Patent Publication Number: US-2002012668-A1

Title: DNA sequence encoding the specific and antigenic outer membrane protein of salmonella typhi

Description:
FIELD OF INVENTION  
       [0001] This invention relates to the field of genetic engineering, diagnostics and vaccinology in relation to the gene encoding for the specific OMP of  S. typhi  (ST50). The protein is estimated to have a molecular weight of 50 kDa. This protein is available as a result of genetic engineering of the gene that encodes it.  
       DESCRIPTION OF THE BACKGROUND  
       [0002] Typhoid fever remains a public health problem in most developing countries. The available conventional methods for the diagnosis of the disease remain unsatisfactory since they are too slow to allow quick decision by the clinician. Culture method may show specificity but it lacked sensitivity and speed. It produced results within 2-7 days and cases of culture negative typhoid were well recognised. The antibody detection test (Widal test) although widely used, lacked speed, sensitivity and specificity. For meaningful interpretation of the test, demonstration of 4-fold rise in antibody titers between acute and convalescent sera 10-14 days later was essential. An ideal diagnostic test for typhoid should be rapid, easy to perform sensitive as well as specific. Neither of the above methods mentioned above satisfied the criteria. Thus there is a need to develop a rapid and specific test. Combined with sensitive diagnosis, the test would provide for prompt, effective and definite management of typhoid fever. In line with the rapid diagnosis for typhoid fever, we have previously made a significant breakthrough in typhoid diagnosis with the discovery of the 50 kDa OMP that is specific for the aetiologic agent,  Salmonella typhi  (Ismail A, et al. 1991 Biochem Biophys Res Commun 27:301-5). The discovery of the specific 50 kDa antigen in the outer membrane of  Salmonella typhi  has been patented in Malaysia (Malaysian patent No: MY-106708-A). Using the isolated OMP, we have successfully developed a rapid dot EIA test (TYPHIDOT™) to detect for the presence of specific IgM and IgG antibodies to the bacteria. The test has a sensitivity of &gt;95%, a high negative predictive value and could produce results within 1-3 hours. The detection of IgM alone or with IgG would suggest acute typhoid while the detection of IgG only posed several interpretations such as convalescence or possible re-infection. Due to the lack of effective immunity to typhoid fever, patients in highly endemic areas often have re-infections. In the event of current re-infection, there will be a secondary immune response with a significant “boosting” effect of IgG over IgM such that the latter may not be detected. A possible strategy to resolve this problem is to “unmask” the presence of IgM by removing total IgG. The development of a 3 hour IgM detection test (TYPHIDOT-M™) is useful in areas of high endemicity since it could differentiate new from convalescent cases. Data from studies to demonstrate the sensitivity, specificity and advantages of the various tests compared to conventional methods showed that the tests provided reliable alternatives to the Widal test. In order to produce the protein on a large scale, we have purified and determined the amino acid sequence of the 50 kDa OMP. Based on this finding we have isolated, cloned and sequenced the DNA encoding for the 50 kDa OMP. Further we have identified the immunogenic epitope of the protein by epitope mapping. This epitope has been used successfully for the upscaling of the 50 kDa OMP in the diagnosis of typhoid fever.  
       SUMMARY OF THE INVENTION  
       [0003] The present invention provides genetic material encoding for the 50 kDa OMP of  Salmonella typhi . The genetic material can be used to produce sufficient quantities of proteins to be used in diagnostic methods for typhoid fever. Additionally, the genetic material can be used as a probe for the detection of  S.typhi . The entire protein or epitopes derived from the protein can be used for the diagnosis and vaccine development for typhoid fever. Further use includes development of DNA/RNA vaccines for typhoid fever. 
     
    
    
     DESCRIPTION OF DRAWINGS  
     [0004]FIG. 1 is a plasmid map of ST50 clone in TOPO 2.1 cloning vector. The antibiotic markers ampicillin (AmpR), kanamycin (KanR), origin of replication sites COLE1 and F1ORI and the ST50 gene is labelled in the map. The size of the clone is 5384 bp.  
     [0005]FIG. 2 is a plasmid map of ST50 clone in pRSETB expression vector. The antibiotic markers ampicillin (AmpR), origin of replication sites F1ORI and the ST50 gene is labeled in the map. The size of the clone is 4401 bp. 
    
