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ToolsSnoeck, Simon, Lee, Hyun Kyung, Schmid, Marc W., Bender, Kyle W., Neeracher, Matthias J., Fernández-Fernández, Alvaro D., Santiago, Julia and Zipfel, Cyril (2024) Leveraging coevolutionary insights and AI-based structural modeling to unravel receptor–peptide ligand-binding mechanisms. Proceedings of the National Academy of Sciences of the United States of America, 121 (33). ISSN 0027-8424
Full text not available from this repository. (Request a copy)Abstract
Secreted signaling peptides are central regulators of growth, development, and stress responses, but specific steps in the evolution of these peptides and their receptors are not well understood. Also, the molecular mechanisms of peptide–receptor binding are only known for a few examples, primarily owing to the limited availability of protein structural determination capabilities to few laboratories worldwide. Plants have evolved a multitude of secreted signaling peptides and corresponding transmembrane receptors. Stress-responsive SERINE RICH ENDOGENOUS PEPTIDES (SCOOPs) were recently identified. Bioactive SCOOPs are proteolytically processed by subtilases and are perceived by the leucine-rich repeat receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2) in the model plant Arabidopsis thaliana. How SCOOPs and MIK2 have (co)evolved, and how SCOOPs bind to MIK2 are unknown. Using in silico analysis of 350 plant genomes and subsequent functional testing, we revealed the conservation of MIK2 as SCOOP receptor within the plant order Brassicales. We then leveraged AI-based structural modeling and comparative genomics to identify two conserved putative SCOOP–MIK2 binding pockets across Brassicales MIK2 homologues predicted to interact with the “SxS” motif of otherwise sequence-divergent SCOOPs. Mutagenesis of both predicted binding pockets compromised SCOOP binding to MIK2, SCOOP-induced complex formation between MIK2 and its coreceptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1, and SCOOP-induced reactive oxygen species production, thus, confirming our in silico predictions. Collectively, in addition to revealing the elusive SCOOP–MIK2 binding mechanism, our analytic pipeline combining phylogenomics, AI-based structural predictions, and experimental biochemical and physiological validation provides a blueprint for the elucidation of peptide ligand–receptor perception mechanisms.
| Item Type: | Article |
|---|---|
| Additional Information: | Data, Materials, and Software Availability: Plasmid maps, predicted protein structures, and source files of blots (Datasets S4–S6) have been deposited in Zenodo (DOI: https://doi.org/10.5281/zenodo.11615633) (61). All other data are included in the article and/or supporting information. Funding Information: This research was supported by the University of Zurich and the European Research Council under Grant Agreement No. 773153 (\u201CIMMUNO-PEPTALK\u201D to C.Z.), and by the University of Lausanne and the Swiss SNF (grant 310030_204526 to J.S.). A.D.F.F. is also supported by a Post-Doctoral Fellowship from the European Molecular Biology Organization (EMBO, ALTF 580-2022). We thank Owen Kentish for assistance with recombinant protein production. We thank members of the Zipfel lab for discussion during this project and feedback on the manuscript, as well as Yasuhiro Kadota and Pok Man (Bruno) Ngou for discussions on RK evolution. |
| Uncontrolled Keywords: | evolution,ligand,peptide,receptor,structure prediction,general ,/dk/atira/pure/subjectarea/asjc/1000 |
| Faculty \ School: | Faculty of Science > The Sainsbury Laboratory |
| UEA Research Groups: | Faculty of Science > Research Groups > Plant Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 24 Oct 2024 08:30 |
| Last Modified: | 24 Oct 2024 08:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97170 |
| DOI: | 10.1073/pnas.2400862121 |
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