Patent Publication Number: US-6706508-B1

Title: Ornithine carbamoyltransferase

Description:
This application is a divisional of U.S. application Ser. No. 08/961,536, filed Oct. 30, 1997, now U.S. Pat. No. 6,165,763. 
    
    
     FIELD OF THE INVENTION 
     This invention relates to newly identified polynucleotides and polypeptides, and their production and uses, as well as their variants, agonists and antagonists, and their uses. In particular, in these and in other regards, the invention relates to novel polynucleotides and polypeptides of the argF/arcB (ornithine carbamoyltransferase) family, hereinafter referred to as “ornithine carbamoyltransferase”. 
     BACKGROUND OF THE INVENTION 
     The Streptococci make up a medically important genera of microbes known to cause several types of disease in humans, including, for example, otitis media, conjunctivitis, pneumonia, bacteremia, meningitis, sinusitis, pleural empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospinal fluid. Since its isolation more than 100 years ago,  Streptococcus pneumoniae  has been one of the more intensively studied microbes. For example, much of our early understanding that DNA is, in fact, the genetic material was predicated on the work of Griffith and of Avery, Macleod and McCarty using this microbe. Despite the vast amount of research with  S. pneumoniae , many questions concerning the virulence of this microbe remain. It is particularly preferred to employ Streptococcal genes and gene products as targets for the development of antibiotics. 
     The frequency of  Streptococcus pneumoniae  infections has risen dramatically in the past 20 years. This has been attributed to the emergence of multiply antibiotic resistant strains and an increasing population of people with weakened immune systems. It is no longer uncommon to isolate  Streptococcus pneumoniae  strains which are resistant to some or all of the standard antibiotics. This has created a demand for both new anti-microbial agents and diagnostic tests for this organism. 
     While certain Streptococcal factors associated with pathogenicity have been identified, e.g., capsule polysaccharides, peptidoglycans, pneumolysins, PspA Complement factor H binding component, autolysin, neuraminidase, peptide permeases, hydrogen peroxide, IgA1 protease, the list is certainly not complete. Moreover, very little is known concerning the temporal expression of such genes during infection and disease progression in a mammalian host. Discovering the sets of genes the bacterium is likely to be expressing at the different stages of infection, particularly when an infection is established, provides critical information for the screening and characterization of novel antibacterials which can interrupt pathogenesis. In addition to providing a fuller understanding of known proteins, such an approach will identify previously unrecognised targets. 
     The reaction catalyzed by ornithine carbamoyltransferase can participate in either the anabolism or the catabolism of arginine. The carbamoylation of ornithine, yielding citrulline, is involved in the biosynthetic sequence; the reverse reaction, the phosphorolysis of citrulline, is the second step of the arginine deiminase pathway. A number of microorganisms which can fulfill both of these functions has been found to possess two distinct ornithine carbamoyltransferases. The kinetic properties of these various enzymes have been determined. All of them, regardless of the role they play in the cell, catalyze both the synthesis and breakdown of citrulline. Enzymes involved in biosynthesis or degradation of aminoacids play a key role in bacterial primary metabolism and therefore inhibitors of these proteins could interfere with the infection process and have utility as antibacterial agents. 
     Clearly, there is a need for factors, such as the novel compounds of the invention, that have a present benefit of being useful to screen compounds for antibiotic activity. Such factors are also useful to determine their role in pathogenesis of infection, dysfunction and disease. There is also a need for identification and characterization of such factors and their antagonists and agonists which can play a role in preventing, ameliorating or correcting infections, dysfunctions or diseases. 
     The polypeptides of the invention have amino acid sequence homology to a known Lactobacillus plantarum argF protein. 
     SUMMARY OF THE INVENTION 
     It is an object of the invention to provide polypeptides that have been identified as novel ornithine carbamoyltransferase polypeptides by homology between the amino acid sequence set out in Table 1 [SEQ ID NO: 2] and a known amino acid sequence or sequences of other proteins such as Lactobacillus plantarum argF protein. 
     It is a further object of the invention to provide polynucleotides that encode ornithine carbamoyltransferase polypeptides, particularly polynucleotides that encode the polypeptide herein designated ornithine carbamoyltransferase. 
     In a particularly preferred embodiment of the invention the polynucleotide comprises a region encoding ornithine carbamoyltransferase polypeptides comprising the sequence set out in Table 1 [SEQ ID NO:1] which includes a full length gene, or a variant thereof. 
     In another particularly preferred embodiment of the invention there is a novel ornithine carbamoyltransferase protein from  Streptococcus pneumoniae  comprising the amino acid sequence of Table 1 [SEQ ID NO:2], or a variant thereof. 
     In accordance with another aspect of the invention there is provided an isolated nucleic acid molecule encoding a mature polypeptide expressible by the  Streptococcus pneumoniae  0100993 strain contained in the deposited strain. 
     A further aspect of the invention there are provided isolated nucleic acid molecules encoding ornithine carbamoyltransferase, particularly  Streptococcus pneumoniae  ornithine carbamoyltransferase, including mRNAs, cDNAs, genomic DNAs. Further embodiments of the invention include biologically, diagnostically, prophylactically, clinically or therapeutically useful variants thereof, and compositions comprising the same. 
     In accordance with another aspect of the invention, there is provided the use of a polynucleotide of the invention for therapeutic or prophylactic purposes, in particular genetic immunization. Among the particularly preferred embodiments of the invention are naturally occurring allelic variants of ornithine carbamoyltransferase and polypeptides encoded thereby. 
     Another aspect of the invention there are provided novel polypeptides of  Streptococcus pneumoniae  referred to herein as ornithine carbamoyltransferase as well as biologically, diagnostically, prophylactically, clinically or therapeutically useful variants thereof, and compositions comprising the same. 
     Among the particularly preferred embodiments of the invention are variants of ornithine carbamoyltransferase polypeptide encoded by naturally occurring alleles of the ornithine carbamoyltransferase gene. 
     In a preferred embodiment of the invention there are provided methods for producing the aforementioned ornithine carbamoyltransferase polypeptides. 
     In accordance with yet another aspect of the invention, there are provided inhibitors to such polypeptides, useful as antibacterial agents, including, for example, antibodies. 
     In accordance with certain preferred embodiments of the invention, there are provided products, compositions and methods for assessing ornithine carbamoyltransferase expression, treating disease, for example, otitis media, conjunctivitis, pneumonia, bacteremia, meningitis, sinusitis, pleural empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospinal fluid, assaying genetic variation, and administering a ornithine carbamoyltransferase polypeptide or polynucleotide to an organism to raise an immunological response against a bacteria, especially a  Streptococcus pneumoniae  bacteria. 
     In accordance with certain preferred embodiments of this and other aspects of the invention there are provided polynucleotides that hybridize to ornithine carbamoyltransferase polynucleotide sequences, particularly under stringent conditions. 
     In certain preferred embodiments of the invention there are provided antibodies against ornithine carbamoyltransferase polypeptides. 
     In other embodiments of the invention there are provided methods for identifying compounds which bind to or otherwise interact with and inhibit or activate an activity of a polypeptide or polynucleotide of the invention comprising: contacting a polypeptide or polynucleotide of the invention with a compound to be screened under conditions to permit binding to or other interaction between the compound and the polypeptide or polynucleotide to assess the binding to or other interaction with the compound, such binding or interaction being associated with a second component capable of providing a detectable signal in response to the binding or interaction of the polypeptide or polynucleotide with the compound; and determining whether the compound binds to or otherwise interacts with and activates or inhibits an activity of the polypeptide or polynucleotide by detecting the presence or absence of a signal generated from the binding or interaction of the compound with the polypeptide or polynucleotide. 
     In accordance with yet another aspect of the invention, there are provided ornithine carbamoyltransferase agonists and antagonists, preferably bacteriostatic or bacteriocidal agonists and antagonists. 
     In a further aspect of the invention there are provided compositions comprising a ornithine carbamoyltransferase polynucleotide or a ornithine carbamoyltransferase polypeptide for administration to a cell or to a multicellular organism. 
     Various changes and modifications within the spirit and scope of the disclosed invention will become readily apparent to those skilled in the art from reading the following descriptions and from reading the other parts of the present disclosure. 
     GLOSSARY 
     The following definitions are provided to facilitate understanding of certain terms used frequently herein. 
     “Host cell” is a cell which has been transformed or transfected, or is capable of transformation or transfection by an exogenous polynucleotide sequence. 
     “Identity,” as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including but not limited to those described in ( Computational Molecular Biology , Lesk, A. M., ed., Oxford University Press, New York, 1988 ; Biocomputing: Informatics and Genome Projects , Smith, D. W., ed., Academic Press, New York, 1993 ; Computer Analysis of Sequence Data , Part I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994 ; Sequence Analysis in Molecular Biology , von Heinje, G., Academic Press, 1987; and  Sequence Analysis Primer , Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991; and Carillo, H., and Lipman, D., SIAM  J. Applied Math ., 48: 1073 (1988). Preferred methods to determine identity are designed to give the largest match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Preferred computer program methods to determine identity and similarity between two sequences include, but are not limited to, the GCG program package (Devereux, J., et al.,  Nucleic Acids Research  12(1): 387 (1984)), BLASTP, BLASTN, and FASTA (Atschul, S. F. et al.,  J. Molec. Biol . 215: 403-410 (1990). The BLAST X program is publicly available from NCBI and other sources ( BLAST Manual , Altschul, S., et al., NCBI NLM NIH Bethesda, Md. 20894; Altschul, S., et al.,  J. Mol. Biol . 215: 403-410 (1990). As an illustration, by a polynucleotide having a nucleotide sequence having at least, for example, 95% “identity” to a reference nucleotide sequence of SEQ ID NO: 1 it is intended that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence of SEQ ID NO: 1. In other words, to obtain a polynucleotide having a nucleotide sequence at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. These mutations of the reference sequence may occur at the 5 or 3 terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence. Analogously , by a polypeptide having an amino acid sequence having at least, for example, 95% identity to a reference amino acid sequence of SEQ ID NO:2 is intended that the amino acid sequence of the polypeptide is identical to the reference sequence except that the polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the reference amino acid of SEQ ID NO: 2. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a reference amino acid sequence, up to 5% of the amino acid residues in the reference sequence may be deleted or substituted with another amino acid, or a number of amino acids up to 5% of the total amino acid residues in the reference sequence may be inserted into the reference sequence. These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence. 
     “Isolated” means altered “by the hand of man” from its natural state, i.e., if it occurs in nature, it has been changed or removed from its original environment, or both. For example, a polynucleotide or a polypeptide naturally present in a living organism is not “isolated,” but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is “isolated”, as the term is employed herein. 
     “Polynucleotide(s)” generally refers to any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. “Polynucleotide(s)” include, without limitation, single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions or single-, double- and triple-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded, or triple-stranded regions, or a mixture of single- and double-stranded regions. In addition, “polynucleotide” as used herein refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The strands in such regions may be from the same molecule or from different molecules. The regions may include all of one or more of the molecules, but more typically involve only a region of some of the molecules. One of the molecules of a triple-helical region often is an oligonucleotide. As used herein, the term “polynucleotide(s)” also includes DNAs or RNAs as described above that contain one or more modified bases. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are “polynucleotide(s)” as that term is intended herein. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples, are polynucleotides as the term is used herein. It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many usefull purposes known to those of skill in the art. The term “polynucleotide(s)” as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including, for example, simple and complex cells. “Polynucleotide(s)” also embraces short polynucleotides often referred to as oligonucleotide(s). 
     “Polypeptide(s)” refers to any peptide or protein comprising two or more amino acids joined to each other by peptide bonds or modified peptide bonds. “Polypeptide(s)” refers to both short chains, commonly referred to as peptides, oligopeptides and oligomers and to longer chains generally referred to as proteins. Polypeptides may contain amino acids other than the 20 gene encoded amino acids. “Polypeptide(s)” include those modified either by natural processes, such as processing and other post-translational modifications, but also by chemical modification techniques. Such modifications are well described in basic texts and in more detailed monographs, as well as in a voluminous research literature, and they are well known to those of skill in the art. It will be appreciated that the same type of modification may be present in the same or varying degree at several sites in a given polypeptide. Also, a given polypeptide may contain many types of modifications. Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains, and the amino or carboxyl termini. Modifications include, for example, acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, glycosylation, lipid attachment, sulfation, gamma-carboxylation of glutamic acid residues, hydroxylation and ADP-ribosylation, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins, such as arginylation, and ubiquitination. See, for instance,  PROTEINS—STRUCTURE AND MOLECULAR PROPERTIES , 2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York (1993) and Wold, F., Posttranslational Protein Modifications: Perspectives and Prospects, pgs. 1-12 in  POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS , B. C. Johnson, Ed., Academic Press, New York (1983); Seifter et al.,  Meth. Enzymol . 182:626-646 (1990) and Rattan et al.,  Protein Synthesis: Posttranslational Modifications and Aging , Ann. N.Y. Acad. Sci. 663: 48-62 (1992). Polypeptides may be branched or cyclic, with or without branching. Cyclic, branched and branched circular polypeptides may result from post-translational natural processes and may be made by entirely synthetic methods, as well. 
     “Variant(s)” as the term is used herein, is a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide respectively, but retains essential properties. A typical variant of a polynucleotide differs in nucleotide sequence from another, reference polynucleotide. Changes in the nucleotide sequence of the variant may or may not alter the amino acid sequence of a polypeptide encoded by the reference polynucleotide. Nucleotide changes may result in amino acid substitutions, additions, deletions, fusions and truncations in the polypeptide encoded by the reference sequence, as discussed below. A typical variant of a polypeptide differs in amino acid sequence from another, reference polypeptide. Generally, differences are limited so that the sequences of the reference polypeptide and the variant are closely similar overall and, in many regions, identical. A variant and reference polypeptide may differ in amino acid sequence by one or more substitutions, additions, deletions in any combination. A substituted or inserted amino acid residue may or may not be one encoded by the genetic code. A variant of a polynucleotide or polypeptide may be a naturally occurring such as an allelic variant, or it may be a variant that is not known to occur naturally. Non-naturally occurring variants of polynucleotides and polypeptides may be made by mutagenesis techniques, by direct synthesis, and by other recombinant methods known to skilled artisans. 
     DESCRIPTION OF THE INVENTION 
     The invention relates to novel ornithine carbamoyltransferase polypeptides and polynucleotides as described in greater detail below. In particular, the invention relates to polypeptides and polynucleotides of a novel ornithine carbamoyltransferase of  Streptococcus pneumoniae , which is related by amino acid sequence homology to Lactobacillus plantarum argF polypeptide. The invention relates especially to ornithine carbamoyltransferase having the nucleotide and amino acid sequences set out in Table 1 [SEQ ID NO: 1] and Table 1 [SEQ ID NO: 2] respectively, and to the ornithine carbamoyltransferase nucleotide sequences of the DNA in the deposited strain and amino acid sequences encoded thereby. 
     
