Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS

Abstract

Summary Small RNA (sRNA) regulators promote efficient responses to stress, but the mechanisms for prioritizing target mRNA regulation remain poorly understood. This study examines mechanisms underlying hierarchical regulation by the sRNA SgrS, found in enteric bacteria and produced under conditions of metabolic stress. SgrS posttranscriptionally coordinates a nine‐gene regulon to restore growth and homeostasis. An in vivo reporter system quantified SgrS‐dependent regulation of target genes and established that SgrS exhibits a clear target preference. Regulation of some targets is efficient even at low SgrS levels, whereas higher SgrS concentrations are required to regulate other targets. In vivo and in vitro analyses revealed that RNA structure and the number and position of base pairing sites relative to the start of translation impact the efficiency of regulation of SgrS targets. The RNA chaperone Hfq uses distinct modes of binding to different SgrS mRNA targets, which differentially influences positive and negative regulation. The RNA degradosome plays a larger role in regulation of some SgrS targets compared to others. Collectively, our results suggest that sRNA selection of target mRNAs and regulatory hierarchy are influenced by several molecular features and that the combination of these features precisely tunes the efficiency of regulation of multi‐target sRNA regulons.

MAPS integrates overlooked regulation of actin-targeting effector SteC into the virulence control network ofSalmonellasmall RNA PinT

“…Binding occurred with an apparent dissociation constant of 533 nM (Supplementary Fig. 2e), similar to other established sRNA-mRNA interactions without addition of Hfq (Bobrovskyy et al, 2019). When Hfq was added to the binding reaction, a further shift occurred, predicting the formation of a super complex of the two RNA partners together with Hfq (Supplementary Fig.…”

The Non-Coding Regulatory RNA Revolution in Archaea

“…Outstanding questions also remain regarding the role of more than 1100 cis -sense sRNAs recently discovered in H. volcanii [ 14 ], the prevalence of regulatory tRNA-derived fragments in the Archaea [ 8 , 47 ] and the potential for sRNAs to encode small peptides such as in Bacteria and Eucarya [ 48 ]. Finally, in vivo quantitative measurements of sRNA-mediated regulation, such as those currently being made in the Bacteria [ 49 ], are necessary to understand, at a system-level, how sRNA-based regulation is integrated within a cell’s regulatory networks.…”

Effects of individual base-pairs onin vivotarget search and destruction kinetics of small RNA

“…19 A disparity between sugar uptake and its metabolism gives rise to stress; a faster uptake leads to an accumulation of glucose-6-phosphate and activation of SgrR, a transcription factor. This stimulates the sgrS gene to transcribe SgrS, which reduces sugar transport, promotes efflux and reroutes cellular metabolism [20][21][22] . Sugar stress conditions are provoked in most studies by subjecting cells to α-methylglucoside (αMG), a sugar analogue that gets phosphorylated during import to form αMG-6-phosphate, which cannot be further processed metabolically.…”