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A molecular roadmap to the plant immune system

Open AccessPublished:August 17, 2020DOI:https://doi.org/10.1074/jbc.REV120.010852
      Plant diseases caused by pathogens and pests are a constant threat to global food security. Direct crop losses and the measures used to control disease (e.g. application of pesticides) have significant agricultural, economic, and societal impacts. Therefore, it is essential that we understand the molecular mechanisms of the plant immune system, a system that allows plants to resist attack from a wide variety of organisms ranging from viruses to insects. Here, we provide a roadmap to plant immunity, with a focus on cell-surface and intracellular immune receptors. We describe how these receptors perceive signatures of pathogens and pests and initiate immune pathways. We merge existing concepts with new insights gained from recent breakthroughs on the structure and function of plant immune receptors, which have generated a shift in our understanding of cell-surface and intracellular immunity and the interplay between the two. Finally, we use our current understanding of plant immunity as context to discuss the potential of engineering the plant immune system with the aim of bolstering plant defenses against disease.
      Plants suffer from disease. Their ability to respond to infection by microbial pathogens and pests is essential for survival. In agriculture, plant disease leads to loss in crop yield and can have devastating effects on both subsistence/small-holder and industrialized farming (
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      ), with subsequent impact on food supply chains and prices. Plant diseases have also shaped our world, with perhaps the best-known example being the Irish potato famine in the mid-1800s, where potato late blight disease (caused by the filamentous plant pathogen Phytophthora infestans) contributed to mass emigration from Ireland (
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      After the famine: Plant pathology, Phytophthora infestans, and the late blight of potatoes, 1845–1960.
      ).
      As a rich source of nutrients, plants are the target of microbial pathogens and pests, including viruses, bacteria, filamentous pathogens (fungi and oomycetes), nematodes, and insects to complete their life cycle (
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      ). Estimates of the impact of pre-harvest yield loss in crops due to disease vary, but at least 30% of global agricultural production is claimed annually (
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      • Nelson A.
      The global burden of pathogens and pests on major food crops.
      ). This can increase to 100% in localized outbreaks and represents a major contributor to food insecurity. In agriculture, plant diseases are largely controlled by chemicals, but this is unsustainable in the long-term due to environmental concerns and the necessity to rethink agricultural practices more generally in light of the climate emergency. Genetic forms of disease resistance offer the potential for environmentally friendly, low-input, sustainable agriculture (
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      Genetic modification to improve disease resistance in crops.
      ). Over the last 25 years, remarkable progress has been made in our understanding of the molecular basis of plant disease resistance mechanisms. Plant immune receptors, encoded by resistance or “R” genes have been cloned and characterized and shown to be the genetic basis of disease resistance phenotypes used by plant breeders for >100 years. Recent studies have extended our knowledge to reveal our first insights into the structural basis of plant immune receptor function (
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      • Zhou J.-M.
      • Chai J.
      Structural Basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex.
      ,
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      Structural basis for recognition of an endogenous peptide by the plant receptor kinase PEPR1.
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      ,
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      • Han Z.
      • Qi Y.
      • Gao N.
      • Wang H.-W.
      • Zhou J.-M.
      • Chai J.
      Ligand-triggered allosteric ADP release primes a plant NLR complex.
      ,
      • Williams S.J.
      • Sohn K.H.
      • Wan L.
      • Bernoux M.
      • Sarris P.F.
      • Segonzac C.
      • Ve T.
      • Ma Y.
      • Saucet S.B.
      • Ericsson D.J.
      • Casey L.W.
      • Lonhienne T.
      • Winzor D.J.
      • Zhang X.
      • Coerdt A.
      • et al.
      Structural basis for assembly and function of a heterodimeric plant immune receptor.
      ,
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      • Ma K.-W.
      • Gao L.
      • Hu Z.
      • Schwizer S.
      • Ma W.
      • Song J.
      Mechanism of host substrate acetylation by a YopJ family effector.
      ,
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      • Collier S.M.
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      • Chai J.
      Structural basis for the interaction between the potato virus X resistance protein (Rx) and its cofactor Ran GTPase-activating protein 2 (RanGAP2).
      ,
      • Hohmann U.
      • Hothorn M.
      Crystal structure of the leucine-rich repeat ectodomain of the plant immune receptor kinase SOBIR1.
      ).
      The immune system of plants shares similarities with the innate immune system of animals (
      • Bentham A.
      • Burdett H.
      • Anderson P.A.
      • Williams S.J.
      • Kobe B.
      Animal NLRs provide structural insights into plant NLR function.
      ,
      • Jones J.D.G.
      • Vance R.E.
      • Dangl J.L.
