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Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium

An increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression during environmental stress. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers of Salmonella stress survival. Generally thought to be 50–500 nucleotides in length and to occur in intergeni...

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Autores principales: Houserova, Dominika, Dahmer, Donovan J., Amin, Shivam V., King, Valeria M., Barnhill, Emmaline C., Zambrano, Mike E., Dean, Meghan A., Crucello, Aline, Aria, Kevin M., Spector, Michael P., Borchert, Glen M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8000849/
https://www.ncbi.nlm.nih.gov/pubmed/33809610
http://dx.doi.org/10.3390/antibiotics10030305
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author Houserova, Dominika
Dahmer, Donovan J.
Amin, Shivam V.
King, Valeria M.
Barnhill, Emmaline C.
Zambrano, Mike E.
Dean, Meghan A.
Crucello, Aline
Aria, Kevin M.
Spector, Michael P.
Borchert, Glen M.
author_facet Houserova, Dominika
Dahmer, Donovan J.
Amin, Shivam V.
King, Valeria M.
Barnhill, Emmaline C.
Zambrano, Mike E.
Dean, Meghan A.
Crucello, Aline
Aria, Kevin M.
Spector, Michael P.
Borchert, Glen M.
author_sort Houserova, Dominika
collection PubMed
description An increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression during environmental stress. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers of Salmonella stress survival. Generally thought to be 50–500 nucleotides in length and to occur in intergenic regions, sRNAs typically regulate protein expression through base pairing with mRNA targets. In this work, through employing a refined definition of sRNAs allowing for shorter sequences and sRNA loci to overlap with annotated protein-coding gene loci, we have identified 475 previously unannotated sRNAs that are significantly differentially expressed during carbon starvation (C-starvation). Northern blotting and quantitative RT-PCRs confirm the expressions and identities of several of these novel sRNAs, and our computational analyses find the majority to be highly conserved and structurally related to known sRNAs. Importantly, we show that deletion of one of the sRNAs dynamically expressed during C-starvation, sRNA4130247, significantly impairs the Salmonella C-starvation response (CSR), confirming its involvement in the Salmonella CSR. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs in Salmonella, experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and more than doubles the Salmonella enterica sRNAs described to date.
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spelling pubmed-80008492021-03-28 Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium Houserova, Dominika Dahmer, Donovan J. Amin, Shivam V. King, Valeria M. Barnhill, Emmaline C. Zambrano, Mike E. Dean, Meghan A. Crucello, Aline Aria, Kevin M. Spector, Michael P. Borchert, Glen M. Antibiotics (Basel) Article An increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression during environmental stress. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers of Salmonella stress survival. Generally thought to be 50–500 nucleotides in length and to occur in intergenic regions, sRNAs typically regulate protein expression through base pairing with mRNA targets. In this work, through employing a refined definition of sRNAs allowing for shorter sequences and sRNA loci to overlap with annotated protein-coding gene loci, we have identified 475 previously unannotated sRNAs that are significantly differentially expressed during carbon starvation (C-starvation). Northern blotting and quantitative RT-PCRs confirm the expressions and identities of several of these novel sRNAs, and our computational analyses find the majority to be highly conserved and structurally related to known sRNAs. Importantly, we show that deletion of one of the sRNAs dynamically expressed during C-starvation, sRNA4130247, significantly impairs the Salmonella C-starvation response (CSR), confirming its involvement in the Salmonella CSR. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs in Salmonella, experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and more than doubles the Salmonella enterica sRNAs described to date. MDPI 2021-03-16 /pmc/articles/PMC8000849/ /pubmed/33809610 http://dx.doi.org/10.3390/antibiotics10030305 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Article
Houserova, Dominika
Dahmer, Donovan J.
Amin, Shivam V.
King, Valeria M.
Barnhill, Emmaline C.
Zambrano, Mike E.
Dean, Meghan A.
Crucello, Aline
Aria, Kevin M.
Spector, Michael P.
Borchert, Glen M.
Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium
title Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium
title_full Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium
title_fullStr Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium
title_full_unstemmed Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium
title_short Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium
title_sort characterization of 475 novel, putative small rnas (srnas) in carbon-starved salmonella enterica serovar typhimurium
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8000849/
https://www.ncbi.nlm.nih.gov/pubmed/33809610
http://dx.doi.org/10.3390/antibiotics10030305
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