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 byin vivoandin vitroanalyses, 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.

Nonspecific N-terminal tetrapeptide insertions disrupt the translation arrest induced by ribosome-arresting peptide sequences

“…1 , B and C ). Next, we calculated the strength of translation arrest from the ratio of the accumulated peptidyl-tRNA to the full-length polypeptide ( 9 , 10 , 11 , 12 , 13 , 22 , 23 , 37 ). The insertion of the SKIK tag did not affect the accumulation of peptidyl-tRNA, consistent with that of the toeprint analysis ( Fig.…”

“…Similarly, translation arrest during the synthesis of E. coli tnaC or speFL also regulates the expression of downstream tryptophanase (TnaA, ( 5 , 6 )) or ornithine decarboxylase (SpeF, ( 7 )), respectively. These ribosome arresting peptides (RAP) with regulatory functions have been identified in various bacteria ( 8 , 9 , 10 , 11 , 12 ) as well as in humans, budding yeast, and plants ( 13 , 14 , 15 , 16 , 17 , 18 ). Although they all depend on the context of the amino acid sequence to arrest translation elongation, each of them exhibits unique amino acid sequences, with little commonality found except in a few instances.…”