The target spectrum of SdsR small RNA inSalmonella

Abstract

Model enteric bacteria such as Escherichia coli and Salmonella enterica express hundreds of small non-coding RNAs (sRNAs), targets for most of which are yet unknown. Some sRNAs are remarkably well conserved, indicating that they serve cellular functions that go beyond the necessities of a single species. One of these ‘core sRNAs’ of largely unknown function is the abundant ∼100-nucleotide SdsR sRNA which is transcribed by the general stress σ-factor, σS and accumulates in stationary phase. In Salmonella, SdsR was known to inhibit the synthesis of the species-specific porin, OmpD. However, sdsR genes are present in almost all enterobacterial genomes, suggesting that additional, conserved targets of this sRNA must exist. Here, we have combined SdsR pulse-expression with whole genome transcriptomics to discover 20 previously unknown candidate targets of SdsR which include mRNAs coding for physiologically important regulators such as the carbon utilization regulator, CRP, the nucleoid-associated chaperone, StpA and the antibiotic resistance transporter, TolC. Processing of SdsR by RNase E results in two cellular SdsR variants with distinct target spectra. While the overall physiological role of this orphan core sRNA remains to be fully understood, the new SdsR targets present valuable leads to determine sRNA functions in resting bacteria.

RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE

“…This notion is consistent with a recent study in E. coli showing functional redundancy for CspC and CspE in regulating the rpoS mRNA (52). Note, however, that, in contrast to E. coli (19, 53), we do not observe CspC/E-dependent changes in rpoS expression in Salmonella or strongly RpoS-dependent transcripts such as the sRNA SdsR (Dataset S2) (54,55), suggesting important differences in CSP-mediated regulation between these closely related species. Functional redundancy might further explain why single-transposon insertions in cspC or cspE did not result in fitness defects within different animal models of salmonellosis (21).…”

Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis

“…Increasingly complex regulatory networks have been discovered, including several direct sRNA-sRNA interactions (Vogel et al, 2003;Lybecker et al, 2014;Miyakoshi et al, 2015;Frohlich et al, 2016). One reported interaction is between sRNAs SraC and SdsR in Escherichia coli, which originates from the same intergenic region, encoded in opposite directions (Vogel et al, 2003).…”

“…However, due to the complete overlap of SdsR in antisense sequence to SraC, the binding of these sRNAs is expected and it results in RNase III-dependent cleaving (Vogel et al, 2003). Although still largely uncharacterized in E. coli, the target network of SdsR has been characterized in Salmonella enterica and includes stress response regulators (Frohlich et al, 2016). Another known interaction is between sRNA GcvB and the RNA sponge SroC, which represses GcvB in E. coli (Miyakoshi et al, 2015).…”

Feedback regulation of small RNA processing by the cleavage product

“…At least in one case, sRNA maturation was shown to be essential for regulation [12]. In addition, processing by RNase E may generate sRNA species with a target spectrum distinct from the genes regulated by the unprocessed sRNA [22]. sRNAs processed in the 5ʹ region carry a 5ʹ monophosphate converting them into preferred substrates for further degradation by RNase E. The sRNA 5ʹ monophosphate may also promote rapid target RNA degradation through interaction with the 5ʹ sensing pocket in RNase E, thereby allosterically activating the enzyme [23].…”