In vivo targets of Salmonella FinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid.

Youssef El Mouali,Raminta Mineikaitė,Milan Gerovac,Jörg Vogel

doi:10.1093/nar/gkab281

Abstract

FinO-domain proteins represent an emerging family of RNA-binding proteins (RBPs) with diverse roles in bacterial post-transcriptional control and physiology. They exhibit an intriguing targeting spectrum, ranging from an assumed single RNA pair (FinP/traJ) for the plasmid-encoded FinO protein, to transcriptome-wide activity as documented for chromosomally encoded ProQ proteins. Thus, the shared FinO domain might bear an unusual plasticity enabling it to act either selectively or promiscuously on the same cellular RNA pool. One caveat to this model is that the full suite of in vivo targets of the assumedly highly selective FinO protein is unknown. Here, we have extensively profiled cellular transcripts associated with the virulence plasmid-encoded FinO in Salmonella enterica. While our analysis confirms the FinP sRNA of plasmid pSLT as the primary FinO target, we identify a second major ligand: the RepX sRNA of the unrelated antibiotic resistance plasmid pRSF1010. FinP and RepX are strikingly similar in length and structure, but not in primary sequence, and so may provide clues to understanding the high selectivity of FinO-RNA interactions. Moreover, we observe that the FinO RBP encoded on the Salmonella virulence plasmid controls the replication of a cohabitating antibiotic resistance plasmid, suggesting cross-regulation of plasmids on the RNA level.

Highlights

Proteins that carry a FinO domain have recently garnered much attention as a new class of widespread RNA-binding proteins (RBPs) in bacteria [1,2]
The homolog of E. coli FinO is located on the so-called virulence plasmid pSLT, which carries the virulence-associated spv operon [50]
By way of inference from E. coli, FinO of Salmonella represses the conjugative transfer of pSLT by interacting with the pSLTencoded traJ mRNA and its antisense RNA, FinP, protecting FinP from degradation and facilitating sense-antisense RNA recognition

Summary

Introduction

Proteins that carry a FinO domain have recently garnered much attention as a new class of widespread RNA-binding proteins (RBPs) in bacteria [1,2] To date, several such proteins have been characterized, some of which in multiple species: FinO itself, FopA, ProQ and RocC. Acting as an RNA chaperone, RocC uses its FinO domain to recognize an inhibitory sRNA (RocR) and several trans-encoded target mRNAs in the competence regulon [10,11] From these and other recent functional studies of ProQ [12,13] or ProQ-associated sRNAs [14,15], a working model has emerged whereby the FinO domain enables these RBPs to act in a transcriptome-wide manner to impact on various aspects of bacterial physiology. Whether the FinO domain recognizes a specific nucleotide sequence or structural element in these many cellular targets is currently unclear; no informative consensus binding motif could be extracted from the large target suite of Salmonella ProQ [7]

Methods

Results

Conclusion