pH-Dependent DNA Distortion and Repression of Gene Expression by Pectobacterium atrosepticum PecS

Abstract

Transcriptional activity is exquisitely sensitive to changes in promoter DNA topology. Transcription factors may therefore control gene activity by modulating the relative positioning of -10 and -35 promoter elements. The plant pathogen Pectobacterium atrosepticum, which causes soft rot in potatoes, must alter gene expression patterns to ensure growth in planta. In the related soft-rot enterobacterium Dickeya dadantii, PecS functions as a master regulator of virulence gene expression. Here, we report that P. atrosepticum PecS controls gene activity by altering promoter DNA topology in response to pH. While PecS binds the pecS promoter with high affinity regardless of pH, it induces significant DNA distortion only at neutral pH, the pH at which the pecS promoter is repressed in vivo. At pH ∼8, DNA distortions are attenuated, and PecS no longer represses the pecS promoter. A specific histidine (H142) located in a crevice between the dimerization- and DNA-binding regions is required for pH-dependent changes in DNA distortion and repression of gene activity, and mutation of this histidine renders the mutant protein incapable of repressing the pecS promoter. We propose that protonated PecS induces a DNA conformation at neutral pH in which -10 and -35 promoter elements are suboptimally positioned for RNA polymerase binding; on deprotonation of PecS, binding is no longer associated with significant changes in DNA conformation, allowing gene expression. We suggest that this mode of gene regulation leads to differential expression of the PecS regulon in response to alkalinization of the plant apoplast.

An EmrB multidrug efflux pump in Burkholderia thailandensis with unexpected roles in antibiotic resistance

“…For example, the redox-sensitive MarR homolog HypR in Bacillus subtilis binds to DNA with similar affinity regardless of redox state, but only oxidized HypR activates target gene expression (29). Similarly, PecS from the plant pathogen Pectobacterium atrosepticum binds to promoter DNA with comparable affinity at pH 7.4 and 8.3, but it represses gene expression only at alkaline pH; in the case of PecS, the differential ability to repress gene activity was ascribed to its pH-dependent ability to alter DNA topology (30). Reduced and oxidized OstR may likewise impose distinct con- 5, and 7).…”

Regulation of Metabolic Pathways by MarR Family Transcription Factors

“…The regulatory function is dictated by the precise location of the binding site, with repressors typically interfering with binding of RNA polymerase or impeding its movement on DNA whereas activators generally bind further upstream to assist in polymerase recruitment. In addition to direct interaction with RNA polymerase, some transcription factors may modulate gene activity by altering promoter DNA topology [3], [4], [5].…”

Transcriptome analysis of the Dickeya dadantii PecS regulon during the early stages of interaction with Arabidopsis thaliana

“…The response to three of these regulators-GacA, MfbR and PecS-has been analysed in planta by quantitative polymerase chain reaction (qPCR) analysis (Lebeau et al, 2008;Mhedbi-Hajri et al, 2011;Reverchon et al, 2010). The PecS major regulator is striking as it belongs to a horizontally acquired genomic island present exclusively in the Dickeya genus and some members of the related soft rot genus Pectobacterium (Deochand et al, 2016). Yet, PecS plays a prominent role in the regulation of virulence, specifically in Dickeya, even though many of the genes it controls are widespread in all soft rot enterobacteria.…”