eg. Robinson & Tones (1997) Seminars in
Immunol 9:271-283; Donnelly et al (1997) Annu Rev Immunol 15:617-648; later herein].
Gene Delivery Vehicles
Gene therapy vehicles for delivery of constructs including a coding sequence of a therapeutic of the invention, to be delivered to
the mammal for expression in the mammal, can be administered either locally or systemically. Those constructs can utilize viral or
non-viral vector approaches in in vivo or ex vivo modality. Expression of such coding sequence can be induced using endogenous
mammalian or heterotogous promoters. Expression of the coding sequence in vivo can be either constitutive or regulated.
The invention includes gene delivery vehicles capable of expressing the contemplated nucleic add sequences. The gene delivery
vehicle is preferably a viral vector and, more preferably, a retroviral, adenovinal, adeno-associated viral (AAV), herpes viral, or
alphavirus vector. The viral vector can also be an astrovirus, coranavirus, orthomyxovirus, papovavirus, paramyxovirus,
parvovirus, picomavirus, poxvirus, or togavirus viral vector. See generally, Jolly (1994) Cancer Gene Therapy 1:51-64; Kimuna
(1994) Human Gene Therapy 5:845-852; Connelly (1995) Human Gene Therapy 6:185-193; and Kaplitt (1994) Nature
Genetics 6:148-153.
Retroviral vectors are well known in the art and we contemplate that any retroviral gene therapy vector is employable in the
invention, including B, C and D type retroviruses, xenotropic rettoviruses (for example, NZB-X1, NZB-X2 and NZB9-1 (see
O'Neill (1985) J. Virol 53:160) polytropic retroviruses eg. MCF and MCF-MLV (see Kelly (1983) J. Virol. 45:291),
spumaviruses and lentrviruses. See RNA Tumor Viruses, Second Edition, Cold Spring Harbor Laboratory, 1985.
Portions of the retroviral gene therapy vector may be derived from different letrovinises. For example, retrovector l.TRs may be
derived from a Murine Sarcoma Virus, a tRNA binding site from a Rous Sarcoma Virus, a packaging signal item a Murine
l.eukemia Virus, and an origin of second strand synthesis from an Avian l.eukosis Virus.
These recombinant retroviral vectors may be used to generate transduction competent retioviral vector particles by introducing
them into appropriate packaging cell lines (see US patent 5,591,624). Retrovirus vectors can be constructed for site-specific
integration into host cell DNA by incorporation of a chimeric integrate enzyme into the retroviral particle (see WO96/37626). It is
preferable that the recombinant viral vector is a replication defective recombinant virus.
Packaging cell lines suitable for use with the above-described retrovirus vectors are well known in the art, are readily prepared
(see WO95/30763 and WO92/05266), and can be used to create producer cell lines (also tamed vector cell lines or "VCLs")
for the production of recombinant vector particles. Preferably, the packaging cell lines are made from human parent cells (eg.
HT1080 cells) or mink patent cell lines, which eliminates inactivation in human serum.
Preferred retroviruses for the construction of retroviral gene therapy vectors include Avian Leukosis Virus, Bovine Leukemia,
Virus, Murine Leukemia Virus, Mink-Cell Focus-Inducing Vims, Murine Sarcoma Virus, Reticuloendotheliosis Virus and Rous
Sarcoma Virus. Particularly preferred Munine Leukemia Viruses include 4070A and 1504A (Hartley and Rowe (1976) J Virol
19:19-25), Abelson (ATCC No. VR499), Friend (ATCC No. VR-245), Graffi, Gross (ATCC No. VR-590), Kirsten, Harvey
Sarcoma Virus and Rauscher (ATCC No. VR-998) and Moloney Murine leukemia Virus (ATCC No. VR-190). Such
retroviruses may be obtained from depositories or collections such as the American Type Culture Collection ("ATCC") in
Rockville, Maryland or isolated from known sources using commonly available techniques.
Exemplary known retroviral gene therapy vectors employable in this invention, include those described in patent applications
GB2200651, EP0415731, EP0345242, EP0334301, WO89/02468; WO89W5349, WO89/09271, WO90/02806,
WO90/07936, WO94/03622, WO93/25698, WO93/25234, WO93/11230, WO93/10218, WO91/02805, WO91/02825,
WO95/07994, US 5,219,740, US 4,405,712, US 4,861,719, US 4,980,289, US 4,777,127, US 5,591,624. See also Vile
(1993) Cancer Res 53:3860-3864; Vile (1993) Cancer Res 53:962-967; Ram (1993) Cancer Res 53 (1993) 83-88;
Takamiva (1992)J Neurosci Res 33:493-503; Baba (1993) J Neurosurg 79:729-735; Mann (1983) Cell 33:153; Cane (1984)
Proc Nail Acad Sci 81:6349; and Miller (1990) Human Gene Therapy 1.
Human adenoviral gene therapy vectors are also known in the art and employable in this invention. See, for example, Berkner
(1988) Biotechniques 6:616 and Rosenfeld (1991) Science 252:431, and WO93/07283, WO93/06223, and WO93/07282.
Exemplary known adenoviral gene therapy vectors employable in this invention include those described in the above referenced
documents and in WO94/12649, WO93/03769, WO93/19191, WO94/28938, WO95/11984, WO95/00655, WO95/27071,
WO95/29993, WO95/34671, WO967/055320, WO94/08026, WO94/11506, WO93/06223, WO94/24299, WO95/14102,
WO95/24297, WO95/02697, WO94/28152, WO94/24299, WO95/09241, WO95/25807, WO95/05835, WO94/18922 and
WO95/09654. Alternatively, administration of DNA linked to killed adenovirus as described in Curiel (1992) Hum. Gene Ther.
3:147-154 may be employed. The gene delivery vehicles of the invention also include adenovirus associated virus (AAV) vectors.
l.eading and preferred examples of such vectors for use in this invention are the AAV-2 based vectors disclosed in Srivastava,
WO93/09239. Most preferred AAV vectors comprise the two AAV inverted terminal repeats in which the native Dsequences
are modified by substitution of nuckotides, such that at least 5 native nudeotides and up to 18 native nudeotides, preferably at
least 10 native nudeotides up to 18 native nudeotides, most preferably 10 native nucleotides are retained and the remaining
nucleotides of the D-sequence are deleted or replaced with non-native nucleotides. The native D-sequences of the AAV inverted
terminal repeats are sequences of 20 consecutive nudeotides in each AAV inverted terminal repeat (ie there is one sequence at
each end) which are not involved in HP formation. The non-native replacement nucleotide may be any nucleotide other than the
nucleotide found in the native Dsequence in the same position. Other employable exemplary AAV vectors are pWP-19,
pWN-1, both of which are disclosed in Nahreini (1993) Gene 124:257-262. Another example of such an AAV vector is
psub201 (see Samulski (1987) J. Virol. 61:3096). Another exemplary AAV vector is the Doubk-D ITR vector. Construction of
the Doubk-D TTR vector is disclosed in US Patent 5,478,745. Still other vectors are those disdosed in Carter US Patent
4,797368 and Muzyczka. US Patent 5,139,941, Chartejee US Patent 5,474,935, and Kotin WO94/288157. Yet a further
example of an AAV vector employable in this invention is SSV9AFABTKneo, which contains the AFP enhancer and albumin
promoter and directs expression predominantly in the liver. Its structure and construction are disdosed in Su (1996) Human
Gene Therapy 7:463470. Additional AAV gene therapy vectors are described in US 5,354,678, US 5,173,414, US
5,139,941, and US 5,252,479.
The gene therapy vectors of the invention also include herpes vectors. Leading and preferred examples are herpes simplex virus
vectors containing a sequence encoding a thymidine kinase polypeptide such as those disclosed in US 5,288,641 and
EP0176170 (Roizman). Additional exemplary herpes simplex virus vectors include HFEM/ICP6-LacZ disdosed in
WO95/04139 (Wistar Institute), pHSVlac described in Geller (1988) Science 241:1667-1669 and in WO90/09441 and
WO92/07945, HSV Us3::pgC-lacZ described in Fink (1992) Human Gene Therapy 3:11-19 and HSV 7134,2 RH 105 and
GAM described in EP 0453242 (Breakefield), and those deposited with (he ATCC with accession numbers VR-977 and
VR-260.
Also contemplated are alpha virus gene therapy vectors that can be employed in mis invention. Preferred alpha virus vectors are
Sindbis viruses vectors. Togaviruses, Semliki Forest virus (ATCC VR-67; ATCC VR-1247), Middkberg virus (ATCC
VR-370), Roes River virus (ATCC VR-373; ATCC VR-1246), Venezndan equine encephalitis virus (ATCC VR923; ATCC
VR-1250; ATCC VR-1249; ATCC VR-532), and those described in US patents 5,091,309, 5,217,879, and WO92/10578.
More particularly, those alpha vinis vectors described in US Serial No. 08/405,627, filed March 15, 1995,WO94/21792,
WO92/10578, WO95/07994, US 5,091,309 and US 5,217,879 are employable. Such alpha viruses may be obtained from
depositories or collections such as the ATCC in Rockville, Maryland or isolated from known sources using commonly available
techniques. Preferably, alphavirus vectors with reduced cytotoxicity are used (see USSN 08/679640).
DNA vector systems such as eukaiyotic layered expression systems are also useful for expressing the nucleic acids of the
invention. See WO95/07994 for a detailed description of eukaryotic layered expression systems. Preferably, the eukaiyotic
layered expression systems of the invention are derived from alphavirus vectore and most preferably from Sindbis viral vectors.
Other viral vectors suitable for use in the present invention include those derived from polioviius, for example ATCC VR-58 and
those described in Evans, Nature 339 (1989) 385 and Sabin (1973) J. Biol. Standardization 1:115; rhimovirus, for example
ATCC VR-1110 and those described in Arnold (1990)J CellBiochem L401; pox viruses such as canary pox virus or vaccinia
virus, for example ATCC VR-111 and ATCC VR-2010 and those described m Fisher-Hoch (1989) Proc Nati Acad Sci
86:317; Flexner (1989) Ann NY Acad Sci 569:86, Eexner (1990) Vaccine 8:17; in US 4,603,112 and US 4,769330 and
WO89/01973; SV40 virus, for example ATCC VR-305 and those described in Mulligan (1979) Nature 277:108 and Madzak
(1992) J Gen Virol 73:1533; influenza virus, for example ATCC VR-797 and recombinant influenza viruses made employing
reverse genetics techniques as described in US 5,166,057 and in Enami (1990) Proc Nad Acad Sci 87:3802-3805; Enami &
Palese (1991) J Virol 65:2711-2713 and Luy^es (1989) Cell 59:110, (see also McMichael (1983) NEJ Med 309:13, and Yap
(1978) Nature 273:238 and Nature (1979) 277:108); human immunodeficiency virus as described in EP-0386882 and in
Buchschacher (1992) J. Virol. 662731; measles virus, for example ATCC VR-67 and VR-1247 and those described in EP-
0440219; Aura virus, for example ATCC VR-368; Bebaru virus, for example ATCC VR-600 and ATCC VR-1240; Cabassou
virus, for example ATCC VR-922; Chiknngunya virus, for example ATCC VR-64 and ATCC VR-1241; Fort Morgan Virus,
for example ATCC VR-924; Getah virus, for example ATCC VR-369 and ATCC VR-1243; Kyzyiagacfa virus, for example
ATCC VR-927; Mayaro virus, for example ATCC VR-66; Mucambo virus, for example ATCC vk-580 and ATCC VR-1244;
Ndumu virus, for example ATCC VR-371; Pixuna virus, for example ATCC VR-372 and ATCC VR-1245; Tonate virus, for
example ATCC VR-925; Triniti virus, for example ATCC VR-469; Una virus, for example ATCC VR-374; Whataroa virus, for
example ATCC VR-926; Y-62-33 virus, for example ATCC VR-375; CTNyang virus, Eastern encephalitis virus, far example
ATCC VR-65 and ATCC VR-1242; Western encephalitis virus, for example ATCC VR-70, ATCC VR-1251, ATCC VR-622
and ATCC VR-1252; and coronavirus, for example ATCC VR-740 and those described in Hamre (1966) Proc Soc Exp Biol
Med 121:190.
Delivery of the compositions of this invention into cells is not limited to the abwe mentioned viral vectors. Other delivery methods
and media may be employed such as, for example, nucleic acid expression vectors, polycatknic condensed DNA linked or
unlinked to lolled adenovirus alone, for example see US Serial No. 08/366,787, filed December 30,1994 and Curiel (1992)
Hum Gene Ther 3:147-154 ligand linked DNA, for example see Wu (1989) J Biol Chem 264:16985-16987, eucaryotic cell
delivery vehicles cells, for example see US Serial No.08/240,030, filed May 9,1994, and US Serial No. 08/404,796, (fcpoatkm
of photoporymerized hydrogel materials, hand-held gene transfer partide gun, as described in US Patent 5,149,655, ionizing
radiation as described in US5,206,152 and in WO92/11033, nucleic charge neutralization or fusion with cell membranes.
Additional approaches are described in Philip (1994) Mol Ceil Biol 14:2411-2418 and in Woffendin (1994) Proc Natl Acad
Sci 91:1581-1585.
Particle mediated gene transfer may be employed, for example see US Serial No. 60/023,867. Briefly, me sequence can be
insetted into conventional vectors that contain conventional control sequences lor high level expression, and then incubated with
synthetic gene transfer molecules such as polymeric DNA-binding cations like rjolylysine, protamine, and albumin, linked to cell
targeting ligands such as asialoorosomucoid, as described in Wu & Wu (1987) J. Biol. Chem. 262:4429-4432, insulin as
described in Hucked (1990) Biochem Pharmacol 40:253-263, galactose as described in Plank (1992) Bioconjugate Chem
