title: Structural basis for transcription regulation by alarmone ppGpp.
abstract: Guanosine-tetraphosphate (ppGpp) is a major regulator of stringent control, an adaptive response of bacteria to amino acid starvation. The 2.7 A resolution structure of the Thermus thermophilus RNA polymerase (RNAP) holoenzyme in complex with ppGpp reveals that ppGpp binds to the same site near the active center in both independent RNAP molecules in the crystal but in strikingly distinct orientations. Binding is symmetrical with respect to the two diphosphates of ppGpp and is relaxed with respect to the orientation of the nucleotide base. Different modes of ppGpp binding are coupled with asymmetry of the active site configurations. The results suggest that base pairing of ppGpp with cytosines in the nontemplate DNA strand might be an essential component of transcription control by ppGpp. We present experimental evidence highlighting the importance of base-specific contacts between ppGpp and specific cytosine residues during both transcription initiation and elongation.
authors.affiliation: Department of Microbiology, Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.
authors.forename: Irina
authors.initials: I
authors.lastname: Artsimovitch
authors.forename: Vsevolod
authors.initials: V
authors.lastname: Patlan
authors.forename: Shun-ichi
authors.initials: S
authors.lastname: Sekine
authors.forename: Marina N
authors.initials: MN
authors.lastname: Vassylyeva
authors.forename: Takeshi
authors.initials: T
authors.lastname: Hosaka
authors.forename: Kozo
authors.initials: K
authors.lastname: Ochi
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
authors.forename: Dmitry G
authors.initials: DG
authors.lastname: Vassylyev
mesh_terms: D019943:Amino Acid Substitution; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D015964:Gene Expression Regulation, Bacterial; D006860:Hydrogen Bonding; D008274:Magnesium / Q000378:metabolism; D008958:Models, Molecular; D011401:Promoter Regions, Genetic; D017433:Protein Structure, Secondary; D021122:Protein Subunits / Q000737:chemistry; D011755:Pyrophosphatases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D015203:Reproducibility of Results; D055672:Static Electricity; D016963:Thermus thermophilus / Q000201:enzymology / Q000235:genetics; D014158:Transcription, Genetic; D014867:Water / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D021122:Protein Subunits; D014867:Water; C027627:guanosine-3',5'-bis(diphosphate) 3'-pyrophosphatase; D011755:Pyrophosphatases; D008274:Magnesium