An antimicrobial protein of the gut symbiont Bacteroides fragilis with a MACPF domain of host immune proteins

Abstract

Summary Bacteroidales are the most abundant Gram negative bacteria of the human intestinal microbiota comprising more than half of the bacteria in many individuals. Some of the factors that these bacteria use to establish and maintain themselves in this ecosystem are beginning to be identified. However, ecological competition, especially interference competition where one organism directly harms another, is largely unexplored. To begin to understand the relevance of this ecological principle as it applies to these abundant gut bacteria and factors that may promote such competition, we screened Bacteroides fragilis for the production of antimicrobial molecules. We found that the production of extracellularly secreted antimicrobial molecules is widespread in this species. The first identified molecule, described in this manuscript, contains a membrane attack complex/perforin (MACPF) domain present in host immune molecules that kill bacteria and virally infected cells by pore formation, and mutations affecting key residues of this domain abrogated its activity. This antimicrobial molecule, termed BSAP-1, is secreted from the cell in outer membrane vesicles and no additional proteins are required for its secretion, processing or immunity of the producing cell. This study provides the first insight into secreted molecules that promote competitive interference among Bacteroidales strains of the human gut.

Bacteroidales Secreted Antimicrobial Proteins Target Surface Molecules Necessary for Gut Colonization and Mediate Competition In Vivo

“…We previously demonstrated that 7/10 B. fragilis strains tested produced secreted antimicrobial molecules (25). In this study, we found that 7/17 B. vulgatus , 2/10 B. dorei , 2/6 B. uniformis , 0/9 B. cellulosilyticus , and 0/6 B. stercoris strains tested secreted antimicrobial molecules detected using an agar overlay assay.…”

“…In both B. fragilis and B. uniformis , the BSAPs are MACPF domain proteins, which we have found to be ubiquitous in Bacteroidetes species, including species that occupy marine and soil habitats (25) (see Fig. S2 and Table S2 in the supplemental material).…”

“…We recently identified a Bacteroidales -secreted antimicrobial protein (BSAP-1) of Bacteroides fragilis that antagonizes in vitro a subset of B. fragilis strains lacking BSAP-1 (25). BSAP-1 contains a membrane attack complex/perforin (MACPF) domain related to the cholesterol-dependent cytolysin (CDC) domain of Gram-positive pore-forming toxins (29).…”

An insider's perspective: Bacteroides as a window into the microbiome

“…Strains of Bacteroides also produce and secrete antimicrobial proteins, such as Bacteroidales secreted antimicrobial protein 1, or BSAP-1 ( B. fragilis ; loaded into OMVs; Fig. 4a) and BSAP-2 ( Bacteroides uniformis ), which contain membrane attack complex/perforin (MACPF) domains and target closely related strains in vitro and in vivo 97,98 . To resist sister-cell killing, bacteriocin producers can directly encode immunity factors that protect against cytotoxicity, or in the case of Bacteroides BSAP producers, encode a non-targeted orthologue of the toxin receptor adjacent to the toxin genes themselves 98,99 .…”

Message in a Biota: Gut Microbes Signal to the Circadian Clock

“…As all human gut Bacteroidales previously analyzed contain genes encoding sulfatases as well as an ortholog of anSME (Benjdia et al, 2011), it is possible that the sulfatases of other species of this order of abundant gut bacteria may be important for inducing intestinal inflammation in this and possibly other models of colitis. In addition, OMVs of Bacteroides species have been shown to mediate important interactions with the host (Shen et al, 2012;Stentz et al, 2014), including protection from disease (Shen et al, 2012), and to mediate both beneficial and competitive interactions with other bacterial members of the microbiota (Chatzidaki-Livanis et al, 2014;Rakoff-Nahoum et al, 2014). Therefore, OMVs that mediate normal microbemicrobe and beneficial microbe-host processes in the healthy gut are also the vehicles that mediate disease in this mouse model of colitis.…”