title: Linking RNA polymerase backtracking to genome instability in E. coli.
abstract: Frequent codirectional collisions between the replisome and RNA polymerase (RNAP) are inevitable because the rate of replication is much faster than that of transcription. Here we show that, in E. coli, the outcome of such collisions depends on the productive state of transcription elongation complexes (ECs). Codirectional collisions with backtracked (arrested) ECs lead to DNA double-strand breaks (DSBs), whereas head-on collisions do not. A mechanistic model is proposed to explain backtracking-mediated DSBs. We further show that bacteria employ various strategies to avoid replisome collisions with backtracked RNAP, the most general of which is translation that prevents RNAP backtracking. If translation is abrogated, DSBs are suppressed by elongation factors that either prevent backtracking or reactivate backtracked ECs. Finally, termination factors also contribute to genomic stability by removing arrested ECs. Our results establish RNAP backtracking as the intrinsic hazard to chromosomal integrity and implicate active ribosomes and other anti-backtracking mechanisms in genome maintenance.
authors.affiliation: Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA.
authors.forename: Dipak
authors.initials: D
authors.lastname: Dutta
authors.forename: Konstantin
authors.initials: K
authors.lastname: Shatalin
authors.forename: Vitaly
authors.initials: V
authors.lastname: Epshtein
authors.forename: Max E
authors.initials: ME
authors.lastname: Gottesman
authors.forename: Evgeny
authors.initials: E
authors.lastname: Nudler
mesh_terms: D004261:DNA Replication; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D042822:Genomic Instability; D012270:Ribosomes / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D012321:DNA-Directed RNA Polymerases