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  • Title: A hyper-mutant of the unusual sigma70-Pr promoter bypasses synergistic ppGpp/DksA co-stimulation.
    Author: Del Peso-Santos T, Bernardo LM, Skärfstad E, Holmfeldt L, Togneri P, Shingler V.
    Journal: Nucleic Acids Res; 2011 Aug; 39(14):5853-65. PubMed ID: 21447563.
    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.
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