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Cited by 46Plant-Microbe Interactions and ImmunityPlant Pathogenic Bacteria StudiesPlant Disease Resistance and Genetics

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Allelic compatibility in plant immune receptors facilitates engineering of new effector recognition specificities

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Bentham, Adam R, De la Concepcion, Juan Carlos, Benjumea, Javier Vega, Kourelis, Jiorgos, Jones, Sally, Mendel, Melanie, Stubbs, Jack, Stevenson, Clare E M, Maidment, Josephine H R, Youles, Mark, Zdrzałek, Rafał, Kamoun, Sophien, Banfield, Mark J·2023·The Plant Cell
DOI 10.1093/plcell/koad204PMC PMC10533329

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Abstract

Engineering the plant immune system offers genetic solutions to mitigate crop diseases caused by diverse agriculturally significant pathogens and pests. Modification of intracellular plant immune receptors of the nucleotide-binding leucine-rich repeat (NLR) receptor superfamily for expanded recognition of pathogen virulence proteins (effectors) is a promising approach for engineering disease resistance. However, engineering can cause NLR autoactivation, resulting in constitutive defense responses that are deleterious to the plant. This may be due to plant NLRs associating in highly complex signaling networks that coevolve together, and changes through breeding or genetic modification can generate incompatible combinations, resulting in autoimmune phenotypes. The sensor and helper NLRs of the rice (Oryza sativa) NLR pair Pik have coevolved, and mismatching between noncoevolved alleles triggers constitutive activation and cell death. This limits the extent to which protein modifications can be used to engineer pathogen recognition and enhance disease resistance mediated by these NLRs. Here, we dissected incompatibility determinants in the Pik pair in Nicotiana benthamiana and found that heavy metal–associated (HMA) domains integrated in Pik-1 not only evolved to bind pathogen effectors but also likely coevolved with other NLR domains to maintain immune homeostasis. This explains why changes in integrated domains can lead to autoactivation. We then used this knowledge to facilitate engineering of new effector recognition specificities, overcoming initial autoimmune penalties. We show that by mismatching alleles of the rice sensor and helper NLRs Pik-1 and Pik-2, we can enable the integration of synthetic domains with novel and enhanced recognition specificities. Taken together, our results reveal a strategy for engineering NLRs, which has the potential to allow an expanded set of integrations and therefore new disease resistance specificities in plants.

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Research works printed but not linked: 64