      Intracellular innate immune surveillance devices in plants and animals.
      ,
      • Meunier E.
      • Broz P.
      Evolutionary convergence and divergence in NLR function and structure.
      ). But as plants lack an adaptive immune system, they rely solely on innate immunity to recognize microbial pathogens and pests. Conceptually, plant immunity can be divided into cell-surface and intracellular immunity (
      • Wang W.
      • Feng B.
      • Zhou J.-M.
      • Tang D.
      Plant immune signaling: advancing on two frontiers.
      ). A full list of the structurally characterized immune receptors and associated ligands can be found in Table 1. Cell-surface immune receptors detect common signatures of pathogens or pests outside the host cell via extracellular domains (ECDs) and initiate cellular responses to resist infection via their intracellular kinase domains (KDs) (
      • Kanyuka K.
      • Rudd J.J.
      Cell surface immune receptors: the guardians of the plant's extracellular spaces.
      ). A subset of cell-surface immune receptors sense damaged “self” as a surrogate for the presence of pathogens or pests (
      • Wang J.
      • Wang J.
      • Hu M.
      • Wu S.
      • Qi J.
      • Wang G.
      • Han Z.
      • Qi Y.
      • Gao N.
      • Wang H.-W.
      • Zhou J.-M.
      • Chai J.
      Ligand-triggered allosteric ADP release primes a plant NLR complex.
      ). Intracellular immune receptors detect signatures of adapted pathogens or pests (
      • van Wersch S.
      • Tian L.
      • Hoy R.
      • Li X.
      Plant NLRs: the whistleblowers of plant immunity.
      ). Typically, these signatures are translocated proteins known as “effectors,” which are delivered inside cells to modulate host physiology to promote colonization and proliferation (
      • Snelders N.C.
      • Rovenich H.
      • Petti G.C.
      • Rocafort M.
      • Vorholt J.A.
      • Mesters J.R.
      • Seidl M.F.
      • Nijland R.
      • Thomma B.P.H.J.
      A plant pathogen utilizes effector proteins for microbiome manipulation.
      ,
      • Varden F.A.
      • De la Concepcion J.C.
      • Maidment J.H.R.
      • Banfield M.J.
      Taking the stage: effectors in the spotlight.
      ) (Fig. 1). Activation of intracellular immunity is generally considered a more robust response and can be associated with localized cell death that constrains the spread of infection. Although often presented as distinct signaling pathways, insights into how cell-surface and intracellular immune pathways in plants overlap and work synergistically to resist infection have recently begun to emerge (
      • Ngou B.P.M.
      • Ahn H.-K.
      • Ding P.
      • Jones J.D.
      Mutual potentiation of plant immunity by cell-surface and intracellular receptors.
      ,
      • Yuan M.
      • Jiang Z.
      • Bi G.
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      • Liu M.
      • He S.Y.
      • Zhou J.-M.
      • Xin X.-F.
      Pattern-recognition receptors are required for NLR-mediated plant immunity.
      ).
      Table 1Structures of plant immune receptors or their domains covered in this review
      ReceptorType: Cell-surfacePlant hostLigandLigand typeCo-receptorPDB codeReferences
      FLS2LRR-RLKArabidopsis thalianaflg22MAMPBAK14MN8
      • Sun Y.
      • Li L.
      • Macho A.P.
      • Han Z.
      • Hu Z.
      • Zipfel C.
      • Zhou J.-M.
      • Chai J.
      Structural Basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex.
      PEPR1LRR-RLKA. thalianaAtpepDAMPBAK15GR8
      • Tang J.
      • Han Z.
      • Sun Y.
      • Zhang H.
      • Gong X.
      • Chai J.
      Structural basis for recognition of an endogenous peptide by the plant receptor kinase PEPR1.
      CERK1LysM-RLKA. thalianaPGNMAMPLYM3/14EBY
      • Liu T.
      • Liu Z.
      • Song C.
      • Hu Y.
      • Han Z.
      • She J.
      • Fan F.
      • Wang J.
      • Jin C.
      • Chang J.
      • Zhou J.-M.
      • Chai J.
      Chitin-induced dimerization activates a plant immune receptor.
      SOBIR1LRR-RLKA. thalianaNA
      NA, not applicable.
      NALRR-RLP, BAK16R1H
      • Hohmann U.
      • Hothorn M.
      Crystal structure of the leucine-rich repeat ectodomain of the plant immune receptor kinase SOBIR1.
      BIR3PseudokinaseA. thalianaNANABRI1/S.E.RK16FG8
      • Hohmann U.
      • Nicolet J.
      • Moretti A.
      • Hothorn L.A.
      • Hothorn M.
