Patchy and widespread distribution of bacterial translation arrest peptides associated with the protein localization machinery

Abstract

Regulatory arrest peptides exert cellular functions via mechanisms involving regulated translational arrest. Monitoring substrates, a class of arrest peptides, feedback-regulate the expression of the Sec or YidC protein localization machinery. Previously, only a limited number of monitoring substrates were identified. In this study, we performed a bacterial domain-wide search, followed by in vivo and in vitro analyses, leading to a comprehensive identification of many novel Sec/YidC-related arrest peptides that showed patchy, but widespread, phylogenetic distribution throughout the bacterial domain. Identification of five novel arrest-inducing sequences suggests that bacteria have evolved various arrest-inducing mechanisms. We also identified many arrest peptides that share an R-A-P-P like sequence, suggesting that this sequence could serve as a common evolutionary seed that could overcome the species-specific structures of ribosomes, to evolve arrest peptides. Our comprehensive phylogenetic study revealed that arrest peptide is a prevalent mechanism for the gene regulation of the protein localization machinery.