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Many genes in bacterial genomes are of unknown function, often referred to as y-genes. Recently, the analytic methods have divided bacterial transcriptomes into independently modulated sets of genes (iModulons). Functionally annotated iModulons that contain y-genes lead to testable hypotheses to elucidate y-gene function. The inversely correlated expression of a putative transporter gene,  ydhC , relative to purine biosynthetic genes, has led to the hypothesis that it encodes a purine-related transporter and revealed a LysR-family regulator, YdhB, with a predicted 23-bp palindromic binding motif. RNA-Seq analysis of a  ydhB  knockout mutant confirmed the YdhB-dependent activation of  ydhC  in the presence of adenosine. The deletion of either the  ydhC  or the  ydhB  gene led to a substantially decreased growth rate for  E. coli  in minimal medium with adenosine, inosine, or guanosine as the nitrogen source. Taken together, we provide clear evidence that YdhB activates the expression of the  ydhC  gene that encodes a purine transporter in  E. coli . We propose that the genes  ydhB  and  ydhC  be re-named as  punR  and  punC , respectively.

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli