title: Eukaryotic and archaeal TBP and TFB/TF(II)B follow different promoter DNA bending pathways.
abstract: During transcription initiation, the promoter DNA is recognized and bent by the basal transcription factor TATA-binding protein (TBP). Subsequent association of transcription factor B (TFB) with the TBP-DNA complex is followed by the recruitment of the ribonucleic acid polymerase resulting in the formation of the pre-initiation complex. TBP and TFB/TF(II)B are highly conserved in structure and function among the eukaryotic-archaeal domain but intriguingly have to operate under vastly different conditions. Employing single-pair fluorescence resonance energy transfer, we monitored DNA bending by eukaryotic and archaeal TBPs in the absence and presence of TFB in real-time. We observed that the lifetime of the TBP-DNA interaction differs significantly between the archaeal and eukaryotic system. We show that the eukaryotic DNA-TBP interaction is characterized by a linear, stepwise bending mechanism with an intermediate state distinguished by a distinct bending angle. TF(II)B specifically stabilizes the fully bent TBP-promoter DNA complex and we identify this step as a regulatory checkpoint. In contrast, the archaeal TBP-DNA interaction is extremely dynamic and TBP from the archaeal organism Sulfolobus acidocaldarius strictly requires TFB for DNA bending. Thus, we demonstrate that transcription initiation follows diverse pathways on the way to the formation of the pre-initiation complex.
authors.affiliation: Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Gietl
authors.affiliation: Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany.
authors.forename: Phil
authors.initials: P
authors.lastname: Holzmeister
authors.affiliation: RNAP Laboratory, University College London, Institute of Structural and Molecular Biology, Division of Biosciences, Gower St., London WC1E 6BT, UK.
authors.forename: Fabian
authors.initials: F
authors.lastname: Blombach
authors.affiliation: Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany.
authors.forename: Sarah
authors.initials: S
authors.lastname: Schulz
authors.affiliation: Department of Chemistry, Center for Nanoscience (CeNS) and Center for Integrated Protein Science Munich (CiPSM), Ludwig Maximilian University, Butenandtstraße 11, 81377 Munich, Germany.
authors.forename: Lena Voith
authors.initials: LV
authors.lastname: von Voithenberg
authors.affiliation: Department of Chemistry, Center for Nanoscience (CeNS) and Center for Integrated Protein Science Munich (CiPSM), Ludwig Maximilian University, Butenandtstraße 11, 81377 Munich, Germany.
authors.forename: Don C
authors.initials: DC
authors.lastname: Lamb
authors.affiliation: RNAP Laboratory, University College London, Institute of Structural and Molecular Biology, Division of Biosciences, Gower St., London WC1E 6BT, UK.
authors.forename: Finn
authors.initials: F
authors.lastname: Werner
authors.affiliation: Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany.
authors.forename: Philip
authors.initials: P
authors.lastname: Tinnefeld
authors.affiliation: Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany d.grohmann@tu-bs.de.
authors.forename: Dina
authors.initials: D
authors.lastname: Grohmann
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D019843:Archaeal Proteins / Q000378:metabolism*; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D035181:TATA-Box Binding Protein / Q000378:metabolism*; D035581:Transcription Factor TFIIB / Q000378:metabolism*; D061785:Transcription Initiation, Genetic
chemical_list: D019843:Archaeal Proteins; C115017:SPT15 protein, S cerevisiae; C073680:SUA7 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D035181:TATA-Box Binding Protein; D035581:Transcription Factor TFIIB; C106466:transcription factor B, Archaea; D004247:DNA
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