# Patent

## Title
Live, oral vaccine for protection against Shigella dysenteriae serotype 1

## Abstract

The invention relates to Salmonella typhi Ty21a comprising core-linked Shigella dysenteriae serotype 1 O-specific polysaccharide (O-Ps) and DNA encoding O antigen biosynthesis, said DNA selected from the group consisting of: a) the DNA sequence set out in any one of SEQ ID NOs: 1 and 2 and species homologs thereof; b) DNA encoding Shigella dysenteriae serotype 1 polypeptides encoded by any one of SEQ ID NOs: 1 and 2, and species homologs thereof; and c) DNA encoding a O antigen biosynthesis gene product that hybridizes under moderately stringent conditions to the DNA of (a) or (b); and related sequences, compositions of matter, vaccines, methods of using, and methods of making.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. patent application Ser. No. 14/145,104, filed Dec. 31, 2013, now U.S. Pat. No. 8,968,719, issued Mar. 3, 2015, which is a continuation of U.S. patent application Ser. No. 13/687,797, filed Nov. 28, 2012, now U.S. Pat. No. 8,790,635, issued Jul. 29, 2014, which is a continuation of U.S. patent application Ser. No. 13/285,614, filed Oct. 31, 2011, now U.S. Pat. No. 8,337,831, issued Dec. 25, 2012; which is a continuation of U.S. patent application Ser. No. 11/597,301, filed Sep. 21, 2007, now U.S. Pat. No. 8,071,113, issued Dec. 6, 2011; which is a national phase entry pursuant to 35 U.S.C. §371 of International Patent Application No. PCT/US2005/018198, filed May 24, 2005; which application claims the benefit of U.S. Provisional Patent Application No. 60/609,494, filed Sep. 13, 2004, and U.S. Provisional Patent Application No. 60/574,279, filed May 24, 2004; the disclosures of all of the foregoing applications are incorporated herein by reference in their entireties.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
The instant application was made with government support; the government has certain rights in this invention.


SEQUENCE LISTING
The Sequence Listing text file attached hereto, created Nov. 28, 2012, size 42 kilobytes, and filed herewith as file name “6137FDA3PUS12_SEQ_ST25.txt” is incorporated herein by reference in its entirety.
BACKGROUND OF THE INVENTION
Shigella cause millions of cases of dysentery (i.e., severe bloody diarrhea) every year, which result in 660,000 deaths worldwide. Shigella dysenteriae serotype 1, one of about 40 serotypes of Shigella, causes a more severe disease with a much higher mortality rate than other serotypes. There are no FDA-licensed vaccines available for protection against Shigella, although a number of institutions are trying various vaccine approaches. The fact that many isolates exhibit multiple antibiotic resistance complicates the management of dysentery infections. The development of an immunogenic composition against Shigella dysenteriae serotype 1 therefore represents a particularly urgent objective.
SUMMARY OF THE INVENTION
The invention relates to Salmonella typhi Ty21a comprising core-linked Shigella dysenteriae serotype 1 O-specific polysaccharide (O-Ps) and DNA encoding O antigen biosynthesis, said DNA selected from the group consisting of:

    
    
        (a) the DNA sequence set out in any one of SEQ ID NOs: 1 and 2 and species homologs thereof;
        (b) DNA encoding Shigella dysenteriae serotype 1 polypeptides encoded by any one of SEQ ID NOs: 1 and 2, and species homologs thereof; and
        (c) DNA encoding a O antigen biosynthesis gene product that hybridizes under moderately stringent conditions to the DNA of (a) or (b);

and related sequences, compositions of matter, vaccines, methods of using, and methods of making.

    
    





BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1. The genes necessary for biosynthesis of the Shigella dysenteriae serotype 1O-antigen.
FIG. 2. E. coli (pGB2-Sd1) was found to express Shigella dysenteriae serotype 1 O-antigen by both slide agglutination and immunoblot assays using Shigella dysenteriae serotype 1-specific antisera.
FIG. 3. Proposed sugar transferase requirements for synthesis of the Shigella dysenteriae serotype 1 O-polysaccharide repeat unit. Rfe is a GlcNac transferase which adds GlcNAc to ACL (antigen carrier lipid/acyl lipid carrier/undecaprenol phosphate); RfbR and RfbQ are Rha transferases; Rfp is a galactosyl transferase (Mol. Microbial. 1995, 18:209)
FIGS. 4A-4B. Expression analyses of LPS from various parental and plasmid-carrying strains. LPS was extracted from various strains as described below and separated on SDS-PAGE gels by electrophoresis. Resulting silver-stained material (4A) and a Western immunoblot (4B) reacted with anti-Shigella dysenteriae serotype 1 antisera are shown. In both parts (4A) and (4B), molecular weight markers are shown in the left-hand lane followed by extracted polysaccharide from E. coli carrying pGB2 (lane pGB2.E. coli), parent S. typhi Ty21a (lane Typhi Ty21a), Ty21a carrying pGB2-Sd1 (lane Sd1.Ty21a), E. coli carrying pGB2-Sd1 (lane Sd1.E. coli), the parent Shigella dysenteriae serotype 1 strain 1617 (lane Sd1 1617), or the rough Shigella dysenteriae serotype 1 strain 60R (lane Sd1 60R).













SEQUENCE SUMMARY








SEQ ID NO.
Description











1
9297 bp. Sequence of rfb locus of Shigella dysenteriae



serotype 1 strain 1617


2
1507 bp. rfp Sequence from Shigella dysenteriae serotype 



1 strain 1617.


3
rfbB


4
rfbC


5
rfbA


6
rfbD


7
rfbX


8
rfc


9
rfbR


10
rfbQ


11
orf9


12
rfp









DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT
Shigella dysenteriae serotype 1 causes the most severe form of shigellosis, often associated with hemolytic uremic syndrome in children, especially in developing countries. Due to the high level of Shiga toxin production and associated high morbidity/mortality, this organism is classified as a Category B bioterrorist threat agent. The lipopolysaccharide of Shigella dysenteriae serotype 1 is essential for virulence, and there is indirect evidence that antibodies against this O-specific polysaccharide (O-Ps) are protective to the host. Thus, there is considerable interest in the development of an O-Ps-based vaccine to protect against Shigella dysenteriae serotype 1. Previous studies showed that the determinants for the production of O antigen lipopolysaccharide in Shigella dysenteriae serotype 1 are distributed on the chromosome (i.e., rfb/rfc genes) and on a small 9-kb plasmid (i.e., rfp gene). The current studies were aimed at cloning the Rfb/Rfc region from strain 1617 to define all essential genes and develop a biosynthetic pathway for O-Ps biosynthesis. The plasmid-carried gene (i.e., the rfp-encoded galactosyl transferase) was also cloned from strain 1617; its 1.6 kb sequence was found to be >99% homologous to rfp previously analyzed from a different Shigella dysenteriae serotype 1 strain. Additionally, the chromosomal Rfb/Rfc region of 9 kb was cloned and sequenced, and found to contain 9 ORFs. Preliminary analysis suggests that all 9 ORFs plus rfp are necessary for serotype 1 LPS biosynthesis. We anticipate that the use of these characterized O-Ps genes in a live, attenuated Salmonella delivery system will lead to a safe, oral vaccine for protection against this severe form of shigellosis.
Introduction
Shigella spp. are the predominant cause of acute bloody diarrhea (dysentery) worldwide, and cause 660,000 deaths globally each year due to shigellosis. Infection with Shigella dysenteriae serotype 1 strains causes a more severe illness with higher mortality than with other Shigellae, particularly in young children and the elderly.
Protective immunity against shigellosis appears to be serotype-specific and protection correlates with the stimulation of immunity against the O-specific surface lipopolysaccharide.
The genes necessary for O-Ps synthesis in Shigella dysenteriae serotype 1 lie on a 9-kb small plasmid (i.e., the rfp gene) and on the chromosome (i.e., rfb cluster). A recombinant plasmid containing the essential Shigella dysenteriae serotype 1 O-antigen biosynthetic genes was previously constructed and introduced into E. coli or attenuated Salmonella spp. This plasmid construct was reported to be unstable when the strains were cultivated without selective pressure, and animal immunization resulted in less than 50% protection (Klee, S. R. et al. 1997 J Bacteriol 179:2421-2425).
The current studies were aimed at cloning the essential O-Ps biosynthetic machinery of Shigella dysenteriae serotype 1, deleting unnecessary adjacent sequences, and completing the DNA sequence analysis of the entire biosynthetic region to define a minimal essential set of genes.
Materials and Methods
1. Shigella dysenteriae serotype 1 strain 1617 was obtained from the culture collection of S. B. Formal, Walter Reed Army Institute of Research (WRAIR). The strain was originally isolated from an outbreak of epidemic Shiga bacillus dysentery in Guatemala, Central America, in 1968 (Mendizabal-Morris, C A. et al. 1971 J Trop Med Hyg 20:927-933). Plasmid and chromosomal DNA used in this study was prepared from this strain.
2. The plasmid rfp region and its cognate promoter and a  ̃9.5 kb rfb locus were first cloned into the pCR 2.1-TOPO vector separately. The insert DNA was confirmed by DNA sequence analysis, and then transferred into the low copy plasmid pGB2 for genetic stabilization.
3. DNA sequence analysis and BLAST homology searches were employed to characterize the essential biosynthetic gene region.
4. The parent Shigella dysenteriae serotype 1 strain 1617 and recombinant E. coli strains expressing the Shigella dysenteriae serotype 1 O-Ps were analyzed for expression by agglutination and immunoblot assays with specific anti-Shigella dysenteriae serotype 1 LPS antisera (Difco, Detroit).