3:533-539, lactose or transfetrin.
Naked DNA may also be employed. Exemplary naked DNA introduction methods arc described in WO 90/11092 and US
5,580,859. Uptake efficiency may be improved using biodegradable latex beads. DNA crated latex beads are efficiently
transported into cells after endocytosis initiation by the beads. Hie method ma}' be improved further by treatment of the beads to
increase hydrophobicity and thereby facilitate disruption of the endosome and release of the DNA into the cytoplasm.
Liposomes that can act as gene delivery vehicles are described in US 5,422,120, WO95/13796, WO94/23697, WO91/14445
and EP-524,968. As described in USSN. 60/023,867, on non-viral delivery, the nucleic acid sequences encoding a polypepnde
can be inserted into conventional vectors that contain conventional control sequences for high level expression, and then be
incubated with synthetic gene transfer molecules such as polymeric DNA-binding cations like polylysine, protamine, and albumin
linked to cell targeting ligands such as asialoorosomucoid, insulin, galactose, lactose, or transferrin. Other delivery systems include
the use of liposomes to encapsulate DNA composing the gene under the control of a variety of tissue-specific or
ubiquitously-active promotes. Further non-viral deliveiy suitable for use includes mechanical delivery systems such as the
approach described in Woffendin et al (1994) Proc. Nad. Acad. Sci. USA 91(24):11581-11585. Moreover, the coding
sequence and the product of expression of such can be delivered through deposition of photopolymerized hydrogel materials.
Other conventional methods for gene delivery that can be used for delivery of the coding sequence include, for example, use of
hand-held gene transfer particle gun, as described in US 5,149,655; use of ionizing radiation for activating tansferred gene, as
described in US 5,206,152 and WO92/11033
Exemplary liposome and polycationic gene delivery vehicles are those described in US 5,422,120 and 4,762,915; in WO
95/13796; WO94/23697; and WO91/14445; in EP-0524968; and in Stryer, Biochemistry, pages 236-240 (1975) W.H
Freeman, San Francisco; Szoka (1960) Biochem Biophys Acta 600:1; Bayer (1979) Biochem Biophys Acta 550:464; Rivnay
(1987) Meth Enzymol 149:119; Wang (1987) Proc Natl Acad Sci 84:7851:. Plant (1989) Anal Biochem 176:420.
A Dolynudeotide composition can comprises therapeutically effective amount of a gene therapy vehicle, as the term is defined
above. For purposes of the present invention, an effective dose will be from about 0.01 mg/ kg to 50 mg/kg or 0.05 mg/kg to
about 10 mg/kg of the DNA constructs in the individual to which it is administered.
Delivery Methods
Once formulated, the polynucleotide compositions of the invention can be administered (1) directly to the subject; (2) delivered ex
vivo, to cells derived from the subject; or (3) in vitro for expression of recombinant proteins. The subjects to be treated can be
mammals or birds. Also, human subjects can be treated.
Direct delivery of the compositions will generally be accomplished by injection, either subcutaneousty, intraperitoneally,
intravenously or intramuscularly or delivered to the interstitial space of a tissue. The compositions can also be administered into a
lesion. Other modes of adminstation include oral and pulmonary administration, suppositories, and transdermal or transcutaneous
applications (eg. see WO98/2Q734), needles, and gene guns or hyposprays. Dosage treatment may be a single dose schedule or
a multiple dose schedule.
Methods for the ex vivo delivery and reimpiantation of transformed cells into a subject are known in the art and described in eg.
WO93/14778. Examples of cells useful in ex vivo applications include, for example, stem cells, particularly hematopoetic, lymph
cells, macrophages, dendritic cells, or tumor cells.
Generally, delivery of nucleic acids far both ex vivo and in vitro applications can be accomplished by the following procedures,
for example, dextran-mediated transfecticn, calcium phosphate precipitation, polybrene mediated tansfection, protoplast fusion,
electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei, all well
known in the art.
Polynucleotide and polypeptide pharmaceutical compositions
In addition to the pharmaceutically acceptable carriers and salts described above; the following additional agents can be used with
polynuckotide and/or polypeptide compositions.
A Polypeptides
One example are polypeptides which include, without limitation: asioloorosomucoid (ASOR); transferrin; asialoglycoproteins;
antibothes; antibody fragments; fernitin; interkukins; interferons, granulocyte, macrophage cokxry stimulating factor (GM-CSF),
gtanulocyte colony stimulating factor (G-CSF), macrophage colony stimulating factor (M-CSF), stem cell factor and
erythropoietia Viral antigens, such as envelope proteins, can also be used. Also, proteins from other invasive organisms, such as
the 17 amino acid peptide from the encumsporozoite protein of plasmodium falciparum known as R1l.
B.Honnones. Vitangns. etc.
Other groups that can be included are, for example: hormones, steroids, androgeiis, estrogens, thyroid hormone, or vitamins, folk
acid
C-Polyalkylenes, Polysaccharides. etc.
Also, polyalkykne glycol can be included with the desiied polynucdeotides/polypeptides. In a preferred embodiment, tbe
poryalkylene glycol is polyethylene glycol. In addition, mono-, di-, or polysaccharides can be included. In a preferred
embodiment of this aspect, the polysaccharide is dextran or DEAE4eKlran. Also, chitosan and poly(lactide-co-glycolide)
D.Lipids. and Liposomes
The desiied polynucleotide/polypeptide can also be encapsulated in lipids or packaged in liposomes prior to delivery to the
subject or to cells derived therefrom.
Lipid encapsulation is generally accomplished using liposomes which are able to stably bind or entrap and retain nucleic acid. The
ratio of condensed polynudeotide to lipid preparation can vary but will generally be around 1:1 (rng DNAmicromoles lipid), or
more of lipid. For a review of tbe use of liposomes as carriers for delivery of nucleic acids, see, Hug and Sleight (1991 )Biochim.
Biophys.Acta. 1097:1-17; Straubinger (1983) Meth.Enzymol 101:512-527.
Liposomal preparations far use in tbe present invention include cationic (positively charged), anionic (negatively charged) and
neutral preparations. Cationic liposomes have been shown to mediate intracellular delivery of plasmid DNA (Feigner 0987)
Proc. Nad. Acad. Sci. USA 84:7413-7416); mRNA (Malone (1989) Proc Natl. Acad Sci. USA 86:6077-6081); and purified
transcription factors (Debs (1990) J. Biol Chein. 265:10189-10192), in functional form.
Cationic Iiposomes are readily available. For example, N[l-2,3-dioleyloxy)propyl]-N,N,N-triethylamonium (DOTMA)
liposomes are available under the trademark Lipofectin, from GIBCO BRI, Grand Island, NY. (See, also Frlgner supra). Other
commercially available lipesomes indude transfectace (DDAB/DOPE) and DOTAP/DOPE (Boerhinger). Other cationic
liposomes can be prepared from readily available meterials using techiques well known in the art See, eg. Szoka (1978) Proc.
Natl. Acad, Sci. USA 75:4194-4198; WO90/11092 for a description of the synthesis of DOTAP
(l,2-bis(oleoyloxy)-3-(trimethylammonio)propane) liposomes.
Similarly, anionic and neutral Iiposomes are readily available, such as from Avanti Polar Lipids (Birmingham, AL), or can be easily
prepared using readily available materials. Such materials include phospharkryi cholrne, cholesterol, phosphatidyl ethanolamme,
dioleoylphospbatidyl cboline (DOPQ, dioleoylphospharklyl gtycerol (DOPG), dioleoyiphoshatdyi ethanolamine (DOPE), among
others. These materials can also be mixed with the DOTMA and DOTAP starting materials in appropriate ratios. Methods for
making liposomes using these materials are well known in the art.
The liposomes can comprise multilammeiar vesicles (Ml.Vs), small unilamellar vesicles (SUVs), or large unflamrilar vesicles
(LUVs). The various liposoms-nucleic acid complexes are prepared using methods known in the sat See eg. Straubinger (1983)
Meth. Immunol. 101^12-527; Szoka (1978) Proc. Nad. Acad. Sci. USA 75:4194-4198; Papahadjopoulos (1975) Biochim.
Biophys. Acta 394:483; Wilson (1979) Cell 17:77); Deamer & Bangbam (1976) Biochim. Biopkys. Ada 443:629; Ostro
(1977) Biochem. Biopkys. Res. Commun. 76:836; Fraley (1979) Proc. Nad. Acad. Scl. USA 763348); Enoch & Stritrmatter
(1979) Proc. Natl. Acad. Sci. USA 76:145; Fraley (1980) /. Biol Chan. (1980) 255:10431; Szoka & Papahadjopoulos
(1978) Proc. Natl. Acad. Sci. USA 75:145; and Schaefer-Ridder (1982) Science 215:166.
ELipoproteins
In addition, lipoproteins can be included with the polvnucfeodde/polypeptide to be delivered. Examples of Kpoproteins to be
utilized include: chyiomicrons, HDL, IDL, LDL, and VLDL Mutants, fragments, or fusions of these proteins can also be used
Abo, modifications of naturally occurring lipoprotons can be used, such as acetybted LDL. These lipoproteins can target the
delivery of pdynucleotides to cells expressing bpoprotein receptors. Preferably, if lipoproteins are including with the
polyriudeotidetobeMvCTedr»otirctarge^
Naturally occurring lipoproteins comprise a lrpid and a protein portion. The protein portion are known as apoproteins. At the
present, apoproteins A, B, C, D, and E have been isolated and identified. At least two of these contain several proteins,
designated by Roman numerals, AI, AII, AIV; CI, CII, CIII.
A Hpoprotein can comprise more than one apoprotein. For example, naturally occurring drykxrncrons comprises of A, B, C & E,
over time these lipoproteins lose A and acquire C & F.. VLDL comprises A, B, C & E apoproteins, LDL comprises apoprotein
B; and HDL comprises apoproteins A, C, & E
The amino acid of these apoproteins are known and are described in, for example, Breslow (1985) Annu Rev. Biochem 54:699;
Law (1986) Adv. Exp Med. Bid 151:162; Chen (1986) J Biol Chem 261:12918; Kane (1980) Proc Natl Acad Soi USA
77:2465; and Utermann (1984) Hum Genet 65:232
Lipoproteins contain a variety of lipids induing, trigrycerides, cholesterol (free and esters), and phosphohpids. The composition
of the lipids varies in naturally occurring lipoproteins. For example, chylomicrons comprise mainly triglycerides. A more detailed
description of the lipid content of naturally occuring lipoproteins can be found, for example, in Meth. Enzymol. 128 (1986). The
composition of the lipids ate chosen to aid in conformation of the apoprotan for receptor binding activity. The composition of
lipids can also be chosen to facititate hydrophobic interaction and association with the polynucleotide binding molecule.
Naturally occuning lipoproteins can be isolated from serum by ultiacentrifugation, for instance. Such methods are described in
Metk Enzymol (supra); Pitas (1980) J. Biochem. 255:5454-5460 and Mahey (1979) J Clin. Invest 64:743-750.
l.ipoproteins can also be produced by in vitro or lecombinant methods by expression of the apopotem genes in a desired host
cell. See for example, Atkinson (1996) Annu Rev Biophys Chem 15:403 and Radding (195$) Biochim Biophys Acta 30.443.
l.ipoproteins can also be purchased from commercial suppliers, such as Biomedical Techniologies, Inc., Stoughton, MA, USA.
Further description of lipoproteins can be found in WO98/06437..
E.Polycationic Agents
Polycationic agents can be included, with or without Hpopnrtein, in a composition with the desired polynucleotide/polypeptide to
be delivered.
Pdycatkric agents, typically, exhibit a net positive charge at physiological relevant pH and are capable of neutralizing the
electrical charge of nucleic acids to facilitate delivery to a desired location. These agents have both, in vitro, ex vivo, and in vivo
applications. Polycatknic agents can be used to deliver nucleic adds to a living subject either intramuscularly, subcutaneousry,efc.
The Mowing are examples of useful polypeptides as polycationic agents: polyrysine, polyarginine, polyomitrrine, and protamine.
Other examples include bistones, protamines, human serum albumin, DNA binding protons, ncoiKtooe chromosomal proteins,
coat proteins from DNA viruses, such as (X174, transcriptional factors also contam domains that bind DNA and therefore may
be useful as nucleic aid condensing agents. Briefly, transcriptional factors such as C/CEBP, ejun, c-fos, AP-1, AP-2, AP-3,
CPF, Prot-1, Sp-1, Oct-1, Oct-2, CREP, andTFUD roiitain bask domaiiis that bind DNA secfiaices.
Organic polycationic agents include: spermine, spemidine, and purtrescine.
The dimensions and of the physical properties of a polycationic agent can be extrapolated from the list above, to construct other
porypeptide polycationic agents or to produce synthetic polycatknic agents.
Synthetic porycationic agents winch are useful include, for example, DEA&dextran, polybreoe. l.ipofectin™, and
lipofedAMINE™ are inononro that fempotycat^^
Immunodiagnostic Assays
Streptococcus antigens of the invention can be used in immunoassays to detect antibody levels (or conversely anti-streptococcus
