Staphylococcus aureus polynucleotides and polypeptides

Abstract

The present invention relates to novel genes from S. aureus and the polypeptides they encode. Also provided are vectors, host cells, antibodies and recombinant methods for producing the same. The invention further relates to screening methods for identifying agonists and antagonists of S. aureus polypeptide activity. The invention additionally relates to diagnostic methods for detecting Staphylococcus nucleic acids, polypeptides and antibodies in a biological sample. The present invention further relates to novel vaccines for the prevention or attenuation of infection by Staphylococcus.

1 . An isolated polynucleotide comprising a nucleic acid sequence encoding an amino acid sequence identical to, except for up to five amino acid alterations per 100 amino acids, an amino acid sequence selected from the group consisting of: 
 (a) the full-length amino acid sequence encoded by the ORF represented by any one odd-numbered sequence of SEQ ID NOS: 1-74; and    (b) the full-length amino acid sequence represented by any one even-numbered sequence of SEQ ID NOS: 1-74.    
     
     
         2 . The isolated polynucleotide of  claim 1  wherein the amino acid sequence is (a).  
     
     
         3 . The isolated polynucleotide of  claim 1  wherein the amino acid sequence is (b).  
     
     
         4 . The isolated polynucleotide of  claim 1 , wherein said polynucleotide comprises a heterologous polynucleotide sequence.  
     
     
         5 . The isolated polynucleotide of  claim 4 , wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.  
     
     
         6 . A method for making a recombinant vector comprising inserting the isolated polynucleotide of  claim 1  into a vector.  
     
     
         7 . A recombinant vector comprising the isolated polynucleotide of  claim 1 .  
     
     
         8 . The recombinant vector of  claim 7 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         9 . A recombinant host cell comprising the isolated polynucleotide of  claim 1 .  
     
     
         10 . The recombinant host cell of  claim 9 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         11 . A method for producing a polypeptide, comprising: 
 (a) culturing a cell under conditions suitable to produce a polypeptide encoded by the polynucleotide of  claim 1;  and    (b) recovering the polypeptide.    
     
     
         12 . A polypeptide produced by the method of  claim 11 .  
     
     
         13 . An isolated polynucleotide comprising a nucleic acid sequence encoding an epitope-bearing portion of an amino acid sequence selected from the group consisting of: 
 (a) the full-length amino acid sequence encoded by the ORF represented by any one odd-numbered sequence of SEQ ID NOS:1-74; and    (b) the full-length amino acid sequence represented by any one even-numbered sequence of SEQ ID NOS:1-74.    
     
     
         14 . The isolated polynucleotide of  claim 13  wherein the amino acid sequence is (a).  
     
     
         15 . The isolated polynucleotide of  claim 13  wherein the amino acid sequence is (b).  
     
     
         16 . The isolated polynucleotide of  claim 13 , wherein said polynucleotide comprises a heterologous polynucleotide sequence.  
     
     
         17 . The isolated polynucleotide of  claim 16 , wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.  
     
     
         18 . A method for making a recombinant vector comprising inserting the isolated polynucleotide of  claim 13  into a vector.  
     
     
         19 . A recombinant vector comprising the isolated polynucleotide of  claim 13 .  
     
     
         20 . The recombinant vector of  claim 19 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         21 . A recombinant host cell comprising the isolated polynucleotide of  claim 13 .  
     
     
         22 . The recombinant host cell of  claim 21 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         23 . A method for producing a polypeptide, comprising: 
 (a) culturing a cell under conditions suitable to produce a polypeptide encoded by the polynucleotide of  claim 13;  and    (b) recovering the polypeptide.    
     
     
         24 . A polypeptide produced by the method of  claim 23 .  
     
     
         25 . An isolated polynucleotide comprising a nucleic acid sequence encoding a fragment of an amino acid sequence identical to, except for up to five amino acid alterations per 100 amino acids, a fragment of an amino acid sequence selected from the group consisting of selected from the group consisting of: 
 (a) the full-length amino acid sequence encoded by the ORF represented by any one odd-numbered sequence of SEQ ID NOS:1-74, wherein said fragment specifically binds an antibody which specifically binds a polypeptide encoded by said full-length amino acid sequence; and    (b) the full-length amino acid sequence represented by any one even-numbered sequence of SEQ ID NOS:1-74, wherein said fragment specifically binds an antibody which specifically binds a polypeptide having said full-length amino acid sequence.    
     
     
         26 . The isolated polynucleotide of  claim 25  wherein the amino acid sequence is (a).  
     
     
         27 . The isolated polynucleotide of  claim 25  wherein the amino acid sequence is (b).  
     
