# Evolutionary adaptation of bacterial proteomes to translation-impeding sequences

## TL;DR

This study explores how bacteria avoid harmful RAPP-like sequences in their proteins while using them as regulatory tools in specific peptides.

## Contribution

The study identifies RAPP and RGPP as robust translation-impeding sequences and shows their dual evolutionary role in exclusion and regulation.

## Key findings

- RAPP-like sequences are strongly underrepresented in bacterial proteomes due to their disruptive potential.
- RAPP and RGPP sequences are used as ribosome-stalling motifs in arrest peptides with diverse regulatory functions.
- RAPP-like sequences are often found at the C-terminus of small secretory and membrane proteins.

## Abstract

Microbial translation arrest peptides monitor intracellular environments and feedback-regulate downstream gene expression. Previous studies have identified a class of bacterial arrest peptides with C-terminal RAPP-like sequences, encoded upstream of genes involved in protein localization. In this study, we found that among RAPP-like sequences, RAPP (Arg-Ala-Pro-Pro) and RGPP (Arg-Gly-Pro-Pro) could more readily evolve into translation-impeding sequences with a particularly robust arrest that is refractory to EF-P. RAPP-like motifs were found to be strongly excluded from bacterial proteomes, likely reflecting the risk of disrupting the cellular translation system. Meanwhile, these motifs tended to occur near the C-terminus of relatively small secretory and membrane proteins. Notably, they were encoded upstream of genes with diverse functions beyond protein localization. Indeed, we identified seven RAPP/RGPP-containing arrest peptides from Streptomyces lividans encoded upstream of genes with diverse functions. These findings illustrate the bidirectional evolution of RAPP-containing proteins: their elimination from bacterial proteomes and their adaptation into arrest peptides with various regulatory roles.

Many bacteria have evolved translation arrest peptides with a C-terminal RAPP-like sequence. This study shows that RAPP-like sequences are widely excluded from bacterial proteomes, while sometimes employed as a ribosome-stalling mechanism in arrest peptides with diverse functions.

RAPP-like sequences, particularly RGPP (Arg-Gly-Pro-Pro) and RAPP (Arg-Ala-Pro-Pro), in combination with various N-terminal sequences readily act as translation-stalling sequences.RAPP-like sequences are strongly underrepresented across bacterial proteomes.RAPP-like sequences tend to occur near the C-terminus of relatively small proteins, where they likely serve as a ribosome-stalling mechanism for regulatory purposes.RAPP-containing arrest peptides are likely involved in diverse biological pathways.

RAPP-like sequences, particularly RGPP (Arg-Gly-Pro-Pro) and RAPP (Arg-Ala-Pro-Pro), in combination with various N-terminal sequences readily act as translation-stalling sequences.

RAPP-like sequences are strongly underrepresented across bacterial proteomes.

RAPP-like sequences tend to occur near the C-terminus of relatively small proteins, where they likely serve as a ribosome-stalling mechanism for regulatory purposes.

RAPP-containing arrest peptides are likely involved in diverse biological pathways.

Analysis of bacterial proteins reveals selection against RAPP-like sequences that serve in ribosome stalling.