antibothes can be used to detect antigen levels). Immunoassays based an well defined, recombmant antigens can be developed to
or serum samples, can be detected Design of the immunoassays is subject to a great deal of variation, and a variety of these are
known in the art Protocols for (he rnimunnassgy may be based, for example, upon competition, type assays. Protocols may also, for example, use solid supports, or may be by unmumprecipitation. Most assays involve the use
Assays which amplify the signals from the probe are also known; examples ofwbicfa are assays wrjkhutifeebictin and avidin, and
enzyme-labeled and mediated immuooassays, such as El.BA assays.
Kits suitable for immunodiagnosis and containing the appropriate labeled reagents are constructed by packaging the appropriate
materials, including the compositions of the invention, in suitable containers, along with the renaming reagents and materials (for
example, suitable buffers, safe solutions, etc.) required for the conduct of the assay, as well as suitable set of assay instructions.
Nucleic Acid Hybridisation
"Hybridization" refers to the association of two nucleic acid sequences to one another by hydrogen bonding. Typically, one
sequence will be fixed to a solid support and the other will be free in solution. Then the two sequeoxs will be placed in contact
with one another under conditions that favor hydrogen bonding. Factors that atfect ths hooding include: the type and volume of
solvent; reaction temperature; time of hybridization; agitation; agents to block the non-specific attachment of the liquid phase
sequence to the solid support (Denhardt's reagent or BLOTTO); concentration of the sequences; use of compounds to increase
the rate of association of sequences (dextan sulfate or polyethylene glycol); and the stringency of tie washing conditions following
hybridization. See Sambrooket al. [supra] Volume 2, chapter 9, pages 9.47 to 9..T.
"Stringency" refers to conditions m a hybridization reaction that favor association of very similar sequences over sequences that
differ. For example, !he combination ofteiupeiuture and salt concentration should be chosen that is approximately 120 to 20CC
below the calculated Tm of the hybrid under study. The temperature and sat conditions can often be determined empirically id
preliminary experiments in which samples of genomic DNA immobilized on fikets are hybridized to the sequence of interest and
then washed under conditions of different stringencies. See Sarnbrook et al., at page 9.50.
Variables to consider when performing, for example, a Southern blot are (1) the complexity of the DNA being blotted and (2) the
homology between the probe and the sequences being detected The total amount of the fragments) to be stuthed can vary a
magnitude of 10, from 0.1 to lug for a plasnrid or phage digest to 10-9 to 10-8 g tor a single copy gene in a highly complex
eukaryotic genome. For lower complexity porynucleotides, substantially shorter blotting, hybridization, and exposure times, a
smaller amount of starting polynucleotides, and lower specific activity of probes can be used. Kor example, a single-copy yeast
gene can be detected with an exposure time of only 1 hour starting with 1 µg of yeast DNA, blotting for two hours, and
hybridizing for 4-8 hours with a probe of 105 cpnVug. For a single-copy mammalian gene a conservative approach would start
with 10 µg of DNA, blot overnight, and hybridize overnight in the presence of 10% dextran sulfaie using a probe of greater than
108 cpm/µg, resulting in an exposure time of ~24 hours.
Several factors can affect the melting temperature (Tin) of a DNA-DNA hybrid between the probe and the fragment of interest,
and consequently, the appropriate conditions for hybridization and washing. In many cases the probe is not 100% homologous to
the fragment Other commonly encountered variables include the, length and total G+C content of the hybridizing sequences and
the ionic strength and formamide content of Ihe hybridization buffer. The effects of all of these factors can be approximated by a
single equation:
Tm= 81 + 16.6(log0Ci) + 0.4[%(G + C)]-0.6(%formamide) - 600/n-1.5(%mismatch).
where Q is the salt concentration (monovalent ions) and n is the length of the hybrid in base pairs (slightly modified from
Meinkoth&Wabl (1984) And. Biochem. 138: 267-284).
In designing a hybridization experiment, some factors affecting nucleic acid hybridization can be conveniently altered. The
temperature of the hybridization and washes and the salt concentration during the washes are the simplest to adjust As the
temperature of the hybridization increases (ie. stringency), it becomes less likely for hybridization to occur between strands that
are nonbomologous, and as a result, background decreases. If the radiolabeled probe is not completely homologous with the
immobilized fragment (as is frequently the case in gene family and interspecies hybridization experiments), the hybridization
temperature must be reduced, and background will increase. The temperature of the washes affects the intensity of the hybridizing
band and the degree of background in a similar manner. The stringency of the washes is also increased with decreasing salt
concentrations.
In general, convenient hybridization temperatures in the presence of 50% formamide are 42°C tor a probe with is 95% to 100%
homologous to the target fragment, 37°C for 90% to 95% homology, and 32°C for 85% to 90% homology. For lower
homologies, fonnamide content should be lowered and temperature adjusted accordingly, usdng the equation above. If the
homology between the probe and the target fragment are not known, the simplest approach is to start with both hybridization and
wash conditions which are nonstringent. If non-specific bands or high background are observed after autoradiography, the filter
can be washed at high stringency and reexposed. If the time required for exposure makes this approach impractical, several
hybridization and/or washing stringencies should be tested in parallel.
Nucleic Acid Probe Assays
Methods such as PCR, branched DNA probe assays, or blotting techniques utilizing nucleic acid probes according to the
invention can determine the presence of cDNA or mRNA. A probe is said to "hybridize' with a sequence of the invention if it can
form a duplex or double stranded complex, which is siable enough to be detected.
The nucleic acid probes will hybridize to the streptococcus nucleotide sequences of the invention (including both sense and
ann'sense strands). Though many different nucleotide sequences will encode the amino acid sequence, the native streptococcus
sequence is preferred because it is the actual sequence present in cells. mRNA represents a coding sequence and so a probe
should be complementary to the coding sequence; single-stranded cDNA is compleraentary tn mRNA, and so a cDNA probe
should be complementary to the non-coding sequence.
The probe sequence need not be identical to the streptococcus sequence (or ils axnpiement) — some variation in the sequence
and length can lead to increased assay sensitivity if the nucleic acid probe can form a duplex with target nucleotides, which can be
detected. Also, the nucleic acid probe can include additional nucleotides to stabilize the formed duplex Additional streptococcus
sequence may also be helpful as a label to detect the formed duplex. For example, a nortcomplernentary nucleotide sequence
may be attached to the 5' end of the probe, with the remainder uf the probe sequence being complementary to a streptococcus
sequence. Alternatively, non-complementary bases or longer sequences can be interspersed into the probe, provided that the
probe sequence has sufficient complementarity with the a streptococcus sequence in order to hybridfe therewith and (hereby
form a duplex which can be detected.
The exact length and sequence of the probe wfll depend on the hybridizaticn conditions (eg. temperature, salt condition etc.). For
example, for diagnostic applications, depending on the complexity of the analyte sequence, the nucleic acid probe typically
contains at least 10-20 nudeotides, preferably 15-25, and more preferably at least 30 nucleotides, although it may be shelter than
this. Short primers generally require cooler temperatures to fismisuflBdenth/stabk hybrid axnplexeswifti the teinplate.
103:3185], or according to Urdea et al [Proc Natl. Acad. Sci. USA (1983) 80: 7461], or using commercially available
automated otigonudeotide synthesizers.
The chemical nature of the probe can be selected according to preference. For certain applications, DNA or RNA are
appropriate. For other applications, modifications may be incorporated eg. backbone modifications, such as phosphorcfthioates
or methylphosphonates, can be used to increase in vivo half-life, alter RNA affinity, increase nuclease resistance etc. [eg. see
Agrawal & Iyer (1995) Curr Opin Biotechnol 6:12-19; Agrawal (1996) JWTECH 14:376-387]; analogues such sis peptide
nucleic acids may also be used [eg. see Corey (1997) TWTECH 15:224-229; Buchardtef ai (1993) TWTECHl 1:384-386].
Alternatively, the poiymerase chain reaction (PCR) is another well-known means for detecting small amounts of target nucleic
acid. The assay is described in NMlis et al [Metk Enzymol. (1987) 155335-350] & US patents 4,683,195 & 4,683,202. Two
"primer" nucleorides hybridize with the target nucleic acids and are used to prime the reaction. The primers can comprise
sequence that does not hybridize to the sequence of the amplification target (or its complement) to Eiid with duplex stability or, for
example, to incorporate a convenient restriction site. Typically, such sequence will flank the desired streptococcus sequence.
A thermostable polymerase creates copies of target nucleic acids from the primers using the original target nucleic acids as a
template. After a threshold amount of target nucleic acids are generated by the porymerase, they can be delected by more
traditional methods, such as Southern blots. When using the Southern Wot method, the labelled probe will hybridize to the
streptococcus sequence (or its complement).
Also, mRNA or cDNA can be detected by traditional blotting techniques described in Sambrook et al [supra]. mRNA, or
cDNA generated from mRNA using a poiymerase enzyme, can be purified and separated using gd dectrcphcresis. The nucleic
acids on the gel are then blotted onto a solid support, such as nitrocellulose. The solid support is exposed to a labelled probe and
then washed to remove any unhybridized probe. Next, the duplexes containing the labeled probe are delected Typically, the
probe is labelled with a radioactive moiety.
BRIEF DESCRIPTION OF DRAWINGS
Figures 1 to 85, 119 to 188, 238 and 239 show SDS-PAGE analysis of total cell extracts from
cultures of recombinant E.coli expressing GBS proteins of the invention. Lane 1 in each gel (except for
Figure 185) contains molecular weight markers. These are 94, 67, 43, 30, 20.1 & 14.4 kDa (except for
Figures 7, 8, 10, 11,13,14,15 and 119-170, which use 250, 150, 100, 75, 50, 37, 25, 15 & 10 kDa).
Figure 86A shows the pDESTIS vector and Figure 86B shows the pDEST17~1 vector.
Figures 88 to 118 and 247 to 319 show protein characterisation data for various proteins of the
invention.
Figures 189 to 237 and 240 to 246 show SDS-PAGE analysis of purified GBS proteins of the
invention. The left-hand lane contains molecular weight markers. These are 94,, 67, 43, 30. 20.1 & 14.4
kDa.
MODES FOR CARRYING OUT THE INVENTION
The following examples describe nucleic acid sequences which have been identified in Streptococcus,
along with their inferred translation products. The examples are generally in the following format.
• a nucleotide sequence which has been identified in Streptococcus
• the inferred translation product of this sequence
• a computer analysis (e.g. PSORT output) of the translation product, indicating antigenicity
Most examples describe nucleotide sequences from S.agalactiae. The specific strain which was
sequenced was from serotype V, and is a clinical strain isolated in Italy which expresses the R antigen
(ISS/Rome/Italy collection, strain2603 V/R). For several of these examples, the corresponding
sequences from S.pyogenes are also given. Where GBS and GAS show homology in this way, there is
conservation between species which suggests an essential function and also gives good cross-species
reactivity.
In contrast, several examples describe nucleotide sequences from GAS for which no homolog in GBS
has been identified.. This lack of homology gives molecules which are useful for distinguishing GAS
from GBS and for making GAS-specific products. The same is true for GBS sequences which lack
GAS homologs e.g. these are useful for making GBS-specific products.
The examples typically include details of homology to sequences in the public databases. Proteins that
are similar in sequence are generally similar in both structure and function, and the homology often
