In vivotargets ofSalmonellaFinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid

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.

Impacts of Small RNAs and Their Chaperones on Bacterial Pathogenicity

“…Deletion of proQ similarly affected levels of mgtCBR mRNA, indicating this mRNA is likely a direct target of ProQ-dependent STnc540 regulation ( Blanc-Potard and Groisman, 1997 ). Two recent reports further demonstrated that FinO-dependent sRNAs regulate copy number of plasmids carrying antibiotic resistance genes in E. coli and S. enterica ( El Mouali et al., 2021 ; Yang et al., 2021 ).…”

Bacterial RNA chaperones and chaperone-like riboregulators: behind the scenes of RNA-mediated regulation of cellular metabolism

“…3C ). Mutations on the NTD RNA-binding surface cause lower intracellular levels of ProQ due to a quality control pathway that prevents cellular accumulation of defective ProQ: such molecules, as well as defective Hfq, are eliminated by the protease Lon [ 62 , 65 ].…”

“…ProQ and other FinO proteins bind to similar RNA motifs. However, ProQ is able to bind to many RNAs, whereas most of the FinO proteins have a small target pool [ 63 , 65 ]. Salmonella FinO, for example, is a plasmid encoded protein that mediates the interaction between the sRNA FinP and the mRNA traJ [ 59 , 63 ].…”

“…Recent studies show that FinO also regulates another sRNA, RepX, different in sequence but similar in structure to FinP, that originates from the replication control locus of another plasmid. This way, the FinO-encoding plasmid influences the copy number of another plasmid via FinO [ 65 ]. ProQ has the C-terminal domain (CTD), that could determine the difference in specificity between ProQ and other FinO proteins, as such extension could directly contribute to the recognition of specific targets [ 66 ] ( Fig.…”

Riboregulation in bacteria: From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products

“…Moreover, asRNAs were found to be associated with Hfq in B. subtilis (Dambach et al, 2013). Finally, FinO and FopA, two members of the emerging FinO/ProQ-like RBPs, act on plasmid-encoded asRNAs (El Mouali et al, 2021;Gerovac et al, 2020;van Biesen & Frost, 1994).…”