Jones, J. D. G. & Dangl, J. L. The plant immune system. Nature 444, 323–329 (2006).
Chisholm, S. T., Coaker, G., Day, B. & Staskawicz, B. J. Host-microbe interactions: shaping the evolution of the plant immune response. Cell 124, 803–814 (2006).
Cui, H., Tsuda, K. & Parker, J. E. Effector-triggered immunity: from pathogen perception to robust defense. Annu. Rev. Plant Biol. 66, 487–511 (2015).
Sarris, P. F. et al. A plant immune receptor detects pathogen effectors that target WRKY transcription factors. Cell 161, 1089–1100 (2015).
Le Roux, C. et al. A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity. Cell 161, 1074–1088 (2015).
Césari, S. et al. The NB-LRR proteins RGA4 and RGA5 interact functionally and physically to confer disease resistance. EMBO J. 33, 1941–1959 (2014).
Deng, Y. et al. Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance. Science 355, 962–965 (2017).
Hou, M. & Xu, G. Growth-defense trade-off in plants: from hypothesis to principle to paradigm. Cell Host Microbe 33, 1222–1226 (2025).
He, Z., Webster, S. & He, S. Y. Growth-defense trade-offs in plants. Curr. Biol. 32, R634–R639 (2022).
Ariga, H. et al. NLR locus-mediated trade-off between abiotic and biotic stress adaptation in Arabidopsis. Nat. Plants 3, 17072 (2017).
Kirkby, E. A. in Marschner’s Mineral Nutrition of Plants 4th edn (eds Rengel, Z. et al.) 3–9 (Academic Press, 2023).
Finney, L. A. & O’Halloran, T. V. Transition metal speciation in the cell: insights from the chemistry of metal ion receptors. Science 300, 931–936 (2003).
Waldron, K. J., Rutherford, J. C., Ford, D. & Robinson, N. J. Metalloproteins and metal sensing. Nature 460, 823–830 (2009).
Williams, R. J. P. The natural selection of the chemical elements. Cell. Mol. Life Sci. 53, 816–829 (1997).
Zhao, F.-J., Tang, Z., Song, J.-J., Huang, X.-Y. & Wang, P. Toxic metals and metalloids: uptake, transport, detoxification, phytoremediation, and crop improvement for safer food. Mol. Plant. 15, 27–44 (2022).
Hou, D. et al. Global soil pollution by toxic metals threatens agriculture and human health. Science 388, 316–321 (2025).
Cobbett, C. & Goldsbrough, P. Phytochelatins and metallothioneins: roles in heavy metal detoxification and homeostasis. Annu. Rev. Plant Biol. 53, 159–182 (2002).
Blum, R. et al. Function of phytochelatin synthase in catabolism of glutathione-conjugates. Plant J. 49, 740–749 (2007).
Rowley, B. & Monestier, M. Mechanisms of heavy metal-induced autoimmunity. Mol. Immunol. 42, 833–838 (2005).
Lv, M. et al. Manganese is critical for antitumor immune responses via cGAS-STING and improves the efficacy of clinical immunotherapy. Cell Res. 30, 966–979 (2020).
Haase, H. & Rink, L. Functional significance of zinc-related signaling pathways in immune cells. Annu. Rev. Nutr. 29, 133–152 (2009).
Wang, Z., Sun, Y., Yao, W., Ba, Q. & Wang, H. Effects of cadmium exposure on the immune system and immunoregulation. Front. Immunol. 12, 695484 (2021).
Zhang, R. et al. Manganese salts function as potent adjuvants. Cell. Mol. Immunol. 18, 1222–1234 (2021).
Du, M. & Chen, Z. J. DNA-induced liquid phase condensation of cGAS activates innate immune signaling. Science 361, 704–709 (2018).
Zhao, Z. et al. Mn2+ directly activates cGAS and structural analysis suggests Mn2+ induces a noncanonical catalytic synthesis of 2′3′-cGAMP. Cell Rep. 32, 108053 (2020).
Poschenrieder, C., Tolrà, R. & Barceló, J. Can metals defend plants against biotic stress?. Trends Plant Sci. 11, 288–295 (2006).