indicates a common evolutionary origin. Comparison with sequences of proteins of known function is
widely used as a guide for the assignment of putative protein function to a new sequence and has proved
particularly useful in whole-genome analyses.
Various tests can be used to assess the in vivo immunogenicity of the proteins identified in the examples.
For example, the proteins can be expressed recombinantly and used to screen patient sera by
immunoblot. A positive reaction between the protein and patient serum indicates that the patient has
previously mounted an immune response to the protein in question i.e. the protein is an immunogen. This
method can also be used to identify immunodominant proteins. The mouse model used in the examples
can also be used.
The recombinant protein can also be conveniently used to prepare antibodies e.g. in a mouse. These can
be used for direct confirmation mat a protein is located on the cell-surface. l.abelled antibody (e.g.
fluorescent labelling for FACS) can be incubated with intact bacteria and the presence of label on the
bacterial surface confirms the location of the protein.
For many GBS proteins, the following data are given:
- SDS-PAGE analysis of total recombinant E.coli cell extracts for GBS protein expression
- SDS-PAGE analysis after the protein purification
- Western-blot analysis of GBS total cell extract using antiseta raised against recombinant proteins
- FACS and ELISA analysis against GBS vising antisera raise against recombinant proteins
- Results of the in vivo passive protection assay
Details of experimental techniques used are presented below:
Sequence analysis
Open reading frames (ORFs) within nucleotide sequences were predicted using the GLIMMER program
[Salzberg et al. (1998) Nucleic Acids Res 26:544-8]. Where necessary, start codons were modified and
corrected manually on the basis of the presence of ribosome-binding sites and promoter regions on the
upstream DNA sequence.
ORFs were then screened against the non-redundant protein databases using the programs BLASTp
[Altschul et al. (1990) J. Mol. Biol. 215:403-410] and PRAZE, a modification of the Smith-Waterman
algorithm [Smith & Waterman (1981) J Mol Biol 147:195-7; see Fleischmann et al (1995) Science
269:496-512].
Leader peptides within the ORFs were located using three different approaches: (i) PSORT [Nakai
(1991) Bull. Inst. Chem. Res., Kyoto Univ. 69:269-291; Horton & Nakai (1996) Intellig. Syst. Mol. Biol.
4:109-115; Horton & Nakai (1997) Intellig. Syst. Mol. Biol. 5:147-152]; (ii) SignalP [Nielsen & Krogh
(1998) in Proceedings of the Sixth International Conference on Intelligent Systems for Molecular
Biology (ISMB 6), AAAI Press, Menlo Park, California, pp. 122-130; Nielsen et al. (1999) Protein
Engineering 12:3-9; Nielsen et al. (1997). Int. J. Neural Sys. 8:581-599]; and (iii) visual inspection of the
ORF sequences. Where a signal sequences is given a "possible site" value, the value represents the
C-terminus residue of the signal peptide e.g. a "possible site" of 26 means that the signal sequence
consists of ammo acids 1-26.
l.ipoprotein-specific signal peptides were located using three different approaches: (i) PSORT [see
above]; (ii) the "prokaryotic membrane lipoprotein lipid attachment site" PROSITE motif [Hefmann et
al. (1999) Nucleic Acids Res. 27:215-219; Bucher & Bairoch (1994) in Proceedings 2nd International
Conference on Intelligent Systems for Molecular Biology (ISMB-94), AAAI Press, pages 53-61]; and
(iii) the FINDPATTERNS program available in the GCG Wisconsin Package, using the pattern
(M,L,V)x(9,35}LxxCx.
Transmembrane domains were located using two approaches: (i) PSORT [see above]; (ii) TopPred [von
Heijne (1992) J. Mol. Biol. 225:487-494]
l.PXTG motifs, characteristic of cell-wall attached proteins in Gram -positive bacteria [Fischetti et al.
(1990) Mol Microbiol 4:1603-5] were located with FIKDPATTERNS using the pattern
(l,i,v,m,y,f)px(t,a,s,g) (g,n,s,t,a,l) .
RGD motife, characteristic of cell-adhesion molecules [D'Souza et al. (1991) Trends Biochem Sci
16:246-50] were located using FINDPATTERNS.
Enzymes belonging to the glycolytic pathway were also selected as antigens, because these have been
found experimentally expressed on the surface of Streptococci [e.g Pancholi & Fischetti (1992) ./ Exp
Med 176:415-26; Pancholi & Fischetti (1998) J Biol Chem 273:14503-15].
Cloning, expression and purification of proteins
GBS genes were cloned to facilitate expression in E.coli as two different types of fusion proteins:
a) proteins having a hexa-histidine tag at the amino-terminus (His-gbs)
b) proteins having a GST fusion partner at the amino-terrmnus (Gst-gbs)
Cloning was performed using the Gateway™ technology (Life Technologies), which is based on the site-
specific recombination reactions that mediate integration and excision of phage lambda into and from the
E.coli genome. A single cloning experiment included the following steps:
1- Amplification of GBS chromosomal DNA to obtain a PCR product coding for a single ORF
flanked by attB recombination sites.
2- Insertion of the PCR product into a pDONR vector (containing attP sites) through a BP reaction
(attB x attP sites). This reaction gives a so called 'pEntry' vector, which now contains atth sites
flanking the insert.
3- Insertion of the GBS gene into E.coli expression vectors (pDestination vectors, containing attR
sites) through a l.R reaction between pEntry and pDestination plasmids (attl. x attR sites).
A) Chromosomal DNA preparation
For chromosomal DNA preparation, GBS strain 2603 V/R (Istituto Superiore Sanita, Rome) was grown
to exponential phase in 2 litres TH Broth (Difco) at 37°C, harvested by centrifugation, and dissolved in
40 ml TES (50 mM Tris pH 8, 5 mM EDTA pH 8, 20% sucrose). After addition of 2.5 ml lysozyme
solution (25 mg/ml in TES) and 0.5 ml mutanolysm (Sigma M-9901, 25000U/ml in I^O), the suspension
was incubated at 37°C for 1 hour. 1 ml RNase (20 mg/ml) and 0.1 ml proteinase K (20 mg/ml) were
added and incubation was continued for 30 min. at 37°C
Cell lysis was obtained by adding 5 ml sarkosyl solution (10% N-laurylsarcosine in 250 mM EDTA pH
8.0), and incubating 1 hour at 37°C with frequent inversion. After sequential extraction with phenol,
phenol-chloroform and chloroform, DNA was precipitated with 0.3M sodium apetate pH 5 1 and 2
volumes of absolute ethanol. The DNA pellet was nnsed with 70% ethanol and dissolved m Tl butler
(10 mM Tris-HCl, 1 mM EDTA, pH 8). DNA concentration was evaluated by OD260.
B) Oligonucleotide design
Synthetic oligonucleotide primers were designed on the basis of the coding sequence of each ORF. The
aim was to express the protein's extracellular region. Accordingly, predicted signal peptides were
omitted (by deducing the 5' end amplification primer sequence immediately downstream from the
predicted leader sequence) and C-terminal cell-wall ancoring regions were removed (e.g. l.PXTG motifs
and downstream amino acids). Where additional nucleotides have been deleted, this is indicated by the
suffix 'd' (e.g. GBS352d' - see Table V). Conversely, a suffix 'l.' refers to expression without these
deletions. Deletions of C- orN-terminal residues were also sometimes made, as indicated by a 'C or 'N'
suffix.
The amino acid sequences of the expressed GBS proteins (including 'd' and 'l.' forms etc.) are
definitively defined by the sequences of the oligonuclotide primers given in Table JH.
5' tails of forward primers and 3' tails of reverse primers included attB 1 and attB2 sites respectively:
Forward primers: 5'-GGGGACAAGTTTGTACAAAAAAGCAGGCT(?r-ORF in frame-31 (the TCT
sequence preceding the ORF was omitted when the ORF's first coding triplet began with T).
Reverse primers: 5'-GGGGACCACTTTGTACAAGAAAGCTGGGTT-ORF reverse complement-3'.
The number of nucleotides which hybridized to the sequence to be amplified depended on the melting
temperature of the primers, which was determined as described by Breslauer et al. [PNAS USA (1986)
83:3746-50]. The average melting temperature of the selected oligos was 50-55 °C for the hybridizing
region and 80-85°C for the whole oligos.
C) Amplification
The standard PCR protocol was as follows: 50 ng genomic DNA were used as template m the presence
of 0.5 µM each primer, 200 µM each dNTP, 1.5 mM MgCfc, Jx bu0er minus Mg (Gibco-BRl.) and 2
units of Taq DNA polymerase (Platinum Taq, Gibco-BRl.) in a final volume of 100 ul. Each sample
underwent a double-step of amplification: 5 cycles performed using as the hybridizing temperature 50°C,
followed by 25 cycles at 68°C.
The standard cycles were as follows:
Denaturation: 94°C, 2 min
5 cycles: Denaturation: 94°C, 30 seconds
Hybridization: 50°C, 50 seconds
Elongation: 72°C, 1 min. or 2 min. and 40 sec.
25 cycles : Denaturation: 94°C, 30 seconds
Hybridization: 68°C, 50 seconds
Elongation: 72°C, 1 min. or 2 min. and 40 sec.
Elongation time was 1 minute for ORFs shorter than 2000bp and 2:40 minutes for ORFs longer than
2000bp. Amplifications were performed using a Gene Amp PCR system 9600 (Perkin Elmer).
To check amplification results, 2µl of each PCR product were loaded onto 1-1.5 agarose gel and the
size of amplified fragments was compared with DNA molecular weight standards (DNA marker DC
Roche, 1kb DNA ladder Biolabs).
Single band PCR products were purified by PEG precipitation: 300 ul of TE buffer and 200 ul of 30%
PEG 8000/30 mM MgCl2 were added to 100 µl PCR reaction. After vortexing, the DNA was centrifuged
for 20 min at 10000g, washed with 1 vol. 70% ethanol and the pellet dissolved in 30 µl TE. PCR
products smaller than 350 bp were purified using a PCR purification Kit (Qiagen) and eluted with 30 p.1
of the provided elution buffer.
In order to evaluate the yield, 2µl of the purified DNA were subjected to agarose gel electrophoresis and
compared to titrated molecular weight standards.
D) Clonine of PCR products into expression vectors
Cloning was performed following the Gateway™ technology's "one-tube protocol", which consists of a
two step reaction (BP and l.R) for direct insertion of PCR products into expression vectors.
BP reaction (attB x attP sites): The reaction allowed insertion of the PCR product into a pDONR
vector. The pDONR™ 201 vector we used contains the killer toxin gene ccdB between attP1 and attP2
sites to minimize background colonies lacking the PCR insert, and a selectable marker gene for
kanamycin resitance. The reaction resulted in a so called pEntry vector, in which the GBS gene was
located between attL1 and attL2 sites.
60 finol of PCR product and 100 ng of pDONR™ 201 vector were incubated with 2.5 ul of BP
clonase™ in a final volume of 12.5 µl for 4 hours at 25°C.
l.R reaction (attLx atiR. sites): The reaction allowed the insertion of the GBS gene, now present in the
pEntry vector, into E.coli expression vectors (pDestination vectors, containing attR sites). Two
pDestination vectors were used (pDEST15 for N- terminal GST fusions - Figure 86; and pDEST17-l
for N-terminal His-tagged fusions — Figure 87). Both allow transcription of the ORF fusion coding
mRNA under T7 RNA polymerase promoter [Stuther et al (1990) Meth. Enzymol 185: 60ff].
To 5 µl of BP reaction were added 0.25 µl of 0.75 M NaCl. 100 ng of destination vector and 1.5 µl of
l.R clonase™ . The reaction was incubated at 25°C for 2 hours and stopped with 1 µl of 1 mg/ml
proteinase K solution at 37°C for 15 min.
1 µl of the completed reaction was used to transform 50 µl electrocompetent Bl.21-SI™ cells (0.1 cm,
200 ohms, 25 µF). BL21-SI cells contain an integrated T7 RNA polymerase gene under the control of
the salt-inducible prU promoter [Gowrishankar (1985) J. Bacterial. 164:434ff]. After electroporation
cells were diluted in lml SOC medium (20 g/1 bacto-tryptone, 5 g/1 yeast extract, 0.58 g/1 NaCl, 0.186 g/1
KC1, 20 mM glucose, 10 mM MgCt) and incubated at 37°C for I hour. 200 ul cells were plated onto
l.BON plates (Luria Broth medium without NaCl) containing 100 µg/ ml ampicillin. Plates were then
incubated for 16 hours at 37°C.
Entry clones: In order to allow the future preparation of Gateway compatible pEntry plasmids
containing genes which might turn out of interest after immunological assays, 2.5 µl of BP reaction were
incubated for 15 min in the presence of 3 ul 0.15 mg/ml proteinase K solution and then kept at -20°C.
The reaction was in this way available to transform E.coli competent cells so as to produce Entry clones
for future introduction of the genes in other Destination vectors.
E) Protein expression
Single colonies derived from the transformation of LR reactions were inoculated as small-scale cultures
in 3 ml l.BON 100 ug/ml ampicillin for overnight growth at 25°C. 50-200 ul of the culture was inoculated
in 3 ml l.BON/Amp to an initial OD600 of 0.1. The cultures were grown at 37°C until OD600 0.4-0.6
and recombinant protein expression was induced by adding NaCl to a final concentration of 0.3 M. After
2 hour incubation the final OD was checked and the cultures were cooled on ice. 0.5 OD^o of cells were
harvested by centrifugation. The cell pellet was suspended in 50 ul of protein l.oading Sample Buffer (50
