Duplex formation between the sRNA DsrA and<i>rpoS</i>mRNA is not sufficient for efficient RpoS synthesis at low temperature

Hämmerle, Hermann; Večerek, Branislav; Resch, Armin; Bläsi, Udo

doi:10.4161/rna.27100

Cited by 11 publications

(8 citation statements)

References 43 publications

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“…These residues were uniformly and moderately modified in the rpoS•Hfq complex, suggesting that Hfq partially opens the mRNA secondary structure. An Hfq-induced structural change in the inhibitory stem was also reported based on RNase footprinting experiments (26).…”

Section: Resultsmentioning

confidence: 68%

“…This unexpected result explains many features of rpoS regulation by sRNAs and Hfq, such as how Hfq brings together the complementary regions of the mRNA and sRNA near the arginine patches along the rim and why sequences upstream and downstream of the sRNA target site are important. Moreover, our SHAPE results show that Hfq partially opens the secondary structure of the inhibitory stem to enhance sRNA annealing and ribosome binding (22,26). Remodeling of the rpoS mRNA requires interactions with both (AAN) 4 and U 5 motifs.…”

Section: Discussionmentioning

confidence: 77%

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Structural model of an mRNA in complex with the bacterial chaperone Hfq

Peng

Curtis

Woodson

2014

Proc. Natl. Acad. Sci. U.S.A.

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The Sm-like protein Hfq (host factor Q-beta phage) facilitates regulation by bacterial small noncoding RNAs (sRNAs) in response to stress and other environmental signals. Here, we present a low-resolution model of Escherichia coli Hfq bound to the rpoS mRNA, a bacterial stress response gene that is targeted by three different sRNAs. Selective 2′-hydroxyl acylation and primer extension, small-angle X-ray scattering, and Monte Carlo molecular dynamics simulations show that the distal face and lateral rim of Hfq interact with three sites in the rpoS leader, folding the RNA into a compact tertiary structure. These interactions are needed for sRNA regulation of rpoS translation and position the sRNA target adjacent to an sRNA binding region on the proximal face of Hfq. Our results show how Hfq specifically distorts the structure of the rpoS mRNA to enable sRNA base pairing and translational control.

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Section: Resultsmentioning

confidence: 68%

Section: Discussionmentioning

confidence: 77%

Structural model of an mRNA in complex with the bacterial chaperone Hfq

Peng

Curtis

Woodson

2014

Proc. Natl. Acad. Sci. U.S.A.

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“…Although the Hfq binding motifs are placed far away from the sRNA interaction sites, it is thought that a flexible linker between the inhibitory stem domain and the upstream A-rich domain in the rpoS 5′-UTR allows optimal positioning of Hfq toward the sRNA binding sites 72 . In addition, Hfq is involved in structural rearrangements of the rpoS 5′-UTR that improve sRNA binding as well as ribosome entry 60 , 73 , 74 . Whether a differential binding mode to the two faces of Hfq contributes to the ability of sRNAs to target rpoS mRNA is not yet clear 71 , 75 .…”

Section: Srnas and The Integration Of Diverse Environmental Signals Imentioning

confidence: 99%

“…Mechanistically, DsrA is the sRNA that is least dependent on Hfq for binding to rpoS mRNA 44 . Yet, this heteroduplex formation does not seem sufficient to allow access of ribosomes to the translation initiation region, but Hfq itself—acting as a RNA chaperone—also contributes to converting rpoS mRNA into a translationally competent conformation 74 . At low temperature, not only DsrA but also the DEAD box helicase CsdA are required for efficient rpoS mRNA translation 86 …”

Section: Srnas and The Integration Of Diverse Environmental Signals Imentioning

confidence: 99%

“…Likewise, high-level production of other sRNAs or Hfq-bound mRNAs has the potential to interfere with efficient rpoS translation 102 , 103 . OxyS binding may also disturb the direct mRNA chaperoning function of Hfq, which in addition to sRNA- rpoS mRNA heteroduplex formation seems to play a role in activating rpoS translation 74 . Finally, Hfq binding leads to a conformational change of OxyS that modulates its degradation by various RNases in ways that differ during growth and stationary phase and may co-modulate rpoS mRNA turnover 48 , 75 …”

Section: Srnas and The Integration Of Diverse Environmental Signals Imentioning

confidence: 99%

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Small RNAs in the control of RpoS, CsgD, and biofilm architecture ofEscherichia coli

Mika¹,

2014

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Amyloid curli fibers and cellulose are extracellular matrix components produced in the stationary phase top layer of E. coli macrocolonies, which confer physical protection, strong cohesion, elasticity, and wrinkled morphology to these biofilms. Curli and cellulose synthesis is controlled by a three-level transcription factor (TF) cascade with the RpoS sigma subunit of RNA polymerase at the top, the MerR-like TF MlrA, and the biofilm regulator CsgD, with two c-di-GMP control modules acting as key switching devices. Additional signal input and fine-tuning is provided by an entire series of small RNAs—ArcZ, DsrA, RprA, McaS, OmrA/OmrB, GcvB, and RydC—that differentially control all three TF modules by direct mRNA interaction. This review not only summarizes the mechanisms of action of these sRNAs, but also addresses the question of how these sRNAs and the regulators they target contribute to building the intriguing three-dimensional microarchitecture and macromorphology of these biofilms.

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