Novel streptococcus pneumoniae open reading frames encoding polypeptide antigents and uses thereof

Abstract

The present invention relates to newly identified open reading frames comprised within the genomic nucleotide sequence of Streptococcus pneumoniae , wherein the open reading frames encode polypeptides that are surface localized on Streptococcus pneumoniae . Thus, the invention relates to Streptococcus pneumoniae open reading frames that encode polypeptide antigens, polypeptides, preferably antigenic polypeptides, encoded by the Streptococcus pneumoniae open reading frames, vectors comprising open reading frame sequences and cells or animals transformed with these vectors. The invention relates also to methods of detecting these nucleic acids or polypeptides and kits for diagnosing Streptococcus pneumoniae infection. The invention finally relates to pharmaceutical compositions, in particular immunogenic compositions, for the prevention and/or treatment of bacterial infection, in particular infections with Streptococcus pneumoniae . In particular embodiments, the immunogenic compositions are used for the treatment or prevention of systemic diseases which are induced or exacerbated by Streptococcus pneumoniae . In other embodiments, the immunogenic compositions are used for the treatment or prevention of non-systemic diseases, particularly of the otitis media, which are induced or exacerbated by Streptococcus pneumoniae.

1 - 105 . (canceled) 
     
     
         106 . An isolated  Streptococcus pneumoniae  polynucleotide comprising at least 95% identity to the full length nucleotide sequence of SEQ ID NO:67, and wherein the polynucleotide encodes an immunogenic polypeptide. 
     
     
         107 . The polynucleotide of  claim 106 , wherein the polynucleotide is a full length complement to the nucleotide sequence of SEQ ID NO:67. 
     
     
         108 . The polynucleotide of  claim 107 , wherein the polynucleotide is selected from the group consisting of DNA, chromosomal DNA, cDNA and RNA. 
     
     
         109 . The polynucleotide of  claim 108 , wherein the polynucleotide further comprises heterologous nucleotides. 
     
     
         110 . An isolated polynucleotide which hybridizes to the full length nucleotide sequence of SEQ ID NO:67, or a complement thereof, under high stringency hybridization conditions, wherein the high stringency hybridization is at 65° C. with 1×SSC followed by a 65° C. wash with 0.3×SSC, and wherein the polynucleotide encodes an immunogenic polypeptide. 
     
     
         111 . An isolated polynucleotide of a  Streptococcus pneumoniae  genomic sequence, wherein the polynucleotide comprises a nucleotide sequence of SEQ ID NO:67, and encodes a polypeptide, selected from the group consisting of: —
 (a) a  Streptococcus pneumoniae  polypeptide having 0, 1 or 2 transmembrane domains;   (b) a  Streptococcus pneumoniae  polypeptide having 3 or more transmembrane domains;   (c) a  Streptococcus pneumoniae  polypeptide having an outer membrane domain or a periplasmic domain;   (d) a  Streptococcus pneumoniae  polypeptide having an inner membrane domain;   (e) a  Streptococcus pneumoniae  polypeptide identified by Blastp analysis;   (f) a  Streptococcus pneumoniae  polypeptide identified by Pfam analysis;   (g) a  Streptococcus pneumoniae  lipoprotein;   (h) a  Streptococcus pneumoniae  polypeptide having a LPXTG motif, wherein the polypeptide is covalently attached to the peptidoglycan layer;   (i) a  Streptococcus pneumoniae  polypeptide having a peptidoglycan binding motif, wherein the polypeptide is associated with the peptidoglycan layer;   (j) a  Streptococcus pneumoniae  polypeptide having a signal sequence and a C-terminal Tyrosine or a C-terminal Phenylalanine amino acid;   (k) a  Streptococcus pneumoniae  polypeptide having a tripeptide RGD amino acid sequence;   (l) a  Streptococcus pneumoniae  polypeptide identified by proteomics as surface exposed; and   (m) a  Streptococcus pneumoniae  polypeptide identified by proteomics as membrane associated.   
     
     
         112 . The polynucleotide of  claim 111 , wherein the polynucleotide is a complement to the nucleotide sequence of SEQ ID NO:67. 
     
     
         113 . The polynucleotide of  claim 112 , wherein the polynucleotide is selected from the group consisting of DNA, chromosomal DNA, cDNA and RNA. 
     
     
         114 . The polynucleotide of  claim 113 , wherein the polynucleotide further comprises heterologous nucleotides. 
     
