Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli

Nucleic Acids Research
Nalini RaghunathanJ Gowrishankar

Abstract

Transcription termination by Rho is essential for viability in various bacteria, including some major pathogens. Since Rho acts by targeting nascent RNAs that are not simultaneously translated, it also regulates antisense transcription. Here we show that RNase H-deficient mutants of Escherichia coli exhibit heightened sensitivity to the Rho inhibitor bicyclomycin, and that Rho deficiency provokes increased formation of RNA-DNA hybrids (R-loops) which is ameliorated by expression of the phage T4-derived R-loop helicase UvsW. We also provide evidence that in Rho-deficient cells, R-loop formation blocks subsequent rounds of antisense transcription at more than 500 chromosomal loci. Hence these antisense transcripts, which can extend beyond 10 kb in their length, are only detected when Rho function is absent or compromised and the UvsW helicase is concurrently expressed. Thus the potential for antisense transcription in bacteria is much greater than hitherto recognized; and the cells are able to retain viability even when nearly one-quarter of their total non-rRNA abundance is accounted for by antisense transcripts, provided that R-loop formation from them is curtailed.

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Citations

Aug 30, 2019·Critical Reviews in Biochemistry and Molecular Biology·David H Bechhofer, Murray P Deutscher
Apr 9, 2019·Nucleic Acids Research·Nalini RaghunathanJayaraman Gowrishankar
Dec 6, 2019·Nucleic Acids Research·Nida Ali, Jayaraman Gowrishankar
Jun 23, 2018·Nucleic Acids Research·Cédric NadirasMarc Boudvillain
Nov 15, 2020·Research in Microbiology·Suraj JoshiBhakti Basu
Jan 15, 2020·Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms·Maxence Lejars, Eliane Hajnsdorf
Apr 18, 2019·Biochimie·Maxence LejarsEliane Hajnsdorf
Jul 14, 2018·Microbiology Spectrum·Jens Georg, Wolfgang R Hess
Jan 10, 2019·Biochemistry·Cédric NadirasMarc Boudvillain
Oct 28, 2021·Transcription·Zhitai HaoEvgeny Nudler

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Datasets Mentioned

BETA
data
GSE103937

Methods Mentioned

BETA
RNA-Seq
electrophoresis
in vitro transcription

Software Mentioned

Contig
Seq
Net

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