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Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli

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-n...

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Autores principales: Huang, Linfeng, Deighan, Padraig, Jin, Jingmin, Li, Yingxue, Cheung, Hung-Chi, Lee, Elaine, Mo, Shirley S., Hoover, Heather, Abubucker, Sahar, Finkel, Nancy, McReynolds, Larry, Hochschild, Ann, Lieberman, Judy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7373196/
https://www.ncbi.nlm.nih.gov/pubmed/32518184
http://dx.doi.org/10.1128/mBio.00485-20
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author Huang, Linfeng
Deighan, Padraig
Jin, Jingmin
Li, Yingxue
Cheung, Hung-Chi
Lee, Elaine
Mo, Shirley S.
Hoover, Heather
Abubucker, Sahar
Finkel, Nancy
McReynolds, Larry
Hochschild, Ann
Lieberman, Judy
author_facet Huang, Linfeng
Deighan, Padraig
Jin, Jingmin
Li, Yingxue
Cheung, Hung-Chi
Lee, Elaine
Mo, Shirley S.
Hoover, Heather
Abubucker, Sahar
Finkel, Nancy
McReynolds, Larry
Hochschild, Ann
Lieberman, Judy
author_sort Huang, Linfeng
collection PubMed
description 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.
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spelling pubmed-73731962020-07-24 Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli Huang, Linfeng Deighan, Padraig Jin, Jingmin Li, Yingxue Cheung, Hung-Chi Lee, Elaine Mo, Shirley S. Hoover, Heather Abubucker, Sahar Finkel, Nancy McReynolds, Larry Hochschild, Ann Lieberman, Judy mBio Research Article 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. American Society for Microbiology 2020-06-09 /pmc/articles/PMC7373196/ /pubmed/32518184 http://dx.doi.org/10.1128/mBio.00485-20 Text en Copyright © 2020 Huang et al. https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research Article
Huang, Linfeng
Deighan, Padraig
Jin, Jingmin
Li, Yingxue
Cheung, Hung-Chi
Lee, Elaine
Mo, Shirley S.
Hoover, Heather
Abubucker, Sahar
Finkel, Nancy
McReynolds, Larry
Hochschild, Ann
Lieberman, Judy
Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli
title Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli
title_full Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli
title_fullStr Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli
title_full_unstemmed Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli
title_short Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli
title_sort tombusvirus p19 captures rnase iii-cleaved double-stranded rnas formed by overlapping sense and antisense transcripts in escherichia coli
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7373196/
https://www.ncbi.nlm.nih.gov/pubmed/32518184
http://dx.doi.org/10.1128/mBio.00485-20
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