Lost in translation: the influence of ribosomes on bacterial mRNA decay: Figure 1.

Deana, Atilio; Belasco, Joel G.

doi:10.1101/gad.1348805

Cited by 275 publications

(277 citation statements)

References 78 publications

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“…initiation of translation upon ligand binding (17,(28)(29)(30)(31). As expected for most translationally repressed mRNAs, the absence of translating ribosomes can reveal critical cleavage site(s) located in the ORF domain that are prone to nuclease attack, ultimately leading to mRNA degradation (32). A clear example has been described for the translationally acting btuB riboswitch from E. coli, for which transcriptional fusions containing only the riboswitch domain showed no modulation as a function of ligand (33).…”

Section: Discussionmentioning

confidence: 99%

“…S3). There is considerable precedence for such a interplay between translation and degradation in which mRNA lifetime is influenced mostly by the time during which it can support protein synthesis (32). In such cases, mRNA decay occurs only as a consequence of translation inhibition and is involved only as a scavenging process, which is referred to as a "nonnucleolytic repression mechanism" (15).…”

Section: Discussionmentioning

confidence: 99%

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Dual-acting riboswitch control of translation initiation and mRNA decay

Caron

Bastet

Lussier

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

149

150

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Riboswitches are mRNA regulatory elements that control gene expression by altering their structure in response to specific metabolite binding. In bacteria, riboswitches consist of an aptamer that performs ligand recognition and an expression platform that regulates either transcription termination or translation initiation. Here, we describe a dual-acting riboswitch from Escherichia coli that, in addition to modulating translation initiation, also is directly involved in the control of initial mRNA decay. Upon lysine binding, the lysC riboswitch adopts a conformation that not only inhibits translation initiation but also exposes RNase E cleavage sites located in the riboswitch expression platform. However, in the absence of lysine, the riboswitch folds into an alternative conformation that simultaneously allows translation initiation and sequesters RNase E cleavage sites. Both regulatory activities can be individually inhibited, indicating that translation initiation and mRNA decay can be modulated independently using the same conformational switch. Because RNase E cleavage sites are located in the riboswitch sequence, this riboswitch provides a unique means for the riboswitch to modulate RNase E cleavage activity directly as a function of lysine. This dual inhibition is in contrast to other riboswitches, such as the thiamin pyrophosphate-sensing thiM riboswitch, which triggers mRNA decay only as a consequence of translation inhibition. The riboswitch control of RNase E cleavage activity is an example of a mechanism by which metabolite sensing is used to regulate gene expression of single genes or even large polycistronic mRNAs as a function of environmental changes.gene regulation | RNA degradosome | translational control S ince the first demonstration that translation attenuation regulates the expression of the tryptophan operon (1), accumulating evidence has revealed the importance of posttranscriptional regulation in prokaryotes and eukaryotes alike. Posttranscriptional regulators include RNA molecules that operate through several mechanisms to control a wide range of physiological responses (2). Among newly identified RNA regulators are riboswitches, which are located in untranslated regions of several mRNAs and that modulate gene expression at the level of transcription, translation, or splicing (3). Riboswitches are highly structured regulatory domains that directly sense cellular metabolites such as amino acids, carbohydrates, coenzymes, and nucleobases. These genetic switches are composed of two modular domains consisting of an aptamer and an expression platform. The aptamer is involved in the specific recognition of the metabolite, and the expression platform is used to control gene expression by altering the structure of the mRNA. Recent bioinformatic analyses have reported the existence of several new RNA motifs exhibiting unconventional expression platforms (4, 5), suggesting that riboswitches using different regulation mechanisms are still likely to be discovered (6).The lysine riboswitch was first...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Dual-acting riboswitch control of translation initiation and mRNA decay

Caron

Bastet

Lussier

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

149

150

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“…Other well-characterized E. coli sRNA-target pairs that are likely to use the same mechanism include DsrA-hns, MicF-ompF, RyhB-sodB, SgrS-ptsG, and Spot42-galK (for review, see Wagner and Darfeuille 2006). Since the half-life of bacterial mRNA is strongly affected by the association with ribosomes (Deana and Belasco 2005), translation inhibition will promote the decay of the repressed target; e.g., by accelerating RNase E-mediated mRNA turnover (Massé et al 2003;Morita et al 2005). Besides RNase E, the bacterial Sm-like protein Hfq has been identified as a key player in this type of translational silencing (Valentin-Hansen et al 2004).…”

mentioning

confidence: 99%

A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites

Sharma¹,

Darfeuille²,

Plantinga³

et al. 2007

Genes Dev.