       
         
           
               
             
               
                 TABLE 1 
               
               
                   
               
               
                 Ornithine carbamoyltransferase Polynucleotide and Polypeptide Sequences 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (A) Sequences from  Streptococcus pneumoniae  ornithine 
               
               
                 carbamoyltransferase polynucleotide sequence [SEQ ID NO:1]. 
               
            
           
           
               
               
            
               
                 5′-1 
                  ATGACAAATT CAGTATTCCA AGGACGCAGC TTCTTAGCAG AAAAAGACTT 
               
               
                   
               
               
                 51 
                 TACCCGTGCA GAGTTAGAAT ACCTTATTGG TCTTTCAGCT CACTTGAAAG 
               
               
                   
               
               
                 101 
                 ATTTGAAAAA ACGCAATATT CAACACCACT ACCTTGCTGG CAAGAATATC 
               
               
                   
               
               
                 151 
                 GCTCTCCTAT TTGAAAAAAC ATCTACTCGT ACTCGTGCAG CCTTTACAAC 
               
               
                   
               
               
                 201 
                 TGCGGCTATC GACCTTGGTG CTCACCCAGA ATACCTCGGA GCAAATGATA 
               
               
                   
               
               
                 251 
                 TTCAGTTGGG TAAAAAAGAA TCTACTGAAG ATACTGCTAA AGTATTGGGA 
               
               
                   
               
               
                 301 
                 CGTATGTTTG ACGGGATTGA ATTCCGCGGA TTCAGCCAAC GTATGGTTGA 
               
               
                   
               
               
                 351 
                 AGAATTGGCA GAATTCTCAG GCGTTCCAGT ATGGAACGGT CTAACTGACG 
               
               
                   
               
               
                 401 
                 AATGGCACCC AACTCAAATG CTCGCTGACT ACTTGACTGT TCAAGAAAAC 
               
               
                   
               
               
                 451 
                 TTCGGTCGCT TGGAAGGCTT GACATTGGTA TACTGTGGTG ATGGACGTAA 
               
               
                   
               
               
                 501 
                 CAACGTTGCC AACAGCTTGC TCGTAACAGG TGCTATCCTT GGTGTCAATG 
               
               
                   
               
               
                 551 
                 TTCACATCTT CTCACCAAAA GAACTCTTCC CAGAAAAAGA AATCGTTGAA 
               
               
                   
               
               
                 601 
                 TTGGCAGAAG GATTTGCTAA AGAAAGTGGC GCACATGTTC TCATCACTGA 
               
               
                   
               
               
                 651 
                 AGATGCTGAT GAAGCAGTTA AAGATGCAGA CGTTCTTTAC ACAGACGTTT 
               
               
                   
               
               
                 701 
                 GGGTATCAAT GGGTGAAGAA GACAAATTCG CAGAACGTGT AGCTCTTCTT 
               
               
                   
               
               
                 751 
                 AAACCTTACC AAGTCAATAT GGACTTAGTT AAAAAAGCAG GCAATGAAAA 
               
               
                   
               
               
                 801 
                 CTTGATCTTC CTACACTGCT TGCCAGCATT CCACGATACT CACACTGTTT 
               
               
                   
               
               
                 851 
                 ATGGTAAAGA CGTTGCTGAA AAATTTGGTG TAGAAGAAAT GGAAGTAACA 
               
               
                   
               
               
                 901 
                 GACGAAGTCT TCCGCAGCAA GTACGCTCGC CACTTCGATC AAGCAGAAAA 
               
               
                   
               
               
                 951 
                 CCGTATGCAC ACTATCAAAG CTGTTATGGC TGCTACACTT GGTAACCTTT 
               
               
                   
               
               
                 1001 
                 ATATTCCTAA AGTATAA-3′ 
               
               
                   
               
            
           
           
               
            
               
                 (B) Ornithine carbamoyltransferase polypeptide sequence deduced from the 
               
               
                 polynucleotide sequence in this table [SEQ ID NO:2]. 
               
            
           
           
               
               
            
               
                 NH 2 -1 
                 MTNSVFQGRS FLAEKDFTRA ELEYLIGLSA HLKDLKKRNI QHHYLAGKNI 
               
               
                   
               
               
                 51 
                 ALLFEKTSTR TRAAFTTAAI DLGAHPEYLG ANDIQLGKKE STEDTAKVLG 
               
               
                   
               
               
                 101 
                 RMFDGIEFRG FSQRMVEELA EFSGVPVWNG LTDEWHPTQM LADYLTVQEN 
               
               
                   
               
               
                 151 
                 FGRLEGLTLV YCGDGRNNVA NSLLVTGAIL GVNVHIFSPK ELFPEKEIVE 
               
               
                   
               
               
                 201 
                 LAEGFAKESG AHVLITEDAD EAVKDADVLY TDVWVSMGEE DKFAERVALL 
               
               
                   
               
               
                 251 
                 KPYQVNMDLV KKAGNENLIF LHCLPAFHDT HTVYGKDVAE KFGVEEMEVT 
               
               
                   
               
               
                 301 
                 DEVFRSKYAR HFDQAENRMH TIKAVMAATL GNLYIPKV -COOH 
               
               
                   
               
            
           
           
               
            
               
                 (C) Polynucleotide sequence embodiments [SEQ ID NO:1]. 
               