    
     DESCRIPTION OF SPECIFIC EMBODIMENTS  
     [0006] The present inventors have identified and obtained for the first time the genetic material encoding for the specific OMP of  S.typhi , which previously has been available only in limited quantities. Since the 50 kDa OMP is central to the detection of specific IgM and IgG antibodies and other antibody classes, availability of the protein in significant quantities in pure form will allow the design of specific diagnostics for typhoid fever. Further, identification and isolation of this specified genetic material allows for production of new vaccines for typhoid. It also provides a source for specific nucleic acid probes for use in hybridization techniques that allow direct detection of  S.typhi . The first residue of the predicted start codon is designated nucleotide 7 and the entire sequence is presented in Table 1. 
               TABLE 1                         Salmonella typhi  ST50 gene DNA and amino acid sequence:       The nucleotide sequences are represented in triplets with their position numbers.       The open reading frame (ORF) starts at 7bp nucleotide position with a start       codon “ATG” and stops with a stop codon “TGA” at 1474bp nucleotide position.       The amino acid coded by the DNA sequence is represented below the DNA       sequence with their position numbers. The signal sequence of the ST50 protein       is a 16 amino acid peptide that starts at 3 rd  amino acid position and ends at 18 th         amino acid position.                                            1   ATG CAA ATG AAG AAA TTG CTC CCC ATC CTT ATC GGC CTG AGC CTG   45       1   Met Gln Met Lys Lys Leu Leu Pro Ile Leu Ile Cly Leu Ser Leu   15               46   TCG GGG TTC AGC ACA CTA AGC GAG GOA GAG AAC CTG ATG CAA GTT   90       16   Ser Gly Phe Ser Thr Leu Ser Gln Ala Glu Asn Leu Met Gln Val   30               91   TAT CAG CAA GCA CGC CTG AGC AAC CCG GAA TTG CGT AAA TCC GCT   135       31   Tyr Gln Gln Ala Arg Leu Ser Asn Pro Glu Leu Arg Lys Ser Ala   45               136   CCC GAT CGC GAT GCT GCA TTC GAA AAA ATT AAC GAA GCG CGT AGT   180       46   Ala Asp Arg Asp Ala Ala Phe Glu Lys Ile Asn Glu Ala Arg Ser   60               181   CCT TTA CTG CCG CAA CTG GGT TTA GGT GCC GAC TAC ACC TAC AGC   225       61   Pro Leu Leu Pro Gln Leu Gly Leu Gly Ala Asp Tyr Thr Tyr Ser   75               226   AAC GGT TAT CGC GAT GCG AAC GGT ATC AAC TCC AAT GAA ACC AGC   270       76   Asn Gly Tyr Arg Asp Ala Asn Gly Ile Asn Ser Asn Glu Thr Ser   90               271   GCT TCT CTG CAA TTA ACG CAG ACG CTA TTT GAT ATG TCG AAA TGG   315       91   Ala Ser Leu Gln Leu Thr Gln Thr Leu Phe Asp Met Ser Lys Trp   105               316   GCT GGG CTC ACC CTG CAA GAA AAA GCA GCA GGC ATT CAG GAT GTC   360       106   Arg Gly Leu Thr Leu Gln Glu Lys Ala Ala gly Ile Gln Asp Val   120               361   ACC TAT CAG ACC GAT CAG CAG ACG CTG ATC CTC AAT ACC GCG AAC   405       121   Thr Tyr Gln Thr Asp Gln Gln Thr Leu Ile Leu Asn Thr Ala Asn   135               406   GCG TAT TTT AAG GTA TTG AAC GCT ATT GAT GTG CTT TCC TAT ACC   450       136   Ala Tyr Phe Lys Val Leu Asn Ala Ile Asp Val Leu Ser Tyr Thr   150               451   CAG GCG CAA AAA GAG GCT ATC TAC CGT CAG TTA GAT CAA ACG ACG   495       151   Gln Ala Gln Lys Glu Ala Ile Tyr Arg Gln Leu Asp Gln Thr Thr   165               496   CAA CGT TTT AAC GTG GGT CTG GTC GCC ATT ACC GAC GTG CAA AAC   540       166   Gln Arg Phe Asn Val Gly Leu Val Ala Ile Thr Asp Val Gln Asn   180               541   GCC CGT GCG CAA TAT GAT ACC GTA CTG GCG AAT GAA GTG ACC GCC   585       181   Ala Arg Ala Gln Tyr Asp Thr Val Leu Ala Asn Glu Val Thr Ala   195               586   CGC AAC AAC CTG GAT AAC GCG GTA GAA GAG CTG CGC CAG GTA ACC   630       196   Arg Asn Asn Leu Asp Asn Ala Val Glu Glu Leu Arg Gln Val Thr   210               631   GGC AAT TAT TAC CCG GAG CTG GCG TCG CTT AAC GTC GAG CAT TTT   675       211   Gly Asn Tyr Tyr Pro Glu Leu Ala Ser Leu Asn Val Glu His Phe   225               676   AAA ACC GAC AAA CCC AAA GCT GTT AAT GCG CTG TTG AAG GAA GCG   720       226   Lys Thr Asp Lys Pro Lys Ala Val Asn Ala Leu Leu Lys Glu Ala   240               721   GAA AAC CGT AAC CTG TCG CTG TTG CAG GCG CGT TTA AGT CAG GAT   765       241   Glu Asn Arg Asn Leu Ser Leu Leu Gln Ala Arg Leu Ser Gln Asp   255               766   CTG GCG CGC GAG CAA ATC CGT CAG GCG CAG GAT GGT CAC CTG CCG   810       256   Leu Ala Arg Glu Gln Ile Arg Gln Ala Gln Asp Gly His Leu Pro   270               811   ACG CTG AAT TTA ACG GCC TCA ACC GGC ATT TCT GAT ACC TCT TAT   855       271   Thr Leu Asn Leu Thr Ala Ser Thr Gly Ile Ser Asp Thr Ser Tyr   285               856   AGC GGT TCT AAA ACC AAC TCC ACC CAG TAG GAG GAT AGC AAC ATG   900       286   Ser Gly Ser Lys Thr Asn Ser Thr Gln Tyr Asp Asp Ser Asn Met   300               901   GGG CAG AAT AAA ATC GGC CTT AAG TTC TCC CTG CCG CTG TAT CAA   945       301   Gly Gln Asn Lys Ile Gly Leu Asn Phe Ser Leu Pro Leu Tyr Gln   315               946   GGT GGG ATG GTT AAC TCG CAG GTA AAA GAG GGG CAG TAT AAG TTC   990       316   Gly Gly Met Val Asn Ser Gln Val Lys Gln Ala Gln Tyr Asn Phe   330               991   GTG GGG GCA AGC GAA CAG CTG GAA AGC GGG GAC CGT AGG GTG GTG   1035       331   Val Gly Ala Ser Glu Gln Leu Glu Ser Ala His Arg Ser Val Val   345               1036   CAG ACC GTA CGT TGT TCG TTT AAG AAT ATT AAG GGC TCC ATC AGC   1080       346   Gln Thr Val Arg Ser Ser Phe Asn Asn Ile Asn Ala Ser Ile Ser   360               1081   AGC ATC AAG GCG TAT AAA GAG GCG GTC GTT TCC GGG GAA AGT TCT   1125       361   Ser Ile Asn Ala Tyr Lys Gln Ala Val Val Ser Ala Gln Ser Ser   375               1126   TTG GAT GCG ATG GAA GCC GGT TAG TGG GTG GGT AGA GGT AGG ATT   1170       376   Leu Asp Ala Met Glu Ala Gly Tyr Ser Val Gly Thr Arg Thr Ile   390               1171   GTT GAG GTA GTG GAT GGG AGG AGG AGT GTG TAT GAT GGG AAG GAG   1215       391   Val Asp Val Leu Asp Ala Thr Thr Thr Leu Tyr Asp Ala Lys Gln   405               1216   GAA GTG GGG AAG GGG GGT TAT AGG TAT TTG ATT AAT GAG TTA AAT   1260       406   Gln Leu Ala Asn Ala Arg Tyr Thr Tyr Leu Ile Asn Gln Leu Asn   420               1261   ATG AAA TAT GGG GTG GGT AGG GTG AAG GAG GAG GAT GTG GTG GGG   1305       421   Ile Lys Tyr Ala Leu Gly Thr Leu Asn Glu Gln Asp Leu Leu Ala   435               1306   GTT AAG AGT AGG TTG GGT AAA GGT ATG GGG AGG TGG GGG GAA AGG   1350       436   Leu Asn Ser Thr Leu Gly Lys Pro Ile Pro Thr Ser Pro Glu Ser   450               1351   GTA GGG GGG GAA AGG GGA GAT GAG GAT GGT GGG GGA GAG GGT TAT   1395       451   Val Ala Pro Glu Thr Pro Asp Gln Asp Ala Ala Ala Asp Gly Tyr   465               1396   AAT GCT CAT AGC GCC GCG CCA GCA GTA CAG CCG ACC GCC GCT CGC   1440       466   Asn Ala His Ser Ala Ala Pro Ala Val Gln Pro Thr Ala Ala Arg   480               1441   GCC AAC AGC AAT AAC GGC AAT CCA TTC CGG CAT TGA   1476       481   Ala Asn Ser Asn Asn Gly Asn Pro Phe Arg His  End     491                  
 
     [0007] The invention has specifically contemplated each and every possible variation of polynucleotide that could be made by selecting combinations based on the possible codon choices listed in Table 1 and Table 2, and all such variations are to be considered as being specifically disclosed. Codons are preferably selected to fit the host cell in which the protein is being produced. Selection of codons to maximize expression of proteins in a heterologous host is a known technique.  
               TABLE 2                          GENETIC CODE       The amino acids and their three letter and single       letter abbreviations are mentioned inside the       parenthesis. The codons are 3-letter triplets       each representing a trinucleotide of DNA       having a 5′ end on the left and a       3′ end on the right. The RNA code is       the same except that U (uracil) replaces T                     Amino acid   Codons                             Alanine (Ala, A),   GCC, GCG, GCT       Arginine (Arg, R),   AGG, CGA, CGC, CGG, CGT       Asparagine (Asn, N)   AAC, AAT       Aspartic acid (Asp, D)   GAC, GAT       Cysteine (Cys, C)   TGC, TGT       Glutamine (Gln, Q)   CAA, CAG       Glutamic acid (Glu, E)   GAA, GAG       Glycine (Gly, G)   GGA, GGC, GGG, GGT               Histidine (His. H)   CAC, CAT       Isoleucine (Ile, I)   ATA, ATC, ATT       Leucine (Leu, L)   CTA, CTC, CTG, CTT, TTA,           TTG       Lysine (Lys, K)   AAA, AAG       Methionine (Met, M)   ATG       Phenylalanine (Phe, F)   TTC, TTT       Proline (Pro, P)   CCA, CCC, CCC, CCT       Serine (Ser, 5)   AGC, ACT, TCA, TCC, TCG,           TCT       Threonine (Thr, T)   ACA, ACC, ACG, ACT       Tryptophan (Trp, W)   TGG       Tyrosine (Tyr, Y)   TAC, TAT       Valine (Val, V)   GTA, GTC, GTG, GTT       Termination signal   TAA, TAG, TGA                  
 
