Analysis of the in vivo decay of the Escherichia coli dicistronic pyrF-orfF transcript: evidence for multiple degradation pathways 1 1Edited by M. Yaniv

Arraiano, Cecília M.; Cruz, Ana; Kushner, Sidney R.

doi:10.1006/jmbi.1997.0962

Cited by 17 publications

(13 citation statements)

References 52 publications

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“…This is consistent with our conclusions that RNase E affects AHL accumulation through targeting the mRNA of sinI. However, we cannot rule out other mechanisms by which RNase E affects AHL accumulation, since multiple pathways of mRNA degradation and interdependence of RNases are known for other bacteria (69)(70)(71).…”

Section: Discussionsupporting

confidence: 90%

RNase E Affects the Expression of the Acyl-Homoserine Lactone Synthase Gene sinI in Sinorhizobium meliloti

et al. 2014

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c Quorum sensing of Sinorhizobium meliloti relies on N-acyl-homoserine lactones (AHLs) as autoinducers. AHL production increases at high population density, and this depends on the AHL synthase SinI and two transcriptional regulators, SinR and ExpR. Our study demonstrates that ectopic expression of the gene rne, coding for RNase E, an endoribonuclease that is probably essential for growth, prevents the accumulation of AHLs at detectable levels. The ectopic rne expression led to a higher level of rne mRNA and a lower level of sinI mRNA independently of the presence of ExpR, the AHL receptor, and AHLs. In line with this, IPTG (isopropyl-␤-D-thiogalactopyranoside)-induced overexpression of rne resulted in a shorter half-life of sinI mRNA and a strong reduction of AHL accumulation. Moreover, using translational sinI-egfp fusions, we found that sinI expression is specifically decreased upon induced overexpression of rne, independently of the presence of the global posttranscriptional regulator Hfq. The 28-nucleotide 5= untranslated region (UTR) of sinI mRNA was sufficient for this effect. Random amplification of 5= cDNA ends (5=-RACE) analyses revealed a potential RNase E cleavage site at position ؉24 between the Shine-Dalgarno site and the translation start site. We postulate therefore that RNase E-dependent degradation of sinI mRNA from the 5= end is one of the steps mediating a high turnover of sinI mRNA, which allows the Sin quorum-sensing system to respond rapidly to changes in transcriptional control of AHL production.

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Section: Discussionsupporting

confidence: 90%

RNase E Affects the Expression of the Acyl-Homoserine Lactone Synthase Gene sinI in Sinorhizobium meliloti

et al. 2014

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“…and M.B., unpublished results). Cleavage at the 5Ј or 3Ј end could facilitate degradation (28), whereas cleavage at the 5Ј end could abolish translation by eliminating initiation. Such a degradation model would prevent translation and thereby offset increases in hns RNA levels caused by reduced H-NS protein levels, because of H-NS autoregulation (4).…”

Section: Discussionmentioning

confidence: 99%

A trans-acting RNA as a control switch in Escherichia coli : DsrA modulates function by forming alternative structures

