Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella

Abstract

Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution but constitutes a complex process that requires synchronization with the physiological state of the host bacteria. Although several host transcription factors are known to regulate plasmid-borne transfer genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. We describe a posttranscriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two separate seed-pairing domains to activate the mRNAs of both the sigma-factor σ S and the RicI protein, a previously uncharacterized membrane protein here shown to inhibit conjugation. Transcription of ricI requires σ S and, together, RprA and σ S orchestrate a coherent feedforward loop with AND-gate logic to tightly control the activation of RicI synthesis. RicI interacts with the conjugation apparatus protein TraV and limits plasmid transfer under membrane-damaging conditions. To our knowledge, this study reports the first small RNA-controlled feedforward loop relying on posttranscriptional activation of two independent targets and an unexpected role of the conserved RprA small RNA in controlling extrachromosomal DNA transfer.RprA | sRNA | feedforward control | plasmid conjugation | Hfq

sRNA-Mediated Control of Transcription Termination in E. coli

“…sRNA-mediated antitermination contributes significantly to the induction of σ S in response to stress, and it appears to work independently of previously described mechanisms involving sRNA-mediated regulation of σ S that relied on inhibition of translation initiation and mRNA degradation (Battesti et al, 2011). The antitermination mechanism may also explain other known instances of sRNA-mediated gene activation, as, for example, in the case of RprA activation of RicI in Salmonella (Papenfort et al, 2015), that lacked obvious features of post-translation control. Indeed, our high-throughput data analysis and its experimental validation show that sRNA-mediated inhibition of Rho activity occurs within the leader sequences of many E. coli genes.…”

Dual-Function RNAs

“…In general, the deep sequencing studies highlight how much remains to be learned about different cellular networks and how even the smallest fragments of RNA can have important functions in the cell. Further identification of more multifunctional RNAs and studies into uncovering their roles in the cell will help to further understand the complex regulatory networks controlling cellular physiology (96). …”

Cross-Regulation between Bacteria and Phages at a Posttranscriptional Level

“…The core-encoded sRNA RprA is induced by both the Rcs and Cpx two component systems in response to cell envelope stress and activates the expression of the core­encoded stationary sigma factor σ S . Like SgrS, RprA has broadened its selection of targets to include two prophage-derived transcripts of S. enterica (SL2594 and SL2705) and several mRNAs encoded by the virulence plasmid pSLT (30). Interestingly, RprA activation of ricI , one of the pSLT encoded-targets that inhibits plasmid transfer, involves regulation of both core-encoded (indirectly through the stationary phase sigma factor σ S which activates ricI transcription) and horizontally-acquired (directly through activation of ricI translation) genes.…”