mM TRIS-HC1 pH 6.8, 0.5% w/v SDS, 2.5% v/'v glycerin, 0.05% w/v Bromophenol Blue, 100 mM
DTT) and incubated at 100 °C for 5 min. 10 µl of sample was analyzed by SDS-PAGE and Coomassie
Blue staining to verify the presence of induced protein band.
F) Purification of the recombinant proteins
Single colonies were inoculated in 25 ml l.BON 100 µg/ml ampicillin and grown at 25°C overnight. The
overnight culture was inoculated in 500 ml l.BON/amp and grown under shaking at 25 °C until OD600
values of 0.4-0.6. Protein expression was then induced by adding NaCl to a final concentration of 0.3 M.
After 3 hours incubation at 25 °C the final OD600 was checked and the cultures were cooled on ice. After
centrifugation at 6000 rpm (JA10 rotor, Beckman) for 20 min., the cell pellet was processed for
purification or frozen at -20 °C.
Proteins were purified in 1 of 3 ways depending on the fusion partner and the protein's solubility
Purification of soluble His-tagged proteins from E.coli
1. Transfer pellets from -20°C to ice bath and reconstitute each pellet with 10 ml B-PERTM solution
(Bacterial-Protein Extraction Reagent, Pierce cat. 78266). 10 µl of a 100 mM MgCl2 solution, 50
µl of DNAse I (Sigma D-4263, 100 Kunits in PBS) and 100 ul of 100 mg/ml lysozyme in PBS
(Sigma l.-7651, final concentration 1 mg/ml).
2. Transfer resuspended pellets in 50 ml centrifuge tubes and leave at room temperature for 30-40
minutes, vortexing 3-4 times.
3. Centrifuge 15-20 minutes at about 30-40000 xg.
4. Prepare Poly-Prep (Bio-Rad) columns containing 1 ml of Fast Flow Ni-activated Chelating
Sepharose (Pharmacia). Equilibrate with 50 mM phosphate buffer, 300 mM MaCl, pH 8.0.
5. Store the pellet at -20°C, and load the supernatant on to the columns.
6. Discard the flow through.
7. Wash with 10 ml 20 mM imidazole buffer, 50 mM phosphate, 300 mM NaCl, pH 8.0.
8. Elute the proteins bound to the columns with 4.5 ml (1.5 ml + 1.5 ml + 1.5 ml) 250 mM imidazole
buffer, 50 mM phosphate, 300 mM NaCl, pH 8.0 and collect three fractions of ~ 1.5 ml each. Add
to each tube 15 ul DTT 200 mM (final concentration 2 mM).
9. Measure the protein concentration of the collected fractions with the Bradford method and analyse
the proteins by SDS-PAGE.
10. Store the collected fractions at +4°C while waiting for the results of the SDS-PAGE analysis.
11. For immunisation prepare 4-5 aliquots of 20-100 µg each in 0.5 ml in 40% glycerol. The dilution
buffer is the above elution buffer, plus 2 mM DTT. Store the aliquots at -20°C until immunisation.
Purification of His-tagged proteins from inclusion bothes
1. Bacteria are collected from 500 ml cultures by centrifugation. If required store bacterial pellets at
-20°C. Transfer the pellets from -20°C to room temperature and reconstitute each pellet with 10
ml B-PER™ solution, 10 ul of a 100 mM MgCU solution (final 1 mM), 50 ul of DNAse I
equivalent to 100 Kimits units in PBS and 100 ul of a 100 mg/ml h/sozime (Sigma l.-7651) solution
in PBS (equivalent to 10 mg, final concentration I mg/ml).
2. Transfer the resuspended pellets in 50 ml centrifuge tubes and let at room temperature for 30-40
minutes, vortexing 3-4 times.
3. Centrifuge 15 minutes at 30-4000 x g and collect the pellets.
4. Dissolve the pellets with 50 mM TRIS-HC1. 1 mM [CEP {Tris(2-carboxyethyl)-phosphine
hydrochloride, Pierce} , 6M guanidine hydrochloride, pH S.5. Stir for ~ l.0 rain, with a magnetic
bar.
5. Centrifuge as described above, and collect the supernatant.
6. Prepare Poly-Prep (Bio-Rad) columns containing 1 ml of Fast Flow Ni-activated Chelating
Sepharose (Pharmacia). Wash the columns twice with 5 ml of H2O and equilibrate with 50 mM
TRIS-HC1, 1 mM TCEP, 6M guanidine hydrochloride, pH 8.5
7. l.oad the supematants from step 5 onto the columns, and wash with 5 ml of 50 mM TRIS-HC1
buffer, 1 mM TCEP, 6M urea, pH 8.5
8. Wash the columns with 10 ml of 20 mM imidazole, 50 mM TRIS-HC1 , 6M urea, 1 mM TCEP,
pH 8.5. Collect and set aside the first 5 ml for possible further controls.
9. Elute proteins bound to columns with 4.5ml buffer containing 250 mM imidazole, 50 mM TRIS-
HC1, 6M urea, 1 mM TCEP, pH 8.5. Add the elution buffer in three 1.5 ml aliquots. and collect
the corresponding three fractions. Add to each fraction 15 µl DTT (final concentration 2 mM).
10. Measure eluted protein concentration with Bradford method and analyse proteins by SDS-PAGE.
11. Dialyse overnight the selected fraction against 50 mM Na phosphate buffer, pH 8.8, containing
10% glycerol, 0.5 M arginine, 5 mM reduced glutathione, 0.5 mM oxidized ghitathione, 2 M urea.
12. Dialyse against 50 mM Na phosphate buffer, pH 8.8, containing 10% glycerol, 0.5 M arginine, 5
mM reduced glutathione, 0.5 mM oxidized glutathione.
13. Clarify the dialysed protein preparation by centrifugation and discard the non-soluble material and
measure the protein concentration with the Bradford method.
14. For each protein destined to the immunization prepare 4-5 aliquot of 20-100 µg each in 0.5 ml
after having adjusted the glycerol content up to 40%. Store the prepared aliquots at -20° C until
immunization.
Purification of GST-fusion proteins from E.coli
1. Bacteria are collected from 500 ml cultures by centrifugation. If required store bacterial pellets at
-20°C. Transfer the pellets from -20°C to room temperature and reconstitute each pellet with 10
ml B-PER™ solution, 10 ul of a 100 mM MgCl2 solution (final 1 mM), 50 ul of DNAse I
equivalent to 100 Kunits units in PBS and 100 ul of a 100 mg/ml lysozime (Sigma l.-7651) solution
in PBS (equivalent to 10 mg, final concentration 1 mg/ml)
2. Transfer the resuspended pellets in 50 ml centrifuge tubes and let at room temperature for 30-40
minutes, vortexing 3-4 times.
3. Centrifuge 15-20 minutes at about 30-40000 x g.
4. Discard centrifugation pellets and load supematants onto the chromatography columns, as
follows.
5. Prepare Poly-Prep (Bio-Rad) columns containing 0.5 ml of Glutaduone-Sepharose 4B resin. Wash
the columns twice with 1 ml of H2O and equilibrate with l.0 ml PBS, pH 7.4.
6. Load supematants on to the columns and discard the flow through.
7. Wash the columns with 10 ml PBS, pH 7.4.
8. Elute proteins bound to columns with 4.5 ml of 50 mM TR1S buffer, 10 mM reduced glutathione,
pH 8.0, adding 1.5 ml + 1.5 ml + 1 5 ml and collecting the respective 3 fractions of ~1.5 ml each.
9. Measure protein concentration of the fractions with the Bradford method and analyse the proteins
by SDS-PAGE.
10. Store the collected fractions at +4°C while waiting for the results of the SDS-PAGE analysis.
11. For each protein destined for immunisation prepare 4-5 aliquots of 20-100 µg each in 0.5 ml of
40% glycerol. The dilution buffer is 50 mM TRIS-HC1, 2 mM DTT, pH 8.0. Store the aliquots at
-20°C until immunisation.
Figures 167 to 170 and 238 to 239
For the experiments shown in Figures 167 to 170, Figure 238 and lanes 2-6 of Figure 239, the GBS
proteins were fused at the N-terminus to thioredoxin and at C-terminus to a poly-His tail. The plasmid
used for cloning is pBAD-DEST49 (Invitrogen Gateway™ technology) and expression is under the
control of an l.(+)-Arabinose dependent promoter. For the production of these GBS antigens, bacteria
are grown on RM medium (6gA Na2HPO4, 3g/l KH2PO4, 0.5 g/1 NaCl, 1 g/1 NR.C1, pH7,4, 2%
casaminoacids, 0.2 % glucose, 1 mM MgCl2) containing 100 µg/ml ampicillin. After incubation at 37°C
until cells reach OD600=0.5, protein expression is induced by adding 0.2% (v/v) l.(+)Axabinose for 3
hours.
Immunisations with GBS proteins
The purified proteins were used to immunise groups of four CD-I mice intraperitoneally. 20 ug of each
purified protein was injected in Freund's adjuvant at days 1, 21 & 35. Immune responses were
monitored by using samples taken on day 0 & 49. Sera were analysed as pools of sera from each group
of mice.
FACScan bacteria Binding Assay procedure.
GBS serotype V 2603 V/R strain was plated on TSA blood agar plates and incubated overnight at 37°C.
Bacterial colonies were collected from the plates using a sterile dracon swab and inoculated into 100ml
Todd Hewitt Broth. Bacterial growth was monitored every 30 minutes by following OD600. Bacteria were
grown until OD600 = 0.7-0.8. The culture was centrifuged for 20 minutes at 5000rpm. The supernatant
was discarded and bacteria were washed once with PBS, resuspended in ½ culture volume of PBS
containing 0.05% paraformaldehyde, and incubated for 1 hour at 37°C and then overnight at 4°C.
50µl bacterial cells (OD600 0.1) were washed once with PBS and resuspended in 20µl blocking serum
(Newborn Calf Serum, Sigma) and incubated for 20 minutes at room temperature. The cells were then
incubated with 100µl diluted sera (1:200) in dilution buffer (20% Newborn Calf Serum 0.1% BSA in
PBS) for 1 hour at 4°C. Cells were centrifuged at 5000rpm, the supernatant aspirated and cells washed
by adding 200µl washing buffer (0.1% BSA in PBS). 50µl R-Phicoerytnn conjugated F(ab)2 goat anti-
mouse, diluted 1:100 in dilution buffer, was added to each sample and incubated for 1 hour at 4°C. Cells
were spun down by centrifugation at 5000rpm and washed by adding 200µl of washing buffer. The
supernatant was aspirated and cells resuspended in 200µl PBS. Samples were transferred to FACScan
tubes and read. The condition for FACScan setting were: Fl.2 on; FSC-H threshold:54; FSC PMT
Voltage: E 02; SSC PMT: 516; Amp. Gains 2.63; Fl.-2 PMT: 728. Compensation values: 0.
Samples were considered as positive if they had a A mean values > 50 channel values.
Whole Extracts preparation
GBS serotype III COH1 strain and serotype V 2603 V/R strain cells were grown overnight in Todd
Hewitt Broth, lml of the culture was inoculated into 100ml Todd Hewitt Broth. Bacterial growth was
monitored every 30 minutes by following OD600. The bacteria were grown until the OD reached 0.7-0.8.
The culture was centrifuged for 20 minutes at 5000 rpm. The supernatant was discarded and bacteria
were washed once with PBS, resuspended in 2ml 50mM Tris-HCl, pH 6.8 adding 400 units of
Mutanolysin (Sigma-Aldrich) and incubated 3 hrs at 37°C. After 3 cycles of freeze/thaw, cellular debris
were removed by centrifugation at 14000g for 15 minutes and the protein concentration of the
supernatant was measured by the Bio-Rad Protein assay, using BSA as a standard.
Western blotting
Purified proteins (50ng) and total cell extracts (25µg) derived from GBS serotype III COH1 strain and
serotype V 2603 V/R strain were loaded on 12% or 15% SDS-PAGE and transferred to a nitrocellulose
membrane. The transfer was performed for 1 hours at 100V at 4°C, in transferring buffer (25mM Tris
base, 192mM glycine, 20% methanol). The membrane was saturated by overnight incubation at 4°C in
saturation buffer (5 % skimmed milk, 0.1% Tween 20 in PBS). The membrane was incubated for 1 hour
at room temperature with 1:1000 mouse sera diluted in saturation buffer. The membrane was washed
twice with washing buffer (3 % skimmed milk, 0.1% Tween 20 in PBS) and incubated for 1 hour with a
1:5000 dilution of horseradish peroxidase labelled anti-mouse Ig (Bio-Rad). The membrane was washed
twice with 0.1% Tween 20 in PBS and. developed with the Opti-4CN Substrate Kit (Bio-Rad). The
reaction was stopped by adding water.
Unless otherwise indicated, lanes 1, 2 and 3 of blots in the drawings are: (1) the purified protein; (2)
GBS-III extracts; and (3) GBS-V extracts. Molecular weight markers are also shown.
In vivo passive protection assay in neonatal sepsis mouse model.
The immune sera collected from the CDI immunized mice were tested in a mouse neonatal sepsis model
to verify their protective efficacy in mice challenged with GBS serotype in. Newborn Balb/C littermates
were randomly divided in two groups within 24 hrs from birth and injected subcutaneously with 25µl of
diluted sera (1:15) from immunized CD1 adult mice. One group received preimmune sera, the other
received immune sera. Four hours later all pups were challenged with a 75% lethal dose of the GBS
serotype III COHl strain. The challenge dose obtained diluting a mid log phase culture was administered
in 25 µl of saline. The number of pups surviving GBS infection was assessed every 12
are in Table III.
SEQ ID 2 (GBS4) was expressed in E.coli as a GST-fasion product. SDS-PAGE analysis of total cell
extract is shown in Figure 9 (lane 3: MW 43.1kD)a) and Figure 63 (lane 4; MW 50kDa). It was also
expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in Figure 12
(lane 7; MW 30kDa), Figure 63 (lane 3; MW 30kDa) and in Figure 178 (lane 3; MW 30kDa)
GBS4-GST was purified as shown in Figure 190 (lane 6) and Figure 209 (lane 8).
Purified GBS4-His is shown in Figures 89A, 191 (lane 10), 209 (lane 7) and 228 (lanes 9 & 10).
The purified GBS4-His fusion product was used to immunise mice (lane 2 product; 201g/mouse). The
resulting antiserum was used for Western blot (Figure 89B), FACS, and in the in vivo passive protection
assay (Table III). These tests confirm that the protein is immunoaccessible on GBS ba.cteria and that it is an