            
           
           
               
               
            
               
                 X—(R 1 ) n -1 
                 ATGACAAATT CAGTATTCCA AGGACGCAGC TTCTTAGCAG AAAAAGACTT 
               
               
                   
               
               
                 51 
                 TACCCGTGCA GAGTTAGAAT ACCTTATTGG TCTTTCAGCT CACTTGAAAG 
               
               
                   
               
               
                 101 
                 ATTTGAAAAA ACGCAATATT CAACACCACT ACCTTGCTGG CAAGAATATC 
               
               
                   
               
               
                 151 
                 GCTCTCCTAT TTGAAAAAAC ATCTACTCGT ACTCGTGCAG CCTTTACAAC 
               
               
                   
               
               
                 201 
                 TGCGGCTATC GACCTTGGTG CTCACCCAGA ATACCTCGGA GCAAATGATA 
               
               
                   
               
               
                 251 
                 TTCAGTTGGG TAAAAAAGAA TCTACTGAAG ATACTGCTAA AGTATTGGGA 
               
               
                   
               
               
                 301 
                 CGTATGTTTG ACGGGATTGA ATTCCGCGGA TTCAGCCAAC GTATGGTTGA 
               
               
                   
               
               
                 351 
                 AGAATTGGCA GAATTCTCAG GCGTTCCAGT ATGGAACGGT CTAACTGACG 
               
               
                   
               
               
                 401 
                 AATGGCACCC AACTCAAATG CTCGCTGACT ACTTGACTGT TCAAGAAAAC 
               
               
                   
               
               
                 451 
                 TTCGGTCGCT TGGAAGGCTT GACATTGGTA TACTGTGGTG ATGGACGTAA 
               
               
                   
               
               
                 501 
                 CAACGTTGCC AACAGCTTGC TCGTAACAGG TGCTATCCTT GGTGTCAATG 
               
               
                   
               
               
                 551 
                 TTCACATCTT CTCACCAAAA GAACTCTTCC CAGAAAAAGA AATCGTTGAA 
               
               
                   
               
               
                 601 
                 TTGGCAGAAG GATTTGCTAA AGAAAGTGGC GCACATGTTC TCATCACTGA 
               
               
                   
               
               
                 651 
                 AGATGCTGAT GAAGCAGTTA AAGATGCAGA CGTTCTTTAC ACAGACGTTT 
               
               
                   
               
               
                 701 
                 GGGTATCAAT GGGTGAAGAA GACAAATTCG CAGAACGTGT AGCTCTTCTT 
               
               
                   
               
               
                 751 
                 AAACCTTACC AAGTCAATAT GGACTTAGTT AAAAAAGCAG GCAATGAAAA 
               
               
                   
               
               
                 801 
                 CTTGATCTTC CTACACTGCT TGCCAGCATT CCACGATACT CACACTGTTT 
               
               
                   
               
               
                 851 
                 ATGGTAAAGA CGTTGCTGAA AAATTTGGTG TAGAAGAAAT GGAAGTAACA 
               
               
                   
               
               
                 901 
                 GACGAAGTCT TCCGCAGCAA GTACGCTCGC CACTTCGATC AAGCAGAAAA 
               
               
                   
               
               
                 951 
                 CCGTATGCAC ACTATCAAAG CTGTTATGGC TGCTACACTT GGTAACCTTT 
               
               
                   
               
               
                 1001 
                 ATATTCCTAA AGTA -(R 2 ) n -Y 
               
               
                   
               
            
           
           
               
            
               
                 (D) Polypeptide sequence embodiments [SEQ ID NO:2]. 
               
            
           
           
               
               
            
               
                 X—(R 1 ) n -1 
                 MTNSVFQGRS FLAEKDFTRA ELEYLIGLSA HLKDLKKRNI QHHYLAGKNI 
               
               
                   
               
               
                 51 
                 ALLFEKTSTR TRAAFTTAAI DLGAHPEYLG ANDIQLGKKE STEDTAKVLG 
               
               
                   
               
               
                 101 
                 RMFDGIEFRG FSQRMVEELA EFSGVPVWNG LTDEWHPTQM LADYLTVQEN 
               
               
                   
               
               
                 151 
                 FGRLEGLTLV YCGDGRNNVA NSLLVTGAIL GVNVHIFSPK ELFPEKEIVE 
               
               
                   
               
               
                 201 
                 LAEGFAKESG AHVLITEDAD EAVKDADVLY TDVWVSMGEE DKFAERVALL 
               
               
                   
               
               
                 251 
                 KPYQVNMDLV KKAGNENLIF LRCLPAFHDT HTVYGKDVAE KFGVEEMEVT 
               
               
                   
               
               
                 301 
                 DEVFRSKYAR HFDQAENRMH TIKAVMAATL GNLYIPKV -(R 2 ) n -Y 
               
               
                   
               
            
           
           
               
            
               
                 (E) Sequences from  Streptococcus pneumoniae  ornithine 
               
               
                 carbamoyltransferase polynucleotide ORF sequence [SEQ ID NO:3]. 
               
               
                 5′- 
               
               
                 ATGACAAATTCAGTATTCCAAGGACGCAGCTTCTTAGCAGAAAAAGACTTTACCCGTGCAGAGTTAGAATACC 
               
               
                 TTATTGG 
               
               
                   
               
               
                 TCTTTCAGCTCACTTGAAAGATTTGAAAAAACGCAATATTCAACACCACTACCTTGCTGGCAAGAATATCGCT 
               
               
                 CTCCTAT 
               
               
                   
               
               
                 TTGAAAAAACATCTACTCGTACTCGTGCAGCCTTTACAACTGCGGCTATCGACCTTGGTGCTCACCCAGAATA 
               
               
                 CCTCGGA 
               
               
                   
               
               
                 GCAAATGATATTCAGTTGGGTAAAAAAGAATCTACTGAAGATACTGCTAAAGTATTGGGACGTATGTTTGACG 
               
               
                 GGATTGA 
               
               
                   
               
               
                 ATTCCGCGGATTCAGCCAACGTTATGGTTGA-3′ 
               
               
                   
               
               
                 (F) Ornithine carbamoyltransferase polypeptide sequence deduced from 
               
               
                 the polynucleotide ORF sequence in this table [SEQ ID NO:4]. 
               
               
                 NH 2 -MTNSVFQGRSFLAEKDFTRAELEYLIGLSAHLKDLKKRNIQHHYLAGKNIALLFEKTSTRTRAAFTTAA 
               
               
                   
               
               
                 IDLGAHPEYLGANDIQLGKKESTEDTAKVLGRMFDGIEFRGFSQRYG -COOH 
               
               
                   
               
            
           
         
       
     
