title: The transcription inhibitor lipiarmycin blocks DNA fitting into the RNA polymerase catalytic site.
abstract: Worldwide spreading of drug-resistant pathogens makes mechanistic understanding of antibiotic action an urgent task. The macrocyclic antibiotic lipiarmycin (Lpm), which is under development for clinical use, inhibits bacterial RNA polymerase (RNAP) by an unknown mechanism. Using genetic and biochemical approaches, we show that Lpm targets the sigma(70) subunit region 3.2 and the RNAP beta' subunit switch-2 element, which controls the clamping of promoter DNA in the RNAP active-site cleft. Lpm abolishes isomerization of the 'closed'-promoter complex to the transcriptionally competent 'open' complex and blocks sigma(70)-stimulated RNA synthesis on promoter-less DNA templates. Lpm activity decreases when the template DNA strand is stabilized at the active site through the interaction of RNAP with the nascent RNA chain. Template DNA-strand fitting into the RNAP active-site cleft directed by the beta' subunit switch-2 element and the sigma(70) subunit region 3.2 is essential for promoter melting and for de novo initiation of RNA synthesis, and our results suggest that Lpm impedes this process.
authors.affiliation: Université de Montpellier 1, Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS, UMR 5236, CPBS, Montpellier, France.
authors.forename: Audrey
authors.initials: A
authors.lastname: Tupin
authors.forename: Maxime
authors.initials: M
authors.lastname: Gualtieri
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Leonetti
authors.forename: Konstantin
authors.initials: K
authors.lastname: Brodolin
mesh_terms: D000617:Aminoglycosides / Q000737:chemistry* / Q000494:pharmacology; D001483:Base Sequence; D020134:Catalytic Domain; D004247:DNA / Q000737:chemistry*; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000378:metabolism; D000077732:Fidaxomicin; D017353:Gene Deletion; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D011401:Promoter Regions, Genetic; D012313:RNA / Q000378:metabolism; D014158:Transcription, Genetic / Q000187:drug effects*
chemical_list: D000617:Aminoglycosides; D012313:RNA; D004247:DNA; D012321:DNA-Directed RNA Polymerases; D000077732:Fidaxomicin