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

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

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Author(s)

  • Padraig Deighan
  • Jingmin Jin
  • Elaine Lee
  • Shirley S. Mo
  • Heather Hoover
  • Sahar Abubucker
  • Nancy Finkel
  • Larry McReynolds
  • Ann Hochschild
  • Judy Lieberman

Detail(s)

Original languageEnglish
Article numbere00485-20
Journal / PublicationmBio
Volume11
Issue number3
Publication statusPublished - May 2020

Link(s)

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 as-RNA 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.

Research Area(s)

  • Antisense RNA, RNase III, Small RNA

Citation Format(s)

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.

In: mBio, Vol. 11, No. 3, e00485-20, 05.2020.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

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