<italic toggle="yes">Tombusvirus</italic> p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in <named-content content-type="genus-species">Escherichia coli</named-content>

ABSTRACT Antisense transcription is widespread in bacteria. By base pairing with overlapping sense RNAs, antisense RNAs (asRNA) can form double-stranded RNAs (dsRNA), which are cleaved by RNase III, a dsRNA endoribonuclease. The ectopic expression of plant Tombusvirus p19 in Escherichia coli stabili...

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Autores principales:	Linfeng Huang, Padraig Deighan, Jingmin Jin, Yingxue Li, Hung-Chi Cheung, Elaine Lee, Shirley S. Mo, Heather Hoover, Sahar Abubucker, Nancy Finkel, Larry McReynolds, Ann Hochschild, Judy Lieberman
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	antisense RNA RNase III small RNA Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/ed7fba3bb00d4c5eb92527be3d3e55a5
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spelling	oai:doaj.org-article:ed7fba3bb00d4c5eb92527be3d3e55a52021-11-15T15:56:47Z<italic toggle="yes">Tombusvirus</italic> p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in <named-content content-type="genus-species">Escherichia coli</named-content>10.1128/mBio.00485-202150-7511https://doaj.org/article/ed7fba3bb00d4c5eb92527be3d3e55a52020-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00485-20https://doaj.org/toc/2150-7511ABSTRACT Antisense transcription is widespread in bacteria. By base pairing with overlapping sense RNAs, antisense RNAs (asRNA) can form double-stranded RNAs (dsRNA), which are cleaved by RNase III, a dsRNA endoribonuclease. The ectopic expression of plant Tombusvirus p19 in Escherichia coli stabilizes ∼21-nucleotide (nt) dsRNA RNase III decay intermediates, which enabled us to characterize otherwise highly unstable asRNA by deep sequencing of p19-captured dsRNA. RNase III-produced small dsRNA were formed at most bacterial genes in the bacterial genome and in a plasmid. We classified the types of asRNA in genomic clusters producing the most abundant p19-captured dsRNA and confirmed RNase III regulation of asRNA and sense RNA decay at three type I toxin-antitoxin loci and at a coding gene, rsd. Furthermore, we provide potential evidence for the RNase III-dependent regulation of CspD protein by asRNA. The analysis of p19-captured dsRNA revealed an RNase III sequence preference for AU-rich sequences 3 nucleotides on either side of the cleavage sites and for GC-rich sequences in the 2-nt overhangs. Unexpectedly, GC-rich sequences were enriched in the middle section of p19-captured dsRNA, suggesting some unexpected sequence bias in p19 protein binding. Nonetheless, the ectopic expression of p19 is a sensitive method for identifying antisense transcripts and RNase III cleavage sites in dsRNA formed by overlapping sense and antisense transcripts in bacteria.Linfeng HuangPadraig DeighanJingmin JinYingxue LiHung-Chi CheungElaine LeeShirley S. MoHeather HooverSahar AbubuckerNancy FinkelLarry McReynoldsAnn HochschildJudy LiebermanAmerican Society for Microbiologyarticleantisense RNARNase IIIsmall RNAMicrobiologyQR1-502ENmBio, Vol 11, Iss 3 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	antisense RNA RNase III small RNA Microbiology QR1-502
spellingShingle	antisense RNA RNase III small RNA Microbiology QR1-502 Linfeng Huang Padraig Deighan Jingmin Jin Yingxue Li Hung-Chi Cheung Elaine Lee Shirley S. Mo Heather Hoover Sahar Abubucker Nancy Finkel Larry McReynolds Ann Hochschild Judy Lieberman <italic toggle="yes">Tombusvirus</italic> p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in <named-content content-type="genus-species">Escherichia coli</named-content>
description	ABSTRACT Antisense transcription is widespread in bacteria. By base pairing with overlapping sense RNAs, antisense RNAs (asRNA) can form double-stranded RNAs (dsRNA), which are cleaved by RNase III, a dsRNA endoribonuclease. The ectopic expression of plant Tombusvirus p19 in Escherichia coli stabilizes ∼21-nucleotide (nt) dsRNA RNase III decay intermediates, which enabled us to characterize otherwise highly unstable asRNA by deep sequencing of p19-captured dsRNA. RNase III-produced small dsRNA were formed at most bacterial genes in the bacterial genome and in a plasmid. We classified the types of asRNA in genomic clusters producing the most abundant p19-captured dsRNA and confirmed RNase III regulation of asRNA and sense RNA decay at three type I toxin-antitoxin loci and at a coding gene, rsd. Furthermore, we provide potential evidence for the RNase III-dependent regulation of CspD protein by asRNA. The analysis of p19-captured dsRNA revealed an RNase III sequence preference for AU-rich sequences 3 nucleotides on either side of the cleavage sites and for GC-rich sequences in the 2-nt overhangs. Unexpectedly, GC-rich sequences were enriched in the middle section of p19-captured dsRNA, suggesting some unexpected sequence bias in p19 protein binding. Nonetheless, the ectopic expression of p19 is a sensitive method for identifying antisense transcripts and RNase III cleavage sites in dsRNA formed by overlapping sense and antisense transcripts in bacteria.
format	article
author	Linfeng Huang Padraig Deighan Jingmin Jin Yingxue Li Hung-Chi Cheung Elaine Lee Shirley S. Mo Heather Hoover Sahar Abubucker Nancy Finkel Larry McReynolds Ann Hochschild Judy Lieberman
author_facet	Linfeng Huang Padraig Deighan Jingmin Jin Yingxue Li Hung-Chi Cheung Elaine Lee Shirley S. Mo Heather Hoover Sahar Abubucker Nancy Finkel Larry McReynolds Ann Hochschild Judy Lieberman
author_sort	Linfeng Huang
title	<italic toggle="yes">Tombusvirus</italic> p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in <named-content content-type="genus-species">Escherichia coli</named-content>
title_short	<italic toggle="yes">Tombusvirus</italic> p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in <named-content content-type="genus-species">Escherichia coli</named-content>
title_full	<italic toggle="yes">Tombusvirus</italic> p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in <named-content content-type="genus-species">Escherichia coli</named-content>
title_fullStr	<italic toggle="yes">Tombusvirus</italic> p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in <named-content content-type="genus-species">Escherichia coli</named-content>
title_full_unstemmed	<italic toggle="yes">Tombusvirus</italic> p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in <named-content content-type="genus-species">Escherichia coli</named-content>
title_sort	<italic toggle="yes">tombusvirus</italic> p19 captures rnase iii-cleaved double-stranded rnas formed by overlapping sense and antisense transcripts in <named-content content-type="genus-species">escherichia coli</named-content>
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/ed7fba3bb00d4c5eb92527be3d3e55a5
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<italic toggle="yes">Tombusvirus</italic> p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in <named-content content-type="genus-species">Escherichia coli</named-content>

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