Liu, H. et al. Copper ion elicits defense response in Arabidopsis thaliana by activating salicylate- and ethylene-dependent signaling pathways. Mol. Plant 8, 1550–1553 (2015).
Kuvelja, A. et al. Zinc priming enhances Capsicum annuum immunity against infection by Botrytis cinerea- from the whole plant to the molecular level. Plant Sci. 343, 112060 (2024).
Morina, F. & Küpper, H. Trace metals at the frontline of pathogen defence responses in non-hyperaccumulating plants. J. Exp. Bot. 73, 6516–6524 (2022).
Howden, R., Goldsbrough, P. B., Andersen, C. R. & Cobbett, C. S. Cadmium-sensitive, cad1 mutants of Arabidopsis thaliana are phytochelatin deficient. Plant Physiol. 107, 1059–1066 (1995).
Ha, S. B. et al. Phytochelatin synthase genes from Arabidopsis and the yeast Schizosaccharomyces pombe. Plant Cell. 11, 1153–1164 (1999).
Narusaka, M. et al. RRS1 and RPS4 provide a dual resistance-gene system against fungal and bacterial pathogens. Plant J. 60, 218–226 (2009).
Van De Weyer, A.-L. et al. A species-wide inventory of NLR genes and alleles in Arabidopsis thaliana. Cell 178, 1260–1272.e14 (2019).
Contreras, M. P., Lüdke, D., Pai, H., Toghani, A. & Kamoun, S. NLR receptors in plant immunity: making sense of the alphabet soup. EMBO Rep. 24, e57495 (2023).
Yu, Y., Zhang, H., Long, Y., Shu, Y. & Zhai, J. Plant Public RNA-seq Database: a comprehensive online database for expression analysis of 45 000 plant public RNA-Seq libraries. Plant Biotechnol. J. 20, 806–808 (2022).
Bjornson, M., Pimprikar, P., Nürnberger, T. & Zipfel, C. The transcriptional landscape of Arabidopsis thaliana pattern-triggered immunity. Nat. Plants 7, 579–586 (2021).
Ding, P. et al. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. J. Exp. Bot. 72, 7927–7941 (2021).
Ngou, B. P. M., Ahn, H.-K., Ding, P. & Jones, J. D. G. Mutual potentiation of plant immunity by cell-surface and intracellular receptors. Nature 592, 110–115 (2021).
Wang, W. et al. WeiTsing, a pericycle-expressed ion channel, safeguards the stele to confer clubroot resistance. Cell 186, 2656–2671.e18 (2023).
Dongus, J. A. & Parker, J. E. EDS1 signalling: at the nexus of intracellular and surface receptor immunity. Curr. Opin. Plant Biol. 62, 102039 (2021).
Lapin, D., Bhandari, D. D. & Parker, J. E. Origins and immunity networking functions of eds1 family proteins. Annu. Rev. Plant Biol. 58, 253–276 (2020).
Martin, R. et al. Structure of the activated ROQ1 resistosome directly recognizing the pathogen effector XopQ. Science 370, eabd9993 (2020).
Yu, H. et al. Activation of a helper NLR by plant and bacterial TIR immune signaling. Science 386, 1413–1420 (2024).
Jia, A. et al. TIR-catalyzed ADP-ribosylation reactions produce signaling molecules for plant immunity. Science 377, eabq8180 (2022).
Huang, S. et al. Identification and receptor mechanism of TIR-catalyzed small molecules in plant immunity. Science 377, eabq3297 (2022).
Wan, L. et al. TIR domains of plant immune receptors are NAD+ -cleaving enzymes that promote cell death. Science 365, 799–803 (2019).
Horsefield, S. et al. NAD+ cleavage activity by animal and plant TIR domains in cell death pathways. Science 365, 793–799 (2019).
Essuman, K. et al. The SARM1 toll/interleukin-1 receptor domain possesses intrinsic NAD+ cleavage activity that promotes pathological axonal degeneration. Neuron 93, 1334–1343.e5 (2017).
Mao, Y. et al. Expanding the target range of base editing in plants without loss of efficiency by blocking RNA-silencing. Plant Biotechnol. J. 19, 2389–2391 (2021).
Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).
Huang, S. et al. NLR signaling in plants: from resistosomes to second messengers. Trends Biochem. Sci 48, 776–787 (2023).
