Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community

ABSTRACT Regulatory small RNAs (sRNAs) play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been extensively studied in model organisms, but very little is known about the dynamics of sRNA synthesis and their roles in the natural environmen...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Diego R. Gelsinger, Gherman Uritskiy, Rahul Reddy, Adam Munn, Katie Farney, Jocelyne DiRuggiero
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	RNA extremophiles gene regulation metagenomics metatranscriptomics microbial communities Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/454f692b70ab473c98167d3d1f931d93
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:454f692b70ab473c98167d3d1f931d93
record_format	dspace
spelling	oai:doaj.org-article:454f692b70ab473c98167d3d1f931d932021-12-02T19:46:19ZRegulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community10.1128/mSystems.00584-192379-5077https://doaj.org/article/454f692b70ab473c98167d3d1f931d932020-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00584-19https://doaj.org/toc/2379-5077ABSTRACT Regulatory small RNAs (sRNAs) play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been extensively studied in model organisms, but very little is known about the dynamics of sRNA synthesis and their roles in the natural environment. In this study, we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs expressed in an extremophilic microbial community inhabiting halite nodules (salt rocks) in the Atacama Desert. For this, we built SnapT, a new sRNA annotation pipeline that can be applied to any microbial community. We found asRNAs with expression levels negatively correlated with that of their overlapping putative target and itsRNAs that were conserved and significantly differentially expressed between 2 sampling time points. We demonstrated that we could perform target prediction and correlate expression levels between sRNAs and predicted target mRNAs at the community level. Functions of putative mRNA targets reflected the environmental challenges members of the halite communities were subjected to, including osmotic adjustments to a major rain event and competition for nutrients. IMPORTANCE Microorganisms in the natural world are found in communities, communicating and interacting with each other; therefore, it is essential that microbial regulatory mechanisms, such as gene regulation affected by small RNAs (sRNAs), be investigated at the community level. This work demonstrates that metatranscriptomic field experiments can link environmental variation with changes in RNA pools and have the potential to provide new insights into environmental sensing and responses in natural microbial communities through noncoding RNA-mediated gene regulation.Diego R. GelsingerGherman UritskiyRahul ReddyAdam MunnKatie FarneyJocelyne DiRuggieroAmerican Society for MicrobiologyarticleRNAextremophilesgene regulationmetagenomicsmetatranscriptomicsmicrobial communitiesMicrobiologyQR1-502ENmSystems, Vol 5, Iss 1 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	RNA extremophiles gene regulation metagenomics metatranscriptomics microbial communities Microbiology QR1-502
spellingShingle	RNA extremophiles gene regulation metagenomics metatranscriptomics microbial communities Microbiology QR1-502 Diego R. Gelsinger Gherman Uritskiy Rahul Reddy Adam Munn Katie Farney Jocelyne DiRuggiero Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community
description	ABSTRACT Regulatory small RNAs (sRNAs) play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been extensively studied in model organisms, but very little is known about the dynamics of sRNA synthesis and their roles in the natural environment. In this study, we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs expressed in an extremophilic microbial community inhabiting halite nodules (salt rocks) in the Atacama Desert. For this, we built SnapT, a new sRNA annotation pipeline that can be applied to any microbial community. We found asRNAs with expression levels negatively correlated with that of their overlapping putative target and itsRNAs that were conserved and significantly differentially expressed between 2 sampling time points. We demonstrated that we could perform target prediction and correlate expression levels between sRNAs and predicted target mRNAs at the community level. Functions of putative mRNA targets reflected the environmental challenges members of the halite communities were subjected to, including osmotic adjustments to a major rain event and competition for nutrients. IMPORTANCE Microorganisms in the natural world are found in communities, communicating and interacting with each other; therefore, it is essential that microbial regulatory mechanisms, such as gene regulation affected by small RNAs (sRNAs), be investigated at the community level. This work demonstrates that metatranscriptomic field experiments can link environmental variation with changes in RNA pools and have the potential to provide new insights into environmental sensing and responses in natural microbial communities through noncoding RNA-mediated gene regulation.
format	article
author	Diego R. Gelsinger Gherman Uritskiy Rahul Reddy Adam Munn Katie Farney Jocelyne DiRuggiero
author_facet	Diego R. Gelsinger Gherman Uritskiy Rahul Reddy Adam Munn Katie Farney Jocelyne DiRuggiero
author_sort	Diego R. Gelsinger
title	Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community
title_short	Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community
title_full	Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community
title_fullStr	Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community
title_full_unstemmed	Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community
title_sort	regulatory noncoding small rnas are diverse and abundant in an extremophilic microbial community
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/454f692b70ab473c98167d3d1f931d93
work_keys_str_mv	AT diegorgelsinger regulatorynoncodingsmallrnasarediverseandabundantinanextremophilicmicrobialcommunity AT ghermanuritskiy regulatorynoncodingsmallrnasarediverseandabundantinanextremophilicmicrobialcommunity AT rahulreddy regulatorynoncodingsmallrnasarediverseandabundantinanextremophilicmicrobialcommunity AT adammunn regulatorynoncodingsmallrnasarediverseandabundantinanextremophilicmicrobialcommunity AT katiefarney regulatorynoncodingsmallrnasarediverseandabundantinanextremophilicmicrobialcommunity AT jocelynediruggiero regulatorynoncodingsmallrnasarediverseandabundantinanextremophilicmicrobialcommunity
_version_	1718376022255075328

Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community

Ejemplares similares