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PreprintCited by 7Bacterial Genetics and BiotechnologyMicrobial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

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Functional and Structural Characterization of an IclR Family Transcription Factor for the Development of Dicarboxylic Acid Biosensors

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Pham, Chester, Nasr, Mohamed, Skarina, Tatiana, Leo, Rosa Di, Kwan, David H., Martin, Vincent J.J., Stogios, Peter J., Mahadevan, Radhakrishnan, Savchenko, Alexei·2023·FEBS Journal
DOI 10.1101/2023.07.27.550818

Preprint — published as 10.1111/febs.17149

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Abstract

Prokaryotic transcription factors (TFs) regulate gene expression in response to small molecules, thus representing promising candidates as versatile small molecule-detecting biosensors valuable for synthetic biology applications. The engineering of such biosensors requires thorough in vitro and in vivo characterization of TF ligand response as well as detailed molecular structure information. In this work we characterize the PcaR TF belonging to the IclR family. We present in vitro functional analysis of PcaR’s ligand profile and construction of genetic circuits for the characterization of PcaR as an in vivo biosensor in the model eukaryote Saccharomyces cerevisiae . We report the crystal structures of PcaR in the apo state and in complex with one of its ligands, succinate, which suggests the mechanism of dicarboxylic acid recognition by this TF. This work provides key structural and functional insights enabling the engineering of PcaR for dicarboxylic acid biosensors. Graphical Abstract: Highlights: PcaR is an IclR family transcription regulator responsive to dicarboxylic acids PcaR was established as an in vivo biosensor in yeast Crystal structure of PcaR in the apo form was solved Crystal structure with PcaR in complex with succinate was solved Sequence alignments unveil ligand-binding positions in the IclR family

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Metadata

Authors
Pham, C., Nasr, M., Skarina, T., Leo, R. D., Kwan, D. H., Martin, V. J. J., Stogios, P. J., Mahadevan, R., & Savchenko, A.
Affiliations
  • University of Toronto (CA)
  • PROTEO (CA)
  • Concordia University (CA)
  • University of Calgary (CA)
Corresponding author
Savchenko, Alexei
ORCID
Venue
FEBS Journal
Publisher
openRxiv
Published
2023-07-27
Volume
291
Issue
15
Pages
3481-3498
ISSN
1742-464X (ISSN-L)
DOI
10.1101/2023.07.27.550818
OpenAlex
W4396575384
Cited by
7
References
1
Citations by year
2026: 3 · 2025: 4
FWCI
1.85
Type
journal article
Language
en
Open access
Licence
cc-by-nc-nd
Locations
  • FEBS Journal (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • Genome Canada
  • Concordia University
  • Natural Sciences and Engineering Research Council of Canada (RGPIN 2017 ?, rgpin-2016-05464, rgpin-2017-06703)
  • Fonds de recherche du Québec – Nature et technologies
  • Argonne National Laboratory
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Keywords
ligand binding, crystal structure, apo state, synthetic gene circuits, Saccharomyces cerevisiae, small molecule detection, synthetic biology
MeSH terms
Dicarboxylic Acids, Ligands, Models, Molecular, Protein Binding, Protein Conformation, Saccharomyces cerevisiae, Transcription Factors, Biosensing Techniques, Crystallography, X-Ray, Succinic Acid, Saccharomyces cerevisiae Proteins

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