  1. Adachi, 2019, NLR singletons, pairs, and networks: evolution, assembly, and regulation of the intracellular immunoreceptor circuitry of plants, Curr Opin Plant Biol, 50, 121, 10.1016/j.pbi.2019.04.007 · DOI
  2. Baggs, 2017, NLR diversity, helpers and integrated domains: making sense of the NLR IDentity, Curr Opin Plant Biol., 38, 59, 10.1016/j.pbi.2017.04.012 · DOI
  3. Bentham, 2020, A molecular roadmap to the plant immune system, J Biol Chem, 295, 14916, 10.1074/jbc.REV120.010852 · DOI
  4. Bentham, 2021, pOPIN-GG: a resource for modular assembly in protein expression vectors, 10.1101/2021.08.10.455798 · DOI
  5. Berrow, 2007, A versatile ligation-independent cloning method suitable for high-throughput expression screening applications, Nucleic Acids Res, 35, e45, 10.1093/nar/gkm047 · DOI
  6. Białas, 2021, Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain, eLife, 10, 10.7554/eLife.66961 · DOI
  7. Białas, 2018, Lessons in effector and NLR biology of plant-microbe systems, Mol Plant Microbe Interact, 31, 34, 10.1094/MPMI-08-17-0196-FI · DOI
  8. Bomblies, 2007, Autoimmune response as a mechanism for a Dobzhansky–Muller-type incompatibility syndrome in plants, PLoS Biol, 5, e236, 10.1371/journal.pbio.0050236 · DOI
  9. Burdett, 2019, Animal NLRs continue to inform plant NLR structure and function, Arch Biochem Biophys, 670, 58, 10.1016/j.abb.2019.05.001 · DOI
  10. Calvo-Baltanás, 2021, Hybrid incompatibility of the plant immune system: an opposite force to heterosis equilibrating hybrid performances, Front Plant Sci., 11, 10.3389/fpls.2020.576796 · DOI
  11. Cesari, 2018, Multiple strategies for pathogen perception by plant immune receptors, New Phytologist, 219, 17, 10.1111/nph.14877 · DOI
  12. Cesari, 2014, A novel conserved mechanism for plant NLR protein pairs: the “integrated decoy” hypothesis, Front Plant Sci, 5, 606, 10.3389/fpls.2014.00606 · DOI
  13. Cesari, 2013, The rice resistance protein pair RGA4/RGA5 recognizes the Magnaporthe oryzae effectors AVR-Pia and AVR1-CO39 by direct binding, Plant Cell, 25, 1463, 10.1105/tpc.112.107201 · DOI
  14. Cesari, 2022, New recognition specificity in a plant homo immune receptor by molecular engineering of its integrated domain, Nat Commun, 13, 1524, 10.1038/s41467-022-29196-6 · DOI
  15. Chae, 2014, Species-wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis, Cell, 159, 1341, 10.1016/j.cell.2014.10.049 · DOI · Paper page
  16. Chen, 2010, Molprobity: all-atom structure validation for macromolecular crystallography, Acta Crystallogr D Biol Crystallogr, 66, 12, 10.1107/S0907444909042073 · DOI · Paper page
  17. Costanzo, 2010, Sequence variation at the rice blast resistance gene Pi-km locus: implications for the development of allele specific markers, Plant Sci., 178, 523, 10.1016/j.plantsci.2010.02.014 · DOI
  18. De la Concepcion, 2019, Protein engineering expands the effector recognition profile of a rice NLR immune receptor, eLife, 8, 10.7554/eLife.47713 · DOI
  19. De la Concepcion, 2018, Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen, Nat Plants., 4, 576, 10.1038/s41477-018-0194-x · DOI
  20. De la Concepcion, 2022, Binding of a blast fungus zinc-finger fold effector to a hydrophobic pocket in the host exocyst subunit Exo70 modulates immune recognition in rice, Proc Natl Acad Sci U S A, 119, 10.1073/pnas.2210559119 · DOI
  21. De la Concepcion, 2021, The allelic rice immune receptor Pikh confers extended resistance to strains of the blast fungus through a single polymorphism in the effector binding interface, PLoS Pathog., 17, 10.1371/journal.ppat.1009368 · DOI
  22. De la Concepcion, 2021, Functional diversification gave rise to allelic specialization in a rice NLR immune receptor pair, eLife, 10, 10.7554/eLife.71662 · DOI
  23. Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr D Biol Crystallogr, 60, 2126, 10.1107/S0907444904019158 · DOI · Paper page
  24. Engler, 2014, A golden gate modular cloning toolbox for plants, ACS Synth Biol, 3, 839, 10.1021/sb4001504 · DOI
  25. Feehan, 2020, Plant NLRs get by with a little help from their friends, Curr Opin Plant Biol, 56, 99, 10.1016/j.pbi.2020.04.006 · DOI
  26. Fridy, 2014, A robust pipeline for rapid production of versatile nanobody repertoires, Nat Methods, 11, 1253, 10.1038/nmeth.3170 · DOI
  27. Fujisaki, 2017, An unconventional NOI/RIN4 domain of a rice NLR protein binds host EXO70 protein to confer fungal immunity, 10.1101/239400 · DOI
  28. Guo, 2018, Specific recognition of two MAX effectors by integrated HMA domains in plant immune receptors involves distinct binding surfaces, Proc Natl Acad Sci U S A, 115, 11637, 10.1073/pnas.1810705115 · DOI
  29. Ho, 2019, Moving beyond P values: data analysis with estimation graphics, Nat Methods, 16, 565, 10.1038/s41592-019-0470-3 · DOI
  30. Jones, 2016, Intracellular innate immune surveillance devices in plants and animals, Science, 354, 10.1126/science.aaf6395 · DOI
  31. Kanzaki, 2012, Arms race co-evolution of Magnaporthe oryzae AVR-Pik and rice Pik genes driven by their physical interactions, Plant J, 72, 894, 10.1111/j.1365-313X.2012.05110.x · DOI
