Gut Symbiont Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism.

Human gut species produce different types of toxins that antagonize closely related members of the gut microbiota. Some are toxic effectors delivered by type VI secretion systems, and others are non-contact-dependent secreted antimicrobial proteins. Many strains of secrete antimicrobial molecules, but only one of these toxins has been described to date ( secreted antimicrobial protein 1 [BSAP-1]). In this study, we describe a novel secreted protein produced by strain 638R that mediated intraspecies antagonism. Using transposon mutagenesis and deletion mutation, we identified a gene encoding a eukaryotic-like ubiquitin protein (BfUbb) necessary for toxin activity against a subset of strains. The addition of into a heterologous background strain conferred toxic activity on that strain. We found this gene to be one of the most highly expressed in the genome. The mature protein is 84% similar to human ubiquitin but has an N-terminal signal peptidase I (SpI) signal sequence and is secreted extracellularly. We found that the mature 76-amino-acid synthetic protein has very potent activity, confirming that BfUbb mediates the activity. Analyses of human gut metagenomic data sets revealed that is present in 12% of the metagenomes that have evidence of As 638R produces both BSAP-1 and BfUbb, we performed a comprehensive analysis of the toxin activity of BSAP-1 and BfUbb against a set of 40 strains, revealing that 75% of strains are targeted by one or the other of these two secreted proteins of strain 638R. We are just beginning to understand some of the important interactions that occur between microbes of the human gut microbiota that dictate the composition and abundance of its constituent members. The ability of one member to produce molecules that directly kill a coresident member has been shown among minor gut species and is just starting to be studied in the abundant species. Here, we show that some strains of have acquired a gene encoding a secreted eukaryotic-like ubiquitin protein with potent inhibitory activity against other stains. This is the first bacterially encoded ubiquitin-like molecule shown to function like a bacterial toxin. This molecule is an example of a gut symbiont acquiring and adapting a eukaryotic molecule likely to increase its competitiveness in the mammalian gut. Understanding antagonistic factors produced by abundant gut symbionts is an important prerequisite to properly engineer strains to colonize the gut for health benefits.