Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA

Desnoyers, Guillaume; Morissette, Audrey; Prévost, Karine; Massé, Éric

doi:10.1038/emboj.2009.116

Cited by 180 publications

(178 citation statements)

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“…For example, Spot42 targets the galETKM mRNA and inhibits galK translation but does not affect the expression of galET or the stability of the mRNA (32,33). RyhB selectively inhibits translation of iscS in the iscRSUA operon and promotes degradation of the iscSUA portion of the transcript, whereas iscR mRNA is stable (34). There are certainly hints from transcriptome studies that bacterial sRNAs commonly target entire operons for coordinate up-or down-regulation (35,36).…”

Section: Discussionmentioning

confidence: 99%

Small RNA binding-site multiplicity involved in translational regulation of a polycistronic mRNA

Rice

Balasubramanian

Vanderpool

2012

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

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In animal systems, mRNAs subject to posttranscriptional regulation by small RNAs (sRNAs) often possess multiple binding sites with imperfect complementarity to a given sRNA. In contrast, small RNA-mRNA interactions in bacteria and plants typically involve a single binding site. In a previous study, we demonstrated that the Escherichia coli sRNA SgrS base pairs with a site in the coding region of the first gene of a polycistronic message, manXYZ. This interaction was shown to be responsible for translational repression of manX and to contribute to destabilization of the manXYZ mRNA. In the current study, we report that translational repression of the manY and manZ genes by SgrS requires a second binding site located in the manX-manY intergenic region. Pairing at this site can repress translation of manY and manZ even when mRNA degradation is blocked. Base pairing between SgrS and the manX site does not affect translation of manY or manZ. Pairing at both sites is required for optimal SgrS-mediated degradation of the fulllength manXYZ mRNA and for a particular stress phenotype. These results suggest that bacterial sRNAs may use target-site multiplicity to enhance the efficiency and stringency of regulation. Moreover, use of multiple binding sites may be particularly important for coordinating regulation of multiple genes encoded in operons.glucose-phosphate stress | Hfq | phosphoenolpyruvate phosphotransferase system | RNase E N ow accepted as fundamentally important players in regulation of gene expression, regulatory RNAs are present in organisms across all domains of life. In many eukaryotic organisms, siRNAs and microRNAs (miRNAs) control gene expression at the posttranscriptional level in diverse pathways (1-3). In bacteria, small RNAs (sRNAs) similarly control gene expression posttranscriptionally, and the principles (if not the details) of sRNA regulatory mechanisms have much in common with miRNA and siRNA regulation. Like miRNAs, many bacterial sRNAs function by base pairing with mRNA targets to affect their translation and stability. Both miRNAs and bacterial sRNAs usually regulate multiple mRNAs through interactions involving short regions (7-10 bases) of imperfect complementarity. In most instances, base pairing between sRNAs or miRNAs and their mRNA targets negatively affects target expression by modulating translation and mRNA stability (2, 4). Bacterial sRNAs usually repress target mRNA translation by base pairing with and sequestering sequences of the ribosome-binding site (RBS) in the 5′ UTR of the mRNA, making it unavailable for ribosome binding. Subsequent mRNA degradation is initiated by the endoribonuclease RNase E and its associated proteins, collectively referred to as the "degradosome" (4).SgrS is a well-studied sRNA found in enteric bacteria and is expressed in response to a metabolic stress known as "glucosephosphate" (GP) stress (5, 6). GP stress is a condition associated with imbalanced glycolytic flux resulting in the accumulation of sugar phosphates. The stress occurs when certain phosp...

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Section: Discussionmentioning

confidence: 99%

Small RNA binding-site multiplicity involved in translational regulation of a polycistronic mRNA

Rice

Balasubramanian

Vanderpool

2012

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

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“…An experiment was then carried out to study RyhB regulation. Wild-type and DryhB strains were grown in M63-glucose medium in the absence of Fe, as RyhB is highly expressed under these conditions (Desnoyers et al 2009). Results showed a threefold increase in SdhC 258 -LacZ fusion activity in the DryhB strain as compared with wild-type (Fig.…”

Section: Spot42 Ryhb and Rybb Regulate Sdhc Expression Post-transcrmentioning

confidence: 99%

“…After migration, the RNA was transferred by capillarity (agarose gel) or electro-transferred (acrylamide gel) to a Hybond-XL membrane (Amersham Biosciences) and UV-cross-linked. Prehybridization, hybridization, and washes were done as described (Desnoyers et al 2009). To analyze RNA retrieved from affinity purification (below), RNA equivalent to 1 OD 600 (input) or 18 OD 600 (output) of culture were sized on polyacrylamide gels (10% bottom/5% top, 8 M urea) and electro-transferred on a Hybond-XL membrane.…”

Section: Rna Extraction and Northern Blot Analysismentioning

confidence: 99%

Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq

Desnoyers¹,

Massé²

2012

Genes Dev.

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136

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The RNA chaperone Hfq is mostly known to help small regulatory RNAs (sRNAs) interact with target mRNAs to block initiating ribosomes. In this model, whereas the sRNA is directly competing with initiating 30S ribosomal subunits, Hfq plays only an indirect role, allowing optimal sRNA-mRNA pairing. Here we report that Hfq is recruited by a sRNA, Spot42, to bind to a precise AU-rich region in the vicinity of the translation initiation region (TIR) of sdhC mRNA and competes directly with 30S ribosomal subunits. We show that the sRNA Spot42 binds sdhC too far upstream of the TIR to directly repress translation initiation in vitro and in vivo. Contrary to the canonical model of sRNA regulation, this suggests a new mechanism where Hfq is directly involved in the translational repression of the target mRNA and where the sRNA acts only as a recruitment factor.

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“…While complete target mRNA degradation seems the most common, RyhB pairing can also result in discoordinated degradation of a polycistronic mRNA, 45 translation activation of a self-repressed mRNA, 46 and translation inhibition without mRNA degradation. 47 Also, RyhB can pair within the first ORF (sdhC) of the polycistronic mRNA sdhCDAB, which induces degradation of the full transcript.…”

Section: Additional Srnas Using Rnase Edependent Mrna Degradationmentioning

confidence: 99%