     [0008] Other DNA molecules that code for such peptides can readily be determined from the list of codons in Table 2 and are likewise contemplated as being equivalent to the DNA sequence of Table 1. In fact since there is a fixed relationship between DNA codons and amino acids in a peptide, any discussion in this application of a replacement or other change in a peptide is equally applicable to the corresponding DNA sequence or to the DNA molecule, recombinant vector, or transformed microorganism in which the sequence is located (and vice versa).  
     [0009] In addition the specific nucleotides listed in Table 1, DNA (or corresponding RNA) molecules of the invention can have additional nucleotides preceding or following those that are specifically listed. For example, a short (e.g. fewer than 20 nucleotides) sequence can be added to the 3′ terminal to provide a terminal sequence corresponding to a restriction endonuclease site, stop codons can follow the peptide sequence to terminate translation, and the like. Additionally, DNA molecules containing a promoter region or other control region upstream from the gene can also be produced. All DNA molecules containing the sequences of the invention will be useful for at least one purpose since all can minimally be fragmented to produce oligonucleotide probes and be used in the isolation or detection of DNA from biological sources.  
     [0010] A number of words used in this specification have specific means in addition to their more common meanings. By “equivalent” is meant, when referring to two nucleotide sequences, that the two nucleotide sequences in question encode the same sequence of amino acids. When “equivalent” is used in referring to two peptides, it means that the two peptides will have a common property (such as antigenic activity, as established by the context). The property does not need to be present to the same extent in both peptides (e.g. two peptides can exhibit different antigenic reactivity), but the properties are preferably substantially the same. “Complementary” , when referring to two nucleotide sequences, means that the two sequences are capable of hybridizing, preferably with less than 25%, more preferably with less than 15%, even more preferably with less than 5%, most preferably with no mismatches between opposed nucleotides. Preferred hybridizing conditions (which are not limited to specific numbers of mismatches) are set forth in the Examples. The term “substantially” varies with the context as understood by those skilled in the relevant art and generally means at least 70%, preferably means at least 80%, more preferably at least 90%, and most preferably at least 95%. The term “isolated” as used herein refers to peptide, DNA, or RNA separated from other peptides, DNAs or RNAs, respectively, and being found in the presence of (if anything) only a solvent, buffer, ion or other component normally present in a biochemical solution of the same. “Isolated” does not encompass either natural materials in their native state or natural materials that have been separated into components (e.g. in an acrylamide gel) but not obtained either as pure substances or as solutions.  
     [0011] Since the DNA sequence of the gene has been identified, it is possible to produce a DNA gene entirely by synthetic chemistry, after which the gene can be inserted into any of the many available DNA vectors using known techniques of recombinant DNA technology. Thus, the present invention can be carried out using reagents, plasmids, and microorganisms which are freely available and in the public domain at the time of filing of this patent application without requiring a deposit of genetic material.  
     [0012] For example, the entire 1476 bp of ST50 gene can be synthesized in a single reaction using specific oligonucleotides of 40 bases spanning both the strands of the gene. This can be done by “assembly PCR technique” that has been described in detail in, for example, Stemmer et al 1995, Gene 164:49-53.  
     [0013] The peptides can then be expressed in a host organism as described herein. Furthermore, automated equipment is also available that makes direct synthesis of many of the peptides disclosed herein readily available, especially peptide fragments of less that the entire 50 kDa OMP of  S.typhi . Such equipment provides ready access to the peptides of the invention, either by direct synthesis or by synthesis of a series of fragments that can be coupled using other known techniques.  
     [0014] In addition to the specific polypeptide sequence shown in Table 1, peptide fragments based on this sequence and fragments and full length sequences representing minor variations thereof will have some of the biological activities of the specific 50 kDa OMP of  S.typhi  and will therefore be useful in vaccine or diagnostic development or other studies. For example, fragments of the 50 kDa OMP sequence can be readily be prepared and can be screened for use as epitope for diagnostic or for DNA vaccine development. Peptide synthesizers can be used to prepare small polypeptide fragments (e.g., less than 100 amino acids) or techniques of genetic engineering can be used to prepare larger fragments. By antibody affinity chromatography using anti-50 kDa OMP antibody immunogenic peptides/epitopes can be derived. Such peptides can also be used (and are indeed more likely to be used) as immunogens for the preparation of antibodies or as standards in assays that use antibodies to the  S.typhi  50 kDa OMP as a method of identifying the presence of a typhoid infection.  
     [0015] The ability to prepare and select peptide fragments having appropriate immunological reactivity from a larger protein is a well known art as described in a number of publications, including patents. For example, U.S. Pat. No. 4,629,783, which describes the preparation of immunologically active fragments of viral proteins that bind with the same antibodies as the entire viral protein.  
     [0016] In addition, minor variations of the previously mentioned peptides and DNA molecules are also contemplated as being equivalent to those peptides and DNA molecules that are set forth in more detail, as will be appreciated by those skilled in the art. For example, it is reasonable to expect that an isolated replacement of a leucine with an isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, or a similar replacement of an amino acid with a structurally related amino acid (i.e., a conservative replacement) will not have a major effect on the biological activity of the resulting molecule, especially if the replacement does not involve an amino acid at a binding site or other site of biologic activity. This is particularly true of the ST50 gene in view of the known significant variations that exist between species. Furthermore, additional amino acids can be present at either of the two termini, or amino acids can be absent, from one or both of the termini, as is known in the art. Peptides in which more than one replacement has taken place can readily be tested in the same manner. Preferred peptides differ at no more than 12, more preferably no more than 5, amino acids in any contiguous group of 20 amino acids. Substitutions of amino acids, when they occur are preferably from within standard conservative groups. Standard conservative groups of amino acids are shown in parenthesis using the one-letter amino acid code (Table 2): nonpolar (A.V, L, I, P, M); aromatic (F, T, W); uncharged polar (G, S, T, C, N, Q); acidic (D, E); basic (K, R, H). The aromatic amino acids are sometimes considered to belong to the broader-defined nonpolar (F, W) or uncharged polar (T) groups. However, such modified protein is less useful in the specific diagnostic assays related to identification of  S.typhi.    
     [0017] Salts of any of the peptides described herein will naturally occur when such peptides are present in (or isolated from) aqueous solutions of various pHs. All salts of peptides having the indicated biological activity are considered to be within the scope of the present invention. Examples include alkali, alkaline earth, and other metal salts of carboxylic acid residues, acid addition salts (e.g., HCl) of amino residues and zwitter ions formed by reactions between carboxylic acid and amino residues within the same molecule.  
