Proteins That Chaperone RNA Regulation

Woodson, Sarah A.; Panja, Subrata; Santiago-Frangos, Andrew

doi:10.1128/microbiolspec.rwr-0026-2018

Cited by 70 publications

(50 citation statements)

References 180 publications

(211 reference statements)

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“…However, the only %three-fold effect measured and the low association rates obtained do not quantitatively match the stronger effects seen in the translation assay (Fig 6B). The capability of the RNA chaperone Hfq to locally unwind and/ or restructure bound RNAs is well established and hardly surprising (e.g., Woodson et al, 2018). Supporting the in vitro translation results (Fig 6A), a distal face mutant Hfq was unable to support OmrA/B-dependent regulation of dgcM::gfp in vivo, even though the sRNA levels were high (Fig 7A and B).…”

Section: Discussionsupporting

confidence: 52%

“…Based on our in vitro results (Fig 6A), proximal and rim interactions contribute only marginally to regulation. The capability of the RNA chaperone Hfq to locally unwind and/ or restructure bound RNAs is well established and hardly surprising (e.g., Woodson et al, 2018). Remodeling has been demonstrated for the sRNAs OxyS, RprA, and DsrA (Zhang et al, 2002;Vecerek et al, 2008;Ribeiro Ede et al, 2012;Henderson et al, 2013), as well as the ompA, sodB, and mutS mRNAs (Moll et al, 2003b;Geissmann & Touati, 2004;Chen & Gottesman, 2017).…”

Section: Discussionmentioning

confidence: 99%

“…In many but not all bacteria, trans-encoded sRNAs require the RNA chaperone Hfq for efficient regulation (Vogel & Luisi, 2011;Holmqvist & Vogel, 2018;Woodson et al, 2018). Hfq is a ring-like homohexamer with at least three distinct RNA-binding surfaces (Updegrove et al, 2016;.…”

Section: Introductionmentioning

confidence: 99%

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Hfq‐dependent mRNA unfolding promotes sRNA ‐based inhibition of translation

et al. 2019

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Small RNAs post‐transcriptionally regulate many processes in bacteria. Base‐pairing of sRNAs near ribosome‐binding sites in mRNAs inhibits translation, often requiring the RNA chaperone Hfq. In the canonical model, Hfq simultaneously binds sRNAs and mRNA targets to accelerate pairing. Here, we show that the Escherichia coli sRNAs OmrA and OmrB inhibit translation of the diguanylate cyclase DgcM (previously: YdaM), a player in biofilm regulation. In OmrA/B repression of dgcM, Hfq is not required as an RNA interaction platform, but rather unfolds an inhibitory RNA structure that impedes OmrA/B binding. This restructuring involves distal face binding of Hfq and is supported by RNA structure mapping. A corresponding mutant protein cannot support inhibition in vitro and in vivo; proximal and rim mutations have negligible effects. Strikingly, OmrA/B‐dependent translational inhibition in vitro is restored, in complete absence of Hfq, by a deoxyoligoribonucleotide that base‐pairs to the biochemically mapped Hfq site in dgcM mRNA. We suggest that Hfq‐dependent RNA structure remodeling can promote sRNA access, which represents a mechanism distinct from an interaction platform model.

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Section: Discussionsupporting

confidence: 52%

Section: Discussionmentioning

confidence: 99%

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Hfq‐dependent mRNA unfolding promotes sRNA ‐based inhibition of translation

et al. 2019

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“…Intriguingly, PUR domain proteins are widespread throughout eukaryotes, where they often perform critical regulatory functions through interactions with nucleic acids (Daniel and Johnson, 2018). Results of these and other studies on BpuR suggest that its functions are distinct from the well-characterized bacterial RNA-binding protein Hfq (Lybecker et al, 2010;Woodson et al, 2018). There are similarities in the apparent effects of BpuR and SpoVG, another bacterial RNA-and DNA-binding proteins that are produced by all firmicutes and spirochetes (Rosenbluh et al, 1981;Jutras et al, 2013b;Burke and Portnoy, 2016;Savage et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

