RESEARCH ARTICLE Analysis of the Outer Membrane Proteome and Secretome of Bacteroides fragilis Reveals a Multiplicity of Secretion Mechanisms

Bacteroides fragilis is a widely distributed member of the human gut microbiome and an op-portunistic pathogen. Cell surface molecules produced by this organism likely play impor-tant roles in colonization, communication with other microbes, and pathogenicity, but the protein composition of the outer membrane (OM) and the mechanisms used to transport polypeptides into the extracellular space are poorly characterized. Here we used LC-MS/ MS to analyze the OM proteome and secretome of B. fragilis NCTC 9343 grown under labo-ratory conditions. Of the 229 OM proteins that we identified, 108 are predicted to be lipopro-teins, and 61 are predicted to be TonB-dependent transporters. Based on their proximity to genes encoding TonB-dependent transporters, many of the lipoprotein genes likely encode proteins involved in nutrient or small molecule uptake. Interestingly, protease accessibility and biotinylation experiments indicated that an unusually large fraction of the lipoproteins are cell-surface exposed. We also identified three proteins that are members of a novel fam-ily of autotransporters, multiple potential type I protein secretion systems, and proteins that appear to be components of a type VI secretion apparatus. The secretome consisted of lipo-proteins and other proteins that might be substrates of the putative type I or type VI secre-tion systems. Our proteomic studies show that B. fragilis differs considerably from well-studied Gram-negative bacteria such as Escherichia coli in both the spectrum of OM pro-teins that it produces and the range of secretion strategies that it utilizes