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 stress survival. Generally thought to be 50-500 nucleotides in length and to occur in intergenic regions,...

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Published in:	Antibiotics (Basel) 2021-03, Vol.10 (3), p.305
Main Authors:	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
Format:	Article
Language:	eng
Subjects:	Annotations Carbon carbon-starvation Computer applications E coli Environmental stress Gene expression Gene loci Genomes Loci noncoding RNA Northern blotting Nucleotides Proteins Salmonella Salmonella enterica sRNA Starvation starvation-stress Survival transcriptomics
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Summary:	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 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 C-starvation response (CSR), confirming its involvement in the CSR. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs in , experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and more than doubles the sRNAs described to date.
ISSN:	2079-6382 2079-6382