Regions 1.2 and 3.2 of the RNA Polymerase σ Subunit Promote DNA Melting and Attenuate Action of the Antibiotic Lipiarmycin. Issue 2 (29th January 2016)

• Record Type: Journal Article
• Authors: Morichaud, Zakia; Chaloin, Laurent; Brodolin, Konstantin
• Is Part Of: Journal of molecular biology. Volume 428:Issue 2:Part B(2016:Jan. 29)
• Page Start: 463
• Page End: 476
• Publication Date: 2016-01-29
• Subjects: RNAP RNA polymerase -- ssDNA single-stranded DNA -- dwDNA downstream DNA duplex -- TB transcription buffer; fidaxomicin -- rpoS -- promoter melting -- switch region -- TFIIB B-reader; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2015.12.017
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract: Initiation of RNA synthesis by bacterial RNA polymerase (RNAP) requires melting of promoter DNA, which is nucleated by the σ subunit during formation of the "open" promoter complex (RPo ). The antibiotic lipiarmycin (Lpm) inhibits promoter melting by blocking access of the template DNA strand to the RNAP active-site cleft. Here we show that Escherichia coli RNAP holoenzymes containing either housekeeping σ 70, with a deletion in the region 3.2, or the stationary phase σ S subunits exhibited hypersensitivity to Lpm and increased cold sensitivity of RPo formation. Similar effects were produced by mutation located ~ 60 Å away from the Lpm binding site within σ 70 region 1.2, controlling − 10 promoter element recognition. Our data suggested that template strand single-stranded DNA competes with Lpm for binding to RNAP and that σ 70 regions 1.2 and 3.2 attenuate Lpm action by promoting DNA duplex opening. Graphical Abstract: Highlights: Promoter DNA opening is a target for genetic regulation and for antibiotics. Regions of the σ 70 factor implicated in DNA opening antagonize the lipiarmycin action. RNAP containing the stationary phase σ S factor displayed hypersensitivity to lipiarmycin. Antibiotic can function as the σ factor selective transcriptional repressor.