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PreprintCited 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, Jones, Sally, Mendel, Melanie, Stubbs, Jack, Stevenson, Clare E. M., Maidment, Josephine H.R., Youles, Mark, Kourelis, Jiorgos, Zdrzałek, Rafał, Kamoun, Sophien, Banfield, Mark J.·2022·The Plant Cell
DOI 10.1101/2022.10.10.511592PMC PMC10533329

Preprint — published as 10.1093/plcell/koad204 · Paper page

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Abstract

Summary: Engineering expanded effector recognition in plant immune receptors is a promising prospect for generating new disease resistant crop varieties. However, modification of plant NLR receptors has proven challenging due to the lack of understanding of their context as part of complex immune systems. Here, we demonstrate a new avenue for NLR-mediated engineering that exploits the allelic diversity in the Pik NLR pair to allow for the generation of receptors with expanded recognition specificities, which would otherwise result in constitutive cell death. This work lays the foundation for the incorporation of new effector recognition motifs into the Pik system and advances the development of designer NLRs that can be tailored to specific secreted pathogen signatures. 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 (NLRs) superfamily for expanded recognition of pathogen virulence proteins (effectors) is a promising approach for engineering novel disease resistance. However, engineering can cause NLR autoactivation, resulting in constitutive defence responses that are deleterious to the plant. This may be due to plant NLRs associating in highly complex signalling networks that co-evolve together, and changes through breeding or genetic modification can generate incompatible combinations, resulting in autoimmune phenotypes. We have previously shown how alleles of the rice NLR pair Pik have differentially co-evolved, and how sensor/helper mismatching between non-co-evolved alleles triggers constitutive activation and cell death (De la Concepcion et al., 2021b). Here, we dissect incompatibility determinants in the Pik pair and found that HMA domains integrated in Pik-1 not only evolved to bind pathogen effectors but also likely co-evolved 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 HMA domains with novel and enhanced recognition of an effector from the rice blast fungus. Taken together, our results reveal a new 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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Metadata

Authors
Bentham, A. R., De la Concepcion, J. C., Benjumea, J. V., Jones, S., Mendel, M., Stubbs, J., Stevenson, C. E. M., Maidment, J. H. R., Youles, M., Kourelis, J., Zdrzałek, R., Kamoun, S., & Banfield, M. J.
Affiliations
  • John Innes Centre (GB)
  • 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
openRxiv
Published
2022-10-11
Volume
35
Issue
10
Pages
3809-3827
ISSN
1040-4651 (ISSN-L)
DOI
10.1101/2022.10.10.511592
PMC
PMC10533329
OpenAlex
W4385186561
Cited by
46
References
1
Citations by year
2026: 13 · 2025: 16 · 2024: 7 · 2023: 10
FWCI
7.23
Type
journal article
Language
en
Open access
Licence
cc-by
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
  • Diamond Light Source
  • UK Research and Innovation (BB/M011216/1)
  • Gatsby Charitable Foundation
  • John Innes Foundation
  • Directorate for Biological Sciences
  • Biotechnology and Biological Sciences Research Council (M011216, BB/P012574/1, BB/M011216/1, BBS/E/J/000PR9797, BBS/E/J/000PR9795, BBS/E/JI/230001A)
  • European Research Council (743165)
  • H2020 European Research Council (743165)
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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