  32. Kourelis, 2022, Activation and regulation of NLR immune receptor networks, Plant Cell Physiol, 63, 1366, 10.1093/pcp/pcac116 · DOI
  33. Kourelis, 2023, NLR Immune receptor–nanobody fusions confer plant disease resistance, Science, 379, 934, 10.1126/science.abn4116 · DOI
  34. Krissinel, 2007, Inference of macromolecular assemblies from crystalline state, J Mol Biol, 372, 774, 10.1016/j.jmb.2007.05.022 · DOI
  35. Kroj, 2016, Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread, New Phytol, 210, 618, 10.1111/nph.13869 · DOI
  36. Le Roux, 2015, A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity, Cell, 161, 1074, 10.1016/j.cell.2015.04.025 · DOI
  37. Liu, 2021, A designer rice NLR immune receptor confers resistance to the rice blast fungus carrying noncorresponding avirulence effectors, Proc Natl Acad Sci U S A., 118, e2110751118, 10.1073/pnas.2110751118 · DOI
  38. Lüdke, 2022, NLR we there yet? Nucleocytoplasmic coordination of NLR-mediated immunity, New Phytol, 236, 24, 10.1111/nph.18359 · DOI
  39. Maidment, 2021, Multiple variants of the fungal effector AVR-Pik bind the HMA domain of the rice protein OsHIPP19, providing a foundation to engineer plant defense, J Biol Chem, 296, 10.1016/j.jbc.2021.100371 · DOI
  40. Maidment, 2022, Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor, 10.1101/2022.06.14.496076 · DOI
  41. Maqbool, 2015, Structural basis of pathogen recognition by an integrated HMA domain in a plant NLR immune receptor, eLife, 4, 10.7554/eLife.08709 · DOI
  42. Marchal, 2022, Show me your ID: NLR immune receptors with integrated domains in plants, Essays Biochem, 66, 527, 10.1042/EBC20210084 · DOI
  43. Maruta, 2022, Structural basis of NLR activation and innate immune signalling in plants, Immunogenetics, 74, 5, 10.1007/s00251-021-01242-5 · DOI
  44. McCoy, 2007, Phaser crystallographic software, J Appl Crystallogr, 40, 658, 10.1107/S0021889807021206 · DOI · Paper page
  45. Monteiro, 2018, Structural, functional, and genomic diversity of plant NLR proteins: an evolved resource for rational engineering of plant immunity, Annu Rev Phytopathol, 56, 243, 10.1146/annurev-phyto-080417-045817 · DOI
  46. Mukhi, 2021, Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor, Proc Natl Acad Sci U S A., 118, 10.1073/pnas.2113996118 · DOI
  47. Murshudov, 1997, Refinement of macromolecular structures by the maximum-likelihood method, Acta Crystallogr D Biol Crystallogr, 53, 240, 10.1107/S0907444996012255 · DOI
  48. Ordon, 2021, Disentangling cause and consequence: genetic dissection of the DANGEROUS MIX2 risk locus, and activation of the DM2h NLR in autoimmunity, Plant J, 106, 1008, 10.1111/tpj.15215 · DOI
  49. Ortiz, 2017, Recognition of the Magnaporthe oryzae effector AVR-Pia by the decoy domain of the rice NLR immune receptor RGA5, Plant Cell, 29, 156, 10.1105/tpc.16.00435 · DOI
  50. Outram, 2022, Seeing is believing: exploiting advances in structural biology to understand and engineer plant immunity, Curr Opin Plant Biol, 67, 10.1016/j.pbi.2022.102210 · DOI
  51. Pettersen, 2021, UCSF Chimerax: structure visualization for researchers, educators, and developers, Protein Sci, 30, 70, 10.1002/pro.3943 · DOI
  52. Rothbauer, 2006, Targeting and tracing antigens in live cells with fluorescent nanobodies, Nat Methods, 3, 887, 10.1038/nmeth953 · DOI
  53. Sarris, 2016, Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens, BMC Biol., 14, 8, 10.1186/s12915-016-0228-7 · DOI
  54. Studier, 2005, Protein production by auto-induction in high-density shaking cultures, Protein Expr Purif., 41, 207, 10.1016/j.pep.2005.01.016 · DOI
  55. Takken, 2012, How to build a pathogen detector: structural basis of NB-LRR function, Curr Opin Plant Biol, 15, 375, 10.1016/j.pbi.2012.05.001 · DOI
  56. Tamborski, ltering specificity and auto-activity of plant immune receptors Sr33 and Sr50 via a rational engineering approach, Mol Plant Microbe Interact
  57. Tran, 2017, Activation of a plant NLR complex through heteromeric association with an autoimmune risk variant of another NLR, Curr Biol., 27, 1148, 10.1016/j.cub.2017.03.018 · DOI
  58. Varden, 2019, Cross-reactivity of a rice NLR immune receptor to distinct effectors from the rice blast pathogen Magnaporthe oryzae provides partial disease resistance, J Biol Chem, 294, 13006, 10.1074/jbc.RA119.007730 · DOI
  59. Wickham, 2016, Ggplot2: elegant graphics for data analysis, 10.1007/978-3-319-24277-4 · DOI
  60. Winn, 2011, Overview of the CCP4 suite and current developments, Acta Crystallogr D Biol Crystallogr, 67, 235, 10.1107/S0907444910045749 · DOI · Paper page
  61. Wu, 2018, Receptor networks underpin plant immunity, Science, 360, 1300, 10.1126/science.aat2623 · DOI
  62. Zdrzałek, 2020, The rice NLR pair Pikp-1/Pikp-2 initiates cell death through receptor cooperation rather than negative regulation, PLoS One, 15, 10.1371/journal.pone.0238616 · DOI
  63. Zhang, 2022, The effector recognition by synthetic sensor NLR receptors requires the concerted action of multiple interfaces within and outside the integrated domain, 10.1101/2022.08.17.504349 · DOI
  64. Zhang, 2017, Mechanism of host substrate acetylation by a YopJ family effector, Nat Plants, 3, 17115, 10.1038/nplants.2017.115 · DOI

