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Highly variable mRNA half‐life time within marine bacterial taxa and functional genes

Messenger RNA can provide valuable insights into the variability of metabolic processes of microorganisms. However, due to uncertainties that include the stability of RNA, its application for activity profiling of environmental samples is questionable. We explored different factors affecting the dec...

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Autores principales: Steiner, Paul A., De Corte, Daniele, Geijo, Javier, Mena, Catalina, Yokokawa, Taichi, Rattei, Thomas, Herndl, Gerhard J., Sintes, Eva
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7379614/
https://www.ncbi.nlm.nih.gov/pubmed/31298776
http://dx.doi.org/10.1111/1462-2920.14737
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author Steiner, Paul A.
De Corte, Daniele
Geijo, Javier
Mena, Catalina
Yokokawa, Taichi
Rattei, Thomas
Herndl, Gerhard J.
Sintes, Eva
author_facet Steiner, Paul A.
De Corte, Daniele
Geijo, Javier
Mena, Catalina
Yokokawa, Taichi
Rattei, Thomas
Herndl, Gerhard J.
Sintes, Eva
author_sort Steiner, Paul A.
collection PubMed
description Messenger RNA can provide valuable insights into the variability of metabolic processes of microorganisms. However, due to uncertainties that include the stability of RNA, its application for activity profiling of environmental samples is questionable. We explored different factors affecting the decay rate of transcripts of three marine bacterial isolates using qPCR and determined mRNA half‐life time of specific bacterial taxa and of functional genes by metatranscriptomics of a coastal environmental prokaryotic community. The half‐life time of transcripts from 11 genes from bacterial isolates ranged from 1 to 46 min. About 80% of the analysed transcripts exhibited half‐live times shorter than 10 min. Significant differences were found in the half‐life time between mRNA and rRNA. The half‐life time of mRNA obtained from a coastal metatranscriptome ranged from 9 to 400 min. The shortest half‐life times of the metatranscriptome corresponded to transcripts from the same clusters of orthologous groups (COGs) in all bacterial classes. The prevalence of short mRNA half‐life time in genes related to defence mechanisms and motility indicate a tight connection of RNA decay rate to environmental stressors. The short half‐life time of RNA and its high variability needs to be considered when assessing metatranscriptomes especially in environmental samples.
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spelling pubmed-73796142020-07-24 Highly variable mRNA half‐life time within marine bacterial taxa and functional genes Steiner, Paul A. De Corte, Daniele Geijo, Javier Mena, Catalina Yokokawa, Taichi Rattei, Thomas Herndl, Gerhard J. Sintes, Eva Environ Microbiol Research Articles Messenger RNA can provide valuable insights into the variability of metabolic processes of microorganisms. However, due to uncertainties that include the stability of RNA, its application for activity profiling of environmental samples is questionable. We explored different factors affecting the decay rate of transcripts of three marine bacterial isolates using qPCR and determined mRNA half‐life time of specific bacterial taxa and of functional genes by metatranscriptomics of a coastal environmental prokaryotic community. The half‐life time of transcripts from 11 genes from bacterial isolates ranged from 1 to 46 min. About 80% of the analysed transcripts exhibited half‐live times shorter than 10 min. Significant differences were found in the half‐life time between mRNA and rRNA. The half‐life time of mRNA obtained from a coastal metatranscriptome ranged from 9 to 400 min. The shortest half‐life times of the metatranscriptome corresponded to transcripts from the same clusters of orthologous groups (COGs) in all bacterial classes. The prevalence of short mRNA half‐life time in genes related to defence mechanisms and motility indicate a tight connection of RNA decay rate to environmental stressors. The short half‐life time of RNA and its high variability needs to be considered when assessing metatranscriptomes especially in environmental samples. John Wiley & Sons, Inc. 2019-07-25 2019-10 /pmc/articles/PMC7379614/ /pubmed/31298776 http://dx.doi.org/10.1111/1462-2920.14737 Text en © 2019 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Steiner, Paul A.
De Corte, Daniele
Geijo, Javier
Mena, Catalina
Yokokawa, Taichi
Rattei, Thomas
Herndl, Gerhard J.
Sintes, Eva
Highly variable mRNA half‐life time within marine bacterial taxa and functional genes
title Highly variable mRNA half‐life time within marine bacterial taxa and functional genes
title_full Highly variable mRNA half‐life time within marine bacterial taxa and functional genes
title_fullStr Highly variable mRNA half‐life time within marine bacterial taxa and functional genes
title_full_unstemmed Highly variable mRNA half‐life time within marine bacterial taxa and functional genes
title_short Highly variable mRNA half‐life time within marine bacterial taxa and functional genes
title_sort highly variable mrna half‐life time within marine bacterial taxa and functional genes
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7379614/
https://www.ncbi.nlm.nih.gov/pubmed/31298776
http://dx.doi.org/10.1111/1462-2920.14737
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