TABLE 1







Summary of Shigella dysenteriae serotype 1 O-Ps ORFs










ORF
Gene name
Location
Proposed function













1
rfbB
756-1841
dTDP-D-glucose 4,6 dehydratase


2
rfbC
1841-2740
dTDP-4-dehydrorhamnose reductase


3
rfbA
2798-3676
Glucose-I-phosphate thymilytransferase


4
rfbD
3679-4236
dTDP-4-dehydrorhamnose 3,5-epimerase


5
rfbX
4233-5423
O-Ag transporter


6
rfc
5420-6562
O-Ag polymerase


7
rfbR
6555-7403
dDTP-rhamnosyl transferase


8
rfbQ
7428-8339
Rhamnosyltransferase


9
orf9
8349-8783
Galactosyltransferase (?)


10
rfp
1134 bp (on
Galactosyltransferase




small plasmid










SUMMARY
Referring to Table 1 and FIGS. 1-3:
1. The O-Ps biosynthetic determinants from Shigella dysenteriae serotype 1 strain 1617 were cloned from both the chromosome (i.e., rfb locus) and a small 9 kb plasmid (i.e., the rfp gene).
2. The separate rfb locus (GenBank accession: AY585348) and rfP region (GenBank accession: AY763519) covering  ̃11 kb total DNA were sequenced entirely and revealed a total of 10 ORFs apparently necessary for O-Ps biosynthesis.
3. A low copy pGB2 vector containing both the rfb and rfp loci in tandem linkage was constructed (i.e., pGB2-Sd1) and found to express Shigella dysenteriae serotype 1 O-Ps antigen.
4. Requirements for sugar linkage in the final O-Ps structure of Shigella dysenteriae serotype 1 are proposed.
5. We anticipate that use of this cloned antigen locus in a live, attenuated Salmonella delivery system will lead to a safe, oral vaccine for protection against this severe form of shigellosis.
Part 1
In one embodiment, the invention comprises a prokaryotic microorganism. Preferably, the prokaryotic microorganism is an attenuated strain of Salmonella. However, alternatively other prokaryotic microorganisms such as attenuated strains of Escherichia coli, Shigella, Yersinia, Lactobacillus, Mycobacteria, Listeria or Vibrio could be used. Examples of suitable strains of microorganisms include Salmonella typhimurium, Salmonella typhi, Salmonella dublin, Salmonella enteritidis, Escherichia coli, Shigella flexneri, Shigella sonnet, Vibrio cholera, and Mycobacterium bovis (BCG).
In a preferred embodiment the prokaryotic microorganism is Salmonella typhi Ty21a. Vivotif® Typhoid Vaccine Live Oral Ty21a is a live attenuated vaccine for oral administration only. The vaccine contains the attenuated strain Salmonella typhi Ty21a. (Germanier et al. 1975 J Infect. Dis. 131:553-558). It is manufactured by Bema Biotech Ltd. Berne, Switzerland. Salmonella typhi Ty21a is also described in U.S. Pat. No. 3,856,935.
As mentioned above, the attenuated strain of the prokaryotic microorganism is transformed with a nucleic acid encoding one or more O-Ps genes. The inventors found for the first time that, when this nucleic acid is expressed in the microorganisms, core-linked O-Ps LPS are generated.
In a further aspect, the present invention provides a composition comprising one or more of above attenuated prokaryotic microorganisms, optionally in combination with a pharmaceutically or physiologically acceptable carrier. Preferably, the composition is a vaccine, especially a vaccine for mucosal immunization, e.g., for administration via the oral, rectal, nasal, vaginal or genital routes. Advantageously, for prophylactic vaccination, the composition comprises one or more strains of Salmonella expressing a plurality of different O-Ps genes.
In a further aspect, the present invention provides an attenuated strain of a prokaryotic microorganism described above for use as a medicament, especially as a vaccine.
In a further aspect, the present invention provides the use of an attenuated strain of a prokaryotic microorganism transformed with nucleic acid encoding enzymes for O-Ps synthesis, wherein the O-Ps are produced in the microorganism, in the preparation of a medicament for the prophylactic or therapeutic treatment of bacterial infection.
Generally, the microorganisms or O-Ps according to the present invention are provided in an isolated and/or purified form, i.e., substantially pure. This may include being in a composition where it represents at least about 90% active ingredient, more preferably at least about 95%, more preferably at least about 98%. Such a composition may, however, include inert carrier materials or other pharmaceutically and physiologically acceptable excipients. A composition according to the present invention may include in addition to the microorganisms or O-Ps as disclosed, one or more other active ingredients for therapeutic or prophylactic use, such as an adjuvant.
The compositions of the present invention are preferably given to an individual in a “prophylactically effective amount” or a “therapeutically effective amount” (as the case may be, although prophylaxis may be considered therapy), this being sufficient to show benefit to the individual. The actual amount administered, and rate and time-course of administration, will depend on the nature and severity of what is being treated. Prescription of treatment, e.g., decisions on dosage etc, is within the responsibility of general practitioners and other medical doctors.
A composition may be administered alone or in combination with other treatments, either simultaneously or sequentially dependent upon the condition to be treated.
Pharmaceutical compositions according to the present invention, and for use in accordance with the present invention, may include, in addition to active ingredient, a pharmaceutically or physiologically acceptable excipient, carrier, buffer, stabilizer or other materials well known to those skilled in the art. Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient. The precise nature of the carrier or other material will depend on the route of administration.
Examples of techniques and protocols mentioned above can be found in Remington's Pharmaceutical Sciences, 16th edition, Osol, A. (ed), 1980.
The invention further relates to the identification and sequencing of 9 ORFs in the rfb locus (GenBank accession number: AY585348) and an ORF in the rfb locus (GenBank accession number: AY763519). These genes may be present in whole or in part in the vaccine strains described herein.
Accordingly, the present invention relates to vaccine strains further characterized by the presence of heterologous genes or a set of heterologous genes coding for O-Ps.
In a preferred embodiment of the vaccine strains, the heterologous gene(s) is (are) present either on a plasmid vector or stably integrated into the chromosome of said strain at a defined integration site which is to be nonessential for inducing a protective immune response by the carrier strain.
In a preferred embodiment, the heterologous genes of the invention, including all 9 ORFs from the rfb locus and the ORF from rfp, are present on a plasmid derived from pGB2 (Churchward et al. 1984 Gene 31:165-171). In another embodiment, the ninth ORF from rfb is not present, because it is not essential for O-Ps biosynthesis.
The ORFs may be under the control of the cognate promoter or other non-cognate promoters. The rfb genes may be separated and present on separate polynucleotide molecules under the control of different promoters, or on the same polynucleotide molecule in any order.
Alternatively, the above vaccine strains contain the rfbB, rfbC, and rfbA and/or any additional gene(s) necessary for the synthesis of complete core-linked O-antigen LPS which are integrated in tandem into a single chromosomal site or independently integrated into individual sites, or cloned into a plasmid or plasmids.
Such vaccine strains allow expression of heterologous O-Ps which is covalently coupled to a heterologous LPS core region, which, preferably, exhibits a degree of polymerization essentially indistinguishable from that of native LPS produced by the enteric pathogen. Such vaccine strains can, if desired, modified in such a way that they are deficient in the synthesis of homologous LPS core.
The invention also relates to a live vaccine comprising the above vaccine strain and optionally a pharmaceutically or physiologically acceptable carrier and/or a buffer for neutralizing gastric acidity and/or a system for delivering said vaccine in a viable state to the intestinal tract.
Said vaccine comprises an immuno-protective or -therapeutic and non-toxic amount of said vaccine strain. Suitable amounts can be determined by the person skilled in the art and are typically 107 to 109 bacteria.
Pharmaceutically and physiologically acceptable carriers, suitable neutralizing buffers, and suitable delivering systems can be selected by the person skilled in the art.
In a preferred embodiment said live vaccine is used for immunization against gram-negative enteric pathogens.
The mode of administration of the vaccines of the present invention may be any suitable route which delivers an immunoprotective or immunotherapeutic amount of the vaccine to the subject. However, the vaccine is preferably administered orally or intranasally.
The invention also relates to the use of the above vaccine strains for the preparation of a live vaccine for immunization against gram-negative enteric pathogens. For such use the vaccine strains are combined with the carriers, buffers and/or delivery systems described above.
