title: Phylogenetic analysis of general bacterial porins: a phylogenomic case study.
abstract: Bacterial porin proteins allow for the selective movement of hydrophilic solutes through the outer membrane of Gram-negative bacteria. The purpose of this study was to clarify the evolutionary relationships among the Type 1 general bacterial porins (GBPs), a porin protein subfamily that includes outer membrane proteins ompC and ompF among others. Specifically, we investigated the potential utility of phylogenetic analysis for refining poorly annotated or mis-annotated protein sequences in databases, and for characterizing new functionally distinct groups of porin proteins. Preliminary phylogenetic analysis of sequences obtained from GenBank indicated that many of these sequences were incompletely or even incorrectly annotated. Using a well-curated set of porins classified via comparative genomics, we applied recently developed bayesian phylogenetic methods for protein sequence analysis to determine the relationships among the Type 1 GBPs. Our analysis found that the major GBP classes (ompC, phoE, nmpC and ompN) formed strongly supported monophyletic groups, with the exception of ompF, which split into two distinct clades. The relationships of the GBP groups to one another had less statistical support, except for the relationships of ompC and ompN sequences, which were strongly supported as sister groups. A phylogenetic analysis comparing the relationships of the GenBank GBP sequences to the correctly annotated set of GBPs identified a large number of previously unclassified and mis-annotated GBPs. Given these promising results, we developed a tree-parsing algorithm for automated phylogenetic annotation and tested it with GenBank sequences. Our algorithm was able to automatically classify 30 unidentified and 15 mis-annotated GBPs out of 78 sequences. Altogether, our results support the potential for phylogenomics to increase the accuracy of sequence annotations.
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA 92182, USA.
authors.forename: Thai X
authors.initials: TX
authors.lastname: Nguyen
authors.forename: Eric R
authors.initials: ER
authors.lastname: Alegre
authors.forename: Scott T
authors.initials: ST
authors.lastname: Kelley
mesh_terms: D000465:Algorithms; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000235:genetics; D030562:Databases, Protein; D019143:Evolution, Molecular; D006090:Gram-Negative Bacteria / Q000737:chemistry* / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D018272:Porins / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D001425:Bacterial Outer Membrane Proteins; D018272:Porins