Hfq‐dependent
            <scp>mRNA</scp>
            unfolding promotes
            <scp>sRNA</scp>
            ‐based inhibition of translation

Hoekzema, Mirthe; Romilly, Cédric; Holmqvist, Erik; Wagner, E. Gerhart H.

doi:10.15252/embj.2018101199

Cited by 40 publications

(43 citation statements)

References 102 publications

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“…Optimal translation of fepA and bamA requires stemloop structures, and OmrA and OmrB repress these targets by disrupting these structures (125). In other examples, such as SgrS and DicF repression of manX, the sRNAs recruit or stabilize Hfq binding, and it is actually Hfq that occludes ribosome binding (126). For OmrAand OmrB-mediated repression of dgcM, Hfq binding leads to a change in the dgcM 5′-UTR secondary structure, which then allows sRNA base pairing to block translation (127).…”

Section: Negative and Positive Regulation Of Translationmentioning

confidence: 99%

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

et al. 2020

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The last few decades have led to an explosion in our understanding of the major roles that small regulatory RNAs (sRNAs) play in regulatory circuits and the responses to stress in many bacterial species. Much of the foundational work was carried out with Escherichia coli and Salmonella enterica serovar Typhimurium. The studies of these organisms provided an overview of how the sRNAs function and their impact on bacterial physiology, serving as a blueprint for sRNA biology in many other prokaryotes. They also led to the development of new technologies. In this chapter, we first summarize how these sRNAs were identified, defining them in the process. We discuss how they are regulated and how they act and provide selected examples of their roles in regulatory circuits and the consequences of this regulation. Throughout, we summarize the methodologies that were developed to identify and study the regulatory RNAs, most of which are applicable to other bacteria. Newly updated databases of the known sRNAs in E. coli K-12 and S. enterica Typhimurium SL1344 serve as a reference point for much of the discussion and, hopefully, as a resource for readers and for future experiments to address open questions raised in this review.

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Section: Negative and Positive Regulation Of Translationmentioning

confidence: 99%

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

et al. 2020

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“…However, the new layer provided by the regulation of flgM could help the bacteria to integrate multiple environmental signals, and combine McaS and OmrA/B to coordinate and promote bacterial motility in response to osmotic and low nutrient stress. This might simultaneously boost their combined negative effect on biofilm formation, tipping the balance towards motility under specific conditions [10,14,17,21].…”

Section: Discussionmentioning

confidence: 99%

“…Chemically competent E. coli Top10 cells were used for all transformations (C404003, Invitrogen). In-frame deletions of flgM and flgM_M1 were obtained using the Lambda red scarless mutagenesis method as described in [17]. For flgM-3xflag transcription, a plasmid with a T7 promoter, the flgM ORF, a 3xflag sequence, and T7 terminator was created using the pET52-b vector from Novagen as backbone.…”

Section: Bacterial Strains and Plasmidsmentioning

confidence: 99%

“…On csgD mRNA, both sRNAs bind far upstream of the ribosome binding site (RBS) to prevent translation initiation by an as yet unknown mechanism [10,21]. Regulation of dgcM mRNA involves Hfq-dependent structure remodelling to facilitate OmrA/B binding, rather than the more common matchmaking activity of this protein [17]. Ultimately, downregulation of these three genes entails inhibition of both curli formation and synthesis of cellulose.…”

Section: Introductionmentioning

confidence: 99%

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Small RNAs OmrA and OmrB promote class III flagellar gene expression by inhibiting the synthesis of anti-Sigma factor FlgM

et al. 2020

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Bacteria can move by a variety of mechanisms, the best understood being flagella-mediated motility. Flagellar genes are organized in a three-tiered cascade allowing for temporally regulated expression that involves both transcriptional and post-transcriptional control. The class I operon encodes the master regulator FlhDC that drives class II gene transcription. Class II genes include fliA and flgM, which encode the Sigma factor σ 28 , required for class III transcription, and the anti-Sigma factor FlgM, which inhibits σ 28 activity, respectively. The flhDC mRNA is regulated by several small regulatory RNAs (sRNAs). Two of these, the sequence-related OmrA and OmrB RNAs, inhibit FlhD synthesis. Here, we report on a second layer of sRNA-mediated control downstream of FhlDC in the flagella pathway. By mutational analysis, we confirm that a predicted interaction between the conserved 5ʹ seed sequences of OmrA/B and the early coding sequence in flgM mRNA reduces FlgM expression. Regulation is dependent on the global RNAbinding protein Hfq. In vitro experiments support a canonical mechanism: binding of OmrA/B prevents ribosome loading and decreases FlgM protein synthesis. Simultaneous inhibition of both FlhD and FlgM synthesis by OmrA/B complicated an assessment of how regulation of FlgM alone impacts class III gene transcription. Using a combinatorial mutation strategy, we were able to uncouple these two targets and demonstrate that OmrA/B-dependent inhibition of FlgM synthesis liberates σ 28 to ultimately promote higher expression of the class III flagellin gene fliC.

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“…Inhibition by sRNA of 30S entry has been observed up to 50 bases upstream of the start codon (Sharma, Darfeuille, Plantinga, & Vogel, 2007). Other RBS-independent mechanisms of sRNAs include suppression of secondary structure that is required for optimal mRNA translation (Hoekzema, Romilly, Holmqvist, & Wagner, 2019;Jagodnik, Chiaruttini, & Guillier, 2017).…”

Section: Mechanisms Of Actionmentioning

confidence: 99%

An RNA biology perspective on species‐specific programmable RNA antibiotics

Vogel

2020

Molecular Microbiology

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Our body is colonized by a vast array of bacteria the sum of which forms our microbiota. The gut alone harbors >1,000 bacterial species. An understanding of their individual or synergistic contributions to human health and disease demands means to interfere with their functions on the species level. Most of the currently available antibiotics are broad‐spectrum, thus too unspecific for a selective depletion of a single species of interest from the microbiota. Programmable RNA antibiotics in the form of short antisense oligonucleotides (ASOs) promise to achieve precision manipulation of bacterial communities. These ASOs are coupled to small peptides that carry them inside the bacteria to silence mRNAs of essential genes, for example, to target antibiotic‐resistant pathogens as an alternative to standard antibiotics. There is already proof‐of‐principle with diverse bacteria, but many open questions remain with respect to true species specificity, potential off‐targeting, choice of peptides for delivery, bacterial resistance mechanisms and the host response. While there is unlikely a one‐fits‐all solution for all microbiome species, I will discuss how recent progress in bacterial RNA biology may help to accelerate the development of programmable RNA antibiotics for microbiome editing and other applications.

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

Cited by 40 publications

References 102 publications

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

Small RNAs OmrA and OmrB promote class III flagellar gene expression by inhibiting the synthesis of anti-Sigma factor FlgM

An RNA biology perspective on species‐specific programmable RNA antibiotics

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