The invention also provides polypeptides and corresponding polynucleotides required for synthesis of core linked O-specific polysaccharide. The invention includes both naturally occurring and unnaturally occurring polynucleotides and polypeptide products thereof. Naturally occurring O antigen biosynthesis products include distinct gene and polypeptide species as well as corresponding species homologs expressed in organisms other than Shigella dysenteriae serotype 1 strains. Non-naturally occurring O antigen biosynthesis products include variants of the naturally occurring products such as analogs and O antigen biosynthesis products which include covalent modifications. In a preferred embodiment, the invention provides O antigen biosynthesis polynucleotides comprising the sequences set forth in SEQ ID NOs: 1 and 2 and species homologs thereof, and polypeptides having amino acids sequences encoded by the polynucleotides.
The present invention provides novel purified and isolated Shigella dysenteriae serotype 1 polynucleotides (e.g., DNA sequences and RNA transcripts, both sense and complementary antisense strands) encoding the bacterial O antigen biosynthesis gene products. DNA sequences of the invention include genomic and cDNA sequences as well as wholly or partially chemically synthesized DNA sequences. Genomic DNA of the invention comprises the protein coding region for a polypeptide of the invention and includes variants that may be found in other bacterial strains of the same species. “Synthesized,” as used herein and is understood in the art, refers to purely chemical, as opposed to enzymatic, methods for producing polynucleotides. “Wholly” synthesized DNA sequences are therefore produced entirely by chemical means, and “partially” synthesized DNAs embrace those wherein only portions of the resulting DNA were produced by chemical means. Preferred DNA sequences encoding Shigella dysenteriae serotype 1 O antigen biosynthesis gene products are set out in SEQ ID NOs: 1 and 2, and species homologs thereof.
The worker of skill in the art will readily appreciate that the preferred DNA of the invention comprises a double-stranded molecule, for example, molecules having the sequences set forth in SEQ ID NOs: 1 and 2 and species homologs thereof, along with the complementary molecule (the “non-coding strand” or “complement”) having a sequence deducible from the sequence of SEQ ID NOs: 1 and 2, according to Watson-Crick basepairing rules for DNA. Also preferred are polynucleotides encoding the gene products encoded by any one of the polynucleotides set out in SEQ ID NOs: 1 and 2 and species homologs thereof.
The invention also embraces DNA sequences encoding bacterial gene products which hybridize under moderately to highly stringent conditions to the non-coding strand, or complement, of any one of the polynucleotides set out in SEQ ID NOs: 1 and 2, and species homologs thereof. DNA sequences encoding O antigen biosynthesis polypeptides which would hybridize thereto but for the degeneracy of the genetic code are contemplated by the invention. Exemplary high stringency conditions include a final wash in buffer comprising 0.2×SSC/0.1% SDS, at 65° C. to 75° C., while exemplary moderate stringency conditions include a final wash in buffer comprising 2×SSC/0.1% SDS, at 35° C. to 45° C. It is understood in the art that conditions of equivalent stringency can be achieved through variation of temperature and buffer, or salt concentration as described in Ausubel, et al. (eds.), Short Protocols in Molecular Biology, John Wiley & Sons (1994), pp. 6.0.3 to 6.4.10. Modifications in hybridization conditions can be empirically determined or precisely calculated based on the length and the percentage of guanosine-cytosine (GC) base pairing of the probe. The hybridization conditions can be calculated as described in Sambrook, et al., (eds.), Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y. (1989), pp. 9.47 to 9.51.
Autonomously replicating recombinant expression constructions such as plasmid and viral DNA vectors incorporating O antigen biosynthesis gene sequences are also provided. Expression constructs wherein O antigen biosynthesis polypeptide-encoding polynucleotides are operatively linked to an endogenous or exogenous expression control DNA sequence and a transcription terminator are also provided. The O antigen biosynthesis genes may be cloned by PCR, using Shigella dysenteriae serotype 1 genomic DNA as the template. For ease of inserting the gene into expression vectors, PCR primers are chosen so that the PCR-amplified gene has a restriction enzyme site at the 5′ end preceding the initiation codon ATG, and a restriction enzyme site at the 3′ end after the termination codon TAG, TGA or TAA. If desirable, the codons in the gene are changed, without changing the amino acids, according to E. coli codon preference described by Grosjean and Fiers, 1982 Gene 18: 199-209; and Konigsberg and Godson, 1983 PNAS USA 80:687-691. Optimization of codon usage may lead to an increase in the expression of the gene product when produced in E. coli. If the gene product is to be produced extracellularly, either in the periplasm of E. coli or other bacteria, or into the cell culture medium, the gene is cloned without its initiation codon and placed into an expression vector behind a signal sequence.
According to another aspect of the invention, host cells are provided, including procaryotic and eukaryotic cells, either stably or transiently transformed, transfected, or electroporated with polynucleotide sequences of the invention in a manner which permits expression of O antigen biosynthesis polypeptides of the invention. Expression systems of the invention include bacterial, yeast, fungal, viral, invertebrate, and mammalian cells systems. Host cells of the invention are a valuable source of immunogen for development of anti-bodies specifically immunoreactive with the O antigen biosynthesis gene product. Host cells of the invention are conspicuously useful in methods for large scale production of O antigen biosynthesis polypeptides wherein the cells are grown in a suitable culture medium and the desired polypeptide products are isolated from the cells or from the medium in which the cells are grown by, for example, immunoaffinity purification or any of the multitude of purification techniques well known and routinely practiced in the art. Any suitable host cell may be used for expression of the gene product, such as E. coli, other bacteria, including P. multocida, Bacillus and S. aureus, yeast, including Pichia pastoris and Saccharomyces cerevisiae, insect cells, or mammalian cells, including CHO cells, utilizing suitable vectors known in the art. Proteins may be produced directly or fused to a peptide or polypeptide, and either intracellularly or extracellularly by secretion into the periplasmic space of a bacterial cell or into the cell culture medium. Secretion of a protein requires a signal peptide (also known as pre-sequence); a number of signal sequences from prokaryotes and eukaryotes are known to function for the secretion of recombinant proteins. During the protein secretion process, the signal peptide is removed by signal peptidase to yield the mature protein.
To simplify the protein purification process, a purification tag may be added either at the 5′ or 3′ end of the gene coding sequence. Commonly used purification tags include a stretch of six histidine residues (U.S. Pat. Nos. 5,284,933 and 5,310,663), a streptavidin affinity tag described by Schmidt and Skerra, (1993 Protein Engineering 6:109-122), a FLAG peptide (Hopp et al. 1988 Biotechnology 6:1205-1210), glutathione 5-transferase (Smith and Johnson, 1988 Gene 67:31-40), and thioredoxin (LaVallie et at. 1993 Bio/Technology 11:187-193). To remove these peptide or polypeptides, a proteolytic cleavage recognition site may be inserted at the fusion junction. Commonly used proteases are factor Xa, thrombin, and enterokinase.
The invention also provides purified and isolated Shigella dysenteriae serotype 1 O antigen biosynthesis polypeptides encoded by a polynucleotide of the invention. Presently preferred are polypeptides comprising the amino acid sequences encoded by any one of the polynucleotides set out in SEQ ID NOs: 1 and 2, and species homologs thereof. The invention embraces O antigen biosynthesis polypeptides encoded by a DNA selected from the group consisting of:
a) the DNA sequence set out in any one of SEQ ID NOs: 1 and 2 and species homologs thereof;
b) DNA molecules encoding Shigella dysenteriae serotype 1 polypeptides encoded by any one of SEQ ID NOs: 1 and 2, and species homologs thereof; and
c) a DNA molecule encoding a O antigen biosynthesis gene product that hybridizes under moderately stringent conditions to the DNA of (a) or (b).
The invention also embraces polypeptides that have at least about 99%, at least about 95%, at least about 90%, at least about 85%, at least about 80%, at least about 75%, at least about 70%, at least about 65%, at least about 60%, at least about 55%, and at least about 50% identity and/or homology to the preferred polypeptides of the invention. Percent amino acid sequence “identity” with respect to the preferred polypeptides of the invention is defined herein as the percentage of amino acid residues in the candidate sequence that are identical with the residues in the O antigen biosynthesis gene product sequence after aligning both sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Percent sequence “homology” with respect to the preferred polypeptides of the invention is defined herein as the percentage of amino acid residues in the candidate sequence that are identical with the residues in one of the O antigen biosynthesis polypeptide sequences after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and also considering any conservative substitutions as part of the sequence identity. Conservative substitutions can be defined as set out in Tables A and B.







