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

Irina A. Rodionova*, Ye Gao, Anand Sastry, Ying Hefner, Hyun Gyu Lim, Dmitry A. Rodionov, Milton H. Saier, Bernhard O. Palsson

*Corresponding author for this work

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Abstract

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.

Original languageEnglish
Article number991
JournalCommunications Biology
Volume4
Issue number1
Number of pages10
ISSN2399-3642
DOIs
Publication statusPublished - Dec 2021

Bibliographical note

Funding Information:
This work was supported by National Institutes of Health (NIH) grants U01AI124316 and GM077402, and Novo Nordisk Foundation Grant Number NNF10CC1016517. We would like to thank A. Bobkova and M. Abrams (UCSD) for editing the manuscript.

Publisher Copyright:
© 2021, The Author(s).

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