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Stael S, Sabljić I, Audenaert D, Andersson T, Tsiatsiani L, Kumpf RP, Vidal-Albalat A, Lindgren C, Vercammen D, Jacques S, Nguyen L, Njo M, Fernández-Fernández ÁD, Beunens T, Timmerman E, Gevaert K, Van Montagu M, Ståhlberg J, Bozhkov PV, Linusson A, Beeckman T, Van Breusegem F. Structure-function study of a Ca 2+-independent metacaspase involved in lateral root emergence. Proc Natl Acad Sci U S A 2023; 120:e2303480120. [PMID: 37216519 PMCID: PMC10235996 DOI: 10.1073/pnas.2303480120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Metacaspases are part of an evolutionarily broad family of multifunctional cysteine proteases, involved in disease and normal development. As the structure-function relationship of metacaspases remains poorly understood, we solved the X-ray crystal structure of an Arabidopsis thaliana type II metacaspase (AtMCA-IIf) belonging to a particular subgroup not requiring calcium ions for activation. To study metacaspase activity in plants, we developed an in vitro chemical screen to identify small molecule metacaspase inhibitors and found several hits with a minimal thioxodihydropyrimidine-dione structure, of which some are specific AtMCA-IIf inhibitors. We provide mechanistic insight into the basis of inhibition by the TDP-containing compounds through molecular docking onto the AtMCA-IIf crystal structure. Finally, a TDP-containing compound (TDP6) effectively hampered lateral root emergence in vivo, probably through inhibition of metacaspases specifically expressed in the endodermal cells overlying developing lateral root primordia. In the future, the small compound inhibitors and crystal structure of AtMCA-IIf can be used to study metacaspases in other species, such as important human pathogens, including those causing neglected diseases.
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Affiliation(s)
- Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Igor Sabljić
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Dominique Audenaert
- VIB Screening Core, VIB,9052Ghent, Belgium
- Centre for Bioassay Development and Screening, Ghent University,9000Ghent, Belgium
| | | | - Liana Tsiatsiani
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | | | | | | | - Dominique Vercammen
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Silke Jacques
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Long Nguyen
- VIB Screening Core, VIB,9052Ghent, Belgium
- Centre for Bioassay Development and Screening, Ghent University,9000Ghent, Belgium
| | - Maria Njo
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Álvaro D. Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Tine Beunens
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Evy Timmerman
- Department of Biomolecular Medicine, Ghent University,9052Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9052Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University,9052Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9052Ghent, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Peter V. Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Anna Linusson
- Department of Chemistry, Umeå University,90187Umeå, Sweden
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
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