TABLE A







Conservative Substitutions I











SIDE CHAIN
CHARACTERISTIC
AMINO ACID







Aliphatic
Non-polar
G, A, P





I, L, V




Polar-uncharged
C, S, T, M





N, Q




Polar-charged
D, E





K, R



Aromatic

H, F, W, Y



Other

N, Q, D, E










Polypeptides of the invention may be isolated from natural bacterial cell sources or may be chemically synthesized, but are preferably produced by recombinant procedures involving host cells of the invention. O antigen biosynthesis gene products of the invention may be full length polypeptides, biologically active fragments, or variants thereof which retain specific biological or immunological activity. Variants may comprise O antigen biosynthesis polypeptide analogs wherein one or more of the specified (i.e., naturally encoded) amino acids is deleted or replaced or wherein one or more non-specified amino acids are added: (1) without loss of one or more of the biological activities or immunological characteristics specific for the O antigen biosynthesis gene product; or (2) with specific disablement of a particular biological activity of the O antigen biosynthesis gene product. Deletion variants contemplated also include fragments lacking portions of the polypeptide not essential for biological activity, and insertion variants include fusion polypeptides in which the wild-type polypeptide or fragment thereof have been fused to another polypeptide.
Variant O antigen biosynthesis polypeptides include those wherein conservative substitutions have been introduced by modification of polynucleotides encoding polypeptides of the invention. Conservative substitutions are recognized in the art to classify amino acids according to their related physical properties and can be defined as set out in Table A (from W097/09433, page 10). Alternatively, conservative amino acids can be grouped as defined in Lehninger, (Biochemistry, Second Edition; W.H. Freeman & Co. 1975, pp.71-77) as set out in Table B.







TABLE B







Conservative Substitutions II










SIDE CHAIN CHARACTERISTIC
AMINO ACID







Non-polar (hydrophobic)




