6S RNA, a Global Regulator of Transcription in <i>Escherichia coli</i>, <i>Bacillus subtilis</i>, and Beyond

Cavanagh, Amy T.; Wassarman, Karen M.

doi:10.1146/annurev-micro-092611-150135

Cited by 100 publications

(94 citation statements)

References 77 publications

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“…Among them, one of the most widespread and abundant (approximately 10,000 copies per cells in stationary phase) is the 6S RNA, a global regulator sRNA that reduces the expression of several σ-70 dependent promoters, favoring the interaction of RNA polymerase with alternate sigma factors, such as RpoS in Bacillus subtilis (Cavanagh and Wassarman 2014), and has been implicated in the down-regulation of the expression of key pathways in response to changing stressful conditions and growth adaptation (Cavanagh et al 2010;Cavanagh and Wassarman 2013). GcvB is also one of the most highly conserved Hfq-associated sRNAs in Gram-negative bacteria and was previously reported to regulate many genes involved in the transport and biosynthesis of oligopeptides and amino acids, such as the branched-chain amino acid (BCAA) transport system (Sharma et al 2011;Stauffer and Stauffer 2013).…”

Section: Discussionmentioning

confidence: 99%

“…Because of this partial complementarity, some of them may rely on the molecular chaperone Hfq to mediate their proper interaction with the cognate mRNAs by remodeling and stabilizing their structure, in addition to stimulating annealing (Vogel and Luisi 2011). sRNAs that interact with proteins include the 6S RNA, which binds to the primary holoenzyme form of RNA polymerase and affects the expression of housekeeping genes under low nutrient conditions (Cavanagh and Wassarman 2014), and the sRNA CsrB, which is the major regulator of the protein CsrA-the effector of the complex network of the carbon storage regulatory (Csr) system controlling various virulence-related and metabolic phenotypes in several bacteria (Vakulskas et al 2015).…”

Section: Introductionmentioning

confidence: 99%

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A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

Rossi

Bossé

et al. 2016

RNA

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Bacterial regulatory small RNAs (sRNAs) play important roles in gene regulation and are frequently connected to the expression of virulence factors in diverse bacteria. Only a few sRNAs have been described for Pasteurellaceae pathogens and no in-depth analysis of sRNAs has been described for Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, responsible for considerable losses in the swine industry. To search for sRNAs in A. pleuropneumoniae, we developed a strategy for the computational analysis of the bacterial genome by using four algorithms with different approaches, followed by experimental validation. The coding strand and expression of 17 out of 23 RNA candidates were confirmed by Northern blotting, RT-PCR, and RNA sequencing. Among them, two are likely riboswitches, three are housekeeping regulatory RNAs, two are the widely studied GcvB and 6S sRNAs, and 10 are putative novel trans-acting sRNAs, never before described for any bacteria. The latter group has several potential mRNA targets, many of which are involved with virulence, stress resistance, or metabolism, and connect the sRNAs in a complex gene regulatory network. The sRNAs identified are well conserved among the Pasteurellaceae that are evolutionarily closer to A. pleuropneumoniae and/or share the same host. Our results show that the combination of newly developed computational programs can be successfully utilized for the discovery of novel sRNAs and indicate an intricate system of gene regulation through sRNAs in A. pleuropneumoniae and in other Pasteurellaceae, thus providing clues for novel aspects of virulence that will be explored in further studies.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

Rossi

Bossé

et al. 2016

RNA

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“…These data implicate RNase BN in contributing to the levels of certain sRNAs in exponential phase cells. To examine this point in more detail, the rest of the study focuses on how RNase BN controls the abundance of 6S RNA, a known regulator of transcription by the RNA polymerase E 70 holoenzyme (14), and an sRNA that increases in stationary phase.…”

Section: Levels Of Small Rnas In Exponential Phase and Stationary Phamentioning

confidence: 99%

“…6S RNA, a stable sRNA, is an important transcription regulator that acts by binding to the sigma 70-containing holoenzyme of RNA polymerase (E 70 ) and reducing its activity (14). In late stationary phase, 6S RNA accumulates to high levels and binds the vast majority of E 70 , leading to reduced transcription of many 70 -dependent genes (15).…”

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confidence: 99%

“…The mechanism driving accumulation of 6S RNA in stationary phase remains unclear. Although regulated transcription contributes to its accumulation in stationary phase (16), increased stability was also suggested to be an important determinant (14). However, ribonucleases that affect 6S RNA stability have not yet been identified in E. coli or any other bacterium (17).…”

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confidence: 99%

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Growth Phase-dependent Variation of RNase BN/Z Affects Small RNAs

Chen

Dutta

Deutscher

2016

Journal of Biological Chemistry

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Edited by Charles SamuelRNase BN, the RNase Z family member in E. coli, can participate in the processing of tRNA precursors. However, this function only becomes apparent when other processing enzymes are absent, raising the question of its primary physiological role. Here, we show that RNase BN itself is subject to growth phasedependent regulation, because both rbn mRNA and RNase BN protein are at their highest levels in early exponential phase, but then decrease dramatically and are essentially absent in stationary phase. As a consequence of this variation, certain small RNAs, such as 6S RNA, remain low in exponential phase cells, and increase greatly in stationary phase. RNase BN affects 6S RNA abundance by decreasing its stability in exponential phase. RNase BN levels increase rapidly as cells exit stationary phase and are primarily responsible for the decrease in 6S RNA that accompanies this process. Purified RNase BN directly cleaves 6S RNA as shown by in vitro assays, and the 6S RNA:pRNA duplex is an even more favorable substrate of RNase BN. The exoribonuclease activity of RNase BN is unnecessary because all its action on 6S RNA is due to endonucleolytic cleavages. These data indicate that RNase BN plays an important role in determining levels of the global transcription regulator, 6S RNA, throughout the growth cycle.The RNase Z family of enzymes is widespread among organisms from prokaryotes to eukaryotes. These RNases generally participate in the 3Ј processing of tRNA precursors lacking an encoded CCA sequence, cleaving right after the discriminator nucleotide to generate a substrate for CCA addition by tRNA nucleotidyltransferase (1). In addition to tRNA precursors, some mRNAs have also been identified as substrates including some in rice (2) and Escherichia coli (3), raising the possibility of other putative substrates (4). This is of particular significance in E. coli, because the precursors of all 86 tRNAs already contain the CCA trinucleotide (5), obviating a need for the action of RNase Z.The RNase Z family member in E. coli is termed RNase BN and was originally identified as an enzyme required for maturation of those bacteriophage T4 tRNA precursors that lacked a CCA sequence (6, 7). In contrast to RNase Z in most organisms, RNase BN can act as an exoribonuclease or an endoribonuclease (8, 9). When acting on CCA-containing tRNA precursors, RNase BN cleaves after the CCA sequence using its endoribonuclease activity or trims up to the CCA sequence using its exoribonuclease activity, keeping the CCA sequence intact (10). Although both activities of RNase BN can function in vivo (9), a role for this enzyme in maturation of tRNA precursors only becomes evident when other processing ribonucleases are inactivated (11), suggesting that its primary function in wild type E. coli cells is still unknown.Ribonucleases play an important role in cellular RNA metabolism, and recent studies have revealed that these enzymes may act as important regulators of small RNAs (sRNAs) 2 by participating in their maturati...

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