     [0018] Peptides of the invention can be prepared for the first time as homogeneous preparations free of other Salmonella materials, either by direct synthesis or by using a cloned gene or a fragment thereof as described herein.  S. typhi  50 kDa OMP was previously available in the form of a crude homogenate with a purity of less than 0.1%. The crude preparation was not free of all other  S. typhi  materials. Although genes and corresponding proteins can be prepared by the totally synthetic techniques discussed above, in preferred embodiments of the invention genetic information is obtained from natural sources and identified as described herein. The genetic material is first obtained in the form of a gene library, using any of numerous existing techniques. The first of these is to randomly shear genomic DNA and insert this sheared material into expression vectors. If enough recombinants are generated, there is a good probability of having at least one recombinant in the population, which is expressing the 50 kDa OMP protein.  
     [0019] Details of this example are set forth below, including details of the experiments that lead to obtaining the complete sequence of the gene. However, there is no reason to believe that the sequence and specific engineered organism prepared by the inventors is any better than other clones that can be prepared using the guidance set forth in this specification. In fact, it is likely that expression of the 50 kDa OMP protein can be enhanced over that described herein by selection of other expression systems.  
     [0020] Now that the sequence of the ST50 gene has been determined, it is no longer necessary to go though these steps to obtain the genetic materials of the present invention. The polymerase chain reaction (PCR) technique can now be used to isolate genes from natural sources in a simpler and more direct manner. The PCR technique, including its use in diagnosis, is disclosed in U.S. Pat. No. 4,683,202, which is, herein incorporated by reference. Since  S.typhi  specimens are readily available from sources such as the American Type Culture Collection of Rockville, Md., and since PCR probes can be prepared using the sequences set forth in this specification, it is possible to obtain any desired segment of the sequences set forth herein using the PCR technique and commercially available sources of the  S.typhi  genomic material. A specific example of such a technique for isolating the  S.typhi  chromosomal gene is described in the examples that follow.  
     [0021] Although the techniques set forth above, when used in combination with the knowledge of those skilled in the art of genetic engineering and the previously stated guidelines, will readily enable isolation of the desired gene and its use in recombinant DNA vectors now that sufficient information is provided to locate the gene, other methods which lead to the same result are also known and may used in the preparation of recombinant DNA vectors of this invention.  
     [0022] Expression of 50 kDa OMP can be enhanced by including multiple copies of the gene in a transformed host; by selecting a vector known to reproduce in the host, thereby producing large quantities of the said protein from exogenous inserted DNA; or by any other known means of enhancing peptide expression. One common variation is the preparation of a polypeptide of the invention in the form of a fused polypeptide. Such peptides are typically prepared by using a plasmid vector with a promoter region of a gene known to be expressed and inserting nucleotides that encode all or a major portion of the amino acid sequence of the invention into the genetic sequence. Examples of such fused proteins include histidine-tag, beta-galactosidase, maltose binding protein and green fluorescent protein. If desired, the fused peptide can be designed so that a site recognized by a proteolytic enzyme (example: enterokinase) is present at the junction between the two fused proteins. The proteolytic enzyme can then be used to cleave the expressed protein so that the desired  S.typhi  specific 50 kDa OMP is available in pure form.  
     [0023] In all cases,  S. typhi  50 kDa OMP protein will be expressed when the DNA sequence is functionally inserted into the vector. By “functionally inserted” is meant in proper reading frame and orientation, as is well understood by those skilled in the art. Typically, a gene will be inserted downstream from a promoter and will be followed by a stop codon, although production as a hybrid protein (possibly followed by cleavage) may be used, if desired.  
     [0024] In addition to the above general procedures which can be used for preparing recombinant DNA molecules and transformed in unicellular organisms in accordance with the practices of this invention, other known techniques and modifications thereof can be used in carrying out the practice of the invention. In particular, techniques relating to genetic engineering have recently undergone explosive growth and development. Many recent U.S. patents disclose plasmids, genetically engineering microorganisms, and methods of conducting genetic engineering, which can be used in the practice of the present invention. For example, U.S. Pat. No. 4,273,875 discloses a plasmid and a process of isolating the same. U.S. Pat. No. 4,304,863 discloses a process for producing bacteria by genetic engineering in which a hybrid plasmid is constructed and used to transform a bacterial host, U.S. Pat. No. 4,419,450 discloses a plasmid useful as a cloning vehicle in recombinant DNA work. U.S. Pat. No. 4,362,867 discloses recombinant cDNA construction methods and hybrid nucleotides produced thereby which are useful in cloning processes. U.S. Pat. No. 4,403,036 discloses genetic reagents for generating plasmids containing multiple copies of DNA segments. U.S. Pat. No. 4,363,877 discloses recombinant DNA transfer vectors. U.S. Pat. No. 4,356,270 discloses a recombinant DNA cloning vehicle and is a particularly useful disclosure for those with limited experience in the area of genetic engineering since it defines many of the terms used in genetic engineering and the basic processes used therein. U.S. Pat. No. 4,336,336 discloses a fused gene and a method of making the same. U.S. Pat. No. 4,349,629 discloses plasmid vectors and the production and use thereof. U.S. Pat. No. 4,332,901 disclose a cloning vector useful in recombinant DNA. Although some of these patents are directed to the production of a particular gene product that is not within the scope of the present invention, the procedures described therein can easily be modified to the practice of the invention described in this specification by those skilled in the art of genetic engineering.  
     [0025] The implications of the present invention are significant in that useful amounts of  S. typhi  specific 50 kDa OMP and genetic material of the invention will become available for use in the development of hybridization assays or in any other type of assay utilizing these materials as a reagent for use in diagnosis, immunization, therapeutics, and research. Transferring the ST50 gene or parts thereof which has been isolated to other expression vectors will produce constructs which improve the expression of the  S. typhi  specific 50 kDa OMP in  E. coli  or express the polypeptide in other hosts.  
     [0026] Particularly contemplated is the isolation of genes from other strains of  S.typhi  using oligonucleotide probes based on the principal and variant nucleotide sequences disclosed herein. Such probes can be considerably shorter than the entire sequence but should be at least 10, preferable at least 14, nucleotides in length. Intermediate oligonucleotides from 20 to 500, especially 30 to 200, nucleotides in length provide particularly specific and rapid-acting probes. Longer oligonucleotides are also useful, up to the full length of the gene. Both RNA and DNA probes can be used.  
     [0027] In use, the probes are typically labelled in a detectable manner (e.g. p 32 , S 35 , biotin, avidin, fluorescein or digoxigenin) and are incubated with single-stranded DNA or RNA from the organism in which a gene is being sought. Hybridization is detected by means of the label denaturing the double-stranded (hybridized) DNA (or DNA/RNA) have been separated (typically using nitrocellulose paper). Hybridization techniques suitable for use with oligonucleotides are well known.  
     [0028] Although probes are normally used with a detectable label that allows easy identification, unlabelled oligonucleotides are also useful, both as precursors of labelled probes and for use in methods that provide for direct detection of double-stranded DNA (or DNA/RNA). Accordingly, the term “oligonucleotide probe” refers to both labelled and unlabelled forms.  