A. Aliphatic:
A, L, I, V, P



B. Aromatic:
F, W



C. Sulfur-containing:
M



D. Borderline:
G



Uncharged-polar




A. Hydroxyl:
S, T, Y



B. Amides:
N, Q



C. Sulfhydryl:
C



D. Borderline:
G



Positively Charged (Basic):
K, R, H



Negatively Charged (Acidic):
D, E










Variant O antigen biosynthesis products of the invention include mature O antigen biosynthesis gene products, i.e., wherein leader or signal sequences are removed, having additional amino terminal residues. O antigen biosynthesis gene products having an additional methionine residue at position −1 are contemplated, as are O antigen biosynthesis products having additional methionine and lysine residues at positions −2 and −1. Variants of these types are particularly useful for recombinant protein production in bacterial cell types. Variants of the invention also include gene products wherein amino terminal sequences derived from other proteins have been introduced, as well as variants comprising amino terminal sequences that are not found in naturally occurring proteins.
The invention also embraces variant polypeptides having additional amino acid residues which result from use of specific expression systems. For example, use of commercially available vectors that express a desired polypeptide as fusion protein with glutathione-S-transferase (GST) provide the desired polypeptide having an additional glycine residue at position −1 following cleavage of the GST component from the desired polypeptide. Variants which result from expression using other vector systems are also contemplated.
Also comprehended by the present invention are antibodies (e.g., monoclonal and polyclonal antibodies, single chain antibodies, chimeric antibodies, humanized, human, and CDR-grafted antibodies, including compounds which include CDR sequences which specifically recognize a polypeptide of the invention) and other binding proteins specific for O antigen biosynthesis gene products or fragments thereof. The term “specific for” indicates that the variable regions of the antibodies of the invention recognize and bind a O antigen biosynthesis polypeptide exclusively (i.e., are able to distinguish a single O antigen biosynthesis polypeptides from related O antigen biosynthesis polypeptides despite sequence identity, homology, or similarity found in the family of polypeptides), but may also interact with other proteins (for example, S. aureus protein A or other antibodies in ELISA techniques) through interactions with sequences outside the variable region of the antibodies, and in particular, in the constant region of the molecule. Screening assays to determine binding specificity of an antibody of the invention are well known and routinely practiced in the art. For a comprehensive discussion of such assays, see Harlow et al. (eds.), Antibodies A Laboratory Manual; Cold Spring Harbor Laboratory; Cold Spring Harbor, N.Y. (1988), Chapter 6. Antibodies that recognize and bind fragments of the O antigen biosynthesis polypeptides of the invention are also contemplated, provided that the antibodies are first and foremost specific for, as defined above, a O antigen biosynthesis polypeptide of the invention from which the fragment was derived.
Part II
Molecular Characterization of Genes for Shigella Dysenteriae Serotype 1 O-Antigen and Expression in a Live Salmonella Vaccine Vector 
Abstract
Shigella dysenteriae serotype 1, a bioterrorist threat agent, causes the most severe form of shigellosis and is typically associated with high mortality rates, especially in developing countries. This severe disease is due largely to Shiga-toxin-induced hemorrhagic colitis, plus hemolytic uremic syndrome in children. The lipopolysaccharide of Shigella dysenteriae serotype 1 is essential for virulence, and there is substantial evidence that antibodies against Shigella O-specific polysaccharide (O-Ps) are protective to the host. Thus, there is considerable interest in the development of an O-Ps-based vaccine to protect against Shigella dysenteriae serotype 1. Previous studies have shown that the genetic determinants for the production of O-Ps antigen in Shigella dysenteriae serotype 1 are uniquely distributed on the chromosome (i.e., rfb genes) and on a small 9 kb plasmid (i.e., the rfp gene). In the current studies, the multi-ORF rfb gene cluster and the rfp gene with their cognate promoter regions have been amplified by PCR from Shigella dysenteriae serotype 1 strain 1617. The two interrelated biosynthetic gene loci were then cloned and sequenced. Sequencing studies revealed 9 ORFs located in the amplified 9.2 kb rfb region. Further deletion studies showed that only eight ORFs in the rfb region are necessary, together with rfp, for Shigella dysenteriae serotype 1 O-Ps biosynthesis. A linked rfb-rfp gene region cassette was constructed and cloned into the low copy plasmid pGB2, resulting in the recombinant plasmid designated pGB2-Sd1. When introduced by transformation into either Salmonella enterica serovar Typhi Ty21a or E. coli K-12, pGB2-Sd1 directed the formation of surface-expressed, core-linked Shigella dysenteriae serotype 1 O-specific lipopolysaccharide. Silver stain and Western immunoblotting analyses showed that the distribution of O repeat units in S. typhi or E. coli K-12 was similar when compared with the pattern observed for the wild type strain 1617 of Shigella dysenteriae serotype 1. In addition, a proposed biopathway, based upon ORF sequence homologies to known genes, was developed. We anticipate that the insertion of these jointly-cloned, O-Ps biosynthetic loci in a live, bacterial vaccine delivery system, such as attenuated S. typhi, will produce a safe, oral vaccine for protection against this severe form of shigellosis.
Introduction
Bacillary dysentery is a severe inflammation of the colon caused classically by the entero-invasive bacterial genus Shigella. The estimated number of bacillary dysentery infections worldwide is over 200 million annually, with more than 650,000 associated deaths globally each year (Kotloff, K. L. et al. 1999 Bull World Health Organ 77:651-66). Shigellosis, especially in developing countries, is predominantly a disease of childhood. More than half of the cases occur in children less than 5 years of age, Shigellosis is highly transmissible due to the very low infective dose of Shigella (i.e., <100 bacteria) and bacterial spread via the fecal-oral route (DuPont, H. L. et al. 1989 J Infect Dis 159:1126-1128). Shigella dysenteriae serotype 1 (Shiga 1) is the primary causative agent of epidemic outbreaks of severe bacillary dysentery which is associated with increased mortality. Due to the presence of high levels of Shiga toxin produced by Shigella dysenteriae serotype 1 strains, infections are more severe than those caused by other Shigella spps. and are often characterized by serious complications (e.g., hemolytic-uremic syndrome, hemorrhagic colitis, sepsis, and purpura) (Levine, M. M. 1982 Med Clin North Am 66:623-638). In addition, the emergence of strains resistant to multiple antibiotics makes therapeutic treatment difficult, particularly in developing countries, and emphasizes the need for vaccines in disease control. For these reasons, the World Health Organization (WHO) has given high priority to the development of a protective vaccine against Shigella dysenteriae serotype 1 (Oberhelman, R. A. et al. 1991 Bull World Health Organ 69:667-676). The increased concern for the potential use of this food- and water-borne pathogen of high morbidity and mortality as a bioterrorist agent has recently amplified the interest in developing an anti-Shiga 1 vaccine.
Protective immunity against shigellosis is serotype-specific and correlates with stimulation of both systemic and local intestinal immunity against the O-specific surface lipopolysaccharide (LPS) (Viret, J. F. et al. 1994 Biologicals 22:361-372; Winsor, D. K. et al. 1988 J Infect Dis 158:1108-1112). Genes for Shigella dysenteriae serotype 1 O antigen biosynthesis are uniquely located in two unlinked gene clusters; one gene, rfp is located unusually on a 9 kb multicopy plasmid (Watanabe, H. et al. 1984 Infect Immun 43:391-396), and the remaining biosynthetic genes are clustered, as usual, in the rfb chromosomal locus (Hale, T. L. et al. 1984 Infect Immun 46:470-5; Sturm, S. et al. 1986 Microb Pathog 1:289-297). The O-Ps of Shigella dysenteriae serotype 1 consists of the repeating tetrasaccharide unit: -3)-alpha-L-Rhap (1-3)-alpha-L-Rhap (1-2)-alpha-D-Galp (1-3)-alpha D-GlcNAcp (1-core oligosaccharide. (Dmitriev, B. A. et al. 1976 Eur J Biochem 66:559-566; Falt, I. C. et al. 1996 Microb Pathog 20:11-30.)
The availability of a safe Salmonella typhi live, oral vaccine strain since late 1970's stimulated new research efforts with the goals of expressing protective antigens (e.g., Shigella O-Ps) in an S. typhi carrier that could be used as a hybrid vaccine (e.g., to protect against bacillary dysentery or other diseases) (Formal, S. B. et al. 1981 Infect Immun 34:746-50). In this initial study, the S. typhi Ty21a strain was employed as a delivery vector for expression of the form 1 O-Ps antigen of S. sonnei. However, the protection in volunteers provided by immunizing with this hybrid vaccine strain varied (Herrington, D. A. et al. 1990 Vaccine 8:353-357), presumably due to spontaneous, high frequency deletion of the form 1 gene region from a very large 300 kb cointegrate plasmid in vaccine strain 5076-IC (Hartman, A. B. et al. 1991 J Clin Microbiol 29:27-32). In more recent studies, we have constructed a refined S. sonnei-Ty21a bivalent vaccine strain by using the defined O antigen gene cluster cloned into a genetically stable low copy plasmid. This refined hybrid vaccine strain showed highly stable expression of form 1 antigen and following immunization it protected mice against a stringent challenge with virulent S. sonnei (Xu, D. Q. et al. 2002 Infect Immun 70:4414-23).
In a similar vaccine development approach, the rfp gene and genes of the rfb cluster of Shigella dysenteriae serotype 1 were introduced together into attenuated strains of S. typhimurium (Falt, I. C. et al. 1996 Microb Pathog 20:11-30), S. typhi (Mills, S. D. et al. 1988 Vaccine 6:11622), or Shigella flexneri (Klee, S. R. et al. 1997 Infect Immun 65:2112-2118) to create vaccine candidates for protection from this Shigella serotype. However, the Shigella dysenteriae serotype 1 O-Ps antigen was expressed as core-linked in Shigella and in S. typhimurium (Falt, I. C. et al. 1996 Microb Pathog 20: 11-30), but was reportedly not core-linked in S. typhi (Mills, S. D. et al. 1988 Vaccine 6:116-22). In the current studies, the Shigella dysenteriae serotype 1 O antigen gene loci were cloned, sequenced completely and analyzed. Putative genes involved in synthesis of the tetrasaccharide O-repeating unit including L-Rhap, L-Rhap, D-Galp, and D-GlcNAcp, as well as genes for O-unit processing and polymerization were identified. The four Rfb genes involved in rhamnose biosynthesis in Shigella dysenteriae serotype 1 were found to be identical to those of E. coli 026, indicating common ancestry. In contrast to a previous report, analyses for the expression of LPS in S. typhi Ty21a carrying the Shigella dysenteriae serotype 1 O-antigen encoding rfb-rfp genes showed that the O-antigen repeat units are linked to the Salmonella typhi core and are envisioned as stimulating protection in mice against challenge with virulent Shigella dysenteriae serotype 1.
Materials and Methods
Bacterial strains, plasmids and growth conditions. The bacterial strains and plasmids utilized are described in Table 2. The wild type parent Shigella dysenteriae serotype 1 strain 1617 was obtained from S. B. Formal, Walter Reed Army Institute of Research (WRAIR) (Neill, R. J. et al. 1988 J Infect Dis 158:737-741). The strain was originally isolated from an outbreak of epidemic Shiga bacillus dysentery in Guatemala, Central America, in 1968 or early 1969 (Mendizabal-Morris, C A. et al. 1971 J Trop Med Hyg 20:927-933). The isolated strain 1617 was lyophilized and has been stored in sealed glass ampules. This strain is sensitive to ampicillin, spectinomycin, streptomycin, tetracycline, chloramphenicol, and kanamycin. Strain 1617 was used to obtain the O-antigen biosynthetic genes and as a positive control for LPS expression analyses. Studies of plasmid-based Shigella dysenteriae serotype 1 LPS expression were performed in Escherichia coli DH5α, and Salmonella enterica serovar Typhi strain Ty21a. Shigella dysenteriae serotype 1 strain 60R (rough strain, Spcr which has lost the small plasmid carrying rfp) was used as an LPS-negative control.







TABLE 2







Bacterial strains and plasmids











Reference or


Strain or plasmid
Genotype or description
source





E. coli DH5α
supE44 hsdR17 recA1 endA1 gyrA96 thi-1 relA1
Sambrook, J. et al.



(E. coli K12-origined)
1989 Molecular




cloning: a laboratory




manual, 2nd ed. Cold




Spring Harbor




Laboratory Press,




Cold Spring Harbor,




N.Y.