     Deposited Materials 
     A deposit containing a  Streptococcus pneumoniae  0100993 strain has been deposited with the National Collections of Industrial and Marine Bacteria Ltd. (herein “NCIMB”), 23 St. Machar Drive, Aberdeen AB2 1RY, Scotland on Apr. 11, 1996 and assigned deposit number 40794. The deposit was described as  Streptococcus peumnoiae  0100993 on deposit. On Apr. 17, 1996 a  Streptococcus peumnoiae  0100993 DNA library in  E. coli  was similarly deposited with the NCIMB and assigned deposit number 40800. The  Streptococcus pneumoniae  strain deposit is referred to herein as “the deposited strain” or as “the DNA of the deposited strain.” 
     The deposited strain contains the full length ornithine carbamoyltransferase gene. The sequence of the polynucleotides contained in the deposited strain, as well as the amino acid sequence of the polypeptide encoded thereby, are controlling in the event of any conflict with any description of sequences herein. 
     The deposit of the deposited strain has been made under the terms of the Budapest Treaty on the International Recognition of the Deposit of Micro-organisms for Purposes of Patent Procedure. The strain will be irrevocably and without restriction or condition released to the public upon the issuance of a patent. The deposited strain is provided merely as convenience to those of skill in the art and is not an admission that a deposit is required for enablement, such as that required under 35 U.S.C. §112. 
     A license may be required to make, use or sell the deposited strain, and compounds derived therefrom, and no such license is hereby granted. 
     Polypeptides 
     The polypeptides of the invention include the polypeptide of Table 1 [SEQ ID NO:2] (in particular the mature polypeptide) as well as polypeptides and fragments, particularly those which have the biological activity of ornithine carbamoyltransferase, and also those which have at least 70% identity to a polypeptide of Table 1 [SEQ ID NOS:2 and 4] or the relevant portion, preferably at least 80% identity to a polypeptide of Table 1 [SEQ ID NOS:2 and 4 ], and more preferably at least 90% similarity (more preferably at least 90% identity) to a polypeptide of Table 1 [SEQ ID NOS:2 and 4] and still more preferably at least 95% similarity (still more preferably at least 95% identity) to a polypeptide of Table 1 [SEQ ID NOS:2 and 4] and also include portions of such polypeptides with such portion of the polypeptide generally containing at least 30 amino acids and more preferably at least 50 amino acids. 
     The invention also includes polypeptides of the formula set forth in Table 1 (D) [SEQ ID NO:2] wherein, at the amino terminus, X is hydrogen, and at the carboxyl terminus, Y is hydrogen or a metal, R 1  and R 2  is any amino acid residue, and n is an integer between 1 and 1000. Any stretch of amino acid residues denoted by either R group, where R is greater than 1, may be either a heteropolymer or a homopolymer, preferably a heteropolymer. 
     A fragment is a variant polypeptide having an amino acid sequence that entirely is the same as part but not all of the amino acid sequence of the aforementioned polypeptides. As with ornithine carbamoyltransferase polypeptides fragments may be “free-standing,” or comprised within a larger polypeptide of which they form a part or region, most preferably as a single continuous region, a single larger polypeptide. 
     Preferred fragments include, for example, truncation polypeptides having a portion of an amino acid sequence of Table 1 [SEQ ID NOS:2 and 4], or of variants thereof, such as a continuous series of residues that includes the amino terminus, or a continuous series of residues that includes the carboxyl terminus. Degradation forms of the polypeptides of the invention in a host cell, particularly a  Streptococcus pneumoniae , are also preferred. Further preferred are fragments characterized by structural or functional attributes such as fragments that comprise alpha-helix and alpha-helix forming regions, beta-sheet and beta-sheet-forming regions, turn and turn-forming regions, coil and coil-forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high antigenic index regions. 
     Also preferred are biologically active fragments which are those fragments that mediate activities of ornithine carbamoyltransferase, including those with a similar activity or an improved activity, or with a decreased undesirable activity. Also included are those figments that are antigenic or immunogenic in an animal, especially in a human. Particularly preferred are fragments comprising receptors or domains of enzymes that confer a function essential for viability of  Streptococcus pneumoniae  or the ability to initiate, or maintain cause disease in an individual, particularly a human. 
     Variants that are fragments of the polypeptides of the invention may be employed for producing the corresponding full-length polypeptide by peptide synthesis; therefore, these variants may be employed as intermediates for producing the full-length polypeptides of the invention. 
     Polynucleotides 
     Another aspect of the invention relates to isolated polynucleotides, including the full length gene, that encode the ornithine carbamoyltransferase polypeptide having a deduced amino acid sequence of Table 1 [SEQ ID NOS:2 and 4] and polynucleotides closely related thereto and variants thereof. 
     Using the information provided herein, such as a polynucleotide sequence set out in Table 1 [SEQ ID NOS:1 and 3], a polynucleotide of the invention encoding ornithine carbamoyltransferase polypeptide may be obtained using standard cloning and screening methods, such as those for cloning and sequencing chromosomal DNA fragments from bacteria using  Streptococcus pneumoniae  0100993 cells as starting material, followed by obtaining a full length clone. For example, to obtain a polynucleotide sequence of the invention, such as a sequence given in Table 1 [SEQ ID NOS:1 and 3], typically a library of clones of chromosomal DNA of  Streptococcus pneumoniae  0100993 in  E. coli  or some other suitable host is probed with a radiolabeled oligonucleotide, preferably a 17-mer or longer, derived from a partial sequence. Clones carrying DNA identical to that of the probe can then be distinguished using stringent conditions. By sequencing the individual clones thus identified with sequencing primers designed from the original sequence it is then possible to extend the sequence in both directions to determine the full gene sequence. Conveniently, such sequencing is performed using denatured double stranded DNA prepared from a plasmid clone. Suitable techniques are described by Maniatis, T., Fritsch, E. F. and Sambrook et al.,  MOLECULAR CLONING, A LABORATORY MANUAL , 2nd Ed.; Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989). (see in particular Screening By Hybridization 1.90 and Sequencing Denatured Double-Stranded DNA Templates 13.70). Illustrative of the invention, the polynucleotide set out in Table 1 [SEQ ID NO:1] was discovered in a DNA library derived from  Streptococcus pneumoniae  0100993. 
     The DNA sequence set out in Table 1 [SEQ ID NOS:1] contains an open reading frame encoding a protein having about the number of amino acid residues set forth in Table 1 [SEQ ID NO:2] with a deduced molecular weight that can be calculated using amino acid residue molecular weight values well known in the art. The polynucleotide of SEQ ID NO: 1, between nucleotide number 1 through number 1014 encodes the polypeptide of SEQ ID NO:2. The stop codon begins at nucleotide number 1015 of SEQ ID NO:1.11014. 
     Ornithine carbamoyltransferase of the invention is structurally related to other proteins of the argF/arcB (ornithine carbamoyltransferase) family, as shown by the results of sequencing the DNA encoding ornithine carbamoyltransferase of the deposited strain. The protein exhibits greatest homology to Lactobacillus plantarum argF protein (GenBank accession no. X99978) among known proteins. Ornithine carbamoyltransferase of Table 1 [SEQ ID NO:2] has about 61% identity over its entire length and about 76% similarity over its entire length with the amino acid sequence of Lactobacillus plantarum argF polypeptide. 
     The invention provides a polynucleotide sequence identical over its entire length to the coding sequence in Table 1 [SEQ ID NO:1]. Also provided by the invention is the coding sequence for the mature polypeptide or a fragment thereof, by itself as well as the coding sequence for the mature polypeptide or a fragment in reading frame with other coding sequence, such as those encoding a leader or secretory sequence, a pre-, or pro- or prepro- protein sequence. The polynucleotide may also contain non-coding sequences, including for example, but not limited to non-coding 5′ and 3′ sequences, such as the transcribed, non-translated sequences, termination signals, ribosome binding sites, sequences that stabilize mRNA, introns, polyadenylation signals, and additional coding sequence which encode additional amino acids. For example, a marker sequence that facilitates purification of the fused polypeptide can be encoded. In certain embodiments of the invention, the marker sequence is a hexa-histidine peptide, as provided in the pQE vector (Qiagen, Inc.) and described in Gentz et al.,  Proc. Natl. Acad. Sci., USA  86: 821-824 (1989), or an HA tag (Wilson et al.,  Cell  37: 767 (1984). Polynucleotides of the invention also include, but are not limited to, polynucleotides comprising a structural gene and its naturally associated sequences that control gene expression. 
     A preferred embodiment of the invention is a polynucleotide of comprising nucleotide 1 to 1014 or 1015 set forth in SEQ ID NO:1 of Table 1 which encode the ornithine carbamoyltransferase polypeptide. 
     The invention also includes polynucleotides of the formula set forth in Table 1 (C)[SEQ ID NO:1] wherein, at the 5′ end of the molecule, X is hydrogen, and at the 3′ end of the molecule, Y is hydrogen or a metal, R 1  and R 2  is any nucleic acid residue, and n is an integer between 1 and 1000. Any stretch of nucleic acid residues denoted by either R group, where n is greater than 1, may be either a heteropolymer or a homopolymer, preferably a heteropolymer. 
     The term “polynucleotide encoding a polypeptide” as used herein encompasses polynucleotides that include a sequence encoding a polypeptide of the invention, particularly a bacterial polypeptide and more particularly a polypeptide of the  Streptococcus pneumoniae  ornithine carbamoyltransferase having the amino acid sequence set out in Table 1 [SEQ ID NO:2]. The term also encompasses polynucleotides that include a single continuous region or discontinuous regions encoding the polypeptide (for example, interrupted by integrated phage or an insertion sequence or editing) together with additional regions, that also may contain coding and/or non-coding sequences. 
     The invention further relates to variants of the polynucleotides described herein that encode for variants of the polypeptide having the deduced amino acid sequence of Table 1 [SEQ ID NO:2]. Variants that are fragments of the polynucleotides of the invention may be used to synthesize full-length polynucleotides of the invention. 
     Further particularly preferred embodiments are polynucleotides encoding ornithine carbamoyltransferase variants, that have the amino acid sequence of ornithine carbamoyltransferase polypeptide of Table 1 [SEQ ID NO:2] in which several, a few, 5 to 10, 1 to 5, 1 to 3, 2, 1 or no amino acid residues are substituted, deleted or added, in any combination. Especially preferred among these are silent substitutions, additions and deletions, that do not alter the properties and activities of ornithine carbamoyltransferase. 
     Further preferred embodiments of the invention are polynucleotides that are at least 70% identical over their entire length to a polynucleotide encoding ornithine carbamoyltransferase polypeptide having an amino acid sequence set out in Table 1 [SEQ ID NOS:2 and 4], and polynucleotides that are complementary to such polynucleotides. Alternatively, most highly preferred are polynucleotides that comprise a region that is at least 80% identical over its entire length to a polynucleotide encoding ornithine carbamoyltransferase polypeptide of the deposited strain and polynucleotides complementary thereto. In this regard, polynucleotides at least 90% identical over their entire length to the same are particularly preferred, and among these particularly preferred polynucleotides, those with at least 95% are especially preferred. Furthermore, those with at least 97% are highly preferred among those with at least 95%, and among these those with at least 98% and at least 99% are particularly highly preferred, with at least 99% being the more preferred. 
     Preferred embodiments are polynucleotides that encode polypeptides that retain substantially the same biological function or activity as the mature polypeptide encoded by the DNA of Table 1 [SEQ ID NO:1]. 
     The invention further relates to polynucleotides that hybridize to the herein above-described sequences. In this regard, the invention especially relates to polynucleotides that hybridize under stringent conditions to the herein above-described polynucleotides. As herein used, the terms “stringent conditions” and “stringent hybridization conditions” mean hybridization will occur only if there is at least 95% and preferably at least 97% identity between the sequences. An example of stringent hybridization conditions is overnight incubation at 42° C. in a solution comprising: 50% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5×Denhardt&#39;s solution, 10% dextran sulfate, and 20 micrograms/ml denatured, sheared salmon sperm DNA, followed by washing the hybridization support in 0.1×SSC at about 65° C. Hybridization and wash conditions are well known and exemplified in Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y., (1989), particularly Chapter 11 therein. 
     The invention also provides a polynucleotide consisting essentially of a polynucleotide sequence obtainable by screening an appropriate library containing the complete gene for a polynucleotide sequence set forth in SEQ ID NO:1 or SEQ ID NO:3 under stringent hybridization conditions with a probe having the sequence of said polynucleotide sequence set forth in SEQ ID NO:1 or a fragment thereof; and isolating said DNA sequence. Fragments useful for obtaining such a polynucleotide include, for example, probes and primers described elsewhere herein. 
     As discussed additionally herein regarding polynucleotide assays of the invention, for instance, polynucleotides of the invention as discussed above, may be used as a hybridization probe for RNA, cDNA and genomic DNA to isolate full-length cDNAs and genomic clones encoding ornithine carbamoyltransferase and to isolate cDNA and genomic clones of other genes that have a high sequence similarity to the ornithine carbamoyltransferase gene. Such probes generally will comprise at least 15 bases. Preferably, such probes will have at least 30 bases and may have at least 50 bases. Particularly preferred probes will have at least 30 bases and will have 50 bases or less. 
     For example, the coding region of the ornithine carbamoyltransferase gene may be isolated by screening using the DNA sequence provided in SEQ ID NO: 1 to synthesize an oligonucleotide probe. A labeled oligonucleotide having a sequence complementary to that of a gene of the invention is then used to screen a library of cDNA, genomic DNA or mRNA to determine which members of the library the probe hybridizes to. 
     The polynucleotides and polypeptides of the invention may be employed, for example, as research reagents and materials for discovery of treatments of and diagnostics for disease, particularly human disease, as further discussed herein relating to polynucleotide assays. 
     Polynucleotides of the invention that are oligonucleotides derived from the sequences of SEQ ID NOS:1 and/or 2 may be used in the processes herein as described, but preferably for PCR, to determine whether or not the polynucleotides identified herein in whole or in part are transcribed in bacteria in infected tissue. It is recognized that such sequences will also have utility in diagnosis of the stage of infection and type of infection the pathogen has attained. 
     The invention also provides polynucleotides that may encode a polypeptide that is the mature protein plus additional amino or carboxyl-terminal amino acids, or amino acids interior to the mature polypeptide (when the mature form has more than one polypeptide chain, for instance). Such sequences may play a role in processing of a protein from precursor to a mature form, may allow protein transport, may lengthen or shorten protein half-life or may facilitate manipulation of a protein for assay or production, among other things. As generally is the case in vivo, the additional amino acids may be processed away from the mature protein by cellular enzymes. 
     A precursor protein, having the mature form of the polypeptide fused to one or more prosequences may be an inactive form of the polypeptide. When prosequences are removed such inactive precursors generally are activated. Some or all of the prosequences may be removed before activation. Generally, such precursors are called proproteins. 
     In sum, a polynucleotide of the invention may encode a mature protein, a mature protein plus a leader sequence (which may be referred to as a preprotein), a precursor of a mature protein having one or more prosequences that are not the leader sequences of a preprotein, or a preproprotein, which is a precursor to a proprotein, having a leader sequence and one or more prosequences, which generally are removed during processing steps that produce active and mature forms of the polypeptide. 
     Vectors, Host Cells, Expression 
     The invention also relates to vectors that comprise a polynucleotide or polynucleotides of the invention, host cells that are genetically engineered with vectors of the invention and the production of polypeptides of the invention by recombinant techniques. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the invention. 
     For recombinant production, host cells can be genetically engineered to incorporate expression systems or portions thereof or polynucleotides of the invention. Introduction of a polynucleotide into the host cell can be effected by methods described in many standard laboratory manuals, such as Davis et al.,  BASIC METHODS IN MOLECULAR BIOLOGY , (1986) and Sambrook et al.,  MOLECULAR CLONING: A LABORATORY MANUAL , 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), such as, calcium phosphate transfection, DEAE-dextran mediated transfection, transvection, microinjection, cationic lipid-mediated transfection, electroporation, transduction, scrape loading, ballistic introduction and infection. 
     Representative examples of appropriate hosts include bacterial cells, such as streptococci, staphylococci, enterococci  E. coli , streptomyces and  Bacillus subtilis  cells; fungal cells, such as yeast cells and Aspergillus cells; insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, 293 and Bowes melanoma cells; and plant cells. 
     A great variety of expression systems can be used to produce the polypeptides of the invention. Such vectors include, among others, chromosomal, episomal and virus-derived vectors, e.g., vectors derived from bacterial plasmids, from bacteriophage, from transposons, from yeast episomes, from insertion elements, from yeast chromosomal elements, from viruses such as baculoviruses, papova viruses, such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids. The expression system constructs may contain control regions that regulate as well as engender expression. Generally, any system or vector suitable to maintain, propagate or express polynucleotides and/or to express a polypeptide in a host may be used for expression in this regard. The appropriate DNA sequence may be inserted into the expression system by any of a variety of well-known and routine techniques, such as, for example, those set forth in Sambrook et al.,  MOLECULAR CLONING, A LABORATORY MANUAL , (supra). 
     For secretion of the translated protein into the lumen of the endoplasmic reticulum, into the periplasmic space or into the extracellular environment, appropriate secretion signals may be incorporated into the expressed polypeptide. These signals may be endogenous to the polypeptide or they may be heterologous signals. 
     Polypeptides of the invention can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography, and lectin chromatography. Most preferably, high performance liquid chromatography is employed for purification. Well known techniques for refolding protein may be employed to regenerate active conformation when the polypeptide is denatured during isolation and or purification. 
     Diagnostic Assays 
     This invention is also related to the use of the ornithine carbamoyltransferase polynucleotides of the invention for use as diagnostic reagents. Detection of ornithine carbamoyltransferase in a eukaryote, particularly a mammal, and especially a human, will provide a diagnostic method for diagnosis of a disease. Eukaryotes (herein also “individual(s)”), particularly mammals, and especially humans, particularly those infected or suspected to be infected with an organism comprising the ornithine carbamoyltransferase gene may be detected at the nucleic acid level by a variety of techniques. 
     Nucleic acids for diagnosis may be obtained from an infected individual&#39;s cells and tissues, such as bone, blood, muscle, cartilage, and skin. Genomic DNA may be used directly for detection or may be amplified enzymatically by using PCR or other amplification technique prior to analysis. RNA or cDNA may also be used in the same ways. Using amplification, characterization of the species and strain of prokaryote present in an individual, may be made by an analysis of the genotype of the prokaryote gene. Deletions and insertions can be detected by a change in size of the amplified product in comparison to the genotype of a reference sequence. Point mutations can be identified by hybridizing amplified DNA to labeled ornithine carbamoyltransferase polynucleotide sequences. Perfectly matched sequences can be distinguished from mismatched duplexes by RNase digestion or by differences in melting temperatures. DNA sequence differences may also be detected by alterations in the electrophoretic mobility of the DNA fragments in gels, with or without denaturing agents, or by direct DNA sequencing. See, e.g., Myers et al.,  Science , 230: 1242 (1985). Sequence changes at specific locations also may be revealed by nuclease protection assays, such as RNase and S1 protection or a chemical cleavage method. See, e.g. Cotton et al.,  Proc. Natl. Acad. Sci., USA , 85:4397-4401 (1985). 
     Cells carrying mutations or polymorphisms in the gene of the invention may also be detected at the DNA level by a variety of techniques, to allow for serotyping, for example. For example, RT-PCR can be used to detect mutations. It is particularly preferred to used RT-PCR in conjunction with automated detection systems, such as, for example, GeneScan. RNA or cDNA may also be used for the same purpose, PCR or RT-PCR. As an example, PCR primers complementary to a nucleic acid encoding ornithine carbamoyltransferase can be used to identify and analyze mutations. Examples of representative primers are shown below in Table 2. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Primers for amplification of ornithine 
               