Lease

Belfort

2000

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

182

183

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DsrA is an 87-nucleotide regulatory RNA of Escherichia coli that acts in trans by RNA-RNA interactions with two different mRNAs, hns and rpoS. DsrA has opposite effects on these transcriptional regulators. H-NS levels decrease, whereas RpoS ( s ) levels increase. Here we show that DsrA enhances hns mRNA turnover yet stabilizes rpoS mRNA, either directly or via effects on translation. Computational and RNA footprinting approaches led to a refined structure for DsrA, and a model in which DsrA interacts with the hns mRNA start and stop codon regions to form a coaxial stack. Analogous bipartite interactions exist in eukaryotes, albeit with different regulatory consequences. In contrast, DsrA base pairs in discrete fashion with the rpoS RNA translational operator. Thus, different structural configurations for DsrA lead to opposite regulatory consequences for target RNAs.natural antisense ͉ RNA turnover ͉ RNA-RNA interactions ͉ structural dynamics ͉ translation R NA plays a variety of regulatory roles in the cell, in addition to its central function in translation processes. These activities are collectively termed riboregulation (1). RNA-RNA interactions provide a basis for sequence-specific RNA regulation of other RNAs in both prokaryotes and eukaryotes (2, 3). DsrA, an 87-nt untranslated RNA in Escherichia coli, is one such regulatory RNA. DsrA contains regions of sequence complementarity to at least five different genes, hns, argR, ilvIH, rpoS, and rbsD (4), and it has been demonstrated to regulate two of these genes, hns and rpoS, by RNA-RNA interactions (4, 5).H-NS is an abundant nucleoid-structuring protein with global transcriptional repressor functions (6, 7). DsrA antagonizes H-NS function by decreasing the levels of H-NS protein in the cell (4). In contrast, the translation of RpoS, the stationary phase and stress-response sigma factor (8), is enhanced by DsrA, especially at low temperatures (9). Thus, DsrA has opposite effects on these two targets, both mediated by RNA-RNA interactions, with global regulatory consequences for the transcriptional state of the cell. Whereas the mechanism of DsrA action at hns is not known, DsrA binds the translational operator of rpoS (4,5) to open a stable stem-loop of rpoS RNA (10), enabling access to the Shine-Dalgarno sequence and thus enhancing translation.Structure predictions based on thermodynamic criteria suggest that DsrA consists of three stem-loops, the third of which is the transcription terminator of DsrA ( Fig. 1A; ref. 11). The hns complementary region, in the center of the molecule, resides within the predicted second stem-loop, whereas the rpoS complementary region occupies the predicted first stemloop and the base of the second stem (4, 5). However, no additional structural data are currently available for DsrA. Mapping of the different regions of complementarity on the structure of DsrA is important for understanding how such a small RNA molecule interacts with multiple targets, and how such interactions might be regulated.Here we show that the basis of D...

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“…This is particularly so for AcnB, which is inactivated (and reactivated) seven (and ten) times faster than AcnA (A. Bradbury & J. R. Guest, unpublished observations). It is known that transcript processing and degradation plays an important part in regulating gene expression in E. coli and that mutations affecting various ribonucleases lower the rate of mRNA decay (Arraiano et al, 1997 ;Kushner, 1996). The apoaconitases could thus regulate Acn synthesis by binding to the 3hUTRs of the acn mRNAs to block transcript processing and 3hexoribonuclease progression.…”

Section: Discussionmentioning

confidence: 99%

Direct evidence for mRNA binding and post-transcriptional regulation by Escherichia coli aconitases

1999

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Escherichia coli contains a stationary-phase aconitase (AcnA) that is induced by iron and oxidative stress, and a major but less stable aconitase (AcnB) synthesized during exponential growth. These enzymes were shown to resemble the bifunctional iron-regulatory proteins (IRP1)/cytoplasmic aconitases of vertebrates in having alternative mRNA-binding and catalytic activities. Affinity chromatography and gel retardation analysis showed that the AcnA and AcnB apo-proteins each interact with the 3' untranslated regions (3'UTRs) of acnA and acnB mRNA at physiologically significant protein concentrations. AcnA and AcnB synthesis was enhanced in vitro by the apoaconitases and this enhancement was abolished by 3'UTR deletion from the DNA templates, presumably by loss of acn-mRNA stabilization by bound apoaconitase. In vivo studies showed that although total aconitase activity is lowered during oxidative stress, synthesis of the AcnA and AcnB proteins and the stabilities of acnA and acnB mRNAs both increase, suggesting that inactive aconitase mediates a post-transcriptional positive autoregulatory switch. Evidence for an iron-sulphur-cluster-dependent switch was inferred from the more than threefold higher mRNA-binding affinities of the apo-aconitases relative to the holo-enzymes. Thus by modulating translation via site-specific interactions between apo-enzyme and relevant transcripts, the aconitases provide a new and rapidly reacting component of the bacterial oxidative stress response.

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Analysis of the in vivo decay of the Escherichia coli dicistronic pyrF-orfF transcript: evidence for multiple degradation pathways 1 1Edited by M. Yaniv

Cited by 17 publications

References 52 publications

RNase E Affects the Expression of the Acyl-Homoserine Lactone Synthase Gene sinI in Sinorhizobium meliloti

RNase E Affects the Expression of the Acyl-Homoserine Lactone Synthase Gene sinI in Sinorhizobium meliloti

A trans-acting RNA as a control switch in Escherichia coli : DsrA modulates function by forming alternative structures

Direct evidence for mRNA binding and post-transcriptional regulation by Escherichia coli aconitases

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