RT Journal Article
SR Electronic
T1 <em>Tombusvirus</em> p19 captures RNase III-cleaved double-stranded RNAs formed by overlapping sense and antisense transcripts in <em>E. coli</em>
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 510842
DO 10.1101/510842
A1 Linfeng Huang
A1 Padraig Deighan
A1 Jingmin Jin
A1 Yingxue Li
A1 Elaine Lee
A1 Shirley S. Mo
A1 Heather Hoover
A1 Sahar Abubucker
A1 Nancy Finkel
A1 Larry McReynolds
A1 Ann Hochschild
A1 Judy Lieberman
YR 2019
UL http://biorxiv.org/content/early/2019/01/04/510842.abstract
AB Antisense transcription is widespread in bacteria. By base pairing with overlapping sense RNAs, antisense RNAs (asRNA) can form long double-stranded RNAs (dsRNA), which are cleaved by RNase III, a dsRNA endoribonuclease. Ectopic expression of plant tombusvirus p19 in E. coli stabilizes ~21 bp dsRNA RNase III decay intermediates, which enabled us to characterize otherwise highly unstable asRNA by deep sequencing of p19-captured dsRNA and total RNA. dsRNA formed at most bacterial genes in the bacterial chromosome and in a plasmid. The most abundant dsRNA clusters were mostly formed by divergent transcription of sense and antisense transcripts overlapping at their 5’-ends. The most abundant clusters included small RNAs, such as ryeA/ryeB, 4 toxin-antitoxin genes, and 3 tRNAs, and some longer coding genes, including rsd and cspD. The sense and antisense transcripts in abundant dsRNA clusters were more plentiful and had longer half-lives in RNase III mutant strains, suggesting that formation of dsRNAs promoted RNA decay at these loci. However, widespread changes in protein levels did not occur in RNase III mutant bacteria. Nonetheless, some proteins involved in antioxidant responses and glycolysis changed reproducibly. dsRNAs accumulated in bacterial cells lacking RNase III, increasing in stationary phase, and correlated with increased cell death in RNase III mutant bacteria in late stationary phase. The physiological importance of widespread antisense transcription in bacteria remains unclear but it may become important during environmental stress. Ectopic expression of p19 is a sensitive method for identifying antisense transcripts and RNase III cleavage sites in bacteria.