Functional diversification gave rise to allelic specialization in a rice NLR immune receptor pair

  1. Juan Carlos De la Concepcion  Is a corresponding author
  2. Javier Vega Benjumea
  3. Aleksandra Bialas
  4. Ryohei Terauchi
  5. Sophien Kamoun
  6. Mark J Banfield  Is a corresponding author
  1. Gregor Mendel Institute of Molecular Plant Biology, Austria
  2. Hospital Universitario Puerta de Hierro, Spain
  3. The Sainsbury Laboratory, University of East Anglia, United Kingdom
  4. Iwate Biotechnology Research Center, Japan
  5. John Innes Centre, United Kingdom

Abstract

Cooperation between receptors from the NLR superfamily is important for intracellular activation of immune responses. NLRs can function in pairs that, upon pathogen recognition, trigger hypersensitive cell death and stop pathogen invasion. Natural selection drives specialization of host immune receptors towards an optimal response, whilst keeping a tight regulation of immunity in the absence of pathogens. However, the molecular basis of co-adaptation and specialization between paired NLRs remains largely unknown. Here, we describe functional specialization in alleles of the rice NLR pair Pik that confers resistance to strains of the blast fungus Magnaporthe oryzae harbouring AVR-Pik effectors. We revealed that matching pairs of allelic Pik NLRs mount effective immune responses whereas mismatched pairs lead to autoimmune phenotypes, a hallmark of hybrid necrosis in both natural and domesticated plant populations. We further showed that allelic specialization is largely underpinned by a single amino acid polymorphism that determines preferential association between matching pairs of Pik NLRs. These results provide a framework for how functionally linked immune receptors undergo co-adaptation to provide an effective and regulated immune response against pathogens. Understanding the molecular constraints that shape paired NLR evolution has implications beyond plant immunity given that hybrid necrosis can drive reproductive isolation.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Plots and Blots.

Article and author information

Author details

  1. Juan Carlos De la Concepcion

    Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
    For correspondence
    juan.concepcion@gmi.oeaw.ac.at
    Competing interests
    No competing interests declared.
  2. Javier Vega Benjumea

    Servicio de Bioquímica-Análisis clínicos, Hospital Universitario Puerta de Hierro, Madrid, Spain
    Competing interests
    No competing interests declared.
  3. Aleksandra Bialas

    The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
    Competing interests
    No competing interests declared.
  4. Ryohei Terauchi

    Division of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate, Japan
    Competing interests
    No competing interests declared.
  5. Sophien Kamoun

    The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
    Competing interests
    Sophien Kamoun, SK receives funding from industry on NLR biology.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0290-0315
  6. Mark J Banfield

    Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
    For correspondence
    Mark.banfield@jic.ac.uk
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8921-3835

Funding

Biotechnology and Biological Sciences Research Council (BB/012574)

  • Sophien Kamoun
  • Mark J Banfield

Biotechnology and Biological Sciences Research Council (BBS/E/J/000PR9795)

  • Sophien Kamoun
  • Mark J Banfield

Biotechnology and Biological Sciences Research Council (BB/M011216/1,project reference 1771322)

  • Aleksandra Bialas

ERC Horizon 2020 (743165)

  • Sophien Kamoun
  • Mark J Banfield

John Innes Foundation

  • Juan Carlos De la Concepcion

Gatsby Charitable Foundation

  • Sophien Kamoun

Erasmus+

  • Javier Vega Benjumea

Japan Society for the Promotion of Science (20H05681)

  • Ryohei Terauchi

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2021, De la Concepcion et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,805
    views
  • 416
    downloads
  • 35
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Juan Carlos De la Concepcion
  2. Javier Vega Benjumea
  3. Aleksandra Bialas
  4. Ryohei Terauchi
  5. Sophien Kamoun
  6. Mark J Banfield
(2021)
Functional diversification gave rise to allelic specialization in a rice NLR immune receptor pair
eLife 10:e71662.
https://doi.org/10.7554/eLife.71662

Share this article

https://doi.org/10.7554/eLife.71662

Further reading

    1. Plant Biology
    Zigmunds Orlovskis, Archana Singh ... Saskia A Hogenhout
    Research Article

    Obligate parasites often trigger significant changes in their hosts to facilitate transmission to new hosts. The molecular mechanisms behind these extended phenotypes - where genetic information of one organism is manifested as traits in another - remain largely unclear. This study explores the role of the virulence protein SAP54, produced by parasitic phytoplasmas, in attracting leafhopper vectors. SAP54 is responsible for the induction of leaf-like flowers in phytoplasma-infected plants. However, we previously demonstrated that the insects were attracted to leaves and the leaf-like flowers were not required. Here, we made the surprising discovery that leaf exposure to leafhopper males is required for the attraction phenotype, suggesting a leaf response that distinguishes leafhopper sex in the presence of SAP54. In contrast, this phytoplasma effector alongside leafhopper females discourages further female colonization. We demonstrate that SAP54 effectively suppresses biotic stress response pathways in leaves exposed to the males. Critically, the host plant MADS-box transcription factor short vegetative phase (SVP) emerges as a key element in the female leafhopper preference for plants exposed to males, with SAP54 promoting the degradation of SVP. This preference extends to female colonization of male-exposed svp null mutant plants over those not exposed to males. Our research underscores the dual role of the phytoplasma effector SAP54 in host development alteration and vector attraction - integral to the phytoplasma life cycle. Importantly, we clarify how SAP54, by targeting SVP, heightens leaf vulnerability to leafhopper males, thus facilitating female attraction and subsequent plant colonization by the insects. SAP54 essentially acts as a molecular ‘matchmaker’, helping male leafhoppers more easily locate mates by degrading SVP-containing complexes in leaves. This study not only provides insights into the long reach of single parasite genes in extended phenotypes, but also opens avenues for understanding how transcription factors that regulate plant developmental processes intersect with and influence plant-insect interactions.

    1. Microbiology and Infectious Disease
    2. Plant Biology
    Nyasha Charura, Ernesto Llamas ... Alga Zuccaro
    Research Article

    Programmed cell death occurring during plant development (dPCD) is a fundamental process integral for plant growth and reproduction. Here, we investigate the connection between developmentally controlled PCD and fungal accommodation in Arabidopsis thaliana roots, focusing on the root cap-specific transcription factor ANAC033/SOMBRERO (SMB) and the senescence-associated nuclease BFN1. Mutations of both dPCD regulators increase colonization by the beneficial fungus Serendipita indica, primarily in the differentiation zone. smb-3 mutants additionally exhibit hypercolonization around the meristematic zone and a delay of S. indica-induced root-growth promotion. This demonstrates that root cap dPCD and rapid post-mortem clearance of cellular corpses represent a physical defense mechanism restricting microbial invasion of the root. Additionally, reporter lines and transcriptional analysis revealed that BFN1 expression is downregulated during S. indica colonization in mature root epidermal cells, suggesting a transcriptional control mechanism that facilitates the accommodation of beneficial microbes in the roots.