Regulation by the Transcriptional Regulator YdcI in E. coli and (p)ppGpp-Dependent Activation of ydcI Expression

YdcI, a LysR-type transcription regulator, has been associated with various phenotypes related to stress response and metabolic adaptation in Escherichia coli and Salmonella enterica. This work addresses regulation of specific target loci by YdcI as well as regulation of ydcI expression and YdcI synthesis in E. coli. DNA binding of YdcI to loci previously identified through ChIP-exo analysis in E. coli K12 was validated for 10 loci by electrophoretic mobility shift assays. Two of these loci, iraP and mqo, are regulated by YdcI as shown using promoter lacZ fusions, while regulation of the other loci is marginal, at least under the conditions tested. Our data suggest that YdcI acts as an H-NS antagonist at the H-NS repressed and (p)ppGpp-dependent stress-induced iraP promoter. Gene iraP encodes the RssB anti-adaptor protein IraP that prevents RssB-mediated targeting of RpoS for degradation. Gene mqo, which is repressed by YdcI, encodes the TCA cycle enzyme malate: quinone oxidoreductase. Other YdcI bound loci encode enzymes involved in the TCA cycle, as well as membrane transport proteins. Furthermore, the transcription of the ydcI gene itself is induced by the alarmone (p)ppGpp under phosphate stress conditions; it is not autoregulated, and a significant increase in YdcI protein levels occurs upon entry from early to mid-exponential growth phase. Taken together, aspects of regulation by YdcI and of ydcI expression as well as YdcI synthesis are presented that relate to its potential role in the response to abiotic stresses and control of metabolism in E. coli.