The Magic Spot: A ppGpp Binding Site on E. coli RNA Polymerase Responsible for Regulation of Transcription Initiation

• Published in: Molecular cell 2013-05, Vol.50 (3), p.420-429
• Main Authors: Ross, Wilma, Vrentas, Catherine E., Sanchez-Vazquez, Patricia, Gaal, Tamas, Gourse, Richard L.
• Format: Article
• Language: English
• Subjects: Alleles; Amino Acid Sequence; binding sites; Binding Sites - genetics; crosslinking; DNA; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - genetics; DNA-Directed RNA Polymerases - metabolism; Escherichia coli; Escherichia coli - enzymology; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; gene expression; Guanosine Tetraphosphate - genetics; Guanosine Tetraphosphate - metabolism; mechanism of action; Molecular Sequence Data; mutants; Mutation; prediction; Promoter Regions, Genetic; Protein Binding; Protein Subunits; proteinases; site; Transcription, Genetic
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2013.03.021

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. [Display omitted] ► We report an RNAP binding site responsible for ppGpp function ► The binding site is at an interface of two RNAP subunits, ω and β′ ► The location of the binding site suggests an allosteric mechanism of action ► The site predicts species in which ppGpp functions by regulating RNAP