340

479

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The interactions of numerous regulatory small RNAs (sRNAs) with target mRNAs have been characterized, but how sRNAs can regulate multiple, structurally unrelated mRNAs is less understood. Here we show that Salmonella GcvB sRNA directly acts on seven target mRNAs that commonly encode periplasmic substrate-binding proteins of ABC uptake systems for amino acids and peptides. Alignment of GcvB homologs of distantly related bacteria revealed a conserved G/U-rich element that is strictly required for GcvB target recognition. Analysis of target gene fusion regulation in vivo, and in vitro structure probing and translation assays showed that GcvB represses its target mRNAs by binding to extended C/A-rich regions, which may also serve as translational enhancer elements. In some cases (oppA, dppA), GcvB repression can be explained by masking the ribosome-binding site (RBS) to prevent 30S subunit binding. However, GcvB can also effectively repress translation by binding to target mRNAs at upstream sites, outside the RBS. Specifically, GcvB represses gltI mRNA translation at the C/A-rich target site located at positions −57 to −45 relative to the start codon. Taken together, our study suggests highly conserved regions in sRNAs and mRNA regions distant from Shine-Dalgarno sequences as important elements for the identification of sRNA targets.[Keywords: Small RNA; riboregulator; post-transcriptional control; translation inhibition; ABC transporter; GcvB] Supplemental material is available at http://www.genesdev.org.

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“…Secondary structures can lower translational frequencies and efficiencies. Posttranscriptional control of mRNA appears to play a major role in controlling gene expression [42,43]. Prokaryotic mRNA transcripts exhibit half-lives as short as a few min in vivo.…”

Section: Rt-qpcrmentioning

confidence: 99%

Shiga Toxin 2 Subtypes of Enterohemorrhagic E. coli O157:H- E32511 Analyzed by RT-qPCR and Top-Down Proteomics Using MALDI-TOF-TOF-MS

Fagerquist

Zaragoza

2015

J. Am. Soc. Mass Spectrom.

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Abstract. We have measured the relative abundance of the B-subunits and mRNA transcripts of two Stx2 subtypes present in Shiga toxin-producing Escherichia coli (STEC) O157:H-strain E32511 using matrix-assisted laser desorption/ionization time-of-flight-time-of-flight tandem mass spectrometry (MALDI-TOF-TOF-MS/MS) with post source decay (PSD) and real time-quantitative polymerase chain reaction (RT-qPCR). Stx2a and Stx2c in STEC strain E32511 were quantified from the integrated peak area of their singly charged disulfide-intact B-subunit ions at m/z 7819 and m/z~7774, respectively. We found that the Stx2a subtype was 21-fold more abundant than the Stx2c subtype. The two amino acid substitutions (16D ↔ 16 N and 24D ↔ 24A) that distinguish Stx2a from Stx2c not only result in a mass difference of 45 Da between their respective B-subunits but also result in distinctly different fragmentation channels by MS/MS-PSD because both substitutions involve an aspartic acid (D) residue. Importantly, these two substitutions have also been linked to differences in subtype toxicity. We measured the relative abundances of mRNA transcripts using RT-qPCR and determined that the stx2a transcript is 13-fold more abundant than stx2c transcript. In silico secondary structure analysis of the full mRNA operons of stx2a and stx2c suggest that transcript structural differences may also contribute to a relative increase of Stx2a over Stx2c. In consequence, toxin expression may be under both transcriptional and post-transcriptional control.

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Lost in translation: the influence of ribosomes on bacterial mRNA decay: Figure 1.

Cited by 275 publications

References 78 publications

Dual-acting riboswitch control of translation initiation and mRNA decay

Dual-acting riboswitch control of translation initiation and mRNA decay

A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites

Shiga Toxin 2 Subtypes of Enterohemorrhagic E. coli O157:H- E32511 Analyzed by RT-qPCR and Top-Down Proteomics Using MALDI-TOF-TOF-MS

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