Positive regulation by small RNAs and the role of Hfq

Abstract

Bacterial small noncoding RNAs carry out both positive and negative regulation of gene expression by pairing with mRNAs; in Escherichia coli, this regulation often requires the RNA chaperone Hfq. Three small regulatory RNAs (sRNAs), DsrA, RprA, and ArcZ, positively regulate translation of the sigma factor RpoS, each pairing with the 5′ leader to open up an inhibitory hairpin. In vitro, rpoS interaction with sRNAs depends upon an ðAANÞ 4 Hfq-binding site upstream of the pairing region. Here we show that both Hfq and this Hfq binding site are required for RprA or ArcZ to act in vivo and to form a stable complex with rpoS mRNA in vitro; both were partially dispensable for DsrA at 37°C. ArcZ sRNA is processed from 121 nt to a stable 56 nt species that contains the pairing region; only the 56 nt ArcZ makes a strong Hfq-dependent complex with rpoS. For each of these sRNAs, the stability of the sRNA • mRNA complexes, rather than their rate of formation, best predicted in vivo activity. These studies demonstrate that binding of Hfq to the rpoS mRNA is critical for sRNA regulation under normal conditions, but if the stability of the sRNA • mRNA complex is sufficiently high, the requirement for Hfq can be bypassed.Sigma 38 | translational control | Sm-like protein | RNA-protein interactions

Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia -specific small, noncoding RNAs required for virulence

“…It is not known if MicA acts similarly in Y. pseudotuberculosis, but we show here that Ysr29 acts to enhance OmpA levels. There are other examples of targets being differently regulated by multiple sRNAs [e.g., RpoS regulation by DsrA, RprA, ArcZ, and OxyS (49,50)] and also of multiple targets under the control of one sRNA [e.g., RybB regulation of outer membrane protein synthesis (51)]. In sum, the global identification of sRNAs in Y. pseudotuberculosis provides an opportunity to discover mechanisms of virulence gene regulation in this pathogenic bacterium, particularly in comparison with closely related species such as Y. pestis and in contrast to other bacteria such as E. coli and Salmonella, the prototype species for studying sRNAs.…”

The stationary phase sigma factor, RpoS, regulates the production of a carbapenem antibiotic, a bioactive prodigiosin and virulence in the enterobacterial pathogen Serratia sp. ATCC 39006

“…Hfq facilitates the complementary base-pairing of three small regulatory RNAs, namely DsrA, RprA and ArcZ, to the 59 UTR, weakening the structure of the inhibitory stem-loop and resulting in increased rpoS translation (Majdalani et al, 1998(Majdalani et al, , 2002Soper et al, 2010). The E. coli rpoS mRNA has been shown to have an unusually long 567 nt 59 UTR, with transcription initiating midway within the upstream nlpD gene (Takayanagi et al, 1994).…”

Disruption of small RNA signaling caused by competition for Hfq

“…The reason for the disparity is unclear. Even with the larger estimate, however, Hfq may be a limiting factor for sRNA activity under some conditions because (i) Hfq mediates duplex formation for more than 100 sRNAs and target mRNAs, some of which are present at high concentrations (19,20); (ii) Hfq can bind to sRNAs and duplexes for an extended period to mediate their degradation or translation as mentioned above; and (iii) multiple Hfq hexamers may bind to each sRNA or target mRNA (21)(22)(23). Therefore, under some circumstances, there may be insufficient Hfq to mediate all these actions (24,25), resulting in sRNAs and target mRNAs competing for Hfq.…”