Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii

Journal of Bacteriology
Diego Rivera Gelsinger, Jocelyne DiRuggiero

Abstract

Haloarchaea in their natural environment are exposed to hypersalinity, intense solar radiation, and desiccation, all of which generate high levels of oxidative stress. Previous work has shown that haloarchaea are an order of magnitude more resistant to oxidative stress than most mesophilic organisms. Despite this resistance, the pathways haloarchaea use to respond to oxidative stress damage are similar to those of nonresistant organisms, suggesting that regulatory processes might be key to their robustness. Recently, small regulatory noncoding RNAs (sRNAs) were discovered in Archaea under a variety of environmental conditions. We report here the transcriptional landscape and functional roles of sRNAs in the regulation of the oxidative stress response of the model haloarchaeon Haloferax volcanii Thousands of sRNAs, both intergenic and antisense, were discovered using strand-specific sRNA sequencing (sRNA-seq), comprising 25 to 30% of the total transcriptome under no-challenge and oxidative stress conditions, respectively. We identified hundreds of differentially expressed sRNAs in response to hydrogen peroxide-induced oxidative stress in H. volcanii The targets of a group of antisense sRNAs decreased in expression when these sRN...Continue Reading

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Citations

Apr 10, 2019·Genes·João Paulo Pereira de AlmeidaTie Koide
Nov 7, 2019·ELife·Maria RojecTobias Warnecke
Mar 15, 2020·Molecular Genetics and Genomics : MGG·Gloria PayáJulia Esclapez
Mar 8, 2018·Genes·Diego Rivera Gelsinger, Jocelyne DiRuggiero
Nov 4, 2020·Antioxidants·Micaela Giani, Rosa María Martínez-Espinosa
Aug 23, 2019·Journal of Molecular Biology·Rylee K Hackley, Amy K Schmid
Sep 26, 2020·Biochemical and Biophysical Research Communications·James A Shapiro
Apr 18, 2019·Biochimie·Maxence LejarsEliane Hajnsdorf
Jun 1, 2021·Frontiers in Molecular Biosciences·Pascal MärkleAnita Marchfelder
Jun 10, 2021·Nature Communications·Phillip NußbaumSonja-Verena Albers
Oct 7, 2021·Nature Reviews. Genetics·Bradley W WrightPaul R Jaschke

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Datasets Mentioned

BETA
PRJNA407425
SRP117726

Methods Mentioned

BETA
RNA-seq
sRNA-seq
dRNA-seq
environmental stresses
deamination
electrophoresis

Software Mentioned

MEME
DAVID
hisat2
house
stringtie
DESeq2
fastqc
gffcompare
Rockhopper2
trim galore

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