title: A hyper-mutant of the unusual sigma70-Pr promoter bypasses synergistic ppGpp/DksA co-stimulation.
abstract: The activities of promoters can be temporally and conditionally regulated by mechanisms other than classical DNA-binding repressors and activators. One example is the inherently weak σ(70)-dependent Pr promoter that ultimately controls catabolism of phenolic compounds. The activity of Pr is up-regulated through the joint action of ppGpp and DksA that enhance the performance of RNA polymerase at this promoter. Here, we report a mutagenesis analysis that revealed substantial differences between Pr and other ppGpp/DksA co-stimulated promoters. In vitro transcription and RNA polymerase binding assays show that it is the T at the -11 position of the extremely suboptimal -10 element of Pr that underlies both poor binding of σ(70)-RNAP and a slow rate of open complex formation--the process that is accelerated by ppGpp and DksA. Our findings support the idea that collaborative action of ppGpp and DksA lowers the rate-limiting transition energy required for conversion between intermediates on the road to open complex formation.
authors: Department of Molecular Biology, Umeå University, Umeå SE 901 87, Sweden.
authors: Teresa
authors: T
authors: Del Peso-Santos
authors: Lisandro M D
authors: LM
authors: Bernardo
authors: Eleonore
authors: E
authors: Skärfstad
authors: Linda
authors: L
authors: Holmfeldt
authors: Peter
authors: P
authors: Togneri
authors: Victoria
authors: V
authors: Shingler
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D006159:Guanosine Tetraphosphate / Q000378:metabolism*; D016296:Mutagenesis; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012808:Sigma Factor / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D012808:Sigma Factor; D014157:Transcription Factors; C090751:dksA protein, E coli; D006159:Guanosine Tetraphosphate; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases