title: Rho-dependent transcription termination is essential to prevent excessive genome-wide R-loops in Escherichia coli.
abstract: Two pathways of transcription termination, factor-independent and -dependent, exist in bacteria. The latter pathway operates on nascent transcripts that are not simultaneously translated and requires factors Rho, NusG, and NusA, each of which is essential for viability of WT Escherichia coli. NusG and NusA are also involved in antitermination of transcription at the ribosomal RNA operons, as well as in regulating the rates of transcription elongation of all genes. We have used a bisulfite-sensitivity assay to demonstrate genome-wide increase in the occurrence of RNA-DNA hybrids (R-loops), including from antisense and read-through transcripts, in a nusG missense mutant defective for Rho-dependent termination. Lethality associated with complete deficiency of Rho and NusG (but not NusA) was rescued by ectopic expression of an R-loop-helicase UvsW, especially so on defined growth media. Our results suggest that factor-dependent transcription termination subserves a surveillance function to prevent translation-uncoupled transcription from generating R-loops, which would block replication fork progression and therefore be lethal, and that NusA performs additional essential functions as well in E. coli. Prevention of R-loop-mediated transcription-replication conflicts by cotranscriptional protein engagement of nascent RNA is emerging as a unifying theme among both prokaryotes and eukaryotes.
authors.affiliation: Laboratory of Bacterial Genetics,  Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 001,  India.
authors.forename: J Krishna
authors.initials: JK
authors.lastname: Leela
authors.forename: Aisha H
authors.initials: AH
authors.lastname: Syeda
authors.forename: K
authors.initials: K
authors.lastname: Anupama
authors.forename: J
authors.initials: J
authors.lastname: Gowrishankar
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004265:DNA Helicases / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010445:Peptide Elongation Factors / Q000235:genetics; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012234:Rho Factor / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D013447:Sulfites; D014157:Transcription Factors / Q000235:genetics; D061806:Transcription Termination, Genetic / Q000502:physiology*; D035602:Transcriptional Elongation Factors; D014764:Viral Proteins / Q000235:genetics
chemical_list: D029968:Escherichia coli Proteins; C070291:NusG protein, E coli; D010445:Peptide Elongation Factors; D012234:Rho Factor; D013447:Sulfites; D014157:Transcription Factors; D035602:Transcriptional Elongation Factors; D014764:Viral Proteins; C068727:nusA protein, E coli; D012313:RNA; D004247:DNA; D004265:DNA Helicases; C107414:UvsW protein, Bacteriophage T4; C009279:sodium bisulfite