Metadata

Authors
Bentham, A. R., De la Concepcion, J. C., Benjumea, J. V., Kourelis, J., Jones, S., Mendel, M., Stubbs, J., Stevenson, C. E. M., Maidment, J. H. R., Youles, M., Zdrzałek, R., Kamoun, S., & Banfield, M. J.
Affiliations
  • John Innes Centre (GB)
  • Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park , Norwich NR4 7UH , UK
  • University of East Anglia (GB)
Corresponding author
  • Benjumea, Javier Vega
  • Mendel, Melanie
  • Stubbs, Jack
  • Maidment, Josephine H R
  • Banfield, Mark J
ORCID
Venue
The Plant Cell
Publisher
Oxford University Press (OUP)
Published
2023-07-24
Volume
35
Issue
10
Pages
3809-3827
ISSN
  • 1040-4651 (ISSN-L)
  • 1532-298X
DOI
10.1093/plcell/koad204
PMC
PMC10533329
OpenAlex
W4385186561
Cited by
46
References
2
Citations by year
2026: 13 · 2025: 16 · 2024: 7 · 2023: 10
FWCI
7.23
Type
journal article
Language
en
Open access
Licence
Locations
  • The Plant Cell (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Durham Research Online (Durham University) (publishedVersion, other-oa)
  • UEA Digital Repository (University of East Anglia) (acceptedVersion)
  • HAL (submittedVersion, cc-by)
  • Durham Research Online (Durham University) (submittedVersion, cc-by)
  • Spiral (Imperial College London) (submittedVersion, cc-by)
  • Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, cc-by)
  • Zenodo (CERN European Organization for Nuclear Research) (cc-by)
Funders
  • Biotechnology and Biological Sciences Research Council (BB/M011216/1, BB/P012574/1, BBS/E/J/000PR9797)
  • European Research Council (743165)
  • John Innes Foundation
  • Gatsby Charitable Foundation
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Pathogenic Bacteria Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Disease Resistance and Genetics
Keywords
plant immune receptors, nucleotide-binding leucine-rich repeat receptors, rice, Nicotiana benthamiana, immune homeostasis
MeSH terms
Alleles, Plant Diseases, Plant Proteins, Plants, Plant Immunity, Disease Resistance

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