     
         28 . The isolated polynucleotide of  claim 25 , wherein said polynucleotide comprises a heterologous polynucleotide sequence.  
     
     
         29 . The isolated polynucleotide of  claim 28 , wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.  
     
     
         30 . A method for making a recombinant vector comprising inserting the isolated polynucleotide of  claim 25  into a vector.  
     
     
         31 . A recombinant vector comprising the isolated polynucleotide of  claim 25 .  
     
     
         32 . The recombinant vector of  claim 31 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         33 . A recombinant host cell comprising the isolated polynucleotide of  claim 25 .  
     
     
         34 . The recombinant host cell of  claim 33 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         35 . A method for producing a polypeptide, comprising: 
 (a) culturing a cell under conditions suitable to produce a polypeptide encoded by the polynucleotide of  claim 25;  and    (b) recovering the polypeptide.    
     
     
         36 . A polypeptide produced by the method of  claim 35 .  
     
     
         37 . An isolated polynucleotide comprising a nucleic acid sequence encoding at least 15 contiguous amino acid residues of an amino acid sequence selected from the group consisting of: 
 (a) the full-length amino acid sequence encoded by the ORF represented by any one odd-numbered sequence of SEQ ID NOS:1-74; and    (b) the full-length amino acid sequence represented by any one even-numbered sequence of SEQ ID NOS:1-74.    
     
     
         38 . The isolated polynucleotide of  claim 37  wherein the amino acid sequence is (a).  
     
     
         39 . The isolated polynucleotide of  claim 37  wherein the amino acid sequence is (b).  
     
     
         40 . The isolated polynucleotide of  claim 37 , wherein said polynucleotide comprises a heterologous polynucleotide sequence.  
     
     
         41 . The isolated polynucleotide of  claim 40 , wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.  
     
     
         42 . A method for making a recombinant vector comprising inserting the isolated polynucleotide of  claim 37  into a vector.  
     
     
         43 . A recombinant vector comprising the isolated polynucleotide of  claim 37 .  
     
     
         44 . The recombinant vector of  claim 43 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         45 . A recombinant host cell comprising the isolated polynucleotide of  claim 37 .  
     
     
         46 . The recombinant host cell of  claim 45 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         47 . A method for producing a polypeptide, comprising: 
 (a) culturing a cell under conditions suitable to produce a polypeptide encoded by the polynucleotide of  claim 37;  and    (b) recovering the polypeptide.    
     
     
         48 . A polypeptide produced by the method of  claim 47 .  
     
     
         49 . The isolated polynucleotide of  claim 37 , wherein said polynucleotide comprises a nucleic acid sequence encoding at least 30 contiguous amino acid residues of an amino acid sequence selected from the group consisting of: 
 (a) the full-length amino acid sequence encoded by the ORF represented by any one odd-numbered sequence of SEQ ID NOS:1-74; and    (b) the full-length amino acid sequence represented by any one even-numbered sequence of SEQ ID NOS:1-74.    
     
     
         50 . The isolated polynucleotide of  claim 49  wherein the amino acid sequence is (a).  
     
     
         51 . The isolated polynucleotide of  claim 49  wherein the amino acid sequence is (b).  
     
     
         52 . The isolated polynucleotide of  claim 49 , wherein said polynucleotide comprises a heterologous polynucleotide sequence.  
     
     
         53 . The isolated polynucleotide of  claim 52 , wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.  
     
     
         54 . A method for making a recombinant vector comprising inserting the isolated polynucleotide of  claim 49  into a vector.  
     
     
         55 . A recombinant vector comprising the isolated polynucleotide of  claim 49 .  
     
     
         56 . The recombinant vector of  claim 55 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         57 . A recombinant host cell comprising the isolated polynucleotide of  claim 49 .  
     
     
         58 . The recombinant host cell of  claim 57 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         59 . A method for producing a polypeptide, comprising: 
 (a) culturing a cell under conditions suitable to produce a polypeptide encoded by the polynucleotide of  claim 49;  and    (b) recovering the polypeptide.    
     
     
         60 . A polypeptide produced by the method of  claim 59 .  
     
     
         61 . An isolated polynucleotide comprising a nucleic acid sequence which hybridizes, at 42° C. in 50% formamide, 5×SSC (750 mM NaCl, 75 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5× Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmon sperm DNA, followed by washing in 0.1×SSC at 65° C., to a nucleic acid sequence complementary to a portion of an ORF encoding an amino acid sequence selected from the group consisting of: 
 (a) the full-length amino acid sequence encoded by the ORF represented by any one odd-numbered sequence of SEQ ID NOS:1-74; and    (b) the full-length amino acid sequence represented by any one even-numbered sequence of SEQ ID NOS:1-74.    
     
