title: Determination of RNA polymerase binding surfaces of transcription factors by NMR spectroscopy.
abstract: In bacteria, RNA polymerase (RNAP), the central enzyme of transcription, is regulated by N-utilization substance (Nus) transcription factors. Several of these factors interact directly, and only transiently, with RNAP to modulate its function. As details of these interactions are largely unknown, we probed the RNAP binding surfaces of Escherichia coli (E. coli) Nus factors by nuclear magnetic resonance (NMR) spectroscopy. Perdeuterated factors with [(1)H,(13)C]-labeled methyl groups of Val, Leu, and Ile residues were titrated with protonated RNAP. After verification of this approach with the N-terminal domain (NTD) of NusG and RNAP we determined the RNAP binding site of NusE. It overlaps with the NusE interaction surface for the NusG C-terminal domain, indicating that RNAP and NusG compete for NusE and suggesting possible roles for the NusE:RNAP interaction, e.g. in antitermination and direct transcription:translation coupling. We solved the solution structure of NusA-NTD by NMR spectroscopy, identified its RNAP binding site with the same approach we used for NusG-NTD, and here present a detailed model of the NusA-NTD:RNAP:RNA complex.
authors.affiliation: Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany.
authors.forename: Johanna
authors.initials: J
authors.lastname: Drögemüller
authors.affiliation: Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Strauß
authors.affiliation: Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany.
authors.forename: Kristian
authors.initials: K
authors.lastname: Schweimer
authors.affiliation: Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany.
authors.forename: Marcel
authors.initials: M
authors.lastname: Jurk
authors.affiliation: Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany.
authors.forename: Paul
authors.initials: P
authors.lastname: Rösch
authors.affiliation: Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany.
authors.forename: Stefan H
authors.initials: SH
authors.lastname: Knauer
mesh_terms: D001665:Binding Sites; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D014176:Protein Biosynthesis; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D012996:Solutions; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D029968:Escherichia coli Proteins; D012996:Solutions; D014157:Transcription Factors; D012321:DNA-Directed RNA Polymerases