An orthogonalized PYR1-based CID module with reprogrammable ligand-binding specificity

Sang-Youl Park; Jingde Qiu; Shuang Wei; Francis C Peterson; Jesús Beltrán; Angélica V Medina-Cucurella; Aditya S Vaidya; Zenan Xing; Brian F Volkman; Dmitri A Nusinow; Timothy A Whitehead; Ian Wheeldon; Sean R Cutler

doi:10.1038/s41589-023-01447-7

An orthogonalized PYR1-based CID module with reprogrammable ligand-binding specificity

Nat Chem Biol. 2024 Jan;20(1):103-110. doi: 10.1038/s41589-023-01447-7. Epub 2023 Oct 23.

Authors

Sang-Youl Park^{1

2}, Jingde Qiu^{1

2}, Shuang Wei³, Francis C Peterson⁴, Jesús Beltrán^{1

2

5}, Angélica V Medina-Cucurella⁶, Aditya S Vaidya^{1

2}, Zenan Xing^{1

2}, Brian F Volkman⁴, Dmitri A Nusinow⁷, Timothy A Whitehead⁸, Ian Wheeldon^{9

10

11}, Sean R Cutler^{12

13}

Affiliations

¹ Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.
² Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA.
³ Department of Biochemistry, University of California, Riverside, Riverside, CA, USA.
⁴ Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
⁵ Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
⁶ Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA.
⁷ Donald Danforth Plant Science Center, St. Louis, MO, USA.
⁸ Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA.
⁹ Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA. wheeldon@ucr.edu.
¹⁰ Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA. wheeldon@ucr.edu.
¹¹ Center for Industrial Biotechnology, University of California, Riverside, Riverside, CA, USA. wheeldon@ucr.edu.
¹² Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA. cutler@ucr.edu.
¹³ Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA. cutler@ucr.edu.

Abstract

Plants sense abscisic acid (ABA) using chemical-induced dimerization (CID) modules, including the receptor PYR1 and HAB1, a phosphatase inhibited by ligand-activated PYR1. This system is unique because of the relative ease with which ligand recognition can be reprogrammed. To expand the PYR1 system, we designed an orthogonal '*' module, which harbors a dimer interface salt bridge; X-ray crystallographic, biochemical and in vivo analyses confirm its orthogonality. We used this module to create PYR1*^MANDI/HAB1* and PYR1*^AZIN/HAB1*, which possess nanomolar sensitivities to their activating ligands mandipropamid and azinphos-ethyl. Experiments in Arabidopsis thaliana and Saccharomyces cerevisiae demonstrate the sensitive detection of banned organophosphate contaminants using living biosensors and the construction of multi-input/output genetic circuits. Our new modules enable ligand-programmable multi-channel CID systems for plant and eukaryotic synthetic biology that can empower new plant-based and microbe-based sensing modalities.

MeSH terms

Abscisic Acid
Arabidopsis Proteins* / metabolism
Arabidopsis* / genetics
Arabidopsis* / metabolism
Dimerization
Ligands
Membrane Transport Proteins / chemistry

Substances

Abscisic Acid
Arabidopsis Proteins
Ligands
Membrane Transport Proteins

Grants and funding

R21 DA053496/DA/NIDA NIH HHS/United States