title: The magic spot: a ppGpp binding site on E. coli RNA polymerase responsible for regulation of transcription initiation.
abstract: The global regulatory nucleotide ppGpp ("magic spot") regulates transcription from a large subset of Escherichia coli promoters, illustrating how small molecules can control gene expression promoter-specifically by interacting with RNA polymerase (RNAP) without binding to DNA. However, ppGpp's target site on RNAP, and therefore its mechanism of action, has remained unclear. We report here a binding site for ppGpp on E. coli RNAP, identified by crosslinking, protease mapping, and analysis of mutant RNAPs that fail to respond to ppGpp. A strain with a mutant ppGpp binding site displays properties characteristic of cells defective for ppGpp synthesis. The binding site is at an interface of two RNAP subunits, ω and β', and its position suggests an allosteric mechanism of action involving restriction of motion between two mobile RNAP modules. Identification of the binding site allows prediction of bacterial species in which ppGpp exerts its effects by targeting RNAP.
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA.
authors.forename: Wilma
authors.initials: W
authors.lastname: Ross
authors.forename: Catherine E
authors.initials: CE
authors.lastname: Vrentas
authors.forename: Patricia
authors.initials: P
authors.lastname: Sanchez-Vazquez
authors.forename: Tamas
authors.initials: T
authors.lastname: Gaal
authors.forename: Richard L
authors.initials: RL
authors.lastname: Gourse
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D006159:Guanosine Tetraphosphate / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D021122:Protein Subunits; D014158:Transcription, Genetic
chemical_list: D029968:Escherichia coli Proteins; D021122:Protein Subunits; D006159:Guanosine Tetraphosphate; D012321:DNA-Directed RNA Polymerases