Helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic Sel1-like genes

• Published in: PLoS computational biology Vol. 3; no. 8; p. e151
• Main Authors: Ogura, Masako, Perez, J Christian, Mittl, Peer R E, Lee, Hae-Kyung, Dailide, Geidrius, Tan, Shumin, Ito, Yoshiyuki, Secka, Ousman, Dailidiene, Daiva, Putty, Kalyani, Berg, Douglas E, Kalia, Awdhesh
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01-08-2007; Public Library of Science (PLoS)
• Subjects: Adaptation (Biology); Adaptation, Physiological - physiology; Amino Acid Sequence; Biological Evolution; Carrier Proteins - genetics; Chromosome Mapping - methods; Computational Biology; Eubacteria; Eukaryotes; Evolution; Evolution, Molecular; Evolutionary Biology; Genes; Genetic aspects; Genetics and Genomics; Genome, Bacterial - genetics; Helicobacter pylori - genetics; Homology (Biology); Infections; Infectious Diseases; Microbiology; Molecular Biology; Molecular Sequence Data; Properties; Proteins; Saccharomyces cerevisiae Proteins - genetics; Sequence Analysis, Protein - methods; Sequence Homology, Amino Acid; Ulcers; United States; Adaptation, Physiological; Biological Evolution; Sequence Homology, Amino Acid; Amino Acid Sequence; Sequence Analysis, Protein; Genome, Bacterial; Helicobacter pylori; Saccharomyces cerevisiae Proteins; Molecular Sequence Data; Chromosome Mapping; Carrier Proteins; Evolution, Molecular
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.0030151

Geographic partitioning is postulated to foster divergence of Helicobacter pylori populations as an adaptive response to local differences in predominant host physiology. H. pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using bacterial proteins that may themselves be targets for adaptive evolution. Sequenced H. pylori genomes encode a family of eight or nine secreted proteins containing repeat motifs that are characteristic of the eukaryotic Sel1 regulatory protein, whereas the related Campylobacter and Wolinella genomes each contain only one or two such "Sel1-like repeat" (SLR) genes ("slr genes"). Signatures of positive selection (ratio of nonsynonymous to synonymous mutations, dN/dS = omega > 1) were evident in the evolutionary history of H. pylori slr gene family expansion. Sequence analysis of six of these slr genes (hp0160, hp0211, hp0235, hp0519, hp0628, and hp1117) from representative East Asian, European, and African H. pylori strains revealed that all but hp0628 had undergone positive selection, with different amino acids often selected in different regions. Most striking was a divergence of Japanese and Korean alleles of hp0519, with Japanese alleles having undergone particularly strong positive selection (omegaJ > 25), whereas alleles of other genes from these populations were intermingled. Homology-based structural modeling localized most residues under positive selection to SLR protein surfaces. Rapid evolution of certain slr genes in specific H. pylori lineages suggests a model of adaptive change driven by selection for fine-tuning of host responses, and facilitated by geographic isolation. Characterization of such local adaptations should help elucidate how H. pylori manages persistent infection, and potentially lead to interventions tailored to diverse human populations.