title: Genome-wide evidence of positive selection in Bacteroides fragilis.
abstract: We used an evolutionary genomics approach to identify genes that are under lineage-specific positive selection in six species of the genus Bacteroides, including three strains of pathogenic Bacteroides fragilis. Using OrthoMCL, we identified 1275 orthologous gene clusters present in all eight Bacteroides genomes. A total of 52 genes were identified as under positive selection in the branch leading to the B. fragilis lineage, including a number of genes encoding cell surface proteins such as TonB-dependent receptor. Three-dimensional structural mapping of positively selected sites indicated that many residues under positive selection occur in the extracellular loops of the proteins. The adaptive changes in these positively selected genes might be related to dynamic interactions between the host immune systems and the surrounding intestinal environment.
authors.affiliation: United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan.
authors.forename: Sumio
authors.initials: S
authors.lastname: Yoshizaki
authors.affiliation: Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Umemura
authors.affiliation: United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan; Division of Anaerobe Research, Life Science Research Center, Gifu University, 1-1, Yanagido, Gifu 501-1194, Japan.
authors.forename: Kaori
authors.initials: K
authors.lastname: Tanaka
authors.affiliation: Division of Anaerobe Research, Life Science Research Center, Gifu University, 1-1, Yanagido, Gifu 501-1194, Japan.
authors.forename: Kunitomo
authors.initials: K
authors.lastname: Watanabe
authors.affiliation: Division of Anaerobe Research, Life Science Research Center, Gifu University, 1-1, Yanagido, Gifu 501-1194, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Hayashi
authors.affiliation: United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan; Department of Functional Bioscience, Gifu University School of Medicine, 1-1, Yanagido, Gifu 501-1193, Japan. Electronic address: ymuto@gifu-u.ac.jp.
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Muto
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D001441:Bacteroides fragilis / Q000235:genetics*; D001483:Base Sequence; D016680:Genome, Bacterial; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012641:Selection, Genetic; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins
keywords: Bacteroides fragilis; Molecular evolution; Pathogenicity; Positive selection