Spot 42 RNA mediates discoordinate expression of the <i>E. coli</i> galactose operon

Møller, Thorleif; Franch, Thomas; Udesen, Christina; Gerdes, Kenn; Valentin‐Hansen, Poul

doi:10.1101/gad.231702

Cited by 277 publications

(292 citation statements)

References 53 publications

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“…Furthermore, we predict that RNase E will be an essential component of the degradation pathway in all of these cases as well. It is less clear how this mechanism will apply to small RNAs that do not cause destruction of their target mRNAs, such as Spot 42 RNA (Møller et al 2002b). Spot 42 down-regulates the translation of the galK gene without causing message degradation; in cells treated with rifampicin, it has a half-life of >30 min (Møller et al 2002b).…”

Section: Mechanism Of Action May Be Conserved For Other Small Rnasmentioning

confidence: 99%

“…It is less clear how this mechanism will apply to small RNAs that do not cause destruction of their target mRNAs, such as Spot 42 RNA (Møller et al 2002b). Spot 42 down-regulates the translation of the galK gene without causing message degradation; in cells treated with rifampicin, it has a half-life of >30 min (Møller et al 2002b). We would argue that it is likely to be degraded during this process, even if the message is not; otherwise it is hard to imagine how it acts as a regulatory molecule or how the down-regulation would be terminated.…”

Section: Mechanism Of Action May Be Conserved For Other Small Rnasmentioning

confidence: 99%

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

Massé¹,

Escorcia²,

Gottesman³

2003

Genes Dev.

653

836

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RyhB is a small antisense regulatory RNA that is repressed by the Fur repressor and negatively regulates at least six mRNAs encoding Fe-binding or Fe-storage proteins in Escherichia coli. When Fe is limiting, RyhB levels rise, and target mRNAs are rapidly degraded. RyhB is very stable when measured after treatment of cells with the transcription inhibitor rifampicin, but is unstable when overall mRNA transcription continues. We propose that RyhB turnover is coupled to and dependent on pairing with the target mRNAs. Degradation of both mRNA targets and RyhB is dependent on RNase E and is slowed in degradosome mutants. RyhB requires the RNA chaperone Hfq. In the absence of Hfq, RyhB is unstable, even when general transcription is inhibited; degradation is dependent upon RNase E. Hfq and RNase E bind similar sites on the RNA; pairing may allow loss of Hfq and access by RNase E. Two other Hfq-dependent small RNAs, DsrA and OxyS, are also stable when overall transcription is off, and unstable when it is not, suggesting that they, too, are degraded when their target mRNAs are available for pairing. Thus, this large class of regulatory RNAs share an unexpected intrinsic mechanism for shutting off their action.

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Section: Mechanism Of Action May Be Conserved For Other Small Rnasmentioning

confidence: 99%

Section: Mechanism Of Action May Be Conserved For Other Small Rnasmentioning

confidence: 99%

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

Massé¹,

Escorcia²,

Gottesman³

2003

Genes Dev.

653

836

View full text Add to dashboard Cite

show abstract

“…RNA-U, A 18 and A 27 were purchased from Dharmacon Research and deprotected following the manufacturer's protocol. RNA quality was assessed by denaturing PAGE and gelpurified as necessary.…”

Section: Rna Preparation For In Vitro Bindingmentioning

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

226

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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“…We next mapped the level of identity among all known spf sequences (120 in total when redundant sequences have been removed) onto a consensus secondary structure model of Spot 42 (based on structure probing by Møller et al 1 ) to find clues to possible structural regions that might be important for target identification and interaction, in general (Fig. 2).…”

Section: Spf Is Restricted To 5 Orders Of Gammaproteobacteriamentioning

confidence: 99%

“…1 In E. coli the spf gene is flanked by polA (upstream) and yihA (downstream), 2,3 and a CRP binding sequence and -10 and -35 promoter sequences are found upstream of spf. spf is also highly conserved within the Vibrionaceae family, and was recently identified in 76 Vibrionaceae genomes that were available at that time (e.g., Vibrio, Aliivibrio, Photobacterium and Grimontia genera).…”

Section: Introductionmentioning

confidence: 99%

The Spot 42 RNA: A regulatory small RNA with roles in the central metabolism

Bækkedal

Haugen

2015

RNA Biology

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T he Spot 42 RNA is a 109 nucleotide long (in Escherichia coli) noncoding small regulatory RNA (sRNA) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the majority of experimental work on Spot 42 RNA has been performed using E. coli, and recently Aliivibrio salmonicida. In the cell Spot 42 RNA plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP complex. Here we summarize the current knowledge on Spot 42, and present the natural distribution of spf, show family-specific secondary structural features of Spot 42, and link highly conserved structural regions to mRNA target binding.

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Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon

Cited by 277 publications

References 53 publications

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

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

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

The Spot 42 RNA: A regulatory small RNA with roles in the central metabolism

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