title: Targeted protein footprinting: where different transcription factors bind to RNA polymerase.
abstract: Gene transcription is regulated through the interactions of RNA polymerase (RNAP) with transcription factors, such as the bacterial sigma proteins. We have devised a new strategy that relies on targeted protein footprinting to make an extensive survey of proximity to the protein surface. This involves attaching cutting reagents randomly to lysine residues on the surface of a protein such as sigma. The lysine-labeled sigma protein is then used to cleave the polypeptide backbones of the RNAP proteins at exposed residues adjacent to the sigma binding site. We used targeted protein footprinting to compare the areas near which sigma(70), sigma(54), sigma(38), sigma(E), NusA, GreA, and omega bind to the protein subunits of Escherichia coli RNAP. The sigma proteins and NusA cut sites in similar regions of the two large RNAP subunits, beta and beta', outlining a common surface. GreA cuts a larger set of sites, whereas omega shows no overlap with the others, cutting only the beta' subunit at a unique location.
authors.affiliation: Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, USA.
authors.forename: S L
authors.initials: SL
authors.lastname: Traviglia
authors.forename: S A
authors.initials: SA
authors.lastname: Datwyler
authors.forename: D
authors.initials: D
authors.lastname: Yan
authors.forename: A
authors.initials: A
authors.lastname: Ishihama
authors.forename: C F
authors.initials: CF
authors.lastname: Meares
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D001665:Binding Sites; D018983:DNA Footprinting / Q000379:methods; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics*; D004926:Escherichia coli; D029968:Escherichia coli Proteins; D010445:Peptide Elongation Factors; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics*; D035602:Transcriptional Elongation Factors
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D010445:Peptide Elongation Factors; D014157:Transcription Factors; D035602:Transcriptional Elongation Factors; C068727:nusA protein, E coli; C075886:GREA protein, Rickettsia prowazekii; D012321:DNA-Directed RNA Polymerases