title: Application of genomics and proteomics for identification of bacterial gene products as potential vaccine candidates.
abstract: The ability of bioinformatics to characterize genomic sequences from pathogenic bacteria for prediction of genes that may encode vaccine candidates, e.g. surface localized proteins, has been evaluated. By applying appropriate tools for genomic mining to the published sequence of Haemophilus influenzae Rd genome, it was possible to identify a putative vaccine candidate, the outer membrane lipoprotein, P6. Proteomics complements genomics by offering abilities to rapidly identify the products of predicted genes, e.g. proteins in outer membrane preparations. The ability to identify the P6 protein uniquely from entries in a sequence database from the expected peptide-mass fingerprint of P6 demonstrates the power of proteomics. The application of proteomics for identification of vaccine candidates for another pathogenic bacterium, Helicobacter pylori using two different approaches is described. The first involves rapid identification of a series of monoclonal antibody reactive proteins from N-terminal sequence tags. The other approach involves identification of proteins in outer membrane preparations by 2-D electrophoresis followed by trypsin digestion and peptide mass map analysis. Our combined studies demonstrate that utilization of genome sequences by application of bioinformatics through genomics and proteomics can expedite the vaccine discovery process by rapidly providing a set of potential candidates for further testing.
authors.affiliation: Wyeth Lederle Vaccines, 211 Bailey Road, West Henrietta, NY 14586, USA. chakradn@war.wyeth.com
authors.forename: D N
authors.initials: DN
authors.lastname: Chakravarti
authors.forename: M J
authors.initials: MJ
authors.lastname: Fiske
authors.forename: L D
authors.initials: LD
authors.lastname: Fletcher
authors.forename: R J
authors.initials: RJ
authors.lastname: Zagursky
mesh_terms: D000907:Antibodies, Bacterial / Q000276:immunology; D000911:Antibodies, Monoclonal / Q000276:immunology; D000942:Antigens, Bacterial / Q000032:analysis; D001425:Bacterial Outer Membrane Proteins / Q000032:analysis; D001426:Bacterial Proteins / Q000032:analysis*; D001428:Bacterial Vaccines / Q000737:chemistry*; D003062:Codon; D019295:Computational Biology; D019992:Databases as Topic; D015180:Electrophoresis, Gel, Two-Dimensional; D004591:Electrophoresis, Polyacrylamide Gel; D020862:GC Rich Sequence; D016680:Genome, Bacterial; D018073:Haemophilus Vaccines / Q000032:analysis; D006193:Haemophilus influenzae / Q000235:genetics; D016480:Helicobacter pylori / Q000737:chemistry / Q000276:immunology; D016366:Open Reading Frames; D010449:Peptide Mapping; D010649:Phenylalanine / Q000032:analysis; D020543:Proteome / Q000737:chemistry* / Q000276:immunology*; D014443:Tyrosine / Q000032:analysis
chemical_list: D000907:Antibodies, Bacterial; D000911:Antibodies, Monoclonal; D000942:Antigens, Bacterial; D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D001428:Bacterial Vaccines; D003062:Codon; D018073:Haemophilus Vaccines; C069990:P6 outer membrane protein, Haemophilus; D020543:Proteome; D014443:Tyrosine; D010649:Phenylalanine