     
         62 . The isolated polynucleotide of  claim 61  wherein the amino acid sequence is (a).  
     
     
         63 . The isolated polynucleotide of  claim 61  wherein the amino acid sequence is (b).  
     
     
         64 . The isolated polynucleotide of  claim 61 , wherein said polynucleotide comprises a heterologous polynucleotide sequence.  
     
     
         65 . The isolated polynucleotide of  claim 64 , wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.  
     
     
         66 . A method for making a recombinant vector comprising inserting the isolated polynucleotide of  claim 61  into a vector.  
     
     
         67 . A recombinant vector comprising the isolated polynucleotide of  claim 61 .  
     
     
         68 . The recombinant vector of  claim 67 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         69 . A recombinant host cell comprising the isolated polynucleotide of  claim 61 .  
     
     
         70 . The recombinant host cell of  claim 69 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         71 . A method for producing a polypeptide, comprising: 
 (a) culturing a cell under conditions suitable to produce a polypeptide encoded by the polynucleotide of  claim 61;  and    (b) recovering the polypeptide.    
     
     
         72 . A polypeptide produced by the method of  claim 71 .  
     
     
         73 . An isolated polynucleotide comprising at least 50 contiguous nucleotides, or the complement thereof, of an ORF encoding an amino acid sequence selected from the group consisting of: 
 (a) the full-length amino acid sequence encoded by the ORF represented by any one odd-numbered sequence of SEQ ID NOS:1-74; and    (b) the full-length amino acid sequence represented by any one even-numbered sequence of SEQ ID NOS:1-74.    
     
     
         74 . The isolated polynucleotide of  claim 73  wherein the amino acid sequence is (a).  
     
     
         75 . The isolated polynucleotide of  claim 73  wherein the amino acid sequence is (b).  
     
     
         76 . The isolated polynucleotide of  claim 73 , wherein said polynucleotide comprises a heterologous polynucleotide sequence.  
     
     
         77 . The isolated polynucleotide of  claim 76 , wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.  
     
     
         78 . A method for making a recombinant vector comprising inserting the isolated polynucleotide of  claim 73  into a vector.  
     
     
         79 . A recombinant vector comprising the isolated polynucleotide of  claim 73 .  
     
     
         80 . The recombinant vector of  claim 79 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         81 . A recombinant host cell comprising the isolated polynucleotide of  claim 73 .  
     
     
         82 . The recombinant host cell of  claim 81 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         83 . A method for producing a polypeptide, comprising: 
 (a) culturing a cell under conditions suitable to produce a polypeptide encoded by the polynucleotide of  claim 73;  and    (b) recovering the polypeptide.    
     
     
         84 . A polypeptide produced by the method of  claim 83 .  
     
     
         85 . The isolated polynucleotide of  claim 73  comprising at least 100 contiguous nucleotides of an ORF encoding an amino acid sequence selected from the group consisting of: 
 (a) the full-length amino acid sequence encoded by the ORF represented by any one odd-numbered sequence of SEQ ID NOS:1-74; and    (b) the full-length amino acid sequence represented by any one even-numbered sequence of SEQ ID NOS:1-74.    
     
     
         86 . The isolated polynucleotide of  claim 85  wherein the amino acid sequence is (a).  
     
     
         87 . The isolated polynucleotide of  claim 85  wherein the amino acid sequence is (b).  
     
     
         88 . The isolated polynucleotide of  claim 85 , wherein said polynucleotide comprises a heterologous polynucleotide sequence.  
     
     
         89 . The isolated polynucleotide of  claim 88 , wherein said heterologous polynucleotide sequence encodes a heterologous polypeptide.  
     
     
         90 . A method for making a recombinant vector comprising inserting the isolated polynucleotide of  claim 85  into a vector.  
     
     
         91 . A recombinant vector comprising the isolated polynucleotide of  claim 85 .  
     
     
         92 . The recombinant vector of  claim 91 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         93 . A recombinant host cell comprising the isolated polynucleotide of  claim 85 .  
     
     
         94 . The recombinant host cell of  claim 93 , wherein said polynucleotide is operably associated with a heterologous regulatory sequence that controls gene expression.  
     
     
         95 . A method for producing a polypeptide, comprising: 
 (a) culturing a cell under conditions suitable to produce a polypeptide encoded by the polynucleotide of  claim 85;  and    (b) recovering the polypeptide.    
     
     
         96 . A polypeptide produced by the method of  claim 95.