Nucleic acid and amino acid sequences relating to Enterococcus faecalis for diagnostics and therapeutics

Abstract

The invention provides isolated polypeptide and nucleic acid sequences derived from Enterococcus faecalis that are useful in diagnosis and therapy of pathological conditions; antibodies against the polypeptides; and methods for the production of the polypeptides. The invention also provides methods for the detection, prevention and treatment of pathological conditions resulting from bacterial infection.

1 . An isolated nucleic acid comprising a nucleotide sequence encoding an  E. faecalis  polypeptide selected from the group consisting of SEQ ID NO: 3406-SEQ ID NO: 6810.  
     
     
         2 . A recombinant expression vector comprising the nucleic acid of  claim 1  operably linked to a transcription regulatory element.  
     
     
         3 . A cell comprising a recombinant expression vector of  claim 2 .  
     
     
         4 . A method for producing an  E. faecalis  polypeptide comprising culturing a cell of  claim 3  under conditions that permit expression of the polypeptide.  
     
     
         5 . An isolated nucleic acid comprising a nucleotide sequence encoding an  E. faecalis  polypeptide or a fragment thereof, said nucleic acid selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 3405.  
     
     
         6 . A recombinant expression vector comprising the nucleic acid of  claim 5  operably linked to a transcription regulatory element.  
     
     
         7 . A cell comprising a recombinant expression vector of  claim 6 .  
     
     
         8 . A method for producing an  E. faecalis  polypeptide comprising culturing a cell of  claim 7  under conditions that permit expression of the polypeptide.  
     
     
         9 . A probe comprising a nucleotide sequence consisting of at least 8 nucleotides of a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 3405.  
     
     
         10 . An isolated nucleic acid comprising a nucleotide sequence of at least 8 nucleotides in length, wherein the sequence is hybridizable to a nucleic acid having a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 3405.  
     
     
         11 . A vaccine composition for prevention or treatment of an  E. faecalis  infection comprising an effective amount of a nucleic acid of  claim 5 .  
     
     
         12 . A vaccine composition of  claim 11 , further comprising a pharmaceutically acceptable carrier.  
     
     
         13 . A vaccine composition of  claim 12 , wherein the pharmaceutically acceptable carrier is an adjuvant.  
     
     
         14 . A method of treating a subject for  E. faecalis  infection comprising administering to a subject a vaccine composition of  claim 11 , such that treatment of  E. faecalis  infection occurs.  
     
     
         15 . A method of  claim 14 , wherein the treatment is a prophylactic treatment.  
     
     
         16 . A method of  claim 14 , wherein the treatment is a therapeutic treatment.  
     
     
         17 . A recombinant or substantially pure preparation of an  E. faecalis  polypeptide or a fragment thereof, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 3406-SEQ ID NO: 6810.  
     
     
         18 . A vaccine composition for prevention or treatment of an  E. faecalis  infection comprising an effective amount of an  E. faecalis  polypeptide of  claim 17 .  
     
     
         19 . A vaccine composition of  claim 18 , further comprising a pharmaceutically acceptable carrier.  
     
     
         20 . A vaccine composition of  claim 19 , wherein the pharmaceutically acceptable carrier is an adjuvant.  
     
     
         21 . A method of treating a subject for  E. faecalis  infection comprising administering to a subject a vaccine composition of  claim 18 , such that treatment of  E. faecalis  infection occurs.  
     
     
         22 . A method of  claim 21 , wherein the treatment is a prophylactic treatment.  
     
     
         23 . A method of  claim 21 , wherein the treatment is a therapeutic treatment.  
     
     
         24 . A method for detecting the presence of an  Enterococcus  nucleic acid in a sample comprising: 
 (a) contacting a sample with a nucleic acid of  claim 5  under conditions in which a hybrid can form between the probe and an  Enterococcus  nucleic acid in the sample; and    (b) detecting the hybrid formed in step (a), wherein detection of a hybrid indicates the presence of an  Enterococcus  nucleic acid in the sample.    
     
     
         25 . A computer readable medium having recorded thereon the nucleotide sequences depicted in SEQ ID NO: 1-SEQ ID NO: 3405 or fragments thereof.  
     
     
         26 . A computer based system for identifying fragments of the  Enterococcus  genome of commercial importance comprising the following elements; 
 a) a data storage means comprising the nucleotide sequences SEQ ID NO: 1-SEQ ID NO: 3405 or fragments thereof,    b) a search means for comparing a target sequence to the nucleotide sequences of the data storage means of step (a) to identify homologous sequences, and;    c) a retrieval means for obtaining said homologous sequences(s) of step (b).    
     
     
         27 . A method of identifying commercially important nucleic acid fragments of the  Enterococcus  genome comprising the step of comparing a database comprising the nucleotide sequences SEQ ID NO: 1-SEQ ID NO: 3405 or fragments thereof with a target sequence to obtain a nucleic acid molecule comprised of a complementary nucleotide sequence to said target sequence, wherein said target sequence is not randomly selected.  
     
     
         28 . A method for identifying an expression modulating fragment of the  Enterococcus  genome comprising the step of comparing a database comprising the nucleotide sequences SEQ ID NO: 1-SEQ ID NO: 3405 or fragments thereof with a target sequence to obtain a nucleic acid molecule comprised of a complementary nucleotide sequence to said target sequence, wherein said target sequence comprises sequences known regulate gene expression.