Comparative genomics of Helicobacter pylori: Analysis of the outer membrane protein families

The two complete genomic sequences of Helicobacter pylori J99 and 26695 wer e used to compare the paralogous families (related genes within one genome, likely to have related function) of genes predicted to encode outer membra ne proteins which were present in each strain. We identified five paralogou s gene families ranging in size from 3 to 33 members; two of these families contained members specific for either H. pylori J99 or H. pylori 26695. Mo st orthologous protein pairs (equivalent genes between two genomes, same fu nction) shared considerable identity between the two strains. The unusual s et of outer membrane proteins and the specialized outer membrane may be a r eflection of the adaptation of H. pylori to the unique gastric environment where it is found. One subfamily of proteins, which contains both channel-f orming and adhesin molecules, is extremely highly related at the sequence l evel and has likely arisen due to ancestral gene duplication. In addition, the largest paralogous family contained two essentially identical pairs of genes in both strains. The presence and genomic organization of these two p airs of duplicated genes were analyzed in a panel of independent H. pylori isolates. While one pair was present in every strain examined, one allele o f the other pair appeared partially deleted in several isolates.