Williams, S. J. et al. Structural basis for assembly and function of a heterodimeric plant immune receptor. Science 344, 299–303 (2014).
Huh, S. U. et al. Protein-protein interactions in the RPS4/RRS1 immune receptor complex. PLoS Pathog. 13, e1006376 (2017).
Bonardi, V., Cherkis, K., Nishimura, M. T. & Dangl, J. L. A new eye on NLR proteins: focused on clarity or diffused by complexity?. Curr. Opin. Immunol. 24, 41–50 (2012).
Guo, H., Wang, S. & Jones, J. D. G. Autoactive Arabidopsis RPS4 alleles require partner protein RRS1-R. Plant Physiol. 185, 761–764 (2021).
Demirjian, C. et al. An atypical NLR gene confers bacterial wilt susceptibility in Arabidopsis. Plant Commun. 4, 100607 (2023).
Zhang, N. et al. Geochemical-integrated machine learning approach predicts the distribution of cadmium speciation in European and Chinese topsoils. Commun. Earth Environ. 6, 548 (2025).
Salas-González, I. et al. Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis. Science 371, eabd0695 (2021).
Kawa, D. & Brady, S. M. Root cell types as an interface for biotic interactions. Trends Plant Sci. 27, 1173–1186 (2022).
Giehl, R. F. H. et al. Cell type-specific mapping of ion distribution in Arabidopsis thaliana roots. Nat. Commun. 14, 3351 (2023).
Munch, D. et al. The Brassicaceae family displays divergent, shoot-skewed NLR resistance gene expression. Plant Physiol. 176, 1598–1609 (2018).
Bernoux, M. et al. Structural and functional analysis of a plant resistance protein TIR domain reveals interfaces for self-association, signaling, and autoregulation. Cell Host Microbe 9, 200–211 (2011).
Ma, S. et al. Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme. Science 370, eabe3069 (2020).
Förderer, A. et al. A wheat resistosome defines common principles of immune receptor channels. Nature 610, 532–539 (2022).
Kim, Y., Schumaker, K. S. & Zhu, J.-K. EMS mutagenesis of Arabidopsis. Methods Mol. Biol. 323, 101–103 (2006).
Abe, A. et al. Genome sequencing reveals agronomically important loci in rice using MutMap. Nat. Biotechnol. 30, 174–178 (2012).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacterium -mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).
Sparkes, I. A., Runions, J., Kearns, A. & Hawes, C. Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants. Nat. Protoc. 1, 2019–2025 (2006).
Xie, X. et al. CRISPR-GE: a convenient software toolkit for CRISPR-based genome editing. Mol. Plant. 10, 1246–1249 (2017).
Ma, X. et al. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol. Plant. 8, 1274–1284 (2015).
Yan, L. et al. High-efficiency genome editing in Arabidopsis using YAO Promoter-driven CRISPR/Cas9 system. Mol. Plant. 8, 1820–1823 (2015).
Falk, A. et al. EDS1, an essential component of R gene-mediated disease resistance in Arabidopsis has homology to eukaryotic lipases. Proc. Natl Acad. Sci. USA 96, 3292–3297 (1999).
Jirage, D. et al. Arabidopsis thaliana PAD4 encodes a lipase-like gene that is important for salicylic acid signaling. Proc. Natl Acad. Sci. USA 96, 13583–13588 (1999).
Dong, O. X. et al. TNL-mediated immunity in Arabidopsis requires complex regulation of the redundant ADR1 gene family. New Phytol. 210, 960–973 (2016).
Castel, B. et al. Diverse NLR immune receptors activate defence via the RPW8-NLR NRG1. New Phytol. 222, 966–980 (2019).
Allasia, V. et al. Quantification of salicylic acid (SA) and SA-glucosides in Arabidopsis thaliana. Bio Protoc. 8, e2844 (2018).
Lapin, D. et al. A coevolved EDS1-SAG101-NRG1 module mediates cell death signaling by tir-domain immune receptors. Plant Cell. 31, 2430–2455 (2019).
Morel, A. et al. in Host-Pathogen Interactions Vol. 1734 (eds Medina, C. & López-Baena, F. J.) 223–239 (Springer, 2018).