effective protective immunogen.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
SEQ ID 8712 (GBS166) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 30 (lane 2; MW 13.1kDa).
The GBS166-His fusion product was purified (Figure 200, lane 10) and used to immunise mice. The
resulting antiserum was used for FACS (Figure 315), which confirmed that the protein is immunoaccessible
on GBS bacteria.
SEQ ID 4 (GBS 15) was expressed in E.coli as a GST-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 9 (lane 5; MW 44.8kDa), Figure 63 (lane 5; MW 44.8kDa) and Figure 66 (lane 7;
MW 45kDa). It was also expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 10 (lane 4; MW 22.3kDa). It was also expressed as GBS15l., with SDS-PAGE
analysis of total cell extract is shown in Figure 185 (lane 1; MW 50kDa).
Purified GBS15-GST is shown in Figure 91A, Figure 190 (lane 9), Figure 210 (lane 4) and Figure 245
(lanes 4 & 5).
The purified GBS15-GST fusion product was used to immunise mice (lane 1+2 products; 20µg/mouse).
The resulting antiserum was used for Western blot (Figure 91B), FACS (Figure 91C ), and in the in vivo
passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS
bacteria and that it is an effective protective immunogen.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
SEQ ID 6 (GBS 103) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 36 (lane 4; MW 32kDa).
The GBS103-His fusion product was purified (Figure 107A; see also Figure 201, lane 9) and used to
immunise mice (lane 2+3 product; 18.5µg/mouse). The resulting antiserum was used for Western blot
(Figure 107B), FACS (Figure 107C ) and in the in vivo passive protection assay (Table III). These tests
confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective
immunogen.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
SEQ ID 8 (GBS 195) was expressed in E.coli as a His-fusion product. SDS-PAGb analysis of total cell
extract is shown in Figure 24 (lane 8). It was also expressed in E.coli as a GST-fusion product. SDS-PAGE
analysis of total cell extract is shown in Figure 31 (lane 5).
GBS195C was expressed in E.coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is
shown tn Figure 175 (lane 6 & 7; MW 8lkDa).
GBS195L was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell extract is
shown in Figure 83 (lane 2; MW 123kDa).
GBS195l.N was expressed in E.coli as a His-fusion product SDS-PAGE analysis of total cell extract is
shown in Figure 83 (lane 3; MW 66kDa).
GBS195-GST was purified as shown in Figure 198, lane 5. GBS195-His was purified as shown in Figure
222, lane 4-5. GBS195N-His was purified as shown in Figure 222, lane 6-7.
The GBS195-GST fusion product was purified (Figure 87A) and used to immunise mice (lane 1 product;
13.6µg/mouse). The resulting antiserum was used for Western blot (Figure 87B), FACS, and in the in vivo
passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS
bacteria and that it is an effective protective immunogen.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 5
A DNA sequence (GBSxG002) was identified in S.agatactiae which encodes the amino
acid sequence . This protein is predicted to be lipoprotein MtsA. Analysis of this protein
sequence reveals the following:
SEQ ED 9404 (GBS679) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 164 (lane 7-9; MW 36kDa) and in Figure 188 (lane 8; MW 36kDa). Purified
protein is shown in Figure 242, lanes 9 & 10.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 6
A DNA sequence (GBSx0003) was identified in S.agalactiae which encodes the amino
acid sequence . This protein is predicted to be ATP-binding protein MtsB. Analysis of this
protein sequence reveals the following:
Example 7
A DNA sequence (GBSx0004) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 18 (GBS205) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 51 (lane 13; MW 31kDa).
GBS205-His was purified as shown in Figure 206, lane 8.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 11
A DNA sequence (GBSx0008) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be sporulation protein SpoIIIE (ftsK). Analysis of this
protein sequence reveals the following:
A related GBS nucleic acid sequence which encodes arnino acid sequence 10036> was also identified.
The protein has homology with the following sequences in the GENPEPI database:
SEQ ID 22 (GBS272d) was expressed in E.coli as a GST-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 147 (lane 9; MW 55kDa + lane 10; MW 70kDa). It was also expressed in E.coli
as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in Figure 147 (lane 11 & 13; MW
85kDa + lane 12; MW 74kDa).
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 12
A DNA sequence (GBSx0009) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be para-aminobenzoate synthetase (pabB) (pabB).
Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 13
A DNA sequence (GBSx00l0) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 17
A DNA sequence (GBSx0014) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be drug transporter. Analysis of this protein sequence
reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 18
A DNA sequence (GBSx0015) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be transposase. Analysis of this protein sequence
reveals the following:
The protein has no significant homology with any sequences in the GENPEPT database
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 19
A DNA sequence (GBSx0016) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be L11 protein (rplK). Analysis of this protein
sequence reveals the following:
A related DNA sequence was identified in S.pyogenes which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 20
A DNA sequence (GBSx0017) was identified in S.agalactiae which encodes the ammo acid
sequence . 'This protein is predicted to be ribosomal protein L1 (rp1A). Analysis of this protein
sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their cpitopes could be useful antigens for
vaccines or diagnostics.
Example 21
A DNA sequence (GBSx0018) was identified in S.agalactiae which encodes the arnino acid
sequence . Analysis of this protein sequence reveals the following:
A related DNA sequence was identified in S.pyogenes which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 8470 (GBS186) was expressed in E.coli as a His-fusion pruduct. SDS-PAGE analysis of total cell
extract is shown in Figure 35 (lane 7; MW 60kDa). It was also expressed in E.coli as a GST-fusion
product. SDS-PAGE analysis of total cell extract is shown in Figure 41 (lane 6; MW 85.7kDa).
GBS186-GST was purified as shown in Figure 202, lane 4.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 22
A DNA sequence (GBSx0019) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 23
A DNA sequence (GBSx0020) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be nickel transport system (permease). Analysis of this
protein sequence reveals the following:
A related GBS gene and protein were also identified. Analysis of this
protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 24
A DNA sequence (GBSx0021) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be peptide ABO transporter, ATP-binding protein.
Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 25
A DNA sequence (GBSx0022) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be peptide ABC transporter, ATP-binding protein.
Analysis of this protein sequence reveals the following:
Example 27
A DNA sequence (GBSx0024) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 28
A DNA sequence (GBSx0025) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be ribosome recycling factor (frr). Analysis of this
protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 29
A DNA sequence (GBSx0026) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 30
A DNA sequence (GBSx0028) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be peptide methionine sulfoxidc reductase (msrA).
Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 31
A DNA sequence (GBSx0029) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 32
A DNA sequence (GBSx0030) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be antigen. 67 kDa (myosin-crossreactive). Analysis
of this protein sequence reveals the following:
SEQ ID 8476 (GBS90) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 18 (lane 6; MW 68.5kDa).
The GBS90-His fusion product was purified (Figure 194, Jane 11) and used to immunise mice. The
resulting antiserum was used for Western blot (Figure 256A), FACS (Figure 256B), and in the in vivo
passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS
bacteria and that it is an effective protective immunogen.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 33
A DNA sequence (GBSx0031) was identified in S.agalactiae which encodes the ammo acid
sequence . This protein is predicted ro be phoh-like protein (phoH). Analysis of this protein
sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 34
A DNA sequence (GBSx0032) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens tor
vaccines or diagnostics.
Example 35
A DNA sequence (GBSx0033) was identified in S.agalactiae which encodes the ammo acid
sequence . This protein is predicted to be MutT/nudix family protein. Analysis of this protein
sequence reveals the following:
A related DNA sequence was identified in S.pyogenes which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 36
A DNA sequence (GBSx0034) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
The protein has no significant homology with any sequences in the GENPEPT database
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 37
A DNA sequence (GBSx0035) was identified in S agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
No corresponding DNA sequence was identified in S.pyogenes.
A related GBS gene and protein were also identified. Analysis of this
protein sequence reveals the following:
SEQ ID 8478 (GBS176) was expressed in E coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 36 (lane 5 & 6; MW 30kDa). It was also expressed in E.coli as a GST-fusion
product. SDS-PAGE analysis of total cell extract is shown in Figure 41 (lane 7; MW 55.4kDa).
The GBS176-GST fusion product was purified (Figure 117A; see also Figure 202, lane 5) and used to
immunise mice (lane 1+2 product; 13.5µg/mouse). The resulting antiserum was used for Western blot
(Figure 117B), FACS (Figure 117C), and in the in vivo passive protection assay (Table III). These tests
confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective
immunogen.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 38
A DNA sequence (GBSx0036) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
A related DNA sequence was identified in S.pyogenes which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 39
A DNA sequence (GBSx0038) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be phosphoglycerate dehydrogenase (serA) (serA).
Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 40
A DNA sequence (GBSx0039) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be alpha-glycerophosphate oxidase. Analysis of this
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens: for
vaccines or diagnostics.
Example 41
A DNA sequence (GBSx0040) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 42
A DNA sequence (GBSx0041) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be lipopolysaccharide core biosynthesis protein kdtB
(kdtB). Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 43
A DNA sequence (GBSx0042) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 44
A DNA sequence (GBSx0043) was identified in S.agalactiae which encodes the amino acid
sequence . Analysts of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 45
A DNA sequence (GBSx0044) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be UDP-sugar hydrolase. Analysis of this protein
sequence reveals the following:
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 46
A DNA sequence (GBSx0045) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be UDP-sugar hydrolase. Analysis of this protein
sequence reveals the following:
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 47
A DNA sequence (GBSx0046) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be unnamed protein product. Analysis of this protein
sequence reveals the following:
A related DNA sequence was identified in S.pyogenes which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 49
A DNA sequence (GBSx0048) was identified in S.agalactiae which encodes the ammo acid
sequence . This protein is predicted to be VanZF. Analysis of this protein sequence reveals
the following:
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 50
A DNA sequence (GBSx0049) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be multidrug resistance-like ATP-binding protein rndl.
Analysis of this protein sequence reveals the following:
There is also homology to SEQ IDs 330, 4634 and 5788.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 52
A DNA sequence (GBSx0051) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 54
A DNA sequence (GBSx0053) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:

