SraL sRNA interaction regulates the terminator by preventing premature transcription termination of
            <i>rho</i>
            mRNA

Silva, Inês J.; Barahona, Susana; Eyraud, Alex; Lalaouna, David; Figueroa‐Bossi, Nara; Massé, Éric; Arraiano, Cecília M.

doi:10.1073/pnas.1811589116

Cited by 44 publications

(38 citation statements)

References 54 publications

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“…Conversely, certain sRNAs may promote translation of their target by unfolding inhibitory structures that otherwise block ribosome binding 67 , 68 . In addition, activating trans -encoded sRNAs in γ - proteobacteria may induce target gene expression by binding to nascent mRNA leaders and interfering with Rho-mediated premature transcription termination 69 , 70 . Besides targeting mRNAs, some sRNAs may bind to, and titrate, regulatory RBPs, thereby indirectly controlling the levels of the target mRNA set of the bound protein 71 .…”

Section: Discussionmentioning

confidence: 99%

A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron

et al. 2020

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Bacteria of the genus Bacteroides are common members of the human intestinal microbiota and important degraders of polysaccharides in the gut. Among them, the species Bacteroides thetaiotaomicron has emerged as the model organism for functional microbiota research. Here, we use differential RNA sequencing (dRNA-seq) to generate a single-nucleotide resolution transcriptome map of B . thetaiotaomicron grown under defined laboratory conditions. An online browser, called ‘Theta-Base’ ( www.helmholtz-hiri.de/en/datasets/bacteroides ), is launched to interrogate the obtained gene expression data and annotations of ~4500 transcription start sites, untranslated regions, operon structures, and 269 noncoding RNA elements. Among the latter is GibS, a conserved, 145 nt-long small RNA that is highly expressed in the presence of N -acetyl- D -glucosamine as sole carbon source. We use computational predictions and experimental data to determine the secondary structure of GibS and identify its target genes. Our results indicate that sensing of N -acetyl- D -glucosamine induces GibS expression, which in turn modifies the transcript levels of metabolic enzymes.

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Section: Discussionmentioning

confidence: 99%

A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron

et al. 2020

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“…DsrA, ArcZ, and RprA binding to the 5′ UTR blocks Rho access to rut sites, thus promoting transcription elongation (141). In a final example, the SraL RNA has been reported to increase synthesis of Rho itself by blocking premature termination (142). Again, one can envision still other mechanisms by which sRNAs can affect transcription termination.…”

Section: Negative and Positive Regulation Of Transcription Terminationmentioning

confidence: 98%

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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“…In another example of an sRNA preventing Rho-dependent termination, the Salmonella SraL sRNA was reported to base-pair with the leader for rho mRNA, protecting it from transcription attenuation and thus increasing levels of full-length rho mRNA (Silva et al, 2019; Figure 2B). While the physiological role of this regulatory interaction is not known, it raises the possibility that under certain conditions the cell might modulate Rho levels and thus Rho-dependent termination via the SraL sRNA.…”

Section: Rho-dependent Transcription Terminationmentioning

confidence: 99%

Regulation of Transcription Termination of Small RNAs and by Small RNAs: Molecular Mechanisms and Biological Functions

Chen

Morita

Gottesman

2019

Front. Cell. Infect. Microbiol.

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Accurate and efficient transcription termination is an important step for cells to generate functional RNA transcripts. In bacteria, two mechanisms are responsible for terminating transcription: intrinsic (Rho-independent) termination and Rho-dependent termination. Growing examples suggest that neither type of transcription termination is static, but instead are highly dynamic and regulated. Regulatory small RNAs (sRNAs) are key players in bacterial stress responses, are frequently expressed under specific growth conditions, and are predominantly terminated through the intrinsic termination mechanism. Once made, sRNAs can base-pair with mRNA targets and regulate mRNA translation and stability. Recent findings suggest that alterations in the efficiency of intrinsic termination for sRNAs under various growth conditions may affect the availability of a given sRNA and the ability of the sRNA to function properly. Moreover, alterations of mRNA structure, translation, and accessibility by sRNAs have the potential to impact the access of Rho factor to mRNAs and thus termination of the mRNA. Indeed, recent studies have revealed that some sRNAs can modulate target gene expression by stimulating or inhibiting Rho-dependent termination, thus expanding the regulatory power of bacterial sRNAs. Here we review the current knowledge on intrinsic termination of sRNAs and sRNA-mediated Rho-dependent termination of protein coding genes in bacteria.

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SraL sRNA interaction regulates the terminator by preventing premature transcription termination of rho mRNA

Abstract: 2 S.B. and A.E. contributed equally to this work.This article contains supporting information online at www.pnas.org/lookup/suppl/

Cited by 44 publications

References 54 publications

A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron

A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron

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

Regulation of Transcription Termination of Small RNAs and by Small RNAs: Molecular Mechanisms and Biological Functions

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