title: Transcription factor-dependent DNA bending governs promoter recognition by the mitochondrial RNA polymerase.
abstract: Promoter recognition is the first and the most important step during gene expression. Our studies of the yeast (Saccharomyces cerevisiae) mitochondrial (mt) transcription machinery provide mechanistic understandings on the basic problem of how the mt RNA polymerase (RNAP) with the help of the initiation factor discriminates between promoter and non-promoter sequences. We have used fluorescence-based approaches to quantify DNA binding, bending, and opening steps by the core mtRNAP subunit (Rpo41) and the transcription factor (Mtf1). Our results show that promoter recognition is not achieved by tight and selective binding to the promoter sequence. Instead, promoter recognition is achieved by an induced-fit mechanism of transcription factor-dependent differential conformational changes in the promoter and non-promoter DNAs. While Rpo41 induces a slight bend upon binding both the DNAs, addition of the Mtf1 results in severe bending of the promoter and unbending of the non-promoter DNA. Only the sharply bent DNA results in the catalytically active open complex. Such an induced-fit mechanism serves three purposes: 1) assures catalysis at promoter sites, 2) prevents RNA synthesis at non-promoter sites, and 3) provides a conformational state at the non-promoter sites that would aid in facile translocation to scan for specific sites.
authors.affiliation: Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine & Dentistry of New Jersey (UMDNJ), Piscataway, New Jersey 08854.
authors.forename: Guo-Qing
authors.initials: GQ
authors.lastname: Tang
authors.affiliation: Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine & Dentistry of New Jersey (UMDNJ), Piscataway, New Jersey 08854.
authors.forename: Aishwarya P
authors.initials: AP
authors.lastname: Deshpande
authors.affiliation: Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine & Dentistry of New Jersey (UMDNJ), Piscataway, New Jersey 08854. Electronic address: patelss@umdnj.edu.
authors.forename: Smita S
authors.initials: SS
authors.lastname: Patel
mesh_terms: D016880:Anisotropy; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods; D007700:Kinetics; D008928:Mitochondria / Q000201:enzymology*; D024101:Mitochondrial Proteins / Q000378:metabolism; D009841:Oligonucleotides / Q000235:genetics; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: C071720:MTF1 protein, S cerevisiae; D024101:Mitochondrial Proteins; D009841:Oligonucleotides; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D004247:DNA; D012321:DNA-Directed RNA Polymerases; C487996:RPO41 protein, S cerevisiae