The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 55
A DNA sequence (GBSx0054) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:

A related GBS nucleic acid sequence which encodes amino acid sequence
was also identified.
The protein has homology with the following sequences in the GENPEPT database:


No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 56
A DNA sequence (GBSx0055) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:

A related GBS nucleic acid sequence which encodes amino acid sequence
was also identified.
The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 57
A DNA sequence (GBSx0056) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:

The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its. epitopes, could be useful antigens tor
vaccines or diagnostics.
Example 58
A DNA sequence (GBSx0057) was identified in S.agalactiae which eacodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 59
A DNA sequence (GBSx0058) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 60
A DNA sequence (GBSx0059) was identified in S. agalactiae which encodes the amino acid
sequence . This protein is predicted to be endonuclease III (pdg). Analysis of this protein
sequence reveals the following:

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 61
A DNA sequence (GBSx0060) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:

The protein has homology with the following sequences in the GENPEPT database:

A related DNA sequence was identified in S.pyogenes which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 62
A DNA sequence (GBSx0061) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
A related DNA sequence was identified in S.pyogenes which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 63
A DNA sequence (GBSx0062) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 8484 (GBS13) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 3 (lane 4; MW 16kDa). It was also expressed in E.coli as a GST-fusion product.
SDS-PAGE analysis of total cell extract is shown in Figure 9 (lane 2; MW 40.5kDa).
The GST-fusion protein was purified as shown in Figure 190, lane 5.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 64
A DNA sequence (GBSx0063) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be regulatory protein TypA (typA). Analysis of this
protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 65
A DNA sequence (GBSx0065) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be D-glutarnic acid adding enzyme MurD (murD).
Analysis of this protein sequence reveals the following:
A related GBS nucleic acid sequence which encodes amino acid sequence
was also identified.
The protein has homology with the following sequences in the GENPEPT database:
SEQ ID 208 (GBS305) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 51 (lane 11; MW 53.7kDa). Ft was also expressed in E.coli as a GST-fusion
product. SDS-PAGE analysis of total cell extract is shown in Figure 56 (lane 3: MW 79kDa).
The GBS305-GST fusion product was purified (Figure 207, lane 8) and used to immunise mice. The
resulting antiserum was used for FACS (Figure 270), which confirmed that the protein is immunoaccessible
on GBS bacteria.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostic;;.
Example 66
A DNA sequence (GBSx0066) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 212 (GBS306) was expressed in E.coli as a His-fusion produce. SDS-PAGE analysis of total cell
extract is shown in Figure 51 (lane 12; MW 43kDa). It was also expressed in E.coli as a GST-fusion
product SDS-PAGE analysis of total cell extract is shown in Figure 56 (lane 4; MW 68kDa).
GBS306-GST was purified as shown in Figure 207. lane 9.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 67
A DNA sequence (GBSx0067) was identified in S.agalactiae which encodes the ammo acid
sequence . This protein is predicted to be cell division protein DivIB. Analysis of this protein
sequence reveals the following:
SEQ ID 216 (GBS85) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 17 (lane 10; MW 45.2kDa).
The GBS85-His fusion product was purified (Figure 105A; see also Figure 193, lane 5) and used to
immunise mice (lane 1 product; 20µg/mouse). The resulting antiserum was used for Western blot (Figure
105B), FACS (Figure 105C), and in the in vivo passive protection assay (Table III). These tests confirm
that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 68
A DNA sequence (GBSx0068) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be cell division protein FtsA (ftsA). Analysis of this
protein sequence reveals the following:
SEQ ID 220 (GBS73) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 17 (lane 5; MW 47.8kDa). It was also expressed in E.coli as a GST-fusion
product SDS-PAGE analysis of total cell extract is shown in Figure 20 (lane 5; MW 70.1kDa).
GBS73-GST was purified as shown in Figure 197, lane 7.
The GBS73-His fusion product was purified (Figure 103A) and used to immunise mice (lane 1 product;
20µg/mouse). The resulting antiserum was used for Western blot (Figure 103B), FACS (Figure 103C ) and
in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible
on GBS bacteria and that it is an effective protective immunogen.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 69
A DNA sequence (GBSx0069) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be cell division protein FtsZ (ftsz). Analysis of this
protein sequence reveals the following:

SEQ ID 224 (GBS163) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 28 (lane 7; MW 44kDa). It was also expressed in E.coli as a GST-fusion
product. SDS-PAGE analysis of total cell extract is shown in Figure 34 (lane 4; MW 69kDa).
The GBS163-GST fusion product was purified (Figure 114A; see also Figure 198, lane 11) and used to
immunise mice (lane 1 product; 20µg/mouse). The resulting antiserum was used for Western blot (Figure
114B), FACS and in the in vivo passive protection assay (Table III). These tests confirm that the protein is
iminunoaccessible on GBS bacteria and that it is an effective protective immunogen.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 70
A DNA sequence (GBSx0070) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:


Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 71
A DNA sequence (GBSx0071) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be YlmF. Analysis of this protein sequence reveals
the following:

Based on this analysis, it was predicted that these proteins and their epitopcs could be useful antigens for
vaccines or diagnostics.
Example 72
A DNA sequence (GBSx0072) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be YlmH. Analysis of this protein sequence reveals
the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 73
A DNA sequence (GBSx0073) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be cell division protein DivIVA (septumplacement).
Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 74
A DNA sequence (GBSx0074) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 75
A DNA sequence (GBSx0075) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 76
A DNA sequence (GBSx0076) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be AP4A hydrolase. Analysis of this protein sequence
reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 77
A DNA sequence (GBSx0077) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be ClpE (clpB-1). Analysis of this protein sequence
reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 78
A DNA sequence (GBSx0078) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be glutamine ABC transporter, permease protein
(glnP). Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopcs could be useful antigens for
vaccines or diagnostics.
Example 79
A DNA sequence (GBSx0079) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be phosphomannomutase (manB). Analysis of this
protein sequence reveals the following:
A related DNA sequence was identified in S.pyogenes which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 81
A DNA sequence (GBSx0081) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 272 (GBS413) was expressed in E.coli as a His-fusion product SDS-PAGE analysis of total cell
extract is shown in Figure 79 (lane 2; MW 34.2kDa). It was also expressed in E.coli as a GST-fusion
product SDS-PAGE analysis of total cell extract is shown in Figure 171 (lane 7; MW 59kDa).
GBS413-GST was purified as shown in Figure 218, lane 12.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 82
A DNA sequence (GBSx0082) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be Exonuclease VII large subunit (xseA). Analysis of
this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 83
A DNA sequence (GBSx0083) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 286 (GBS310) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 57 (lane 3; MW 34kDa). It was also expressed in E.coli as a GST-fusion
product. SDS-PAGE analysis of total cell extract is shown in Figure 61 (lane 4; MW S8.8kDa).
The GBS310-GST fusion product was purified (Figure 210, lane 10) and used to immunise mice. The
resulting antiserum was used for FACS (Figure 282), which confirmed that the protein is immunoaccessible
on GBS bacteria.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 86
A DNA sequence (GBSx0086) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 87
A DNA sequence (GBSx0088) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:

