A Genomic Survey of Reb Homologs Suggests Widespread Occurrence of R-Bodies in Proteobacteria

Abstract

Bacteria and eukaryotes are involved in many types of interaction in nature, with important ecological consequences. However, the diversity, occurrence, and mechanisms of these interactions often are not fully known. The obligate bacterial endosymbionts of Paramecium provide their hosts with the ability to kill sensitive Paramecium strains through the production of R-bodies, highly insoluble coiled protein ribbons. R-bodies have been observed in a number of free-living bacteria, where their function is unknown. We have performed an exhaustive survey of genes coding for homologs of Reb proteins (R-body components) in complete bacterial genomes. We found that reb genes are much more widespread than previously thought, being present in representatives of major Proteobacterial subdivisions, including many free-living taxa, as well as taxa known to be involved in various kinds of interactions with eukaryotes, from mutualistic associations to pathogenicity. Reb proteins display very good conservation at the sequence level, suggesting that they may produce functional R-bodies. Phylogenomic analysis indicates that reb genes underwent a complex evolutionary history and allowed the identification of candidates potentially involved in R-body assembly, functioning, regulation, or toxicity. Our results strongly suggest that the ability to produce R-bodies is likely widespread in Proteobacteria. The potential involvement of R-bodies in as yet unexplored interactions with eukaryotes and the consequent ecological implications are discussed.

Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits

“…This enables them to kill symbiont-free competitors by an unknown mechanism. Recently a study demonstrated that Reb homologs are widely distributed in members of proteobacteria (Raymann et al, 2013). In the present study, although we did not observe R-body structures in cultured strains of V. nigripulchritudo or V. coralliilyticus, the induction of the expression of V. nigripulchritudo reb genes in E. coli was sufficient to produce R-bodies, suggesting that specific conditions are required for reb gene expression in Vibrio.…”

Growth on Chitin Impacts the Transcriptome and Metabolite Profiles of Antibiotic-Producing Vibrio coralliilyticus S2052 and Photobacterium galatheae S2753

“…We believe that these genes were misannotated since their encoded products contain a RebB domain, necessary for the production of R-bodies. These are cytoplasmic inclusions occurring widely in Proteobacteria whose exact function is not known, but they have been suggested to play a role during host infection (33). …”

Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics

“…They encode R-bodies, highly insoluble protein ribbons that are typically coiled into cylindrical structures but can unroll under certain conditions (Pond et al, 1989) and are associated with the killing trait toward sensitive Paramecia (Dilts and Quackenbush, 1986). Orthologs of reb were found to be present in many free-living bacteria, but their function remains unclear to date (Raymann et al, 2013).…”