Regulatory roles of pyruvate-sensing two-component system PyrSR (YpdAB) in Escherichia coli K-12

Abstract When the rate of production of metabolites in bacteria exceeds the amounts needed for cell growth, excess metabolites are secreted into the extracellular environment. Upon entry into poor nutrient conditions, overflowed exometabolites are reused to continue cell growth and survival. At present, however, the genetic system for utilization of exometabolites is poorly understood even for the best-characterized model prokaryote Escherichia coli. A two-component system YpdAB of E. coli K-12 was predicted to participate in regulation of this process, and the yhjX gene encoding the MFS-family transporter with an as yet unidentified function was identified as a single regulatory target of YpdB. Using gSELEX screening in vitro, however, we have identified up to eight regulatory targets, including the yhjX gene. The predicted regulatory targets were all confirmed to be under the direct control of YpdB by gel shift assay in vitro and reporter assay in vivo. For induction of YpdAB function, the major exometabolite pyruvate in growing E. coli K-12 was identified as the inducer. We then propose to rename YpdAB as PyrSR (regulator of pyruvate reutilization). One unique feature of PyrSR is its cross-talk with another pyruvate-sensing BtsSR at the TCS stage 1 for fine-tuning of pyruvate reutilization. The poorly characterized two-component PyrSR (YpdAB) system of Escherichia coli K-12 was found to monitor high concentrations of the major exometabolite pyruvate and regulates a set of the genes for reutilization of pyruvate.