title: Stopped in its tracks: the RNA polymerase molecular motor as a robust sensor of DNA damage.
abstract: DNA repair is often a complex, multi-component, multi-step process; this makes detailed kinetic analysis of the different steps of repair a challenging task using standard biochemical methods. At the same time, single-molecule methods are well-suited for extracting kinetic information despite time-averaging due to diffusion of biochemical components and stochasticity of chemical reaction steps. Here we discuss recent experiments using DNA nanomanipulation in a magnetic trap to study the initiation of transcription-coupled repair in a model bacterial system comprising the canonical Escherichia coli RNA polymerase and the Mfd translocase which specifically binds to it. These experiments provide kinetic insight into the reaction process, helping to explain how Mfd discriminates between transcribing RNAP and stalled RNAP. They also identify a reliably long-lived intermediate containing Mfd translocase and, potentially, RNA polymerase. This intermediate presumably serves as a platform for assembly of downstream repair components UvrAB(C).
authors.affiliation: Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
authors.forename: K
authors.initials: K
authors.lastname: Howan
authors.affiliation: Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
authors.forename: J
authors.initials: J
authors.lastname: Monnet
authors.affiliation: Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
authors.forename: J
authors.initials: J
authors.lastname: Fan
authors.affiliation: Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France. Electronic address: trs9898@hotmail.com.
authors.forename: T R
authors.initials: TR
authors.lastname: Strick
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004249:DNA Damage; D004260:DNA Repair; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism*; D004706:Endodeoxyribonucleases / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000737:chemistry / Q000201:enzymology / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D020409:Molecular Motor Proteins / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D020409:Molecular Motor Proteins; D014157:Transcription Factors; C072103:transcription repair coupling factor protein, Bacteria; D004247:DNA; D012321:DNA-Directed RNA Polymerases; D004706:Endodeoxyribonucleases; C036385:endodeoxyribonuclease uvrABC
keywords: Helicase; Magnetic trapping; Repair; Single-molecule; Transcription