               
                 carbamoyltransferase polynucleotides 
               
            
           
           
               
               
               
            
               
                   
                 SEQ ID NO 
                 PRIMER SEQUENCE 
               
               
                   
                   
               
               
                   
                 5 
                 5′ AAAAACGCAATATTCAACACCACT -3′ 
               
               
                   
                 6 
                 5′ TCCTTCTGCCAATTCAACGAT -3′ 
               
               
                   
                   
               
            
           
         
       
     
     The invention further provides these primers with 1, 2, 3 or 4 nucleotides removed from the 5′ and/or the 3′ end. These primers may be used for, among other things, amplifying ornithine carbamoyltransferase DNA isolated from a sample derived from an individual. The primers may be used to amplify the gene isolated from an infected individual such that the gene may then be subject to various techniques for elucidation of the DNA sequence. In this way, mutations in the DNA sequence may be detected and used to diagnose infection and to serotype and/or classify the infectious agent. 
     The invention further provides a process for diagnosing, disease, preferably bacterial infections, more preferably infections by  Streptococcus pneumoniae , and most preferably otitis media, conjunctivitis, pneumonia, bacteremia, meningitis, sinusitis, pleural empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospinal fluid, comprising determining from a sample derived from an individual a increased level of expression of polynucleotide having the sequence of Table 1 [SEQ ID NO: 1]. Increased or decreased expression of ornithine carbamoyltransferase polynucleotide can be measured using any on of the methods well known in the art for the quantation of polynucleotides, such as, for example, amplification, PCR, RT-PCR, RNase protection, Northern blotting and other hybridization methods. 
     In addition, a diagnostic assay in accordance with the invention for detecting over-expression of ornithine carbamoyltransferase protein compared to normal control tissue samples may be used to detect the presence of an infection, for example. Assay techniques that can be used to determine levels of a ornithine carbamoyltransferase protein, in a sample derived from a host are well-known to those of skill in the art. Such assay methods include radioimmunoassays, competitive-binding assays, Western Blot analysis and ELISA assays. 
     Antibodies 
     The polypeptides of the invention or variants thereof, or cells expressing them can be used as an inimunogen to produce antibodies immunospecific for such polypeptides. “Antibodies” as used herein includes monoclonal and polyclonal antibodies, chimeric, single chain, simianized antibodies and humanized antibodies, as well as Fab fragments, including the products of an Fab immunolglobulin expression library. 
     Antibodies generated against the polypeptides of the invention can be obtained by administering the polypeptides or epitope-bearing fragments, analogues or cells to an animal, preferably a nonhuman, using routine protocols. For preparation of monoclonal antibodies, any technique known in the art that provides antibodies produced by continuous cell line cultures can be used. Examples include various techniques, such as those in Kohler, G. and Milstein, C.,  Nature  256: 495-497 (1975); Kozbor et al.,  Immunology Today  4: 72 (1983); Cole et al., pg. 77-96 in  MONOCLONAL ANTIBODIES AND CANCER THERAPY , Alan R. Liss, Inc. (1985). 
     Techniques for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce single chain antibodies to polypeptides of this invention. Also, transgenic mice, or other organisms such as other mammals, may be used to express humanized antibodies. 
     Alternatively phage display technology may be utilized to select antibody genes with binding activities towards the polypeptide either from repertoires of PCR amplified v-genes of lymphocytes from humans screened for possessing anti-ornithine carbamoyltransferase or from naive libraries (McCafferty, J. et al., (1990), Nature 348, 552-554; Marks, J. et al., (1992) Biotechnology 10, 779-783). The affinity of these antibodies can also be improved by chain shuffling (Clackson, T. et al., (1991) Nature 352, 624-628). 
     If two antigen binding domains are present each domain may be directed against a different epitope—termed ‘bispecific’ antibodies. 
     The above-described antibodies may be employed to isolate or to identify clones expressing the polypeptides to purify the polypeptides by affinity chromatography. 
     Thus, among others, antibodies against ornithine carbamoyltransferase- polypeptide may be employed to treat infections, particularly bacterial infections and especially otitis media, conjunctivitis, pneumonia, bacteremia, meningitis, sinusitis, pleural empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospinal fluid. 
     Polypeptide variants include antigenically, epitopically or immunologically equivalent variants that form a particular aspect of this invention. The term “antigenically equivalent derivative” as used herein encompasses a polypeptide or its equivalent which will be specifically recognized by certain antibodies which, when raised to the protein or polypeptide according to the invention, interfere with the immediate physical interaction between pathogen and mammalian host. The term “immunologically equivalent derivative” as used herein encompasses a peptide or its equivalent which when used in a suitable formulation to raise antibodies in a vertebrate, the antibodies act to interfere with the immediate physical interaction between pathogen and mammalian host. 
     The polypeptide, such as an antigenically or immunologically equivalent derivative or a fusion protein thereof is used as an antigen to immunize a mouse or other animal such as a rat or chicken. The fusion protein may provide stability to the polypeptide. The antigen may be associated, for example by conjugation, with an immunogenic carrier protein for example bovine serum albumin (BSA) or keyhole limpet haemocyanin (KLH). Alternatively a multiple antigenic peptide comprising multiple copies of the protein or polypeptide, or an antigenically or immunologically equivalent polypeptide thereof may be sufficiently antigenic to improve immunogenicity so as to obviate the use of a carrier. 
     Preferably, the antibody or variant thereof is modified to make it less immunogenic in the individual. For example, if the individual is human the antibody may most preferably be “humanized”; where the complimentarity determining region(s) of the hybridoma-derived antibody has been transplanted into a human monoclonal antibody, for example as described in Jones, P. et al. (1986),  Nature  321, 522-525 or Tempest et al., (1991)  Biotechnology  9, 266-273. 
     The use of a polynucleotide of the invention in genetic immunization will preferably employ a suitable delivery method such as direct injection of plasmid DNA into muscles (Wolff et al., Hum Mol Genet 1992, 1:363, Manthorpe et al., Hum. Gene Ther. 1963:4, 419), delivery of DNA complexed with specific protein carriers (Wu et al.,  J Biol Chem . 1989: 264,16985), coprecipitation of DNA with calcium -phosphate (Benvenisty &amp; Reshef,  PNAS USA , 1986:83,9551), encapsulation of DNA in various forms of liposomes (Kaneda et al.,  Science  1989:243,375), particle bombardment (Tang et al.,  Nature  1992, 356:152, Eisenbraun et al.,  DNA Cell Biol  1993, 12:791) and in vivo infection using cloned retroviral vectors (Seeger et al.,  PNAS USA  1984:81,5849). 
     Antagonists and Agonists—Assays and Molecules 
     Polypeptides of the invention may also be used to assess the binding of small molecule substrates and ligands in, for example, cells, cell-free preparations, chemical libraries, and natural product mixtures. These substrates and ligands may be natural substrates and ligands or may be structural or functional mimetics. See, e.g., Coligan et al.,  Current Protocols in Immunology  1(2): Chapter 5 (1991). 
     The invention also provides a method of screening compounds to identify those which enhance (agonist) or block (antagonist) the action of ornithine carbamoyltransferase polypeptides or polynucleotides, particularly those compounds that are bacteriostatic and/or bacteriocidal. The method of screening may involve high-throughput techniques. For example, to screen for agonists or antagonists, a synthetic reaction mix, a cellular compartment, such as a membrane, cell envelope or cell wall, or a preparation of any thereof, comprising ornithine carbamoyltransferase polypeptide and a labeled substrate or ligand of such polypeptide is incubated in the absence or the presence of a candidate molecule that may be a ornithine carbamoyltransferase agonist or antagonist. The ability of the candidate molecule to agonize or antagonize the ornithine carbamoyltransferase polypeptide is reflected in decreased binding of the labeled ligand or decreased production of product from such substrate. Molecules that bind gratuitously, i.e., without inducing the effects of ornithine carbamoyltransferase polypeptide are most likely to be good antagonists. Molecules that bind well and increase the rate of product production from substrate are agonists. Detection of the rate or level of production of product from substrate may be enhanced by using a reporter system. Reporter systems that may be useful in this regard include but are not limited to colorimetric labeled substrate converted into product, a reporter gene that is responsive to changes in ornithine carbamoyltransferase polynucleotide or polypeptide activity, and binding assays known in the art. 
     Another example of an assay for ornithine carbamoyltransferase antagonists is a competitive assay that combines ornithine carbamoyltransferase and a potential antagonist with ornithine carbamoyltransferase-binding molecules, recombinant ornithine carbamoyltransferase binding molecules, natural substrates or ligands, or substrate or ligand mimetics, under appropriate conditions for a competitive inhibition assay. Ornithine carbamoyltransferase can be labeled, such as by radioactivity or a colorimetric compound, such that the number of ornithine carbamoyltransferase molecules bound to a binding molecule or converted to product can be determined accurately to assess the effectiveness of the potential antagonist. 
     Potential antagonists include small organic molecules, peptides, polypeptides and antibodies that bind to a polynucleotide or polypeptide of the invention and thereby inhibit or extinguish its activity. Potential antagonists also may be small organic molecules, a peptide, a polypeptide such as a closely related protein or antibody that binds the same sites on a binding molecule, such as a binding molecule, without inducing ornithine carbamoyltransferase-induced activities, thereby preventing the action of ornithine carbamoyltransferase by excluding ornithine carbamoyltransferase from binding. 
     Potential antagonists include a small molecule that binds to and occupies the binding site of the polypeptide thereby preventing binding to cellular binding molecules, such that normal biological activity is prevented. Examples of small molecules include but are not limited to small organic molecules, peptides or peptide-like molecules. Other potential antagonists include antisense molecules (see Okano,  J. Neurochem . 56: 560 (1991);  OLIGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORS OF GENE EXPRESSION , CRC Press, Boca Raton, Fla. (1988), for a description of these molecules). Preferred potential antagonists include compounds related to and variants of ornithine carbamoyltransferase. 
     Each of the DNA sequences provided herein may be used in the discovery and development of antibacterial compounds. The encoded protein, upon expression, can be used as a target for the screening of antibacterial drugs. Additionally, the DNA sequences encoding the amino terminal regions of the encoded protein or Shine-Delgarno or other translation facilitating sequences of the respective mRNA can be used to construct antisense sequences to control the expression of the coding sequence of interest. 
     The invention also provides the use of the polypeptide, polynucleotide or inhibitor of the invention to interfere with the initial physical interaction between a pathogen and mammalian host responsible for sequelae of infection. In particular the molecules of the invention may be used: in the prevention of adhesion of bacteria, in particular gram positive bacteria, to mammalian extracellular matrix proteins on in-dwelling devices or to extracellular matrix proteins in wounds; to block ornithine carbamoyltransferase protein-mediated mammalian cell invasion by, for example, initiating phosphorylation of mammalian tyrosine kinases (Rosenshine et al.,  Infect. Immun . 60:2211 (1992); to block bacterial adhesion between mammalian extracellular matrix proteins and bacterial ornithine carbamoyltransferase proteins that mediate tissue damage and; to block the normal progression of pathogenesis in infections initiated other than by the implantation of in-dwelling devices or by other surgical techniques. 
