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

Publication ,  Journal Article
Huang, L; Deighan, P; Jin, J; Li, Y; Cheung, H-C; Lee, E; Mo, SS; Hoover, H; Abubucker, S; Finkel, N; McReynolds, L; Hochschild, A; Lieberman, J
Published in: mBio
June 2020

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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Published In

mBio

DOI

EISSN

2150-7511

ISSN

2150-7511

Publication Date

June 2020

Volume

11

Issue

3

Start / End Page

e00485 / e00420

Related Subject Headings

  • Tombusvirus
  • Ribonuclease III
  • RNA, Double-Stranded
  • RNA, Antisense
  • RNA Stability
  • Genome, Bacterial
  • Gene Expression Regulation, Bacterial
  • Escherichia coli
  • 3207 Medical microbiology
  • 3107 Microbiology
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Huang, L., Deighan, P., Jin, J., Li, Y., Cheung, H.-C., Lee, E., … Lieberman, J. (2020). Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli. MBio, 11(3), e00485–e00420. https://doi.org/10.1128/mbio.00485-20
Huang, Linfeng, Padraig Deighan, Jingmin Jin, Yingxue Li, Hung-Chi Cheung, Elaine Lee, Shirley S. Mo, et al. “Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli.MBio 11, no. 3 (June 2020): e00485–e00420. https://doi.org/10.1128/mbio.00485-20.
Huang L, Deighan P, Jin J, Li Y, Cheung H-C, Lee E, et al. Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli. mBio. 2020 Jun;11(3):e00485–e00420.
Huang, Linfeng, et al. “Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli.MBio, vol. 11, no. 3, June 2020, pp. e00485–e00420. Epmc, doi:10.1128/mbio.00485-20.
Huang L, Deighan P, Jin J, Li Y, Cheung H-C, Lee E, Mo SS, Hoover H, Abubucker S, Finkel N, McReynolds L, Hochschild A, Lieberman J. Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli. mBio. 2020 Jun;11(3):e00485–e00420.

Published In

mBio

DOI

EISSN

2150-7511

ISSN

2150-7511

Publication Date

June 2020

Volume

11

Issue

3

Start / End Page

e00485 / e00420

Related Subject Headings

  • Tombusvirus
  • Ribonuclease III
  • RNA, Double-Stranded
  • RNA, Antisense
  • RNA Stability
  • Genome, Bacterial
  • Gene Expression Regulation, Bacterial
  • Escherichia coli
  • 3207 Medical microbiology
  • 3107 Microbiology