Molecular evolution of the major outer-membrane protein gene (oprF) of Pseudomonas

• Published in: Microbiology (Society for General Microbiology) 2006-04, Vol.152 (4), p.1075-1088
• Main Authors: Bodilis, Josselin, Barray, Sylvie
• Format: Article
• Language: English
• Subjects: Bacterial Outer Membrane Proteins - genetics; Bacteriology; Base Composition; Biological and medical sciences; Codon - genetics; Evolution, Molecular; Fundamental and applied biological sciences. Psychology; Gene Order; Gene Transfer, Horizontal; Genetics; Genome, Bacterial - genetics; Microbiology; Mutation; Pathogenicity, virulence, toxins, bacteriocins, pyrogens, host-bacteria relations, miscellaneous strains; Phylogeny; Porins - genetics; Pseudomonas; Pseudomonas - classification; Pseudomonas - genetics; Pseudomonas fluorescens; Sequence Homology
• ISSN: 1350-0872; 1465-2080
• DOI: 10.1099/mic.0.28656-0

LMDF (Laboratoire de Microbiologie Du Froid), UPRES 2123, ABISS (Atelier de Biologie, Informatique, Statistique et Sociolinguistinque), Université de Rouen, 76821 Mont Saint Aignan, France Correspondence Josselin Bodilis josselin.bodilis{at}univ-rouen.fr The major outer-membrane protein of Pseudomonas , OprF, is multifunctional. It is a non-specific porin that plays a role in maintenance of cell shape, in growth in a low-osmolarity environment, and in adhesion to various supports or molecules. OprF has been studied extensively for its utility as a vaccine component, its role in antimicrobial drug resistance, and its porin function. The authors have previously shown important differences between the OprF and 16S rDNA phylogenies: Pseudomonas fluorescens isolates split into two quite separate clusters, probably according to their ecological niche. In this study, the evolutionary history of the oprF gene was investigated further. The study of G+C content at the third codon position, synonymous codon usage (codon adaptation index, CAI) and genomic context showed no evidence of horizontal transfer or gene duplication. Similarly, a robust likelihood test of incongruence showed no significant incongruence between the oprF phylogeny and the species phylogeny. In addition, the ratio of nonsynonymous mutations to synonymous mutations ( K a / K s ) is high between the different clusters, especially between the two clusters containing P. fluorescens isolates, highlighting important modifications in evolutionary constraints during the history of the oprF gene. Since OprF is known as a pleiotropic protein, modifications in evolutionary constraints could have resulted from variations in cryptic functions, correlated with the ecological fingerprint. Finally, relaxed constraints and/or episodic positive evolution, especially for some P. fluorescens strains, could have led to a phylogeny reconstruction artifact. Abbreviations: CAI, codon adaptation index; GC3, G+C content at the third codon position; ML, maxiumum likelihood