RNA Sequencing Identifies New RNase III Cleavage Sites in <italic toggle="yes">Escherichia coli</italic> and Reveals Increased Regulation of mRNA

ABSTRACT Ribonucleases facilitate rapid turnover of RNA, providing cells with another mechanism to adjust transcript and protein levels in response to environmental conditions. While many examples have been documented, a comprehensive list of RNase targets is not available. To address this knowledge...

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Autores principales: Gina C. Gordon, Jeffrey C. Cameron, Brian F. Pfleger
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Publicado: American Society for Microbiology 2017
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spelling oai:doaj.org-article:03b9810c445b4c19a2aa297414444f732021-11-15T15:51:00ZRNA Sequencing Identifies New RNase III Cleavage Sites in <italic toggle="yes">Escherichia coli</italic> and Reveals Increased Regulation of mRNA10.1128/mBio.00128-172150-7511https://doaj.org/article/03b9810c445b4c19a2aa297414444f732017-05-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00128-17https://doaj.org/toc/2150-7511ABSTRACT Ribonucleases facilitate rapid turnover of RNA, providing cells with another mechanism to adjust transcript and protein levels in response to environmental conditions. While many examples have been documented, a comprehensive list of RNase targets is not available. To address this knowledge gap, we compared levels of RNA sequencing coverage of Escherichia coli and a corresponding RNase III mutant to expand the list of known RNase III targets. RNase III is a widespread endoribonuclease that binds and cleaves double-stranded RNA in many critical transcripts. RNase III cleavage at novel sites found in aceEF, proP, tnaC, dctA, pheM, sdhC, yhhQ, glpT, aceK, and gluQ accelerated RNA decay, consistent with previously described targets wherein RNase III cleavage initiates rapid degradation of secondary messages by other RNases. In contrast, cleavage at three novel sites in the ahpF, pflB, and yajQ transcripts led to stabilized secondary transcripts. Two other novel sites in hisL and pheM overlapped with transcriptional attenuators that likely serve to ensure turnover of these highly structured RNAs. Many of the new RNase III target sites are located on transcripts encoding metabolic enzymes. For instance, two novel RNase III sites are located within transcripts encoding enzymes near a key metabolic node connecting glycolysis and the tricarboxylic acid (TCA) cycle. Pyruvate dehydrogenase activity was increased in an rnc deletion mutant compared to the wild-type (WT) strain in early stationary phase, confirming the novel link between RNA turnover and regulation of pathway activity. Identification of these novel sites suggests that mRNA turnover may be an underappreciated mode of regulating metabolism. IMPORTANCE The concerted action and overlapping functions of endoribonucleases, exoribonucleases, and RNA processing enzymes complicate the study of global RNA turnover and recycling of specific transcripts. More information about RNase specificity and activity is needed to make predictions of transcript half-life and to design synthetic transcripts with optimal stability. RNase III does not have a conserved target sequence but instead recognizes RNA secondary structure. Prior to this study, only a few RNase III target sites in E. coli were known, so we used RNA sequencing to provide a more comprehensive list of cleavage sites and to examine the impact of RNase III on transcript degradation. With this added information on how RNase III participates in transcript regulation and recycling, a more complete picture of RNA turnover can be developed for E. coli. Similar approaches could be used to augment our understanding of RNA turnover in other bacteria.Gina C. GordonJeffrey C. CameronBrian F. PflegerAmerican Society for MicrobiologyarticleEscherichia coliRNA degradationRNA sequencingRNA stabilityRNase IIIMicrobiologyQR1-502ENmBio, Vol 8, Iss 2 (2017)
institution DOAJ
collection DOAJ
language EN
topic Escherichia coli
RNA degradation
RNA sequencing
RNA stability
RNase III
Microbiology
QR1-502
spellingShingle Escherichia coli
RNA degradation
RNA sequencing
