title: Role of the σ54Activator Interacting Domain in Bacterial Transcription Initiation.
abstract: Bacterial sigma factors are subunits of RNA polymerase that direct the holoenzyme to specific sets of promoters in the genome and are a central element of regulating transcription. Most polymerase holoenzymes open the promoter and initiate transcription rapidly after binding. However, polymerase containing the members of the σ54family must be acted on by a transcriptional activator before DNA opening and initiation occur. A key domain in these transcriptional activators forms a hexameric AAA+ ATPase that acts through conformational changes brought on by ATP hydrolysis. Contacts between the transcriptional activator and σ54are primarily made through an N-terminal σ54activator interacting domain (AID). To better understand this mechanism of bacterial transcription initiation, we characterized the σ54AID by NMR spectroscopy and other biophysical methods and show that it is an intrinsically disordered domain in σ54alone. We identified a minimal construct of the Aquifex aeolicus σ54AID that consists of two predicted helices and retains native-like binding affinity for the transcriptional activator NtrC1. Using the NtrC1 ATPase domain, bound with the non-hydrolyzable ATP analog ADP-beryllium fluoride, we studied the NtrC1-σ54AID complex using NMR spectroscopy. We show that the σ54AID becomes structured after associating with the core loops of the transcriptional activators in their ATP state and that the primary site of the interaction is the first predicted helix. Understanding this complex, formed as the first step toward initiation, will help unravel the mechanism of σ54bacterial transcription initiation.
authors.affiliation: Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA.
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Siegel
authors.affiliation: Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, CA 94720, USA. Electronic address: dewemmer@berkeley.edu.
authors.forename: David E
authors.initials: DE
authors.lastname: Wemmer
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D001419:Bacteria / Q000737:chemistry* / Q000201:enzymology* / Q000235:genetics; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D000072417:Protein Domains; D051877:RNA Polymerase Sigma 54 / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D000255:Adenosine Triphosphate; D051877:RNA Polymerase Sigma 54
keywords: NMR spectroscopy; bacterial transcription initiation; sigma54; transcriptional activators