     [0029] Monoclonal or polyclonal antibodies to recombinant ST50 protein can be produced using the known technologies. Antibodies produced against the ST50 recombinant protein could be used to develop an antigen detection immuno assay for the detection of  S. typhi  or for use with other technologies which use antibody as an ingredient. In addition, parts of the DNA or the peptides or proteins derived from the ST50 gene can be used as an immunogen in vaccine formulations to protect against  S. typhi  infections. The immunogen may be incorporated into liposomes, or conjugated to polysaccharides and/or other polymers for use in a vaccine formulation. The DNA sequence of ST50 gene can also be used to develop a DNA vaccine formulation. Many methods may be used by those skilled in the art, to introduce the vaccine formulations into human. These include, but are not limited to intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, oral and intranasal routes of administration.  
     [0030] In summary,  S.typhi  specific ST50 gene have been isolated, cloned, sequenced and expressed in  E. coli . The open-reading frame of this gene directs the synthesis of a 50,000 Dalton protein with identifiable similarities to the 50 kDa OMP of  S.typhi . The sequence of the entire ST50 gene was 1476 base pairs (bp) with GC and AT composition of 52.03% and 47.97% respectively. The open reading frame (ORF) starts at 7 bp nucleotide position with a start codon “ATG” and a stop codon “TGA” at 1474 bp nucleotide position. The predicted amino acid of the ST50 gene consisted of 491 amino acids. The signal sequence of the 50 kDa OMP is a 16 amino acid peptide that extends between the 3rd and 18th amino acid position. The 50 kDa OMP has been expressed in large quantities in  E. coli , which provides a source for large quantities of pure protein for future diagnostic and vaccine studies.  
     [0031] The expressed 50 kDa OMP has been purified to the homogeneity by IMAC chromatography. The specific immuno reactivity of the recombinant ST50 protein has been evaluated by Western blot and Dot immuno assay at IgM and IgG level. With the availability of information about the DNA sequence, it should not be difficult to use the same or parts of it as DNA probe or PCR primer for the diagnosis of typhoid. This invention now being generally described, the same will be better understood by reference to the following examples, which are provided for purposes of illustration only and are not to be considered limiting of the invention unless so specified.  
     EXAMPLES  
     Bacterial Strains and Media  
     [0032] Salmonella typhi  (USM1) strain was isolated from a patient with typhoid fever and has been maintained in our laboratory since 1987. Blood agar and nutrient broth was used to propagate the  S. typhi  strain. For molecular biology experiments, the  S. typhi  was cultured on Luria broth.  
     Isolation of Outer Membrane Protein  
     [0033] Partially purified OMP of  S. typhi  were obtained as described in Schnaitman et al (1971), 108: 553-556. Briefly  S. typhi  was grown in nutrient broth and incubated in a shaker at 37° C. for 18 h until late log phase (OD=0.8 at 660 nm). Cells were harvested and suspended in 0.01M HEPES buffer (pH 7.4). Bacterial cells were disrupted by vortexing with glass beads (0.15 mm diameter) for 1.5 h with 1 minute alternate on ice until 95% breakage was obtained as monitored by serial Gram stain. The cell lysate was aspirated and the glass beads washed with 0.01M HEPES buffer. Cell debris and unbroken cells were removed by centrifugation at 5,000 g for 15 min at 4° C. The supernatant fluid was centrifuged at 200,000 g for 1 h to obtain cell envelopes. The cytoplasmic membrane was removed by 0.01M HEPES containing 2% Triton X-100 and was allowed to stand for 10 min at room temperature. This was followed by centrifugation at 200,000 g for 1 h, 4° C. to pellet the insoluble outer membrane. Protein concentration of OMP was determined by the calorimetric microassay using the Bio-Rad protein assay dye reagent (Bio-Rad, Richmond, Calif.) using bovine serum albumin as standard.  
     Purification of 50 kDa OMP from  S. typhi    
     [0034] The 50 kDa OMP of  S. typhi  was isolated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and electro elution. SDS-PAGE was performed under reducing conditions using the discontinuous buffer systems (Lammli, 1970) with a vertical slab electrophoresis unit (Bio-Rad). The stacking and separating gels contained 4.5% and 9% acrylamide respectively. Each preparative gel was loaded with 500 μg of OMP and was run at constant current setting of 25 mA per plate at 4° C. for 4 h. The separated OMPs were stained with Coomassie blue, and the molecular weights were established with molecular weight markers of 14.4-94 kDa.  
     [0035] For N terminal amino acid sequencing the OMP was run on SDS-PAGE and electroblotted onto Polyvinylidene difluoride (PVDF) membrane. After staining with Coomassie blue, the 50 kDa band of interest was excised carefully and sent for amino acid sequencing (MidWest Analytical, USA).  
     Cloning of ST50 Gene  
     [0036] (i) Primer Designing  
     [0037] Amino acid sequence obtained from the N terminal amino acid sequencing of the ST50 OMP was analysed. Based on the analysis, a pair of PCR primers STPCS1-ATG CM ATG MG AM TTG CTC and STR1-TCA ATG CCG GM TGG ATT GC were designed to PCR amplify the ST50 gene.  
     [0038] (ii) Polymerase Chain Reaction (PCR)  
     [0039] S. typhi  (USM1) genomic DNA was extracted by standard protocol and the 50 ng of the DNA was used as a template for the PCR amplification using STPS1 and STR1. PCR amplification was performed under following conditions. 200 μM of each dNTP, 1×PCR buffer (50 mM KCl, 10 mM Tris.Cl, pH 8.3), 2.5 mM MgCl 2 , 20 pmol of STPCSI and STR1 primer, and 1 unit of TAQ DNA polymerase. PCR was performed on a Perkin-Elmer 9600 Thermal cycler. The optimal annealing temperature of 50° C. was used for the primer sets. The PCR parameters used are as follows: Initial denaturation at 95° C. for 5 minutes, followed by additional 1 minute. Primer annealing and extension was carried out at 55° C. and 72° C. respectively for 1 minute. The steps were repeated for 30 cycles. Finally a temperature of 72° C. was included for 5 minutes as a final extension. The PCR products were analyzed by agarose gel electrophoresis and the size of the PCR product was 1476 bp. The PCR products were specific for  S. typhi  since the primers did not amplify any products when  E.coli  genomic DNA was used as template.  
     [0040] (iii) PCR Cloning of ST50 Gene  
     [0041] The amplified 1476 bp PCR product of the ST50 gene was cloned on to PCR cloning vector (TOPO 2.1, invitrogen) as per the manufacturer instructions. The clones were screened using an internal primer STPR1:GGC CGT TM ATT CAG CGT CG and M13 reverse primer: CAG GM ACA GCT ATG AC. The map of the ST50 clone pST50-USM1 is depicted in FIG. 1.  
     Sequence of ST50 Gene  
     [0042] The DNA sequencing of the ST50 gene was carried out using pST50-USM1 and M13-20 forward CTG GCC GTC GTT TTA C and M13 reverse primers CAG GM ACA GCT ATG AC through a commercial DNA sequencing company (ACGT Inc, USA). The sequence of the entire ST50 gene was 1476 base pairs (bp) with GC and AT composition of 52.03% and 47.97%. The open reading frame (ORF) starts at 7 bp nucleotide position with a start codon “ATG” and with a stop codon “TGA” at 1474 bp nucleotide position. The ST50 gene code for 491 amino acids and the predicted size of the protein is 53682 Daltons. The signal sequence of the ST50 protein is a 16 amino acid peptide that extends between 3rd and 18th amino acid position. The DNA sequence and the predicted amino acid sequence are given in Table 1. The presence of signal sequence indicates that this protein is localized in the periplasmic region.  
     Cloning of ST50 Gene in Expression Vector  
     [0043] For the expression of ST50 gene, we choose a T7 promoter based expression vector system, pRSETB vector (Invitrogen), The advantage of pRSETB vector is that it contains T7 promoter, which is highly specific for T7 RNA Polymerase. Transcription by T7 polymerase is selective and 5 times faster than  E. coli  RNA polymerase thus leading to higher expression of genes cloned under T7 promoter. This vector also contains a nucleotide sequence that encodes a metal binding domain, a series of six consecutive histidine amino acids expressed as N-terminal fusion to the protein of interest. This metal binding domain (six-tagged histidine moieties) on the fusion peptide has high affinity for the divalent ions (like nickel, copper and cobalt) and facilitates one step purification of the protein using (IMAC) immobilized metal affinity columns.  
