Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions

Small regulatory RNAs play a major role in bacterial gene regulation by binding their target mRNAs, which mostly influences the stability or translation of the target. Expression levels of sRNAs are often regulated by their own promoters, but recent reports have highlighted the presence and importan...

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Autores principales:	Daniel-Timon Spanka, Gabriele Klug
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	UTR-derived sRNA sRNA processing and maturation ribonucleases RNase E <i>Rhodobacter sphaeroides</i> Alphaproteobacteria Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/008dfdc8df3844ce98446c5302cd59b4
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id	oai:doaj.org-article:008dfdc8df3844ce98446c5302cd59b4
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spelling	oai:doaj.org-article:008dfdc8df3844ce98446c5302cd59b42021-11-25T17:54:49ZMaturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions10.3390/ijms2222122601422-00671661-6596https://doaj.org/article/008dfdc8df3844ce98446c5302cd59b42021-11-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/22/12260https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067Small regulatory RNAs play a major role in bacterial gene regulation by binding their target mRNAs, which mostly influences the stability or translation of the target. Expression levels of sRNAs are often regulated by their own promoters, but recent reports have highlighted the presence and importance of sRNAs that are derived from mRNA 3′ untranslated regions (UTRs). In this study, we investigated the maturation of 5′ and 3′ UTR-derived sRNAs on a global scale in the facultative phototrophic alphaproteobacterium <i>Rhodobacter sphaeroides</i>. Including some already known UTR-derived sRNAs like UpsM or CcsR1-4, 14 sRNAs are predicted to be located in 5 UTRs and 16 in 3′ UTRs. The involvement of different ribonucleases during maturation was predicted by a differential RNA 5′/3′ end analysis based on RNA next generation sequencing (NGS) data from the respective deletion strains. The results were validated in vivo and underline the importance of polynucleotide phosphorylase (PNPase) and ribonuclease E (RNase E) during processing and maturation. The abundances of some UTR-derived sRNAs changed when cultures were exposed to external stress conditions, such as oxidative stress and also during different growth phases. Promoter fusions revealed that this effect cannot be solely attributed to an altered transcription rate. Moreover, the RNase E dependent cleavage of several UTR-derived sRNAs varied significantly during the early stationary phase and under iron depletion conditions. We conclude that an alteration of ribonucleolytic processing influences the levels of UTR-derived sRNAs, and may thus indirectly affect their mRNA targets.Daniel-Timon SpankaGabriele KlugMDPI AGarticleUTR-derived sRNAsRNA processing and maturationribonucleasesRNase E<i>Rhodobacter sphaeroides</i>AlphaproteobacteriaBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 12260, p 12260 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	UTR-derived sRNA sRNA processing and maturation ribonucleases RNase E <i>Rhodobacter sphaeroides</i> Alphaproteobacteria Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	UTR-derived sRNA sRNA processing and maturation ribonucleases RNase E <i>Rhodobacter sphaeroides</i> Alphaproteobacteria Biology (General) QH301-705.5 Chemistry QD1-999 Daniel-Timon Spanka Gabriele Klug Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions
description	Small regulatory RNAs play a major role in bacterial gene regulation by binding their target mRNAs, which mostly influences the stability or translation of the target. Expression levels of sRNAs are often regulated by their own promoters, but recent reports have highlighted the presence and importance of sRNAs that are derived from mRNA 3′ untranslated regions (UTRs). In this study, we investigated the maturation of 5′ and 3′ UTR-derived sRNAs on a global scale in the facultative phototrophic alphaproteobacterium <i>Rhodobacter sphaeroides</i>. Including some already known UTR-derived sRNAs like UpsM or CcsR1-4, 14 sRNAs are predicted to be located in 5 UTRs and 16 in 3′ UTRs. The involvement of different ribonucleases during maturation was predicted by a differential RNA 5′/3′ end analysis based on RNA next generation sequencing (NGS) data from the respective deletion strains. The results were validated in vivo and underline the importance of polynucleotide phosphorylase (PNPase) and ribonuclease E (RNase E) during processing and maturation. The abundances of some UTR-derived sRNAs changed when cultures were exposed to external stress conditions, such as oxidative stress and also during different growth phases. Promoter fusions revealed that this effect cannot be solely attributed to an altered transcription rate. Moreover, the RNase E dependent cleavage of several UTR-derived sRNAs varied significantly during the early stationary phase and under iron depletion conditions. We conclude that an alteration of ribonucleolytic processing influences the levels of UTR-derived sRNAs, and may thus indirectly affect their mRNA targets.
format	article
author	Daniel-Timon Spanka Gabriele Klug
author_facet	Daniel-Timon Spanka Gabriele Klug
author_sort	Daniel-Timon Spanka
title	Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions
title_short	Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions
title_full	Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions
title_fullStr	Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions
title_full_unstemmed	Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions
title_sort	maturation of utr-derived srnas is modulated during adaptation to different growth conditions
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/008dfdc8df3844ce98446c5302cd59b4
work_keys_str_mv	AT danieltimonspanka maturationofutrderivedsrnasismodulatedduringadaptationtodifferentgrowthconditions AT gabrieleklug maturationofutrderivedsrnasismodulatedduringadaptationtodifferentgrowthconditions
_version_	1718411841128890368

Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions

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