The Lyme disease spirochete's BpuR DNA/RNA‐binding protein is differentially expressed during the mammal–tick infectious cycle, which affects translation of the SodA superoxide dismutase

Jutras

Savage

Arnold

et al. 2019

Molecular Microbiology

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Summary When the Lyme disease spirochete, Borrelia burgdorferi, transfers from a feeding tick into a human or other vertebrate host, the bacterium produces vertebrate‐specific proteins and represses factors needed for arthropod colonization. Previous studies determined that the B. burgdorferi BpuR protein binds to its own mRNA and autoregulates its translation, and also serves as co‐repressor of erp transcription. Here, we demonstrate that B. burgdorferi controls transcription of bpuR, expressing high levels of bpuR during tick colonization but significantly less during mammalian infection. The master regulator of chromosomal replication, DnaA, was found to bind specifically to a DNA sequence that overlaps the bpuR promoter. Cultured B. burgdorferi that were genetically manipulated to produce elevated levels of BpuR exhibited altered levels of several proteins, although BpuR did not impact mRNA levels. Among these was the SodA superoxide dismutase, which is essential for mammalian infection. BpuR bound to sodA mRNA in live B. burgdorferi, and a specific BpuR‐binding site was mapped 5′ of the sodA open reading frame. Recognition of posttranscriptional regulation of protein levels by BpuR adds another layer to our understanding of the B. burgdorferi regulome, and provides further evidence that bacterial protein levels do not always correlate directly with mRNA levels.

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“…Global RNA binding proteins such as Hfq and FinO-like proteins are mediators of sRNA-target interactions in many Gram-negative bacteria (Holmqvist and Vogel 2018;Woodson et al 2018). The role of Hfq has been extensively studied in Proteobacteria, particularly in E. coli and S. enterica, where it forms a homohexameric ring with three RNA-interacting surfaces to stabilize the bound sRNA and facilitate its annealing to target mRNAs (Kavita et al 2018;Santiago-Frangos and Woodson 2018;Vogel and Luisi 2011).…”

Section: Rbp Candidates and Ribonucleases In Bacteroidetesmentioning

confidence: 99%

An RNA-centric view on gut Bacteroidetes

Ryan

Prezza

Westermann

2020

Biological Chemistry

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Bacteria employ noncoding RNAs to maintain cellular physiology, adapt global gene expression to fluctuating environments, sense nutrients, coordinate their interaction with companion microbes and host cells, and protect themselves against bacteriophages. While bacterial RNA research has made fundamental contributions to biomedicine and biotechnology, the bulk of our knowledge of RNA biology stems from the study of a handful of aerobic model species. In comparison, RNA research is lagging in many medically relevant obligate anaerobic species, in particular the numerous commensal bacteria comprising our gut microbiota. This review presents a guide to RNA-based regulatory mechanisms in the phylum Bacteroidetes, focusing on the most abundant bacterial genus in the human gut, Bacteroides spp. This includes recent case reports on riboswitches, an mRNA leader, and cis- and transencoded small RNAs (sRNAs) in Bacteroides spp. and a survey of CRISPR-Cas systems across Bacteroidetes. Recent work from our laboratory now suggests the existence of hundreds of noncoding RNA candidates in Bacteroides thetaiotaomicron, the emerging model organism for functional microbiota research. Based on these collective observations, we predict mechanistic and functional commonalities and differences between Bacteroides sRNAs and those of other model bacteria, and outline open questions and tools needed to boost Bacteroidetes RNA research.

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Proteins That Chaperone RNA Regulation

Cited by 70 publications

References 180 publications

Hfq‐dependent mRNA unfolding promotes sRNA ‐based inhibition of translation

Hfq‐dependent mRNA unfolding promotes sRNA ‐based inhibition of translation

The Lyme disease spirochete's BpuR DNA/RNA‐binding protein is differentially expressed during the mammal–tick infectious cycle, which affects translation of the SodA superoxide dismutase

An RNA-centric view on gut Bacteroidetes

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