# Extended Shine-Dalgarno motifs govern translation initiation in Staphylococcus aureus

## TL;DR

This paper shows how Staphylococcus aureus uses unique RNA structures to control protein production, which differs from other bacteria and affects biofilm formation.

## Contribution

The study reveals extended Shine-Dalgarno motifs in S. aureus that enable species-specific translation initiation and uORF-mediated regulation.

## Key findings

- Extended Shine-Dalgarno motifs in S. aureus enable specific translation initiation incompatible with E. coli ribosomes.
- Non-canonical start codons and uORF-mediated regulation modulate biofilm regulator expression in S. aureus.
- Codon rarity, ribosome pausing, and arginine availability link nutrient sensing to biofilm formation in S. aureus.

## Abstract

Regulation of translation initiation is central to bacterial adaptation, but species-specific mechanisms remain poorly understood. We present high-resolution mapping of translation start sites in Staphylococcus aureus, revealing distinct features of initiation alongside numerous unannotated small ORFs. Our analysis, combined with cryo-EM of a native mRNA-ribosome complex, shows that S. aureus relies on extended, start codon proximal Shine-Dalgarno (SD) interactions, creating specificity against phylogenetically distant bacteria. Several natural S. aureus initiation sites are not correctly decoded by E. coli ribosomes. We identify new and conserved non-canonical start codons, whose regulatory initiation sites contain these characteristic extended SD sequence motifs. Finally, we characterize a novel example of uORF-mediated translational control in S. aureus, demonstrating that translation of a small leader peptide modulates expression of a key biofilm regulator. The described mechanism involves codon rarity, ribosome pausing, and arginine availability, linking nutrient sensing to biofilm formation in this major human pathogen.

Kohl et al. combine high-resolution Ribo-seq and cryo electron microscopy to show that the bacterium Staphylococcus aureus uses extended Shine-Dalgarno motifs to initiate translation, which can make start-site decoding incompatible with phylogenetically distant ribosomes.