YmdB: a stress-responsive ribonuclease-binding regulator of <i>E. coli</i> RNase III activity

Kim, Kwang-sun; Manasherob, Robert; Cohen, Stanley N.

doi:10.1101/gad.1729508

Cited by 70 publications

(109 citation statements)

References 57 publications

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“…One possibility is that RNase III activity is controlled by interaction with a protein. Kim et al 13 identified the cold-shock induced RNase III modulator protein YmdB, which inhibits processing of the rnc and pnp transcripts by RNase III under cold-shock conditions. Sim et al 12 proposed that RNase III is inhibited by hyperosmotic stress, and demonstrated that expression of rnc, pnp, and bdm, which are likewise processed by RNase III, is induced by hyper-osmotic stress.…”

Section: Discussionmentioning

confidence: 99%

“…11,12 Interestingly, environmental cues such as temperature and osmolarity affect processing by RNase III. 12,13 The cold-shock induced protein YmdB interacts with the catalytic region of RNase III and thereby inhibits processing of rnc and pnp mRNA under cold-shock. 13 Similarly, the activity of RNase III is inhibited at high osmolarity resulting in upregulation of the rnc, pnp, and bdm mRNAs.…”

mentioning

confidence: 99%

“…12,13 The cold-shock induced protein YmdB interacts with the catalytic region of RNase III and thereby inhibits processing of rnc and pnp mRNA under cold-shock. 13 Similarly, the activity of RNase III is inhibited at high osmolarity resulting in upregulation of the rnc, pnp, and bdm mRNAs. 12 The mechanism of osmoregulation of RNase III activity is still unclear.…”

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confidence: 99%

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RNase III initiates rapid degradation ofproUmRNA upon hypo-osmotic stress inEscherichia coli

2012

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RNase III initiates rapid degradation ofproUmRNA upon hypo-osmotic stress inEscherichia coli

2012

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“…These results suggest that the SraG-mediated regulation of pnp may act as an additional factor in the control of PNPase expression to supplement its autoregulation and CsrA-dependent control of translation. The physiological role of SraG might be more important in conditions where RNase III activity is down-regulated, e.g., in response to stresses (Kim et al 2008). This interplay in the control of SraG processing and PNPase expression thus contributes to PNPase homeostasis.…”

Section: Discussionmentioning

confidence: 99%

The small RNA SraG participates in PNPase homeostasis

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Gasiorowski

Gracia

et al. 2016

RNA

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The rpsO-pnp operon encodes ribosomal protein S15 and polynucleotide phosphorylase, a major 3 ′ -5 ′ exoribonuclease involved in mRNA decay in Escherichia coli. The gene for the SraG small RNA is located between the coding regions of the rpsO and pnp genes, and it is transcribed in the opposite direction relative to the two genes. No function has been assigned to SraG. Multiple levels of post-transcriptional regulation have been demonstrated for the rpsO-pnp operon. Here we show that SraG is a new factor affecting pnp expression. SraG overexpression results in a reduction of pnp expression and a destabilization of pnp mRNA; in contrast, inhibition of SraG transcription results in a higher level of the pnp transcript. Furthermore, in vitro experiments indicate that SraG inhibits translation initiation of pnp. Together, these observations demonstrate that SraG participates in the post-transcriptional control of pnp by a direct antisense interaction between SraG and PNPase RNAs. Our data reveal a new level of regulation in the expression of this major exoribonuclease.

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“…As the activity of RNase III is downregulated in response to different stresses (41), it is possible that the relative effects of the two PNPase autoregulation pathways change under different physiological conditions. The two sides of the autogenous regulation process highlight the interplay between translation and RNA decay machineries in fine-tuning the expression of a pleiotropic gene.…”

Section: Discussionmentioning

confidence: 99%

RNase III-Independent Autogenous Regulation of Escherichia coli Polynucleotide Phosphorylase via Translational Repression

2015

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The complex posttranscriptional regulation mechanism of the Escherichia coli pnp gene, which encodes the phosphorolytic exoribonuclease polynucleotide phosphorylase (PNPase), involves two endoribonucleases, namely, RNase III and RNase E, and PNPase itself, which thus autoregulates its own expression. The models proposed for pnp autoregulation posit that the target of PNPase is a mature pnp mRNA previously processed at its 5= end by RNase III, rather than the primary pnp transcript (RNase III-dependent models), and that PNPase activity eventually leads to pnp mRNA degradation by RNase E. However, some published data suggest that pnp expression may also be regulated through a PNPase-dependent, RNase III-independent mechanism. To address this issue, we constructed isogenic ⌬pnp rnc ؉ and ⌬pnp ⌬rnc strains with a chromosomal pnp-lacZ translational fusion and measured ␤-galactosidase activity in the absence and presence of PNPase expressed by a plasmid. Our results show that PNPase also regulates its own expression via a reversible RNase III-independent pathway acting upstream from the RNase III-dependent branch. This pathway requires the PNPase RNA binding domains KH and S1 but not its phosphorolytic activity. We suggest that the RNase III-independent autoregulation of PNPase occurs at the level of translational repression, possibly by competition for pnp primary transcript between PNPase and the ribosomal protein S1. IMPORTANCEIn Escherichia coli, polynucleotide phosphorylase (PNPase, encoded by pnp) posttranscriptionally regulates its own expression. The two models proposed so far posit a two-step mechanism in which RNase III, by cutting the leader region of the pnp primary transcript, creates the substrate for PNPase regulatory activity, eventually leading to pnp mRNA degradation by RNase E. In this work, we provide evidence supporting an additional pathway for PNPase autogenous regulation in which PNPase acts as a translational repressor independently of RNase III cleavage. Our data make a new contribution to the understanding of the regulatory mechanism of pnp mRNA, a process long since considered a paradigmatic example of posttranscriptional regulation at the level of mRNA stability.A wealth of mechanisms that control gene expression and an intricate network of regulatory interactions subtly and promptly adapt the presence and concentration of gene products to a variety of environmental and developmental conditions. Autogenous regulation of the pnp gene in Escherichia coli has long since been considered an example of regulation at the level of mRNA stability. This gene codes for polynucleotide phosphorylase (PNPase), a phosphorolytic 3=-to-5= exoribonuclease and a template-independent, nucleoside diphosphate-dependent RNA polymerase that is conserved in bacteria and eukaryotic organelles (1, 2). E. coli PNPase plays a major role in RNA turnover and metabolism (3) and has been implicated in several processes, such as adaptation and growth in the cold, biofilm formation, and responses to oxidative stress...

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YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity

Cited by 70 publications

References 57 publications

RNase III initiates rapid degradation ofproUmRNA upon hypo-osmotic stress inEscherichia coli

RNase III initiates rapid degradation ofproUmRNA upon hypo-osmotic stress inEscherichia coli

The small RNA SraG participates in PNPase homeostasis

RNase III-Independent Autogenous Regulation of Escherichia coli Polynucleotide Phosphorylase via Translational Repression

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