DksA Is Required for Growth Phase-Dependent Regulation, Growth Rate-Dependent Control, and Stringent Control offisExpression inEscherichia coli

Abstract

DksA is a critical transcription factor in Escherichia coli that binds to RNA polymerase and potentiates control of rRNA promoters and certain amino acid promoters. Given the kinetic similarities between rRNA promoters and the fis promoter (Pfis), we investigated the possibility that DksA might also control transcription from Pfis. We show that the absence of dksA extends transcription from Pfis well into the late logarithmic and stationary growth phases, demonstrating the importance of DksA for growth phase-dependent regulation of fis. We also show that transcription from Pfis increases with steady-state growth rate and that dksA is absolutely required for this regulation. In addition, both DksA and ppGpp are required for inhibition of Pfis promoter activity following amino acid starvation, and these factors act directly and synergistically to negatively control Pfis transcription in vitro. DksA decreases the half-life of the intrinsically short-lived fis promoter-RNA polymerase complex and increases its sensitivity to the concentration of CTP, the predominant initiating nucleotide triphosphate for this promoter. This work extends our understanding of the multiple factors controlling fis expression and demonstrates the generality of the DksA requirement for regulation of kinetically similar promoters.

Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria

“…To validate this prediction, we analyzed the changes in the rplY promoter activity after induction of the stringent response by serine-hydroxamate (SHX). The treatment with SHX has been widely applied for triggering the RelA-dependent ppGpp synthesis in studies of individual promoters (e.g., Mallik et al 2006;Lemke et al 2011) as well as of the global effect of ppGpp on gene expression (Durfee et al 2008). The changes in the transcription level were first evaluated by RT-PCR analysis of individual transcripts in total RNA isolated from the wild-type (relA + , dksA + ) strain and its derivatives deficient in ppGpp (relA::kan) or its cofactor DksA (dksA::tet) (Fig.…”

Cholera Toxin Production during Anaerobic Trimethylamine N-Oxide Respiration Is Mediated by Stringent Response in Vibrio cholerae

“…The negative influence of DksA on bacterial growth has been well studied. In an E. coli strain defective in DksA protein, transcription of the fis operon, expression of which was known to actively occur during exponential growth, was extended into the stationary phase (51). In addition, P. aeruginosa DksA represses rRNA gene expression under both actively growing and stringent response conditions (52).…”

Transcription Profiling of the Stringent Response in Escherichia coli

“…The other genes that were immediately repressed included two genes encoding nucleoid-associated factors: fis, a known stringent gene (68), and stpA (102). Fis positively regulates rRNA and certain tRNA-encoding operons (67,80), and its down-regulation is coordinated with an effect on stable RNA synthesis (62). Expression of rnpA, encoding a subunit of RNase P which is required for processing of both 4.5S RNA and tRNAs, was also down-regulated, although the rnpB gene, which was previously shown to be stringently regulated (49), was not significantly affected in these experiments.…”