The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 88
A DNA sequence (GBSx0089) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be DNA repair protein recn (recN). Analysis of this
protein sequence reveals the following:

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 89
A DNA sequence (GBSx0090) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be degV protein. Analysis of this protein sequence
reveals the following:
A related DNA sequence was identified in S.pyogenes which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 300 (GBS113) was expressed in E.coli as a His-fusion product. Purified protein is shown in Figure
201, lane 8.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 90
A DNA sequence (GBSx0092) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
A related GBS gene and protein were also identified. Analysis of this
protein sequence reveals the following:
SEQ ID 308 (GBS20) was expressed in E.coli as a His-fusion product SDS-PAGE analysis of total cell
extract is shown in Figure 4 (lane 5; MW 25kDa) and in Figure 167 0ane 12-14; MW 37kDa - thioredoxin
fusion). It was also expressed in E.coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is
shown in Figure 9 (lane 7; MW 47.6kDa). Purified Thio-GBS20-His is shown in Figure 244, lane 12.
Example 91
A DNA sequence (GBSx0093) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be histone-like DNA-binding protein. Analysis of this
protein sequence reveals the following:
SEQ ID 9294 (GBS663) was expressed in E.coli as a GST-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 137 (lane 3; MW 89.5kDa). It was also expressed in E.coli as a His-fusion
product. SDS-PAGE analysis of total cell extract is shown in Figure 137 (lane 5-7; MW 64.5kDa), in Figure
179 (lane 11; MW 65kDa) and in Figure 65 (lane 2; MW 61kDa) Purified GBS663-His is shown in Figure
231, lane 3-4. Purified GBS324-His is shown in lane 6 of Figure 210.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 93
A DNA sequence (GBSx0095) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be transmembrane protein OppB (oppB). Analysis of
this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 95
A DNA sequence (GBSx0097) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be ATPase OppD (oppD). Analysis of this protein
sequence reveals the following:
There is also homology to SEQ ID 72.
SEQ ID 326 (GBS375) was expressed in E.coli as a His-fusion product SDS-PAGE analysis of total cell
extract is shown in Figure 64 (lane 9; MW 42kDa). It was also expressed in E.coli as a GST-fusion
product SDS-PAGE analysis of total cell extract is shown in Figure 71 (lane 3; MW 67kDa).
GBS375-GST was purified as shown in Figure 215, lane 10.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 97
A repeated DNA sequence (GBSx0099) was identified in S.agalactiae which encodes the
amino acid sequence . Analysis of this protein sequence reveals the following:

The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 98
A repeated DNA sequence (GBSx0l00) was identified in S.agalactiae which encodes the
amino acid sequence . Analysis of this protein sequence reveals the following:

The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 99
A repeated DNA sequence (GBSxOlOl) was identified in S.agalactiae which encodes the
amino acid sequence . Analysis of this protein sequence reveals the following:

The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 100
A repeated DNA sequence (GBSx0103) was identified in S.agalactiae which encodes the
amino acid sequence . Analysis of this protein sequence reveals the following:

The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 101
A repeated DNA sequence (GBSx0104) was identified in S.agalactiae which encodes the
amino acid sequence . Analysis of this protein sequence reveals the following:

The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 102
A repeated DNA sequence (GBSx0105) was identified in S.agalactiae which encodes the
amino acid sequence . Analysis of this protein sequence reveals the following:
The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 103
A repeated DNA sequence (GBSx0106) was identified in S.agalactiae which encodes the
amino acid sequence . Analysis of this protein sequence reveals the following:
The protein has do significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 104
A repeated DNA sequence (GBSx0107) was identified in S.agalactiae which encodes the
amino acid sequence . Analysis of this protein sequence reveals the following:
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 105
A DNA sequence (GBSx0108) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on tins analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 106
A DNA sequence (GBSx0109) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be AdcR protein. Analysis of this protein sequence
reveals the following:
Based cm this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 107
A DNA sequence (GBSx0110) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be AdcC protein. Analysis of this protein sequence
reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 108
A DNA sequence (GBSx0111) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 374 (GBS64d) was expressed in E.coli as a GST-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 120 (lane 2-4; MW 107kDa). It was also expressed in E.coli as a His-fusion
product. SDS-PAGE analysis of total cell extract is shown in Figure 120 (lane 5-7; MW 82kDa) and in
Figure 179 (lane 2; MW 82kDa).
GBS64d-His was purified as shown in Figure 231, lane 7-8.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 113
A DNA sequence (GBSx0116) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be DNA-dependent RNA polymerase subunit beta
(rpoB). Analysis of this protein sequence reveals the following:
Example 114
A DNA sequence (GBSxO118) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be DNA-directed RNA polymerase, beta subunit
(rpoC). Analysis of this protein sequence reveals the following:
A related DNA sequence was identified in S.pyogenes which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 390 (GBS63) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 5 (lane 5; MW 39kDa). It was also expressed in E.coli as a GST-fusion product.
SDS-PAGE analysis of total cell extract is shown in Figure 13 (lane 2; MW 64kDa).
The GBS63-GST fusion product was purified (Figure 101A; see also Figure 191, lane 3) and used to
immunise mice (lane 1 product; 20µg/mouse). The resulting antiserum was used for Western blot (Figure
101B), FACS (Figure 101C ), and in the in vivo passive protection assay (Table III). These tests confirm
that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.
SEQ ID 8494 (GBS49) was expressed in E.coli as a His-fusion product SDS-PAGE analysis of total cell
extract is shown in Figure 11 (lane 3; MW 15kDa). It was also was expressed in E.coli as a GST-fusion
product. SDS-PAGE analysis of total cell extract is shown in Figure 15 (lane 5; MW 60kDa).
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 118
A DNA sequence (GBSx0123) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be Com YD or ComGD. Analysis of this protein
sequence reveals the following:
SEQ ID 398 (GBS6) was expressed in E.coli as a GST-fusion product SDS-PAGE analysis of total cell
extract is shown in Figure 1 (lane 2; MW 40kDa). It was also expressed in E.coli as a His-fusion product.
SDS-PAGE analysis of total cell extract is shown in Figure 2 (lane 2; MW 15kDa). The GBS6-GST fusion
product was purified (Figure 189, lane 2) and used to immunise mice. The resulting antiserum was used for
FACS (Figure 260), which confirmed that the protein is immunoaccessible on GBS bacteria.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 120
A DNA sequence (GBSx0125) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be acetate kinase (ackA-1). Analysis of this protein
sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 121
A DNA sequence (GBSx0126) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be repressor protein. Analysis of this protein sequence
reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 122
A DNA sequence (GBSx0127) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on tins analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 12S
A DNA sequence (GBSx0130) was identified in S.agalactiae which encodes tire amino acid
sequence . Analysis of this protein sequence reveals the following:
The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 126
A DNA sequence (GBSx0131) was identified in S.agalactiae which encodes the ammo acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 8498 (GBS214) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 40 (lane 3; MW 13.9kDa). It was also expressed in E.coli as a GST-fusion
product. SDS-PAGE analysis of total cell extract is shown in Figure 46 (lane 6; MW 39kDa).
Based on this analysis, it was predicted that these proteins and their epitopcs could be useful antigens for
vaccines or diagnostics.
Example 127
A DNA sequence (GBSx0132) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be thioredoxin H1 (trxA). Analysis of this protein
sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 128
A DNA sequence (GBSxO133) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be phenylalanyl-tRNA synthetase beta subunit, non-
spirochete. Analysis of this protein sequence reveals the following:
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 130
A DNA sequence (GBSx0136) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 131
A DNA sequence (GBSx0137) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S-pyagenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 134
A DNA sequence (GBSx0140) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 454 (GBS248d) was expressed in E.coli as a GST-fusion product SDS-PAGE analysis of total cell
extract is shown in Figure 124 (lane 2-4; MW 71kDa). It was also expressed in E.coli as a His-fusion
product. SDS-PAGE analysis of total cell extract is shown in Figure 124 (lane 5-7; MW 46kDa) and in
Figure 180 (lane 2; MW 46kDa).
GBS248d-His was purified as shown in Figure 234, lane 3-4.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 135
A DNA sequence (GBSx014l) was identified in S.agalactiae which encodes the amino acid
sequence . This protein is predicted to be two-component response regulator (lytT). Analysis
of this protein sequence reveals the following:
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 136
A DNA sequence (GBSx0142) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DMA. sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 137
A DNA sequence (GBSx0143) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 8502 (GBS106) was expressed in E.coli as a His-fusion product. SDS-PAGE analysis of total cell
extract is shown in Figure 18 (lane 3; MW The GBS106-His fusion product was purified (Figure 194, lane 2) and used to immunise mice. The
resulting antiserum was used for Western blot (Figure 255A), FACS (Figure 255B), and in the in vivo
passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS
bacteria and that it is an effective protective immunogen.
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 140
A DNA sequence (GBSx0146) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
The protein has no significant homology with any sequences in the GENPEPT database.
No corresponding DNA sequence was identified in S.pyogenes.
Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for
vaccines or diagnostics.
Example 141
A DNA sequence (GBSx0147) was identified in S.agalactiae which encodes the amino acid
sequence . Analysis of this protein sequence reveals the following:
SEQ ID 8472 (GBS436) was expressed in E.coli as a GST-fusion product SDS-PAGE analysis of total cell
extract is shown in Figure 173 (lane 9; MW 54kDa).
Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for
vaccines or diagnostics.
Example 142
A DNA sequence (GBSx0148) was identified in S.agalactiae which encodes the amino acid

Documents:

226459-FORM 27.pdf

461-KOLNP-2003-(04-10-2012)-FORM-27.pdf

461-KOLNP-2003-FORM-27-1.1.pdf

461-KOLNP-2003-FORM-27-1.pdf

461-KOLNP-2003-FORM-27.pdf

461-kolnp-2003-granted-abstract.pdf

461-kolnp-2003-granted-claims.pdf

461-kolnp-2003-granted-correspondence.pdf

461-kolnp-2003-granted-drawings.pdf

461-kolnp-2003-granted-examination report.pdf

461-kolnp-2003-granted-form 1.pdf

461-kolnp-2003-granted-form 18.pdf

461-kolnp-2003-granted-form 2.pdf

461-kolnp-2003-granted-form 26.pdf

461-kolnp-2003-granted-form 3.pdf

461-kolnp-2003-granted-form 5.pdf

461-kolnp-2003-granted-reply to examination report.pdf


Patent Number 226459
Indian Patent Application Number 461/KOLNP/2003
PG Journal Number 51/2008
Publication Date 19-Dec-2008
Grant Date 17-Dec-2008
Date of Filing 16-Apr-2003
Name of Patentee CHIRON S.P.A.
Applicant Address VIA FIORENTIMA 1,53100 SIENA
Inventors:
# Inventor's Name Inventor's Address
1 TELFORD JHON C/O CHIRON SPA, OF VIA FIORENTIMA 1,53100 SIENA
2 MASIGNANI VEGA C/O CHIRON SPA, OF VIA FIORENTIMA 1,53100 SIENA
3 MARGARIT Y ROS IMMACULADA C/O CHIRON SPA, OF VIA FIORENTIMA 1,53100 SIENA
4 GRANDI GUIDO C/O CHIRON SPA, OF VIA FIORENTIMA 1,53100 SIENA
5 FRASER CLAIRE C/O THE INSTITUTE FOR GENOMIC RESEARCH 9712 MEDICAL CENTER DRIVE, ROCKVILLE, MARYLAND 20850
6 TETTELIN HERVE C/O THE INSTITUTE FOR GENOMIC RESEARCH 9712 MEDICAL CENTER DRIVE, ROCKVILLE, MARYLAND 20850
PCT International Classification Number C07K 14/195
PCT International Application Number PCT/GB01/04789
PCT International Filing date 2001-10-29
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 0105640.7 2001-03-07 U.K.
2 0026333.5 2000-10-27 U.K.
3 0028727.6 2000-11-24 U.K.