     The antagonists and agonists of the invention may be employed, for instance, to inhibit and treat otitis media, conjunctivitis, pneumonia, bacteremia, meningitis, sinusitis, pleural empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospinal fluid. 
       Helicobacter pylori  (herein  H. pylori ) bacteria infect the stomachs of over one-third of the world&#39;s population causing stomach cancer, ulcers, and gastritis (International Agency for Research on Cancer (1994) Schistosomes, Liver Flukes and  Helicobacter Pylori  (International Agency for Research on Cancer, Lyon, France; http://www.uicc.ch/ecp/ecp2904.htm). Moreover, the international Agency for Research on Cancer recently recognized a cause-and-effect relationship between  H. pylori  and gastric adenocarcinoma, classifying the bacterium as a Group I (definite) carcinogen. Preferred antimicrobial compounds of the invention (agonists and antagonists of ornithine carbamoyltransferase) found using screens provided by the invention, particularly broad-spectrum antibiotics, should be useful in the treatment of  H. pylori  infection. Such treatment should decrease the advent of  H. pylori -induced cancers, such as gastrointestinal carcinoma. Such treatment should also cure gastric ulcers and gastritis. 
     Vaccines 
     Another aspect of the invention relates to a method for inducing an immunological response in an individual, particularly a mammal which comprises inoculating the individual with ornithine carbamoyltransferase, or a fragment or variant thereof, adequate to produce antibody and/or T cell immune response to protect said individual from infection, particularly bacterial infection and most particularly  Streptococcus pneumoniae  infection. Also provided are methods whereby such immunological response slows bacterial replication. Yet another aspect of the invention relates to a method of inducing immunological response in an individual which comprises delivering to such individual a nucleic acid vector to direct expression of ornithine carbamoyltransferase, or a fragment or a variant thereof, for expressing ornithine carbamoyltransferase, or a fragment or a variant thereof in vivo in order to induce an immunological response, such as, to produce antibody and/or T cell immune response, including, for example, cytokine-producing T cells or cytotoxic T cells, to protect said individual from disease, whether that disease is already established within the individual or not. One way of administering the gene is by accelerating it into the desired cells as a coating on particles or otherwise. Such nucleic acid vector may comprise DNA, RNA, a modified nucleic acid, or a DNA/RNA hybrid. 
     A further aspect of the invention relates to an immunological composition which, when introduced into an individual capable or having induced within it an immunological response, induces an immunological response in such individual to a ornithine carbamoyltransferase or protein coded therefrom, wherein the composition comprises a recombinant ornithine carbamoyltransferase or protein coded therefrom comprising DNA which codes for and expresses an antigen of said ornithine carbamoyltransferase or protein coded therefrom. The immunological response may be used therapeutically or prophylactically and may take the form of antibody immunity or cellular immunity such as that arising from CTL or CD4+T cells. 
     A ornithine carbamoyltransferase polypeptide or a fragment thereof may be fused with co-protein which may not by itself produce antibodies, but is capable of stabilizing the first protein and producing a fused protein which will have immunogenic and protective properties. Thus fused recombinant protein, preferably further comprises an antigenic co-protein, such as lipoprotein D from Hemophilus influenzae, Glutathione-S-transferase (GST) or beta-galactosidase, relatively large co-proteins which solubilize the protein and facilitate production and purification thereof. Moreover, the co-protein may act as an adjuvant in the sense of providing a generalized stimulation of the immune system. The co-protein may be attached to either the amino or carboxy terminus of the first protein. 
     Provided by this invention are compositions, particularly vaccine compositions, and methods comprising the polypeptides or polynucleotides of the invention and immunostimulatory DNA sequences, such as those described in Sato, Y. et al. Science 273: 352 (1996). 
     Also, provided by this invention are methods using the described polynucleotide or particular fragments thereof which have been shown to encode non-variable regions of bacterial cell surface proteins in DNA constructs used in such genetic immunization experiments in animal models of infection with  Streptococcus pneumoniae  will be particularly useful for identifying protein epitopes able to provoke a prophylactic or therapeutic immune response. It is believed that this approach will allow for the subsequent preparation of monoclonal antibodies of particular value from the requisite organ of the animal successfully resisting or clearing infection for the development of prophylactic agents or therapeutic treatments of bacterial infection, particularly  Streptococcus pneumoniae  infection, in mammals, particularly humans. 
     The polypeptide may be used as an antigen for vaccination of a host to produce specific antibodies which protect against invasion of bacteria, for example by blocking adherence of bacteria to damaged tissue. Examples of tissue damage include wounds in skin or connective tissue caused, e.g., by mechanical, chemical or thermal damage or by implantation of indwelling devices, or wounds in the mucous membranes, such as the mouth, mammary glands, urethra or vagina. 
     The invention also includes a vaccine formulation which comprises an immunogenic recombinant protein of the invention together with a suitable carrier. Since the protein may be broken down in the stomach, it is preferably administered parenterally, including, for example, administration that is subcutaneous, intramuscular, intravenous, or intradermal. Formulations suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation insotonic with the bodily fluid, preferably the blood, of the individual; and aqueous and non-aqueous sterile suspensions which may include suspending agents or thickening agents. The formulations may be presented in unit-dose or multi-dose containers, for example, sealed ampules and vials and may be stored in a freeze-dried condition requiring only the addition of the sterile liquid carrier immediately prior to use. The vaccine formulation may also include adjuvant systems for enhancing the immunogenicity of the formulation, such as oil-in water systems and other systems known in the art. The dosage will depend on the specific activity of the vaccine and can be readily determined by routine experimentation. 
     While the invention has been described with reference to certain ornithine carbamoyltransferase protein, it is to be understood that this covers fragments of the naturally occurring protein and similar proteins with additions, deletions or substitutions which do not substantially affect the immunogenic properties of the recombinant protein. 
     Compositions, Kits and Administration 
     The invention also relates to compositions comprising the polynucleotide or the polypeptides discussed above or their agonists or antagonists. The polypeptides of the invention may be employed in combination with a non-sterile or sterile carrier or carriers for use with cells, tissues or organisms, such as a pharmaceutical carrier suitable for administration to a subject. Such compositions comprise, for instance, a media additive or a therapeutically effective amount of a polypeptide of the invention and a pharmaceutically acceptable carrier or excipient. Such carriers may include, but are not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol and combinations thereof. The formulation should suit the mode of administration. The invention further relates to diagnostic and pharmaceutical packs and kits comprising one or more containers filled with one or more of the ingredients of the aforementioned compositions of the invention. 
     Polypeptides and other compounds of the invention may be employed alone or in conjunction with other compounds, such as therapeutic compounds. 
     The pharmaceutical compositions may be administered in any effective, convenient manner including, for instance, administration by topical, oral, anal, vaginal, intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal or intradermal routes among others. 
     In therapy or as a prophylactic, the active agent may be administered to an individual as an injectable composition, for example as a sterile aqueous dispersion, preferably isotonic. 
     Alternatively the composition may be formulated for topical application for example in the form of ointments, creams, lotions, eye ointments, eye drops, ear drops, mouthwash, impregnated dressings and sutures and aerosols, and may contain appropriate conventional additives, including, for example, preservatives, solvents to assist drug penetration, and emollients in ointments and creams. Such topical formulations may also contain compatible conventional carriers, for example cream or ointment bases, and ethanol or oleyl alcohol for lotions. Such carriers may constitute from about 1% to about 98% by weight of the formulation; more usually they will constitute up to about 80% by weight of the formulation. 
     For administration to mammals, and particularly humans, it is expected that the daily dosage level of the active agent will be from 0.01 mg/kg to 10 mg/kg, typically around 1 mg/kg. The physician in any event will determine the actual dosage which will be most suitable for an individual and will vary with the age, weight and response of the particular individual. The above dosages are exemplary of the average case. There can, of course, be individual instances where higher or lower dosage ranges are merited, and such are within the scope of this invention. 
     In-dwelling devices include surgical implants, prosthetic devices and catheters, i.e., devices that are introduced to the body of an individual and remain in position for an extended time. Such devices include, for example, artificial joints, heart valves, pacemakers, vascular grafts, vascular catheters, cerebrospinal fluid shunts, urinary catheters, continuous ambulatory peritoneal dialysis (CAPD) catheters. 
     The composition of the invention may be administered by injection to achieve a systemic effect against relevant bacteria shortly before insertion of an in-dwelling device. Treatment may be continued after surgery during the in-body time of the device. In addition, the composition could also be used to broaden perioperative cover for any surgical technique to prevent bacterial wound infections, especially  Streptococcus pneumoniae  wound infections. 
     Many orthopaedic surgeons consider that humans with prosthetic joints should be considered for antibiotic prophylaxis before dental treatment that could produce a bacteremia. Late deep infection is a serious complication sometimes leading to loss of the prosthetic joint and is accompanied by significant morbidity and mortality. It may therefore be possible to extend the use of the active agent as a replacement for prophylactic antibiotics in this situation. 
     In addition to the therapy described above, the compositions of this invention may be used generally as a wound treatment agent to prevent adhesion of bacteria to matrix proteins exposed in wound tissue and for prophylactic use in dental treatment as an alternative to, or in conjunction with, antibiotic prophylaxis. 
     Alternatively, the composition of the invention may be used to bathe an indwelling device immediately before insertion. The active agent will preferably be present at a concentration of 1 μg/ml to 10 mg/ml for bathing of wounds or indwelling devices. 
     A vaccine composition is conveniently in injectable form. Conventional adjuvants may be employed to enhance the immune response. A suitable unit dose for vaccination is 0.5-5 microgram/kg of antigen, and such dose is preferably administered 1-3 times and with an interval of 1-3 weeks. With the indicated dose range, no adverse toxicological effects will be observed with the compounds of the invention which would preclude their administration to suitable individuals. 
     Each reference disclosed herein is incorporated by reference herein in its entirety. Any patent application to which this application claims priority is also incorporated by reference herein in its entirety. 
    
