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

Journal Article (Journal 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.

Full Text

Duke Authors

Cited Authors

  • 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 Date

  • June 2020

Published In

Volume / Issue

  • 11 / 3

Start / End Page

  • e00485 - e00420

PubMed ID

  • 32518184

Pubmed Central ID

  • PMC7373196

Electronic International Standard Serial Number (EISSN)

  • 2150-7511

International Standard Serial Number (ISSN)

  • 2150-7511

Digital Object Identifier (DOI)

  • 10.1128/mbio.00485-20

Language

  • eng