Coupled degradation of a small regulatory RNA and its mRNA targets in <i>Escherichia coli</i>

Massé, Éric; Escorcia, Freddy E.; Gottesman, Susan

doi:10.1101/gad.1127103

Cited by 651 publications

(876 citation statements)

References 56 publications

(67 reference statements)

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“…In one setup we employed the temperature-sensitive allele rne-3071 from strain EM1277. 55 The timing of the shift to the non-permissive temperature relative to the induction of starvation was an important consideration for this experiment, because the activation of one stress response may alter the cellular response to a second stressor. Namely, cells experiencing a heat shock at the time of amino acid deprivation might alter their response to amino acid starvation and consequently reduce or increase the degree of tRNA decay.…”

Section: Ribonuclease Ementioning

confidence: 99%

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

2018

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Production of the translation apparatus of E. coli is carefully matched to the demand for protein synthesis posed by a given growth condition. For example, the fraction of RNA polymerases that transcribe rRNA and tRNA drops from 80% during rapid growth to 24% within minutes of a sudden amino acid starvation. We recently reported in Nucleic Acids Research that the tRNA pool is more dynamically regulated than previously thought. In addition to the regulation at the level of synthesis, we found that tRNAs are subject to demand-based regulation at the level of their degradation. In this point-of-view article we address the question of why this phenomenon has not previously been described. We also present data that expands on the mechanism of tRNA degradation, and we discuss the possible implications of tRNA instability for the ability of E. coli to cope with stresses that affect the translation process.

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Section: Ribonuclease Ementioning

confidence: 99%

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

2018

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“…RNA lifetime analysis has been used as another measure of Hfq activity in vivo 7,16,38 . In the presence of Hfq, DsrA has been shown to degrade significantly more slowly than when Hfq is absent 7 .…”

Section: Assessment Of Dsra Stability In Vivomentioning

confidence: 99%

“…Escherichia coli Hfq mutants show disrupted signaling in stress response pathways 7,8 , arising from the need for Hfq to mediate base-pairing between regulatory ncRNAs and their mRNA targets. Examples of these partnerships include DsrA-rpoS 7,9,10 , OxyS-fhlA 11,12 , OxyS-rpoS 13 , RprA-rpoS 14 , RyhBsodB [15][16][17] .…”

Section: Introductionmentioning

confidence: 99%

Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs

Mikulecky

Kaw

Brescia

et al. 2004

Nat Struct Mol Biol

225

395

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The bacterial Sm-like protein Hfq facilitates RNA-RNA interactions involved in posttranscriptional regulation of the stress response. Specifically, Hfq helps pair noncoding RNAs (ncRNAs) with complementary regions of target mRNAs. To probe the mechanism of this pairing, we generated a series of Hfq mutants and measured their affinity for RNAs like those with which Hfq must associate in vivo. We tested the mutants' DsrA-dependent activation of rpoS, and their ability to stabilize DsrA ncRNA against degradation in vivo. Our results suggest that Hfq has two independent RNA-binding surfaces. In addition to a well-known site around the core of the Hfq hexamer, we observe interactions with the distal face of Hfq, a new locus with which mRNAs and poly(A) sequences associate. Our model explains how Hfq can simultaneously bind a ncRNA and its mRNA target to facilitate the strand displacement reaction required for Hfq-dependent translational regulation.Hfq protein from Escherichia coli was first described in connection with Qβ-phage replication 1,2 . Hfq has recently emerged as a central player in post-transcriptional gene regulation as mediated by bacterial ncRNAs [3][4][5][6] . Escherichia coli Hfq mutants show disrupted signaling in stress response pathways 7,8 , arising from the need for Hfq to mediate base-pairing between regulatory ncRNAs and their mRNA targets. Examples of these partnerships include DsrA-rpoS 7,9,10 , OxyS-fhlA 11,12 , OxyS-rpoS 13 , RprA-rpoS 14 , RyhBsodB [15][16][17] .Complexes between ncRNAs and their mRNA targets function in several ways. Most commonly, complexed structures lead to translational activation or repression by remodeling mRNA regulatory regions containing the ribosome-binding site (RBS) and/or start codon. Alternatively, the interaction can enhance decay of the target mRNA16 or simply block translation11. Clearly, Hfq facilitates base-pairing between ncRNAs and their targets, but how it does so is poorly understood. How the chaperone function relates to other Hfq activities such as the control of poly(A) tail elongation19 , 20 and regulation of mRNA stability21 , 22 is also unknown. COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests. NIH Public Access Author ManuscriptNat Struct Mol Biol. Author manuscript; available in PMC 2011 April 5. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptHfq shares sequence similarity to the eukaryotic Lsm proteins [23][24][25][26][27] We addressed these questions through a mutational analysis of Hfq, probing in vitro binding to several model RNAs that represent species with which Hfq must interact. Hfq mutants were assayed in vivo using a reporter assay and RNA lifetime experiments. Together, the results support a model wherein at least two independent RNA-binding sites exist on the Hfq hexamer, and juxtaposition of bound RNAs facilitates base-pairing. RESULTS Hfq mutagenesisTo identify amino acids essential for RNA binding, we constructed a series of E. coli Hfq misse...

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“…As noted above, for many sRNAs, down-regulation of the promoter is sufficient to lead to rapid degradation of the sRNA (Massé et al 2003). However, this does not seem to be the case for ChiX.…”

Section: Abundance Of the Chix Srna Is Regulated By A Target Decoy Amentioning

confidence: 97%

“…1A). Under biologically relevant conditions, many Hfq-dependent sRNAs turn over relatively rapidly (within minutes) (Massé et al 2003). However, if all cellular transcription is inhibited with rifampicin, the sRNA is then stable.…”

Section: Bacterial Pairing Rnas: On and Off Switchesmentioning

confidence: 99%

Regulating the regulator: an RNA decoy acts as an OFF switch for the regulation of an sRNA: Figure 1.

Mandin

Gottesman²

2009

Genes Dev.

Self Cite

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Many bacterial small regulatory RNAs (sRNAs) pair with mRNA targets, stimulating or inhibiting mRNA stability and/or translation. Regulation of these sRNAs is usually due to tight transcriptional regulation of synthesis.In this issue of Genes & Development and a related paper in Molecular Microbiology, Figueroa-Bossi and colleagues (pp. 2004–2015) and Overgaard and colleagues report a novel regulatory mechanism in which induction of a competing mRNA acts to titrate away the sRNA, allowing expression of an otherwise strongly inhibited target gene.

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Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli

Cited by 651 publications

References 56 publications

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs

Regulating the regulator: an RNA decoy acts as an OFF switch for the regulation of an sRNA: Figure 1.

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