The <i>Arabidopsis</i> TIRome informs the design of artificial TIR (Toll/interleukin-1 receptor) domain proteins
The TIR (Toll/interleukin-1 receptor) domain is an ancient protein module that functions in immune and cell death responses across the Tree of Life. TIR domains encoded by plants and prokaryotes function as enzymes to produce diverse small molecule immune signals. Plant genomes can encode hundreds of TIR-domain containing proteins-many of which confer important agricultural disease resistance as TIR-NLR (nucleotide-binding, leucine-rich repeat) immune receptors. Despite their importance, how natural variation influences TIR enzymatic output and immunity-associated cell death is largely unexplored. We assayed a complete collection of the TIR domains of <i>Arabidopsis thaliana</i> Col-0 (the "AtTIRome") to explore variation in TIR metabolite production and cell death signaling. Roughly half of the AtTIRome triggered cell death in transient assays. Artificial TIR proteins designed based on consensus sequences of the AtTIRome's cell death phenotypic classes revealed polymorphisms controlling variation in TIR cell death elicitation and metabolite production. Structure-function analyses of artificial TIRs revealed that natural variation in the "BB-loop", a flexible region overlying the catalytic pocket, determines differences in function across <i>Arabidopsis</i> TIR-containing proteins. We further demonstrate that artificial TIRs are functional on an NLR chassis and that BB-loop variation can tune the activity of a natural TIR-NLR protein. These findings shed light on the diversity of TIR outputs and reveal methods to design and engineer TIR-based immune receptors.
Authors
- Marc T. Nishimura (ORCID: https://orcid.org/0000-0003-4666-6900)
- Andrew Flint (ORCID: https://orcid.org/0000-0002-8340-4726)
- Mitchell Sorbello (ORCID: https://orcid.org/0000-0001-9442-5170)
- Mehdi Mobli (ORCID: https://orcid.org/0000-0003-2420-4262)
- Li Wan (ORCID: https://orcid.org/0000-0002-0839-3748)
- Natsumi Maruta (ORCID: https://orcid.org/0000-0002-6246-6346)
- Murray Grant (ORCID: https://orcid.org/0000-0003-3357-0264)
- Mikhail S. Drenichev (ORCID: https://orcid.org/0000-0001-7624-8801)
- Boštjan Kobe (ORCID: https://orcid.org/0000-0001-9413-9166)
- Thomas Ve (ORCID: https://orcid.org/0000-0002-0113-1905)
- Lijiang Song (ORCID: https://orcid.org/0000-0002-5843-005X)
- Vardis Ntoukakis (ORCID: https://orcid.org/0000-0003-0069-6004)
- Adam M. Bayless (ORCID: https://orcid.org/0000-0002-8773-4482)
- Jeffery L. Dangl (ORCID: https://orcid.org/0000-0003-3199-8654)
- Sam C. Ogden (ORCID: https://orcid.org/0000-0002-4244-8095)
- Qingli Liu (ORCID: https://orcid.org/0009-0007-4665-376X)
- T Todd
- Jedidiah Tulu
Institutions
- Engelhardt Institute of Molecular Biology (RU)
- University of North Carolina at Chapel Hill (US)
- Griffith University (AU)
- The University of Queensland (AU)
- University of Warwick (GB)
- Institute of Bioengineering and Nanotechnology (SG)
- Institute for Biomedicine (IT)
- Center for Excellence in Molecular Plant Sciences (CN)
- AgriBio (AU)
- Syngenta (Switzerland) (CH)
- Colorado State University (US)
Publication Details
- Journal
- Proceedings of the National Academy of Sciences
- Published
- 2025-09-12
- DOI
- https://doi.org/10.1073/pnas.2505893122
- Citations
- 4
- Primary Topic
- Plant-Microbe Interactions and Immunity
- Type
- article
- Field-Weighted Citation Impact
- 7.00
Funders
- National Science Foundation
- Howard Hughes Medical Institute
- Colorado State University
- Chinese Academy of Sciences
- National Key Laboratory of Plant Molecular Genetics
- National Institutes of Health
- Directorate for Biological Sciences
- Medical Research Council
- National Health and Medical Research Council
- National Institute of General Medical Sciences