    
     EXAMPLES 
     The examples below are carried out using standard techniques, which are well known and routine to those of skill in the art, except where otherwise described in detail. The examples are illustrative, but do not limit the invention. 
     Example 1 
     Strain Selection, Library Production and Sequencing 
     The polynucleotide having the DNA sequence given in SEQ ID NO:1 was obtained from a library of clones of chromosomal DNA of  Streptococcus pneumoniae  in  E. coli . The sequencing data from two or more clones containing overlapping  Streptococcus pneumoniae  DNAs was used to construct the contiguous DNA sequence in SEQ ID NO:1. Libraries may be prepared by routine methods, for example: 
     Methods 1 and 2 below. 
     Total cellular DNA is isolated from  Streptococcus pneumoniae  0100993 according to standard procedures and size-fractionated by either of two methods. 
     Method 1 
     Total cellular DNA is mechanically sheared by passage through a needle in order to size-fractionate according to standard procedures. DNA fragments of up to 11kbp in size are rendered blunt by treatment with exonuclease and DNA polymerase, and EcoRI linkers added. Fragments are ligated into the vector Lambda ZapII that has been cut with EcoRI, the library packaged by standard procedures and  E. coli  infected with the packaged library. The library is amplified by standard procedures. 
     Method 2 
     Total cellular DNA is partially hydrolyzed with a one or a combination of restriction enzymes appropriate to generate a series of fragments for cloning into library vectors (e.g., RsaI, PalI, AluI, Bshl235I), and such fragments are size-fractionated according to standard procedures. EcoRI linkers are ligated to the DNA and the fragments then ligated into the vector Lambda ZapII that have been cut with EcoRI, the library packaged by standard procedures, and  E. coli  infected with the packaged library. The library is amplified by standard procedures. 
     Example 2 
     The Determination of Expression During Infection of a Gene from  Streptococcus pneumoniae    
     Excised lungs from a 48 hour respiratory tract infection of  Streptococcus pneumoniae  0100993 in the mouse is efficiently disrupted and processed in the presence of chaotropic agents and RNAase inhibitor to provide a mixture of animal and bacterial RNA. The optimal conditions for disruption and processing to give stable preparations and high yields of bacterial RNA are followed by the use of hybridisation to a radiolabelled oligonucleotide specific to  Streptococcus pneumoniae  16S RNA on Northern blots. The RNAase free, DNAase free, DNA and protein free preparations of RNA obtained are suitable for Reverse Transcription PCR (RT-PCR) using unique primer pairs designed from the sequence of each gene of  Streptococcus pneumoniae  0100993. 
     a) Isolation of Tissue Infected with  Streptococcus pneumoniae  0100993 from a Mouse Animal Model of Infection (Lungs) 
       Streptococcus pneumoniae  0100993 is grown either on TSA/5%horse blood plates or in AGCH medium overnight, 37° C., 5%CO 2 . Bacteria are then collected and resuspended in phosphate-buffered saline to an A 600  of approximately 0.4. Mice are anaesthetized with isofluorane and 50 ml of bacterial suspension (approximately 2×10 5  bacteria) is administered intranasally using a pipetman. Mice are allowed to recover and have food and water ad libitum. After 48 hours, the mice are euthanized by carbon dioxide overdose, and lungs are aseptically removed and snap-frozen in liquid nitrogen. 
     b) Isolation of  Streptococcus pneumoniae  0100993 RNA from Infected Tissue Samples 
     Infected tissue samples, in 2-ml cryo-strorage tubes, are removed from −80° C. storage into a dry ice ethanol bath. In a microbiological safety cabinet the samples are disrupted up to eight at a time while the remaining samples are kept frozen in the dry ice ethanol bath. To disrupt the bacteria within the tissue sample, 50-100 mg of the tissue is transfered to a FastRNA tube containing a silica/ceramic matrix (BIO101). Immediately, 1 ml of extraction reagents (FastRNA reagents, BIO101) are added to give a sample to reagent volume ratio of approximately 1 to 20. The tubes are shaken in a reciprocating shaker (FastPrep FP120, BIO101) at 6000 rpm for 20-120 sec. The crude RNA preparation is extracted with chloroform/isoamyl alcohol, and precipitated with DEPC-treated/Isopropanol Precipitation Solution (BIO101). RNA preparations are stored in this isopropanol solution at −80° C. if necessary. The RNA is pelleted (12,000 g for 10 min.), washed with 75% ethanol (v/v in DEPC-treated water), air-dried for 5-10 min, and resuspended in 0.1 ml of DEPC-treated water, followed by 5-10 minutes at 55° C. Finally, after at least 1 minute on ice, 200 units of Rnasin (Promega) is added. 
     RNA preparations are stored at −80° C. for up to one month. For longer term storage the RNA precipitate can be stored at the wash stage of the protocol in 75% ethanol for at least one year at −20° C. 
     Quality of the RNA isolated is assessed by running samples on 1% agarose gels. 1×TBE gels stained with ethidium bromide are used to visualise total RNA yields. To demonstrate the isolation of bacterial RNA from the infected tissue 1×MOPS, 2.2M formaldehyde gels are run and vacuum blotted to Hybond-N (Amersham). The blot is then hybridised with a  32 P-labelled oligonucletide probe, of sequence 5′ AACTGAGACTGGCTTTAAGAGATTA 3′ (SEQ ID NO:7), specific to 16S rRNA of  Streptococcus pneumoniae . The size of the hybridising band is compared to that of control RNA isolated from in vitro grown  Streptococcus pneumoniae  0100993 in the Northern blot. Correct sized bacterial 16S rRNA bands can be detected in total RNA samples which show degradation of the mammalian RNA when visualised on TBE gels. 
     c) The Removal of DNA from  Streptococcus pneumoniae -derived RNA 
     DNA is removed from 50 microgram samples of RNA by a 30 minute treatment at 37° C. with 20 units of RNAase-free DNAaseI (GenHunter) in the buffer supplied in a final volume of 57 microliters. 
     The DNAase is inactivated and removed by treatment with TRIzol LS Reagent (Gibco BRL, Life Technologies) according to the manufacturers protocol. DNAase treated RNA is resuspended in 100 microlitres of DEPC treated water with the addition of Rnasin as described before. 
     d) The Preparation of cDNA from RNA Samples Derived from Infected Tissue 
     3 microgram samples of DNAase treated RNA are reverse transcribed using.a SuperScript Preamplification System for First Strand cDNA Synthesis kit (Gibco BRL, Life Technologies) according to the manufacturers instructions. 150 nanogram of random hexamers is used to prime each reaction. Controls without the addition of SuperScriptII reverse transcriptase are also run. Both +/−RT samples are treated with RNaseH before proceeding to the PCR reaction. 
     e) The Use of PCR to Determine the Presence of a Bacterial cDNA Species 
     PCR reactions are set up on ice in 0.2 ml tubes by adding the following components: 43 microlitres PCR Master Mix (Advanced Biotechnologies Ltd.); 1 microlitre PCR primers (optimally 18-25 basepairs in length and designed to possess similar annealing temperatures), each primer at 10 mM initial concentration; and 5 microlitres cDNA. 
     PCR reactions are run on a Perkin Elmer GeneAmp PCR System 9600 as follows: 2 minutes at 94° C., then 50 cycles of 30 seconds each at 94° C., 50° C. and 72° C. followed by 7 minutes at 72° C. and then a hold temperature of 20° C. (the number of cycles is optimally 30-50 to determine the appearance or lack of a PCR product and optimally 8-30 cycles if an estimation of the starting quantity of cDNA from the RT reaction is to be made); 10 microlitre aliquots are then run out on 1% 1×TBE gels stained with ethidium bromide, with PCR product, if present, sizes estimated by comparison to a 100 bp DNA Ladder (Gibco BRL, Life Technologies). Alternatively if the PCR products are conveniently labelled by the use of a labelled PCR primer (e.g. labelled at the 5′end with a dye) a suitable aliquot of the PCR product is run out on a polyacrylamide sequencing gel and its presence and quantity detected using a suitable gel scanning system (e.g. ABI Prism™ 377 Sequencer using GeneScan™ software as supplied by Perkin Elmer). 
     RT/PCR controls may include +/− reverse transcriptase reactions, 16S rRNA primers or DNA specific primer pairs designed to produce PCR products from non-transcribed  Streptococcus pneumoniae  0100993 genomic sequences. 
     To test the efficiency of the primer pairs they are used in DNA PCR with  Streptococcus pneumoniae  0100993 total DNA. PCR reactions are set up and run as described above using approx. 1 microgram of DNA in place of the cDNA. 
     Primer pairs which fail to give the predicted sized product in either DNA PCR or RT/PCR are PCR failures and as such are uninformative. Of those which give the correct size product with DNA PCR two classes are distinguished in RT/PCR: 1.Genes which are not transcribed in vivo reproducibly fail to give a product in RT/PCR; and 2.Genes which are transcribed in vivo reproducibly give the correct size product in RT/PCR and show a stronger signal in the +RT samples than the signal (if at all present) in −RT controls. 
     