     [0044] From the TOPO vector the ST50 gene was excised using EcoRI restriction enzyme. The excised ST50 kDa gene was ligated on to EcoRI site of pRSETB vector. The clones were screened using an internal primer STPR1: GGC CGT TAA ATT CAG CGT CG and T7 terminator primer: GCT AGT TAT TGC TCA GCG G. The map of the ST50 gene in pRSETB vector, pST50-USM2, is depicted in (FIG. 2). The presence of ST50 gene in pRSETB vector was confirmed by restriction analysis using Eco RI restriction enzyme.  
     Protein Expression  
     [0045] The protein expression of ST50 protein from the pST50-USM2 clone was carried out in BL21(DE3)  E. coli  host. The  E. coli  BL21(DE3) contains chromosomal copy of T7 RNA polymerase gene under the control of lac UV5 promoter and hence expression of genes cloned under T7 promoter can be induced with gratuitous inducer such as IPTG. Further BL21(DE3) being a Ion protease deficient strain which protects the expressed heterologous proteins from proteolytic cleavage. The ST50 protein was expressed in  E. coli  BL21(DE3) after inducing with IPTG.  
     [0046] Briefly the following protocol was followed for expression of the recombinant proteins:(Luria broth was supplemented with 100 μg/ml ampicillin for the following experiment)  
     [0047] a)  E. coli  BL21(DE3) was transformed with the pST50-USM2 clone using protocol mentioned in ‘(Sambrook et al 1989) Molecular Cloning—A Laboratory Manual (second edition)’, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.  
     [0048] b) A single colony of fresh transformant was inoculated into 1.5 ml LB and grown overnight (o/n) at 37° C., at static condition.  
     [0049] c) 50 μl of the o/n culture was inoculated into 10 ml LB in 100 ml conical flask and grown at 37° C. with 150 rpm shaking, till OD 600  of the culture reached 0.6.  
     [0050] d) IPTG was added to a final concentration of 1 mM and the culture was grown for 3 hours at 37° C. with 150 rpm shaking.  
     [0051] e) The culture was centrifuged at 10,000 g for 5 minutes. The supernatant was discarded and  E. coli  pellet containing the recombinant protein was stored at 20° C.  
     [0052] The recombinant ST50 protein was analysed by SDS-PAGE. The size of recombinant ST50 protein was 59 kDa, that is larger than native 50 kDa OMP, because of the presence of additional 52 amino acids derived from the pRSETB vector.  
     Purification of the Recombinant ST50 Protein  
     [0053] The purification of recombinant ST50 protein was carried out by Immobilized metal affinity chromatography (IMAC). IMAC is a special form of affinity chromatography in which an immobilized metal ion such as copper, zinc or a transition metal ion such as cobalt or nickel is used to bind protein selectively by reaction with imidazole group of histidine residues. (Porath et al, 1975). The elution of the protein can be achieved either by lowering the pH, thereby destabilizing the protein-metal complex or by using competitive ligands like imidazole or by using complexing agents like EDTA.  
     [0054] In the clone pST50-USM2, the recombinant ST50 protein was expressed in the form of inclusion bodies. Therefore the recombinant ST50 proteins was solubilized with 8M urea and the protein was purified under denaturing conditions.  
     [0055] The following chromatography protocol was followed to purify the recombinant ST50 protein:  
     [0056] The NiNTA matrix was purchased from (Qiagen) and used for the purification of the recombinant ST50 protein. The column was prepared as described by the manufacture&#39;s instructions. Initially the matrix was equilibriated with the starting column buffer (0.1M phosphate buffer pH 8.0, 0.01M Tris pH 8.0 with 8M urea). The recombinant ST50 protein was solubilized by using lysis buffer (0.1M phosphate buffer pH 8.0, 0.01M Tris pH 8.0 and 8M Urea) for 8 hours at 40° C. and spun at 12K for 15 minutes to remove the debris. The supernatant containing the solubilized recombinant protein was passed through the column and allowed to bind for 4 hours. The unbound protein was removed by washing the column with 5 to 10 columns volumes of start buffer (0.1M phosphate buffer pH 8.0 containing 8M urea) until the fractions showed zero at A 280 . The elution of the protein was achieved by 0.1M phosphate buffer pH 4.5 containing 8M Urea. The eluted fractions were collected and the protein concentration quantitated by measuring the absorbance at 280 nm. The eluted fractions containing the protein were pooled and urea was removed by stepwise dialysis. SDS-PAGE analysis was carried out with the wash and the eluted fractions to check the purity of the eluted protein  
     Immunoreactivity of Recombinant ST50 Protein  
     [0057] (i) Western Blotting  
     [0058] The immuno reactivity of the recombinant ST50 protein was analysed by western blotting. Briefly, the recombinant ST50 protein was run on a 8% SDS-PAGE. After electrophoresis the gel was incubated for 10 minutes in transfer buffer (25 mM Tris, 192 mM glycine, 20% methanol). Nitrocellulose membrane (NCP) cut to the exact size of separating gel was incubated for 10 minutes in transfer buffer. Without trapping air-bubbles the NCP was overlaid on the gel and sandwiched between filter papers and scotch brite pads. Electrophoretic transfer was carried out in the cold room at 200 mA for 3 hours using Transblot (Bio Rad, USA) electroblotting apparatus. After transfer, the molecular weight marker lane was cut and stained with amido black (100 mg Amido block in 45% methanol, 10% acetic acid). The rest of the NCP was stained with Ponceau S (0.2% Ponceau S, Sigma, USA, in 0.3% trichloro acetic acid and 0.3% sulfosalicylic acid) to ensure the transfer of the proteins. Membrane was washed in PBS and blocked o/n at 4° C. with 5% non-fat milk powder in PBS.  
     [0059] The NCP was washed in wash buffer (PBS) thrice 5 minutes duration each, and then incubated over night with 1:200 dilution of pooled normal sera, pooled typhoid sera, sera from patients with fevers common in this region such as dengue, hepatitis, scrub typhus, paratyphi A, B and C. The pooled normal sera was obtained from 5 healthy individuals while pooled typhoid sera was obtained from typhoid patient who&#39;s blood samples were positive by culture. After washing in the wash buffer the membrane was incubated for 2 hours with peroxidase-conjugated anti-human IgM and IgG. After extensive washing the blot was developed using H 2 O 2  and 4-chloro-1-naphthol reagent for 15 minutes and the blot was rinsed in distilled water to stop the reaction. The recombinant ST50 protein specifically reacted with  S. typhi  patients sera at the IgG and at the IgM antibody level but not with sera obtained from other infections.  
     [0060] (ii) Dot Enzyme Immuno Assay  
     [0061] A nitrocellulose membrane of 0.45μ pore size (Microfiltration system, CA, USA) was used in this assay. One μl of the recombinant ST50 protein i.e., protein was dotted onto nitrocellulose using a microsyringe and allowed to dry. The strips were dipped into blocking buffer (3% skimmed milk, 0.9% NaCl, 10 mM Tris-HCl, pH 7.4), and placed on a rocker platform for 30 minutes at room temperature. The blocked strips were rinsed 3 times for 15 minutes with NETG buffer (150 mM NaCl, 50 mM Tris-HCl, 5 mM EDTA and 0.25% gelatin), allowed to dry and kept at 4° C. until use. The strip was then probed with one ml of 1:100 dilution of the different sera sample and incubated on a rocker platform for 1 hour at room temperature. The strips were then washed with 3 times for 15 minutes with 1M NETG buffer and further incubated on a rocker platform with 1: 1,600 dilution of peroxidase conjugated antihuman IgG (Dakopafts, Glostrup, Denmark) or 1:800 dilution of antihuman IgM (Dakopatts, Glostrup, Denmark). After extensive washing the blot was developed using H 2 O 2  and 4-chloro-1-naphthol reagent for 15 minutes and the blot was rinsed in distilled water to stop the reaction. The recombinant ST50 protein showed specific reactivity with  S. typhi  patients sera at the IgM and at the IgG antibody level whereas no reactivity was seen with sera obtained from other infections.  
     [0062] The isolated DNA or RNA molecule (ST50) of the invention are useful as sources of immunological protection against diseases such as typhoid fever in an animal, example, a mammal, example, a human, in particular as the basis of a vaccine capable of provoking a strong immune reaction. Appropriate dosages and conditions of administrations are known in the art.  
     [0063] All publications and patent applications mentioned in this specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.  
     [0064] The invention now being fully described, it will be apparent to one of ordinary skill in the art that many changes and modifications can be made thereto without departing from the spirit or scope of the appended claims.  
    
