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Synthesis of the novel transporter YdhC, is regulated by the YdhB transcription factor controlling adenosine and adenine uptake

View ORCID ProfileIrina A. Rodionova, Ye Gao, Anand Sastry, Reo Yoo, Dmitry A. Rodionov, Milton H. Saier Jr, Bernhard Ø. Palsson
doi: https://doi.org/10.1101/2020.05.03.074617
Irina A. Rodionova
1Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA 92093, USA
2Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA
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  • ORCID record for Irina A. Rodionova
  • For correspondence: irodionova@ucsd.edu palsson@ucsd.edu msaier@ucsd.edu
Ye Gao
1Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA 92093, USA
2Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA
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Anand Sastry
2Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA
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Reo Yoo
2Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA
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Dmitry A. Rodionov
3Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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Milton H. Saier Jr
2Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA
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  • For correspondence: irodionova@ucsd.edu palsson@ucsd.edu msaier@ucsd.edu
Bernhard Ø. Palsson
1Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA 92093, USA
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  • For correspondence: irodionova@ucsd.edu palsson@ucsd.edu msaier@ucsd.edu
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Abstract

The YdhB transcriptional factor, re-named here AdnB, homologous to the allantoin regulator, AllS, was shown to regulate ydhC gene expression in Escherichia coli, which is divergently transcribed from adnB, and this gene arrangement is conserved in many Protreobacteria. The predicted consensus DNA binding sequence for YdhB is also conserved in Entrobacterial genomes. RNA-seq data confirmed the activation predicted due to the binding of AdnB as shown by Chip-Exo results. Fluorescent polarization experiments revealed binding of YdhB to the predicted binding site upstream of ydhC in the presence of 0.35 mM adenine, but not in its absence. The E. coli MG1655, strain lacking the ydhB gene, showed a lower level of ydhC mRNA in cells grown in M9-glucose supplemented with 2 mM adenosine. Adenosine and adenine are products of purine metabolism and provide sources of ammonium for many organisms. They are utilized under nitrogen starvation conditions as single nitrogen sources. Deletion of either the ydhC or the ydhB gene leads to a substantially decreased growth rate for E. coli in minimal M9 medium with glycerol as the carbon source and adenosine or adenine as the single nitrogen source. The ydhC mutant showed increased resistance to Paromomycine, Sulfathiazole and Sulfamethohazole using Biolog plates. We provide evidence that YdhB, (a novel LysR family regulator) activates expression of the ydhC gene, encoding a novel adenosine/adenine transporter in E. coli. The YdhB binding consensus for different groups of Enterobacteria was predicted.

Competing Interest Statement

The authors have declared no competing interest.

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Posted May 03, 2020.
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Synthesis of the novel transporter YdhC, is regulated by the YdhB transcription factor controlling adenosine and adenine uptake
Irina A. Rodionova, Ye Gao, Anand Sastry, Reo Yoo, Dmitry A. Rodionov, Milton H. Saier Jr, Bernhard Ø. Palsson
bioRxiv 2020.05.03.074617; doi: https://doi.org/10.1101/2020.05.03.074617
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Synthesis of the novel transporter YdhC, is regulated by the YdhB transcription factor controlling adenosine and adenine uptake
Irina A. Rodionova, Ye Gao, Anand Sastry, Reo Yoo, Dmitry A. Rodionov, Milton H. Saier Jr, Bernhard Ø. Palsson
bioRxiv 2020.05.03.074617; doi: https://doi.org/10.1101/2020.05.03.074617

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