E. coli XL 1-blue
supE44 hsdR17 rec A1 endA1 gyrA96 thi-1 relA1
Sambrook, J. et al.



lac[F′ proAB lacIq ZM15Tn10 (Tetr)] (K12-
1989 (supra)



DH5α-origined)



E. coli TOP10F′
F′ {lacIq Tn10 (Tetr} mcrA Δ(mmr-hsdRMS-
Invitrogen



mcrBC) φ80lacZ ΔM15 Δ lacX74 recA1araD139




Δ(ara-leu)7697 galU galK rpsL (Strr) endA1 nupG



Salmonella enterica
serovar Typhi Ty21a galE ilvD viaB (Vi) h2S
Germanier, R. and E.




Furer 1975 J Infect




Dis 131: 553-558


Shigella dysenteriae
1617, virulent
S. Formal (Neill, R. J.


serotype 1

et al. 1988 J Infect Dis




158: 737-741)


Shigella dysenteriae
rough LPS mutant missing rfp plasmid
S. Formal (Neill, R. J.


serotype 1 60R

et al. 1988 J Infect Dis




158: 737-741)







Plasmid









pGB2
pSC101 derivative, low copy plasmid; Smr, Spcr
Churchward, G. et al.




1984 Gene 31: 165-171


pCR2.1-TOPO
PCR TA cloning vector, pUC origin, Ampr Kanr
Invitrogen


pXK-Tp
pCR2.1-TOPO containing rfp gene of strain 1617,
this study



Ampr Kanr



pXK-Bp56
pGB2 containing rfp gene of strain 1617, Spcr
this study


pXK-T4
pCR2.1-TOPO containing rfb gene cluster, Ampr
this study



Kanr



pGB2-Sd1
pGB2 containing S. dysenteriae rfb-rfp gene
this study



cassette, Spcr









Plasmids pGB2 (which is derived from plasmid pSC101) and pCR2.1-TOPO (Invitrogen) were used for cloning and subcloning. Bacterial strains were grown at 37° C. in Luria-Bertani (LB) broth or on LB agar (Difco). S. enterica serovar Typhi Ty21a strain was grown in SOB (soy broth) medium (Difco). Plasmid-containing strains were selected in medium containing ampicillin (Amp; 100 μg/ml for E. coli and 25 μg/ml for S. enterica serovar Typhi or spectinomycin (Spc; 100 μg for E. coli, 50 μg/ml for S. enterica serovar Typhi Ty21a).
PCR and DNA cloning. Unless otherwise noted all DNA manipulations were performed essentially by following the procedures outlined by Sambrook et al. (Sambrook, J. et al. 1989 Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.) or by following instructions provided with various commercially available reagents and kits, including a genomic DNA purification kit, plasmid purification kits and PCR products purification kits (Promega, Madison Wis.). Restriction enzymes (Roche) were used with the supplied buffers. Plasmid electroporation was performed with a Gene Pulser (Bio-Rad). All PCR reactions were conducted with ExTaq or LA-Taq (Takara Co).
Genomic DNA of Shigella dysenteriae serotype 1 strain 1617, isolated with a genomic DNA purification kit, was used as a PCR template to generate the 9.2 kb DNA fragment containing the rfb locus. A 1.6 kb DNA fragment containing the rfp gene was synthesized by PCR from Shigella dysenteriae serotype 1 strain 1617 genomic template material-treated by boiling. The PCR products were used for sequencing studies and for construction of the rfb-rfp linked gene region cassette. Sequencing templates included PCR products from 1.6 kb to 9.2 kb in Size.
O-Ps expression analyses. Slide agglutination was performed with rabbit antisera against Shigella dysenteriae serotype 1 (B-D Co., Sparks, Md. USA). For immunoblotting, Salmonella, Shigella, and E. coli strains with or without various recombinant plasmids were grown overnight with aeration at 37° C. in LB media containing appropriate antibiotics. Bacteria were pelleted by centrifugation and were lysed in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) sample buffer containing 4% 2-mercaptoethanol. The samples were heated at 95° C. for 5 min, and treated with proteinase K for 1 hr, and LPS samples were fractionated by 16% Tris-Glycine-SDS-PAGE on a Novex mini-cell gel apparatus (Invitrogen Life Technologies) at 30 mA until tracing dye had left the gel. For immunoblotting, LPS bands were transferred to polyvinylidene floride membranes (Schleicher & Schuell, Germany). The membranes were blocked with 5% nonfat dry milk in Tris-buffered saline (TBS: 20 mM Tris-HCl, 150 mM NaCl, pH 7.5) and were reacted with rabbit polyclonal antibodies against the O antigen of either Shigella dysenteriae serotype 1 or Salmonella typhi (Difco Laboratories, Michigan, USA), followed by protein A-alkaline phosphatase conjugate. The developing solution consisted of 200 mg of Fast Red TR salt and 100 mg of Naphthol NS-MX phosphate (Sigma) in 50 mM Tris buffer, pH 8.0). The silver staining analysis was performed using SilverXpress Silver Staining Kit (Invitrogen) according to the manufacturer's instructions.
DNA sequence and analysis. DNA sequencing was performed with Ready Reactions DyeDeoxy Terminator cycle sequencing kits (Applied Biosystems) and an ABI model 373A automated sequencer. The PCR products including the 9.2 kb rfb region and the 1.6 kb rfp gene region, amplified from genomic DNA of Shigella dysenteriae serotype 1 strain 1617, were used for sequencing and construction of the linked rfb-rfp gene cassette. Sequences were assembled and analyzed by using the Vector NTI suite 9.0 software (InforMax, Inc.). DNA homology searches were performed by using the Basic Local Alignment Search Tool (BLAST) of National Center for Biotechnology Information. Putative promoters were identified by using MacVector 6.5 (Accelrys, Burlington, Mass.). The JUMPstart sequence was found by using NIH Computational Molecular Biology software, GCG-Left Sequence Comparison Tools, and the JUMPstart sequence identified from our previous studies at an upstream region of the S. sonnei O antigen locus (Xu, D. Q. et al. 2002 Infect Immun 70:4414-23). In order to confirm the fidelity of our sequence data obtained from LA Taq PCR products, the Computational Molecular Biology software, GCG-Left Sequence Comparison Tools was also used to compare with homologous sequences from a different Shigella dysenteriae serotype 1 strain provided by the Sanger Sequencing Institute.
Growth curves and stability of O-antigen expression in the recombinant vaccine strain. Several studies were conducted to determine if the Salmonella vaccine strains carrying a rfb/rfp recombinant expression plasmid are efficient for growth and stably express the Shiga-1 O-antigen. First, growth curves of recombinant strains and control bacteria under different growth conditions were compared. Shigella dysenteriae serotype 1 O-antigen-specific positive colonies of Sd1-Ty21a and Sd1-E. coli were inoculated into LB broth with or without antibiotic. Overnight cultures of each strain were diluted to an OD600 of approximately 0.1, and growth to the stationary phase was monitored.
Animal immunization study. We are in the process of conducting animal protection studies to confirm safety and efficacy. In another embodiment, we envision removing any antibiotic resistance gene from the final plasmid construct and inserting a different selection marker (e.g., a heavy metal ion resistance gene, such as mercury resistance gene) in place of antibiotic resistance to allow for genetic manipulations. In yet another embodiment, we envision inserting a gene encoding for the Shiga toxin B subunit, which is nontoxic but stimulates immunity to whole Shiga toxin, into the final vaccine strain. Thus, in this embodiment, the final vaccine will trigger antibodies against Shigella dysenteriae serotype 1 LPS and against Shiga toxin to give better protection against Shigella dysenteriae serotype 1, and it is envisioned as providing protection against Shiga toxin-producing E. coli strains to prevent the occurrence of hemolytic uremic syndrome caused by Shiga toxin-mediated damage to the kidneys.
Results
Cloning the essential Shigella dysenteriae serotype 1 O-Ps biosynthetic genes and construction of an O-antigen gene expression cassette. Previous studies showed that the determinants for the production of O antigen lipopolysaccharide in Shigella dysenteriae serotype 1 are distributed on the chromosome (i.e., rfb genes) and on a small 9-kb plasmid (FIG. 1). The DNA fragment containing the rfp gene was first synthesized by PCR from the whole cell lysate (treated by boiling) of Shigella dysenteriae serotype 1 strain 1617 with the two primers listed below and based upon the previously published DNA sequence (GenBank Accession #: M96064): dy5: ttatttccagactccagctgtcattatg (SEQ ID NO: 13); dy6: ccatcgatattggctgggtaaggtcat (SEQ ID NO: 14).
The 1.6 kb PCR fragment was cloned into the pCR 2.1-TOPO cloning vector (Invitrogen). The resulting TOPO-rfp recombinant plasmid, designated pXK-Tp, was digested with EcoRI, then the EcoRI fragment containing the rfp gene was cloned into the EcoRI site of the low copy plasmid pGB2. The resulting pGB2-rfp recombinant plasmid was designated pXK-Bp56.
The large DNA fragment containing the 9.2 kb rfb gene cluster was amplified from Shigella dysenteriae serotype 1 genomic DNA directly by using LA Taq polymerase (Takara) cocktail that combines the proven performance of Taq polymerase with an efficient 3′-5′ exonuclease activity for increased proofreading fidelity. The primers used in this amplification are: SalI-N: cgtatgtcgactgagctctctgaatactctgtcatccagaccaaa (SEQ ID NO: 15) (ref. to GenBank Accession #: AF529080) (a Sail restriction site is created); BamHI-C: tatcagcttttcactcaactcggcggatccgccctcatac (SEQ ID NO: 16) (ref. to GenBank Accession #: L07293) (a BamHI-C restriction site is created).
Using BLAST, we found that one of four genes which encodes enzymes involved in rhamnose biosynthesis of E. coli 026 strain has extensive homology with a gene (rfbD) of Shigella dysenteriae serotype 1 which has predicted involvement in rhamnose biosynthesis. In order to identify a potential primer binding site adjacent to the N-terminal region of the rfb gene cluster of Shigella dysenteriae serotype 1, a series of primers recognizing the N-terminal sequence adjacent to the O-antigen gene cluster of E. coli 026 were synthesized. We successfully produced a 9.2 kb DNA fragment by PCR using a primer (i.e., SalI-N) synthesized from the N-terminus of the O-antigen gene cluster of E. coli 026 and another primer (i.e., BamHI-C) synthesized from the previously defined C-terminal region adjacent to the rfb gene cluster of Shigella dysenteriae serotype 1 and using genomic DNA of Shigella dysenteriae serotype 1 1617 as a template. Previous studies indicated that this 9.2 kb DNA fragment contained all essential ORFs of the rfb gene cluster.
The 9.2 kb PCR DNA fragment containing the rfb gene locus was first cloned into the pCR 2.I-TOPO cloning vector (Invitrogen), resulting in plasmid pXK-T4. In order to combine this rfb gene cluster with the cloned rfp gene, plasmid pXK-T4 was digested with BamHI and SalI, and the 9.2 kb BamHI-SalI fragment was cloned into plasmid pXK-Bp56, which had been cleaved with BamHI and SalI, to produce the linked rfb-rfp gene expression cassette. The resulting new recombinant low copy pGB-2 derivative plasmid was designated pGB2-Sd1 (FIG. 2). As shown in FIG. 2, the rfp gene encoding galactosyl transferase is located downstream of the rfb gene cluster and both contain their cognate promoter regions. After pGB2-Sd1 electroporation into E. coli or S. typhi, colonies that express Shigella dysenteriae serotype 1 O-antigen were identified by colony immunoblotting with Shiga 1-specific antiserum.
Expression of Shigella dysenteriae serotype 1 O-antigen in Salmonella typhi vaccine strain Ty21a. Plasmid pGB2-Sd1 was transferred by electroporation into S. enterica serovar Typhi Ty21a. Resulting electroporants were characterized by colony immunoblot for Shigella dysenteriae serotype 1 O-antigen expression. All colonies showed strong positive reaction by colony immunoblot screening, and all selected Ty21a (pGB2-Sd1) colonies directed expression of Shiga 1 O-antigen as determined by slide agglutination with Shigella dysenteriae serotype 1-specific antiserum.
Plasmid-based expression of Shigella dysenteriae serotype 1 O-antigen in each host was further examined by SDS-PAGE followed by silver staining and Western immunoblotting with Shigella dysenteriae serotype 1-specific antisera. LPS from wild type Shigella dysenteriae serotype 1 strain 1617 gave a typical O-antigen ladder pattern with the predominant chain length of 17 to 21 O units as detected by both silver stain or immunoblotting (FIGS. 4A and B).
Silver stain analyses of lipopolysaccharide from various strains (FIG. 4A) revealed a series of prominent protein bands that were resistant to protease K digestion. Despite the presence of these interfering bands, several observations could be made. The control rough E. coli K12 carrying the empty pGB2 plasmid vector (lane pGB2.E. coli) as well as the Shigella dysenteriae serotype 1 60R rough strain (lane Sd1 60R) showed no evidence of LPS ladders, as expected. A faint LPS ladder pattern was seen with the wild type Shigella dysenteriae serotype 1 1617 strain (lane Sd1.1617), but was obscured by heavy protein bands in the bottom half of the gel. A similar Shiga 1 ladder pattern was observed more clearly in the E. coli or Ty21a strains carrying pGB2-Sd1 (lanes Sd1.E. coli and Sd1.Ty21a, respectively). S. typhi Ty21a alone showed the typical repeats of the 9,12 ladder pattern of this serovar (lane Typhi Ty21a).
As shown in FIG. 4B, anti-Shigella dysenteriae serotype 1 O-antigen reactive material was not detected with Shigella dysenteriae serotype 1 rough strain 60R (lane Sd1 60R), rough E. coli K-12 carrying pGB-2 (lane pGB-2.E. coli) or S. typhi Ty21a alone (lane Sd1.Ty21a). However, recipient S. typhi Ty21a or E. coli strains carrying pGB2-Sd1 (lanes Sd1.Ty21a and Sd1.E. coli) showed typical LPS patterns like that seen with the Shigella dysenteriae serotype 1 wild type strain (lane Sd1.1617).
In this study, the S. enterica serovar Typhi Ty21a-bearing pGB2-Sd1 clearly exhibited the typical Shigella dysenteriae serotype 1-specific O-antigen LPS ladder. In contrast to the findings reported earlier, the Shigella dysenteriae serotype 1 O-Ps in vaccine strain Ty21a showed a core-linked LPS pattern.
Sequence analysis and a proposed biopathway for Shigella dysenteriae serotype 1 O-antigen synthesis. A contiguous segment of about 9.2 kb (rfb/rfc region) (GenBank #AY585348) and a 1.6 kb (rfp fragment) (GenBank #AY763519) were sequenced to characterize the Shigella dysenteriae serotype 1 O-antigen biosynthetic genes. Primary analysis of the 9.2 kb sequence revealed 9 open reading frames (ORFs); the last open reading frame (orf9) was identified as a small protein coding sequence. In order to demonstrate whether orf9 is essential for Shiga 1 O-antigen biosynthesis, plasmid pGB2-Sd1 was subjected to digestion with SspBI and BstXI (which are uniquely located in the middle of orf 9), followed by religation. The new construct, containing a deletion of the middle of orf9, showed identical O-antigen expression compared with the original plasmid pGB2-Sd1, indicating that orf9 is not involved in O-antigen biosynthesis.
To confirm the fidelity of the resulting sequence data obtained from PCR products synthesized using LA Taq polymerase, our 9.2 kb sequence was compared with an homologous Shiga 1 rfb region available from unpublished data using GCG Molecular Comparison Program of the Sanger Sequencing Center. The results showed 99.98% identity with the Sanger sequence from S. dysenteriae strain M131649(M131) and only one nucleotide change (i.e., a G to C transition at position 2450 within rfbB; accession #: AY585348). In addition, the presumed transcriptional antiterminator JUMPstart sequence: cagtggctctggtagctgtaaagccaggggcggtagcgt (SEQ ID NO: 17) was identified at by 643-680 (GenBank accession#:AY585348) of the amplified rfb region of Shiga 1 strain 1617.
The Shigella dysenteriae serotype 1 O antigen genes. The properties of the nine essential genes including eight ORFs from the rfb locus plus the rfp gene, summarized in Table 2, were obtained from homology searches. The putative genes involved in biosynthesis of the tetrasaccharide repeating unit: L-Rhap, L-Rhap, D-Galp, and D-GlcNAcp as well as genes for a unit processing (e.g., encoding O antigen transporter/flipase and polymerase) were identified. The genes involved in the rhamnose biopathway, rfbB, rfbC, rfbA and rfbD, (Klena, J. D. et al. 1993 Molec Microbio 19:393-402) share 98.5, 99, 99, and 93% identity, respectively, with the rhamnose biosynthetic genes rmlB, rmlD, rmlA and rmlC of E. coli 026. The enzymatic working order of the four proteins in this pathway are: RfbA, RfbB, RfbC and RfbD. RfbA/RmlA is a glucose-1-phosphatate thymidylytransferase, which links Glu-1-P to a carrier nucleotide creating dTDP-glucose for further chemical transformation. RfbB/RmlB is an dTDP-D-glucose 4,6-dehydratase, which catalyzes the second step in the rhamnose biosynthetic pathway: the dehydration of dTDP-D-glucose to form dTDP-4-keto 6-deoxy-D-glucose. RfbC/RmlC is dTDP-4-dyhydrorhamnose reductase. RfbD/RmlD is a dTDP-4-dehydrorhamnose 3,5-epimerase, which catalyses the terminal reaction in dTDP-L-rhamnose biosynthesis, reducing the C4-keto group of dTDP-L-lyxo-6-deoxy-4-hexulose to a hydroxyl resulting in the product dTDP-L-rhamnose. RfbX is putative O antigen transporter, which belongs to the Wzx gene family involved in the export of O antigen and teichoic acid. This protein shows only 53% identity to that of E. coli K-12. The next Orf is rfc, which was a member of the Wzy protein family of O antigen polymerases. Wzy proteins usually have several transmembrane segments and a large periplasmic loop which interacts with the O antigen chain length determinant Cld/wzz to control O-Ps repeat unit chain length and distribution on the cell surface. There are two putative rhamnosyltransferases which are located at the end of this rfb locus. The transferase must recognize both the sugar nucleotide and the recipient polymer to which the sugar is transferred, forming a specific glycosidic linkage. There are two rhamnosyltranferases which work in tandem to link the 2 rhamnoses at the end of the O-repeat unit. We suggest that the S. typhi chromosomal Rfe, which is very conserved in gram-negative bacteria, is a GlcNac transferase which first adds GlcNAc to the ACL (antigen carrier lipid/acyl lipid carrier/undecaprenol phosphate). Rfp is a galactosyl transferase, which normally transfers the Gal moiety from UDP-Gal to the GluNAc-bound ACL. Following these two sugars, the 2 terminal rhamnoses are transferred to complete the tetrasaccharide O-repeat unit.
Summary
The O-Ps biosynthetic determinants from Shigella dysenteriae serotype 1 strain 1617 were cloned from both the chromosome (i.e., rfb locus) and a small 9 kb plasmid (i.e., the rfp gene). The separate rfb locus and ifp region covering  ̃11 kb total DNA were sequenced entirely. Sequencing data and genetic deletion studies in one terminal orf revealed that 8 Rib orf's and the single Rfp orf are necessary for O-Ps biosynthesis. A low copy pGB2 vector containing both the rfb and rfp loci in tandem linkage with their cognate promoters was constructed (i.e., pGB2-Sd1). This plasmid is genetically stable and promotes the expression of Shigella dysenteriae serotype 1 O-Ps antigen as a typical core-linked structure in both E. coli and S. Typhi recipients. Sequence comparisons revealed proposed gene functions for the 9 required Orf's that result in the biosynthesis of a tetrasaccharide repeat O-unit as well 9*as its processing, transport and linkage to core oligosaccharide. We anticipate that use of this cloned antigen locus in a live, attenuated Salmonella delivery system will lead to a safe, oral vaccine for protection against this severe form of shigellosis.
While the present invention has been described in some detail for purposes of clarity and understanding, one skilled in the art will appreciate that various changes in form and detail can be made without departing from the true scope of the invention. All figures, tables, and appendices, as well as patents, applications, and publications, referred to above, are hereby incorporated by reference.

## Claims

1. An attenuated strain of Salmonella comprising core-linked Shigella dysenteriae serotype 1 O-specific polysaccharide (O-Ps) and DNA encoding O antigen biosynthesis, said DNA selected from the group consisting of:
a) the DNA sequence set out in any one of SEQ ID NOs: 1 and 2 and nucleic acid molecules from the species Shigella dysenteriae serotype 1 that share at least about 90% sequence identity with the nucleic acid molecule of SEQ ID NO: 1 or 2;
b) DNA encoding Shigella dysenteriae serotype 1 polypeptides encoded by any one of SEQ ID NOs: 1 and 2 and nucleic acid molecules from the species Shigella dysenteriae serotype 1 that share at least about 90% sequence identity with the nucleic acid molecule of SEQ ID NO: 1 or 2; and
c) DNA encoding variants of Shigella dysenteriae serotype 1 biosynthesis polypeptides encoded by any one of SEQ ID NOs: 1 and 2, wherein each variant comprises O antigen biosynthesis polypeptide, and wherein one or more of the specified amino acids is deleted or replaced, or wherein one or more non-specified amino acids are added without loss of Shigella dysenteriae serotype 1 O antigen or protective immunological activity of the O antigen biosynthesis gene product.

2. The attenuated strain of claim 1, said DNA being present on a plasmid.

3. The attenuated strain of claim 1, said DNA being under the control of its cognate promoters.

4. A composition of matter comprising the attenuated strain of claim 1 in combination with a physiologically acceptable carrier.

5. A method of prophylactic or therapeutic treatment of bacterial infection comprising administering a prophylactically or therapeutically effective amount of the attenuated strain of claim 1 to an individual for prescription of said treatment.

6. A method of making a vaccine comprising combining the attenuated strain of claim 1 with a physiologically acceptable carrier.

7. The attenuated strain of claim 1, wherein the Salmonella is selected from the group consisting of Salmonella typhimurium and Salmonella typhi.

8. An attenuated strain of Shigella comprising core-linked Shigella dysenteriae serotype 1 O-specific polysaccharide (O-Ps) and DNA encoding O antigen biosynthesis, said DNA selected from the group consisting of:
a) the DNA sequence set out in any one of SEQ ID NOs: 1 and 2 and nucleic acid molecules from the species Shigella dysenteriae serotype 1 that share at least about 90% sequence identity with the nucleic acid molecule of SEQ ID NO: 1 or 2;
b) DNA encoding Shigella dysenteriae serotype 1 polypeptides encoded by any one of SEQ ID NOs: 1 and 2 and nucleic acid molecules from the species Shigella dysenteriae serotype 1 that share at least about 90% sequence identity with the nucleic acid molecule of SEQ ID NO: 1 or 2; and
c) DNA encoding variants of Shigella dysenteriae serotype 1 biosynthesis polypeptides encoded by any one of SEQ ID NOs: 1 and 2, wherein each variant comprises O antigen biosynthesis polypeptide, and wherein one or more of the specified amino acids is deleted or replaced, or wherein one or more non-specified amino acids are added without loss of Shigella dysenteriae serotype 1 O antigen or protective immunological activity of the O antigen biosynthesis gene product.

9. The attenuated strain of claim 8, wherein the Shigella is selected from the group consisting of Shigella flexneri and Shigella sonnei.

10. The attenuated strain of claim 8, said DNA being present on a plasmid.

11. The attenuated strain of claim 8, said DNA being under the control of its cognate promoter.

12. A composition of matter comprising the attenuated strain of claim 8 in combination with a physiologically acceptable carrier.

13. A method of prophylactic or therapeutic treatment of bacterial infection comprising administering a prophylactically or therapeutically effective amount of the attenuated strain of claim 8 to an individual for prescription of said treatment.

14. A method of making a vaccine comprising combining the attenuated strain of claim 8 with a physiologically acceptable carrier.