     
       
         1 
         
           
             2  
           
           
             1  
             1476  
             DNA  
             Salmonella typhi  
             
               CDS  
               (1)..(1476)  
             
           
            1 

atg caa atg aag aaa ttg ctc ccc atc ctt atc ggc ctg agc ctg tcg       48 
Met Gln Met Lys Lys Leu Leu Pro Ile Leu Ile Gly Leu Ser Leu Ser 
1               5                   10                  15 

ggg ttc agc aca cta agc cag gca gag aac ctg atg caa gtt tat cag       96 
Gly Phe Ser Thr Leu Ser Gln Ala Glu Asn Leu Met Gln Val Tyr Gln 
            20                  25                  30 

caa gca cgc ctg agc aac ccg gaa ttg cgt aaa tcc gct gcc gat cgc      144 
Gln Ala Arg Leu Ser Asn Pro Glu Leu Arg Lys Ser Ala Ala Asp Arg 
        35                  40                  45 

gat gct gca ttc gaa aaa att aac gaa gcg cgt agt cct tta ctg ccg      192 
Asp Ala Ala Phe Glu Lys Ile Asn Glu Ala Arg Ser Pro Leu Leu Pro 
    50                  55                  60 

caa ctg ggt tta ggt gcc gac tac acc tac agc aac ggt tat cgc gat      240 
Gln Leu Gly Leu Gly Ala Asp Tyr Thr Tyr Ser Asn Gly Tyr Arg Asp 
65                  70                  75                  80 

gcg aac ggt atc aac tcc aat gaa acc agc gct tct ctg caa tta acg      288 
Ala Asn Gly Ile Asn Ser Asn Glu Thr Ser Ala Ser Leu Gln Leu Thr 
                85                  90                  95 

cag acg cta ttt gat atg tcg aaa tgg cgt ggg ctc acc ctg caa gaa      336 
Gln Thr Leu Phe Asp Met Ser Lys Trp Arg Gly Leu Thr Leu Gln Glu 
            100                 105                 110 

aaa gca gca ggc att cag gat gtc acc tat cag acc gat cag cag acg      384 
Lys Ala Ala Gly Ile Gln Asp Val Thr Tyr Gln Thr Asp Gln Gln Thr 
        115                 120                 125 

ctg atc ctc aat acc gcg aac gcg tat ttt aag gta ttg aac gct att      432 
Leu Ile Leu Asn Thr Ala Asn Ala Tyr Phe Lys Val Leu Asn Ala Ile 
    130                 135                 140 

gat gtg ctt tcc tat acc cag gcg caa aaa gag gct atc tac cgt cag      480 
Asp Val Leu Ser Tyr Thr Gln Ala Gln Lys Glu Ala Ile Tyr Arg Gln 
145                 150                 155                 160 

tta gat caa acg acg caa cgt ttt aac gtg ggt ctg gtc gcc att acc      528 
Leu Asp Gln Thr Thr Gln Arg Phe Asn Val Gly Leu Val Ala Ile Thr 
                165                 170                 175 

gac gtg caa aac gcc cgt gcg caa tat gat acc gta ctg gcg aat gaa      576 
Asp Val Gln Asn Ala Arg Ala Gln Tyr Asp Thr Val Leu Ala Asn Glu 
            180                 185                 190 

gtg acc gcc cgc aac aac ctg gat aac gcg gta gaa gag ctg cgc cag      624 
Val Thr Ala Arg Asn Asn Leu Asp Asn Ala Val Glu Glu Leu Arg Gln 
        195                 200                 205 

cta acc ggc aat tat tac ccg gag ctg gcg tcg ctt aac gtc gag cat      672 
Leu Thr Gly Asn Tyr Tyr Pro Glu Leu Ala Ser Leu Asn Val Glu His 
    210                 215                 220 

ttt aaa acc gac aaa ccc aaa gct gtt aat gcg ctg ttg aag gaa gcg      720 
Phe Lys Thr Asp Lys Pro Lys Ala Val Asn Ala Leu Leu Lys Glu Ala 
225                 230                 235                 240 

gaa aac cgt aac ctg tcg ctg ttg cag gcg cgt tta agt cag gat ctg      768 
Glu Asn Arg Asn Leu Ser Leu Leu Gln Ala Arg Leu Ser Gln Asp Leu 
                245                 250                 255 

gcg cgc gag caa atc cgt cag gcg cag gat ggt cac ctg ccg acg ctg      816 
Ala Arg Glu Gln Ile Arg Gln Ala Gln Asp Gly His Leu Pro Thr Leu 
            260                 265                 270 

aat tta acg gcc tca acc ggc att tct gat acc tct tat agc ggt tct      864 
Asn Leu Thr Ala Ser Thr Gly Ile Ser Asp Thr Ser Tyr Ser Gly Ser 
        275                 280                 285 

aaa acc aac tcc acc cag tac gac gat agc aac atg ggg cag aat aaa      912 
Lys Thr Asn Ser Thr Gln Tyr Asp Asp Ser Asn Met Gly Gln Asn Lys 
    290                 295                 300 

atc ggc ctt aac ttc tcc ctg ccg ctg tat caa ggt ggg atg gtt aac      960 
Ile Gly Leu Asn Phe Ser Leu Pro Leu Tyr Gln Gly Gly Met Val Asn 
305                 310                 315                 320 

