DksA: A potentiator of regulation of transcription by small molecules in <i>Escherichia coli</i>
The initiation of transcription often serves as a key point in the regulation of gene expression. Regulation of transcription initiation in Escherlchia coli can occur by changes in the concentrations of the small molecules guanosine 5′ diphosphate 3′-diphosphate (ppGpp) and initiating NTPs (iNTPs). Ribosomal RNA (rRNA) promoters and certain amino acid promoters are both regulated by ppGpp, while rRNA promoters are also regulated by iNTPs. It has been proposed that the small molecules regulate these promoters because of their intrinsic kinetic characteristics. We show that the small protein DksA is required for the proper regulation of rRNA and certain amino acid promoters in vivo by potentiating the effects of the small molecule regulators.
DksA was found to bind directly to RNA polymerase (RNAP) and increase the rate of dissociation of RNAP from all tested promoters, thereby decreasing the lifetime of the open complex. DksA also increased the rate of isomerization from the closed to the open complex at an amino acid promoter. In vitro, DksA increased the inhibitory effect of ppGpp and increased dependence on iNTPs.
In vivo, rRNA and certain amino acid promoters did not respond properly to changes in the concentrations of the small molecules in a Δ dksA strain. rRNA promoters were no longer growth phase or growth rate regulated, nor did they respond to nutrient shifts. The activities of certain amino acid promoters were also affected during a nutrient shift and/or steady-state growth. DksA's role in regulation by the small molecular effectors in vivo is proposed to be that of a facilitator, rather than a direct regulator, since its levels were relatively constant under all conditions that were tested.
Classical mechanisms of regulation of transcription initiation in E. coli occur by proteins whose effects are directed to specific promoters by DNA binding sites. In contrast, the small molecules and DksA are likely present at all transcription initiation complexes, but are proposed to have specific effects on transcription because of the intrinsic kinetic characteristics of promoters. DksA alters the kinetic characteristics of promoters, leading to regulation of specific promoters by small molecule effectors.
0307: Molecular biology