PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | https://doi.org/10.1186/s12864-018-5259-8 |
Resumo: | Background: Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives in the stationary phase. The genome-wide mRNA half-lives were determined by a dynamic analysis of transcriptomes after transcription arrest. We have combined the analysis of mRNA half-lives with the steady-state concentrations (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. Results: The values of mRNA half-lives demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. Conclusions: This work had identified PNPase as a central player associated with mRNA degradation in stationary phase. |
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PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coliE. coliGene expression regulationPNPaseRNA decayRNase RTranscriptomeBiotechnologyGeneticsBackground: Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives in the stationary phase. The genome-wide mRNA half-lives were determined by a dynamic analysis of transcriptomes after transcription arrest. We have combined the analysis of mRNA half-lives with the steady-state concentrations (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. Results: The values of mRNA half-lives demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. Conclusions: This work had identified PNPase as a central player associated with mRNA degradation in stationary phase.Instituto de Tecnologia Química e Biológica António Xavier (ITQB)Molecular, Structural and Cellular Microbiology (MOSTMICRO)RUNDressaire, ClémentinePobre, VâniaLaguerre, SandrineGirbal, LaurenceArraiano, Cecilia MariaCocaign-Bousquet, Muriel2019-04-26T22:14:13Z2018-11-292018-11-29T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://doi.org/10.1186/s12864-018-5259-8engPURE: 12361305http://www.scopus.com/inward/record.url?scp=85057566097&partnerID=8YFLogxKhttps://doi.org/10.1186/s12864-018-5259-8info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T04:32:01Zoai:run.unl.pt:10362/67797Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:34:39.857691Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli |
title |
PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli |
spellingShingle |
PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli Dressaire, Clémentine E. coli Gene expression regulation PNPase RNA decay RNase R Transcriptome Biotechnology Genetics |
title_short |
PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli |
title_full |
PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli |
title_fullStr |
PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli |
title_full_unstemmed |
PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli |
title_sort |
PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli |
author |
Dressaire, Clémentine |
author_facet |
Dressaire, Clémentine Pobre, Vânia Laguerre, Sandrine Girbal, Laurence Arraiano, Cecilia Maria Cocaign-Bousquet, Muriel |
author_role |
author |
author2 |
Pobre, Vânia Laguerre, Sandrine Girbal, Laurence Arraiano, Cecilia Maria Cocaign-Bousquet, Muriel |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Instituto de Tecnologia Química e Biológica António Xavier (ITQB) Molecular, Structural and Cellular Microbiology (MOSTMICRO) RUN |
dc.contributor.author.fl_str_mv |
Dressaire, Clémentine Pobre, Vânia Laguerre, Sandrine Girbal, Laurence Arraiano, Cecilia Maria Cocaign-Bousquet, Muriel |
dc.subject.por.fl_str_mv |
E. coli Gene expression regulation PNPase RNA decay RNase R Transcriptome Biotechnology Genetics |
topic |
E. coli Gene expression regulation PNPase RNA decay RNase R Transcriptome Biotechnology Genetics |
description |
Background: Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives in the stationary phase. The genome-wide mRNA half-lives were determined by a dynamic analysis of transcriptomes after transcription arrest. We have combined the analysis of mRNA half-lives with the steady-state concentrations (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. Results: The values of mRNA half-lives demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. Conclusions: This work had identified PNPase as a central player associated with mRNA degradation in stationary phase. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-11-29 2018-11-29T00:00:00Z 2019-04-26T22:14:13Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://doi.org/10.1186/s12864-018-5259-8 |
url |
https://doi.org/10.1186/s12864-018-5259-8 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
PURE: 12361305 http://www.scopus.com/inward/record.url?scp=85057566097&partnerID=8YFLogxK https://doi.org/10.1186/s12864-018-5259-8 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
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application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
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RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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