       
         
           
             7 
           
           
             
               1017 base pairs 
               nucleic acid 
               double 
               linear 
             
              1
ATGACAAATT CAGTATTCCA AGGACGCAGC TTCTTAGCAG AAAAAGACTT TACCCGTGCA     60
GAGTTAGAAT ACCTTATTGG TCTTTCAGCT CACTTGAAAG ATTTGAAAAA ACGCAATATT    120
CAACACCACT ACCTTGCTGG CAAGAATATC GCTCTCCTAT TTGAAAAAAC ATCTACTCGT    180
ACTCGTGCAG CCTTTACAAC TGCGGCTATC GACCTTGGTG CTCACCCAGA ATACCTCGGA    240
GCAAATGATA TTCAGTTGGG TAAAAAAGAA TCTACTGAAG ATACTGCTAA AGTATTGGGA    300
CGTATGTTTG ACGGGATTGA ATTCCGCGGA TTCAGCCAAC GTATGGTTGA AGAATTGGCA    360
GAATTCTCAG GCGTTCCAGT ATGGAACGGT CTAACTGACG AATGGCACCC AACTCAAATG    420
CTCGCTGACT ACTTGACTGT TCAAGAAAAC TTCGGTCGCT TGGAAGGCTT GACATTGGTA    480
TACTGTGGTG ATGGACGTAA CAACGTTGCC AACAGCTTGC TCGTAACAGG TGCTATCCTT    540
GGTGTCAATG TTCACATCTT CTCACCAAAA GAACTCTTCC CAGAAAAAGA AATCGTTGAA    600
TTGGCAGAAG GATTTGCTAA AGAAAGTGGC GCACATGTTC TCATCACTGA AGATGCTGAT    660
GAAGCAGTTA AAGATGCAGA CGTTCTTTAC ACAGACGTTT GGGTATCAAT GGGTGAAGAA    720
GACAAATTCG CAGAACGTGT AGCTCTTCTT AAACCTTACC AAGTCAATAT GGACTTAGTT    780
AAAAAAGCAG GCAATGAAAA CTTGATCTTC CTACACTGCT TGCCAGCATT CCACGATACT    840
CACACTGTTT ATGGTAAAGA CGTTGCTGAA AAATTTGGTG TAGAAGAAAT GGAAGTAACA    900
GACGAAGTCT TCCGCAGCAA GTACGCTCGC CACTTCGATC AAGCAGAAAA CCGTATGCAC    960
ACTATCAAAG CTGTTATGGC TGCTACACTT GGTAACCTTT ATATTCCTAA AGTATAA      1017
 
           
           
             
               338 amino acids 
               amino acid 
               single 
               linear 
             
              2
Met Thr Asn Ser Val Phe Gln Gly Arg Ser Phe Leu Ala Glu Lys Asp
 1               5                  10                  15
Phe Thr Arg Ala Glu Leu Glu Tyr Leu Ile Gly Leu Ser Ala His Leu
            20                  25                  30
Lys Asp Leu Lys Lys Arg Asn Ile Gln His His Tyr Leu Ala Gly Lys
        35                  40                  45
Asn Ile Ala Leu Leu Phe Glu Lys Thr Ser Thr Arg Thr Arg Ala Ala
    50                  55                  60
Phe Thr Thr Ala Ala Ile Asp Leu Gly Ala His Pro Glu Tyr Leu Gly
65                  70                  75                  80
Ala Asn Asp Ile Gln Leu Gly Lys Lys Glu Ser Thr Glu Asp Thr Ala
                85                  90                  95
Lys Val Leu Gly Arg Met Phe Asp Gly Ile Glu Phe Arg Gly Phe Ser
            100                 105                 110
Gln Arg Met Val Glu Glu Leu Ala Glu Phe Ser Gly Val Pro Val Trp
        115                 120                 125
Asn Gly Leu Thr Asp Glu Trp His Pro Thr Gln Met Leu Ala Asp Tyr
    130                 135                 140
Leu Thr Val Gln Glu Asn Phe Gly Arg Leu Glu Gly Leu Thr Leu Val
145                 150                 155                 160
Tyr Cys Gly Asp Gly Arg Asn Asn Val Ala Asn Ser Leu Leu Val Thr
                165                 170                 175
Gly Ala Ile Leu Gly Val Asn Val His Ile Phe Ser Pro Lys Glu Leu
            180                 185                 190
Phe Pro Glu Lys Glu Ile Val Glu Leu Ala Glu Gly Phe Ala Lys Glu
        195                 200                 205
Ser Gly Ala His Val Leu Ile Thr Glu Asp Ala Asp Glu Ala Val Lys
    210                 215                 220
Asp Ala Asp Val Leu Tyr Thr Asp Val Trp Val Ser Met Gly Glu Glu
225                 230                 235                 240
Asp Lys Phe Ala Glu Arg Val Ala Leu Leu Lys Pro Tyr Gln Val Asn
                245                 250                 255
Met Asp Leu Val Lys Lys Ala Gly Asn Glu Asn Leu Ile Phe Leu His
            260                 265                 270
Cys Leu Pro Ala Phe His Asp Thr His Thr Val Tyr Gly Lys Asp Val
        275                 280                 285
Ala Glu Lys Phe Gly Val Glu Glu Met Glu Val Thr Asp Glu Val Phe
    290                 295                 300
Arg Ser Lys Tyr Ala Arg His Phe Asp Gln Ala Glu Asn Arg Met His
305                 310                 315                 320
Thr Ile Lys Ala Val Met Ala Ala Thr Leu Gly Asn Leu Tyr Ile Pro
                325                 330                 335
Lys Val
 
           
           
             
               351 base pairs 
               nucleic acid 
               double 
               linear 
             
              3
ATGACAAATT CAGTATTCCA AGGACGCAGC TTCTTAGCAG AAAAAGACTT TACCCGTGCA     60
GAGTTAGAAT ACCTTATTGG TCTTTCAGCT CACTTGAAAG ATTTGAAAAA ACGCAATATT    120
CAACACCACT ACCTTGCTGG CAAGAATATC GCTCTCCTAT TTGAAAAAAC ATCTACTCGT    180
ACTCGTGCAG CCTTTACAAC TGCGGCTATC GACCTTGGTG CTCACCCAGA ATACCTCGGA    240
GCAAATGATA TTCAGTTGGG TAAAAAAGAA TCTACTGAAG ATACTGCTAA AGTATTGGGA    300
CGTATGTTTG ACGGGATTGA ATTCCGCGGA TTCAGCCAAC GTTATGGTTG A             351
 
           
           
             
               116 amino acids 
               amino acid 
               single 
               linear 
             
              4
Met Thr Asn Ser Val Phe Gln Gly Arg Ser Phe Leu Ala Glu Lys Asp
 1               5                  10                  15
Phe Thr Arg Ala Glu Leu Glu Tyr Leu Ile Gly Leu Ser Ala His Leu
            20                  25                  30
Lys Asp Leu Lys Lys Arg Asn Ile Gln His His Tyr Leu Ala Gly Lys
        35                  40                  45
Asn Ile Ala Leu Leu Phe Glu Lys Thr Ser Thr Arg Thr Arg Ala Ala
    50                  55                  60
Phe Thr Thr Ala Ala Ile Asp Leu Gly Ala His Pro Glu Tyr Leu Gly
65                  70                  75                  80
Ala Asn Asp Ile Gln Leu Gly Lys Lys Glu Ser Thr Glu Asp Thr Ala
                85                  90                  95
Lys Val Leu Gly Arg Met Phe Asp Gly Ile Glu Phe Arg Gly Phe Ser
            100                 105                 110
Gln Arg Tyr Gly
        115
 
           
           
             
               24 base pairs 
               nucleic acid 
               single 
               linear 
             
              5
AAAAACGCAA TATTCAACAC CACT                                            24
 
           
           
             
               21 base pairs 
               nucleic acid 
               single 
               linear 
             
              6
TCCTTCTGCC AATTCAACGA T                                               21
 
           
           
             
               25 base pairs 
               nucleic acid 
               single 
               linear 
             
              7
AACTGAGACT GGCTTTAAGA GATTA                                           25