RNA stability
RNase III
Microbiology
QR1-502
Gina C. Gordon
Jeffrey C. Cameron
Brian F. Pfleger
RNA Sequencing Identifies New RNase III Cleavage Sites in <italic toggle="yes">Escherichia coli</italic> and Reveals Increased Regulation of mRNA
description ABSTRACT Ribonucleases facilitate rapid turnover of RNA, providing cells with another mechanism to adjust transcript and protein levels in response to environmental conditions. While many examples have been documented, a comprehensive list of RNase targets is not available. To address this knowledge gap, we compared levels of RNA sequencing coverage of Escherichia coli and a corresponding RNase III mutant to expand the list of known RNase III targets. RNase III is a widespread endoribonuclease that binds and cleaves double-stranded RNA in many critical transcripts. RNase III cleavage at novel sites found in aceEF, proP, tnaC, dctA, pheM, sdhC, yhhQ, glpT, aceK, and gluQ accelerated RNA decay, consistent with previously described targets wherein RNase III cleavage initiates rapid degradation of secondary messages by other RNases. In contrast, cleavage at three novel sites in the ahpF, pflB, and yajQ transcripts led to stabilized secondary transcripts. Two other novel sites in hisL and pheM overlapped with transcriptional attenuators that likely serve to ensure turnover of these highly structured RNAs. Many of the new RNase III target sites are located on transcripts encoding metabolic enzymes. For instance, two novel RNase III sites are located within transcripts encoding enzymes near a key metabolic node connecting glycolysis and the tricarboxylic acid (TCA) cycle. Pyruvate dehydrogenase activity was increased in an rnc deletion mutant compared to the wild-type (WT) strain in early stationary phase, confirming the novel link between RNA turnover and regulation of pathway activity. Identification of these novel sites suggests that mRNA turnover may be an underappreciated mode of regulating metabolism. IMPORTANCE The concerted action and overlapping functions of endoribonucleases, exoribonucleases, and RNA processing enzymes complicate the study of global RNA turnover and recycling of specific transcripts. More information about RNase specificity and activity is needed to make predictions of transcript half-life and to design synthetic transcripts with optimal stability. RNase III does not have a conserved target sequence but instead recognizes RNA secondary structure. Prior to this study, only a few RNase III target sites in E. coli were known, so we used RNA sequencing to provide a more comprehensive list of cleavage sites and to examine the impact of RNase III on transcript degradation. With this added information on how RNase III participates in transcript regulation and recycling, a more complete picture of RNA turnover can be developed for E. coli. Similar approaches could be used to augment our understanding of RNA turnover in other bacteria.
format article
author Gina C. Gordon
Jeffrey C. Cameron
Brian F. Pfleger
author_facet Gina C. Gordon
Jeffrey C. Cameron
Brian F. Pfleger
author_sort Gina C. Gordon
title RNA Sequencing Identifies New RNase III Cleavage Sites in <italic toggle="yes">Escherichia coli</italic> and Reveals Increased Regulation of mRNA
title_short RNA Sequencing Identifies New RNase III Cleavage Sites in <italic toggle="yes">Escherichia coli</italic> and Reveals Increased Regulation of mRNA
title_full RNA Sequencing Identifies New RNase III Cleavage Sites in <italic toggle="yes">Escherichia coli</italic> and Reveals Increased Regulation of mRNA
title_fullStr RNA Sequencing Identifies New RNase III Cleavage Sites in <italic toggle="yes">Escherichia coli</italic> and Reveals Increased Regulation of mRNA
title_full_unstemmed RNA Sequencing Identifies New RNase III Cleavage Sites in <italic toggle="yes">Escherichia coli</italic> and Reveals Increased Regulation of mRNA
title_sort rna sequencing identifies new rnase iii cleavage sites in <italic toggle="yes">escherichia coli</italic> and reveals increased regulation of mrna
publisher American Society for Microbiology
publishDate 2017
url https://doaj.org/article/03b9810c445b4c19a2aa297414444f73
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