     
         115 . The polynucleotide of  claim 114 , wherein the polynucleotide encodes a fusion polypeptide. 
     
     
         116 . The polynucleotide of  claim 111 , wherein the polynucleotide of SEQ ID NO:67 encodes a polypeptide having 0, 1 or 2 transmembrane domains. 
     
     
         117 . The polynucleotide of  claim 111 , wherein the polynucleotide of SEQ ID NO:67 encodes a polypeptide having an inner membrane domain. 
     
     
         118 . The polynucleotide of  claim 111 , wherein the polynucleotide of SEQ ID NO:67 encodes a polypeptide identified by proteomics as surface exposed. 
     
     
         119 . A recombinant expression vector comprising a polynucleotide having at least 95% identity to the full length nucleotide sequence of SEQ ID NO:67, wherein the polynucleotide encodes for an immunogenic polypeptide. 
     
     
         120 . The vector of  claim 119 , wherein the polynucleotide is selected from the group consisting of DNA, chromosomal DNA, cDNA, RNA and antisense RNA. 
     
     
         121 . The vector of  claim 120 , wherein the polynucleotide comprises heterologous nucleotide sequences. 
     
     
         122 . The vector of  claim 121 , wherein the polynucleotide is operatively linked to one or more gene expression regulatory elements. 
     
     
         123 . The vector of  claim 122 , wherein the polynucleotide encodes a polypeptide comprising an amino acid sequence having at least 95% identity to the amino acid sequence of SEQ ID NO:282. 
     
     
         124 . The vector of  claim 119 , wherein the vector is a plasmid. 
     
     
         125 . A genetically engineered host cell, transfected, transformed or infected with the vector of  claim 119 . 
     
     
         126 . The host cell of  claim 125 , wherein the host cell is a bacterial cell. 
     
     
         127 . The host cell of  claim 126 , wherein the polynucleotide is expressed to produce the encoded polypeptide. 
     
     
         128 . An immunogenic composition comprising a polynucleotide having a nucleotide sequence of SEQ ID NO:67 and is comprised in an expression vector. 
     
     
         129 . The immunogenic composition of  claim 128 , wherein the vector is plasmid DNA. 
     
     
         130 . The immunogenic composition of  claim 129 , wherein the polynucleotide comprises heterologous nucleotides. 
     
     
         131 . The immunogenic composition of  claim 130  wherein the polynucleotide is operatively linked to one or more gene expression regulatory elements. 
     
     
         132 . The immunogenic composition of  claim 131 , wherein the polynucleotide directs the expression of a neutralizing epitope of  Streptococcus pneumoniae.    
     
     
         133 . The immunogenic composition of  claim 132 , further comprising one or more adjuvants. 
     
     
         134 . A DNA chip comprising an array of polynucleotides, wherein at least one of the polynucleotides comprises a nucleotide sequence identical or complementary to a segment of at least 25 to about 70 contiguous bases of the sequence of SEQ ID NO:67, or a complement thereof. 
     
     
         135 . A kit comprising a container containing an isolated polynucleotide comprising a nucleotide sequence of a segment of at least 10 to about 70 contiguous bases of the nucleotide sequence of SEQ ID NO:67. 
     
     
         136 . The kit of  claim 135 , wherein the polynucleotide is a primer or a probe. 
     
     
         137 . The kit of  claim 136 , wherein the polynucleotide is a primer and the kit further comprises a container containing a polymerase. 
     
     
         138 . The kit of  claim 135 , wherein the kit further comprises a container containing dNTP. 
     
     
         139 . A method for producing a polypeptide which comprises culturing the genetically engineered host cell of  claim 126  under conditions suitable to produce the polypeptide and recovering the polypeptide from the culture. 
     
     
         140 . An isolated polynucleotide of a  Streptococcus pneumoniae  genomic sequence, wherein the polynucleotide encodes a polypeptide comprising an amino acid sequence of SEQ ID NO:282. 
     
     
         141 . An isolated polynucleotide comprising the nucleotide sequence of SEQ ID NO: 67. 
     
     
         142 . An isolated polynucleotide that encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 282. 
     
     
         143 . An isolated polynucleotide that encodes a polypeptide comprising an amino acid sequence having at least 95% identity to the amino acid sequence of SEQ ID NO: 282, wherein the polypeptide is an immunogenic polypeptide.