tcg cag gta aaa cag gcg cag tat aac ttc gtc ggc gca agc gaa cag     1008 
Ser Gln Val Lys Gln Ala Gln Tyr Asn Phe Val Gly Ala Ser Glu Gln 
                325                 330                 335 

ctg gaa agc gcg cac cgt agc gtg gtg cag acc gta cgt tct tcc ttt     1056 
Leu Glu Ser Ala His Arg Ser Val Val Gln Thr Val Arg Ser Ser Phe 
            340                 345                 350 

aac aat att aac gcc tcc atc agc agc atc aac gcg tat aaa cag gcg     1104 
Asn Asn Ile Asn Ala Ser Ile Ser Ser Ile Asn Ala Tyr Lys Gln Ala 
        355                 360                 365 

gtc gtt tcc gcg caa agt tct ttg gat gcc atg gaa gcc ggt tac tcg     1152 
Val Val Ser Ala Gln Ser Ser Leu Asp Ala Met Glu Ala Gly Tyr Ser 
    370                 375                 380 

gtc ggt aca cgt acc att gtt gac gta ctg gat gcc acc acc act ctg     1200 
Val Gly Thr Arg Thr Ile Val Asp Val Leu Asp Ala Thr Thr Thr Leu 
385                 390                 395                 400 

tat gat gcc aag cag caa ctg gcc aac gcg cgt tat acc tat ttg att     1248 
Tyr Asp Ala Lys Gln Gln Leu Ala Asn Ala Arg Tyr Thr Tyr Leu Ile 
                405                 410                 415 

aat cag tta aat atc aaa tat gcg ctc ggt acg ctg aac gag cag cat     1296 
Asn Gln Leu Asn Ile Lys Tyr Ala Leu Gly Thr Leu Asn Glu Gln His 
            420                 425                 430 

ctg ctc gcg ctt aac agt acg ttg ggt aaa cct atc ccg acg tcg ccg     1344 
Leu Leu Ala Leu Asn Ser Thr Leu Gly Lys Pro Ile Pro Thr Ser Pro 
        435                 440                 445 

gaa agc gta gcg ccg gaa acg cca gat cag gat gct gcc gca gac ggt     1392 
Glu Ser Val Ala Pro Glu Thr Pro Asp Gln Asp Ala Ala Ala Asp Gly 
    450                 455                 460 

tat aat gct cat agc gcc gcg cca gca gta cag ccg acc gcc gct cgc     1440 
Tyr Asn Ala His Ser Ala Ala Pro Ala Val Gln Pro Thr Ala Ala Arg 
465                 470                 475                 480 

gcc aac agc aat aac ggc aat cca ttc cgg cat tga                     1476 
Ala Asn Ser Asn Asn Gly Asn Pro Phe Arg His 
                485                 490 

 
           
             2  
             491  
             PRT  
             Salmonella typhi  
           
            2 

Met Gln Met Lys Lys Leu Leu Pro Ile Leu Ile Gly Leu Ser Leu Ser 
1               5                   10                  15 

Gly Phe Ser Thr Leu Ser Gln Ala Glu Asn Leu Met Gln Val Tyr Gln 
            20                  25                  30 

Gln Ala Arg Leu Ser Asn Pro Glu Leu Arg Lys Ser Ala Ala Asp Arg 
        35                  40                  45 

Asp Ala Ala Phe Glu Lys Ile Asn Glu Ala Arg Ser Pro Leu Leu Pro 
    50                  55                  60 

Gln Leu Gly Leu Gly Ala Asp Tyr Thr Tyr Ser Asn Gly Tyr Arg Asp 
65                  70                  75                  80 

Ala Asn Gly Ile Asn Ser Asn Glu Thr Ser Ala Ser Leu Gln Leu Thr 
                85                  90                  95 

Gln Thr Leu Phe Asp Met Ser Lys Trp Arg Gly Leu Thr Leu Gln Glu 
            100                 105                 110 

Lys Ala Ala Gly Ile Gln Asp Val Thr Tyr Gln Thr Asp Gln Gln Thr 
        115                 120                 125 

Leu Ile Leu Asn Thr Ala Asn Ala Tyr Phe Lys Val Leu Asn Ala Ile 
    130                 135                 140 

Asp Val Leu Ser Tyr Thr Gln Ala Gln Lys Glu Ala Ile Tyr Arg Gln 
145                 150                 155                 160 

Leu Asp Gln Thr Thr Gln Arg Phe Asn Val Gly Leu Val Ala Ile Thr 
                165                 170                 175 

Asp Val Gln Asn Ala Arg Ala Gln Tyr Asp Thr Val Leu Ala Asn Glu 
            180                 185                 190 

Val Thr Ala Arg Asn Asn Leu Asp Asn Ala Val Glu Glu Leu Arg Gln 
        195                 200                 205 

Leu Thr Gly Asn Tyr Tyr Pro Glu Leu Ala Ser Leu Asn Val Glu His 
    210                 215                 220 

Phe Lys Thr Asp Lys Pro Lys Ala Val Asn Ala Leu Leu Lys Glu Ala 
225                 230                 235                 240 

Glu Asn Arg Asn Leu Ser Leu Leu Gln Ala Arg Leu Ser Gln Asp Leu 
                245                 250                 255 

Ala Arg Glu Gln Ile Arg Gln Ala Gln Asp Gly His Leu Pro Thr Leu 
            260                 265                 270 

Asn Leu Thr Ala Ser Thr Gly Ile Ser Asp Thr Ser Tyr Ser Gly Ser 
        275                 280                 285 

Lys Thr Asn Ser Thr Gln Tyr Asp Asp Ser Asn Met Gly Gln Asn Lys 
    290                 295                 300 

Ile Gly Leu Asn Phe Ser Leu Pro Leu Tyr Gln Gly Gly Met Val Asn 
305                 310                 315                 320 

Ser Gln Val Lys Gln Ala Gln Tyr Asn Phe Val Gly Ala Ser Glu Gln 
                325                 330                 335 

Leu Glu Ser Ala His Arg Ser Val Val Gln Thr Val Arg Ser Ser Phe 
            340                 345                 350 

Asn Asn Ile Asn Ala Ser Ile Ser Ser Ile Asn Ala Tyr Lys Gln Ala 
        355                 360                 365 

Val Val Ser Ala Gln Ser Ser Leu Asp Ala Met Glu Ala Gly Tyr Ser 
    370                 375                 380 

Val Gly Thr Arg Thr Ile Val Asp Val Leu Asp Ala Thr Thr Thr Leu 
385                 390                 395                 400 

Tyr Asp Ala Lys Gln Gln Leu Ala Asn Ala Arg Tyr Thr Tyr Leu Ile 
                405                 410                 415 

Asn Gln Leu Asn Ile Lys Tyr Ala Leu Gly Thr Leu Asn Glu Gln His 
            420                 425                 430 

Leu Leu Ala Leu Asn Ser Thr Leu Gly Lys Pro Ile Pro Thr Ser Pro 
        435                 440                 445 

Glu Ser Val Ala Pro Glu Thr Pro Asp Gln Asp Ala Ala Ala Asp Gly 
    450                 455                 460 

Tyr Asn Ala His Ser Ala Ala Pro Ala Val Gln Pro Thr Ala Ala Arg 
465                 470                 475                 480 

Ala Asn Ser Asn Asn Gly Asn Pro Phe Arg His 
                485                 490