      The SERK3 elongated allele defines a role for BIR ectodomains in brassinosteroid signalling.
      BIK1RLCKA. thalianaNANABAK1, FLS25TOS
      • Lal N.K.
      • Nagalakshmi U.
      • Hurlburt N.K.
      • Flores R.
      • Bak A.
      • Sone P.
      • Ma X.
      • Song G.
      • Walley J.
      • Shan L.
      • He P.
      • Casteel C.
      • Fisher A.J.
      • Dinesh-Kumar S.P.
      The receptor-like cytoplasmic kinase BIK1 localizes to the nucleus and regulates defense hormone expression during plant innate immunity.
      CEBiPLysM-RLPOryza sativaChitinMAMPOsCERK15JCD, 5JCE
      • Liu S.
      • Wang J.
      • Han Z.
      • Gong X.
      • Zhang H.
      • Chai J.
      Molecular mechanism for fungal cell wall recognition by rice chitin receptor OsCEBiP.
      ReceptorType: IntracellularPlant hostLigand(s)Ligand typeCo-receptorPDB codeReferences
      MLA10 CCCC-NLRHordeum vulgareNANANA3QFL, 5T1Y
      • Maekawa T.
      • Cheng W.
      • Spiridon L.N.
      • Töller A.
      • Lukasik E.
      • Saijo Y.
      • Liu P.
      • Shen Q.H.
      • Micluta M.A.
      • Somssich I.E.
      • Takken F.L.W.
      • Petrescu A.J.
      • Chai J.
      • Schulze-Lefert P.
      Coiled-coil domain-dependent homodimerization of intracellular barley immune receptors defines a minimal functional module for triggering cell death.
      ,
      • Casey L.W.
      • Lavrencic P.
      • Bentham A.R.
      • Cesari S.
      • Ericsson D.J.
      • Croll T.
      • Turk D.
      • Anderson P.A.
      • Mark A.E.
      • Dodds P.N.
      • Mobli M.
      • Kobe B.
      • Williams S.J.
      The CC domain structure from the wheat stem rust resistance protein Sr33 challenges paradigms for dimerization in plant NLR proteins.
      Pikp-1 HMACC-NLRO. sativaAVR-PikD, AVR-PikE, AVR-PikA, AVR-PiaMAX effectorPikp-25A6W, 5A6P, 6G11, 6G10, 6Q76
      • Maqbool A.
      • Saitoh H.
      • Franceschetti M.
      • Stevenson C.E.M.
      • Uemura A.
      • Kanzaki H.
      • Kamoun S.
      • Terauchi R.
      • Banfield M.J.
      Structural basis of pathogen recognition by an integrated HMA domain in a plant NLR immune receptor.
      ,
      • De la Concepcion J.C.
      • Franceschetti M.
      • Maqbool A.
      • Saitoh H.
      • Terauchi R.
      • Kamoun S.
      • Banfield M.J.
      Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen.
      ,
      • Varden F.A.
      • Saitoh H.
      • Yoshino K.
      • Franceschetti M.
      • Kamoun S.
      • Terauchi R.
      • Banfield M.J.
      Cross-reactivity of a rice NLR immune receptor to distinct effectors from the rice blast pathogen Magnaporthe oryzae provides partial disease resistance.
      Pikm-1 HMACC-NLRO. sativaAVR-PikE, AVR-PikA, AVR-PikDMAX effectorPikm-26FUB, 6FUD, 6FU9
      • De la Concepcion J.C.
      • Franceschetti M.
      • Maqbool A.
      • Saitoh H.
      • Terauchi R.
      • Kamoun S.
      • Banfield M.J.
      Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen.
      Pia HMACC-NLRO. sativaAvr1-CO39MAX effectorRGA45ZNG, 5ZNE
      • Guo L.
      • Cesari S.
      • de Guillen K.
      • Chalvon V.
      • Mammri L.
      • Ma M.
      • Meusnier I.
      • Bonnot F.
      • Padilla A.
      • Peng Y.-L.
      • Liu J.
      • Kroj T.
      Specific recognition of two MAX effectors by integrated HMA domains in plant immune receptors involves distinct binding surfaces.
      RRS1 WRKYTIR-NLRA. thalianaPopP2T3SERPS45W3X
      • Zhang Z.-M.
      • Ma K.-W.
      • Gao L.
      • Hu Z.
      • Schwizer S.
      • Ma W.
      • Song J.
      Mechanism of host substrate acetylation by a YopJ family effector.
      ZAR1CC-NLRA. thalianaAvr-ACT3SERKS16J5T, 6J6I, 6J5W, 6J5V
      • Wang J.
      • Hu M.
      • Wang J.
      • Qi J.
      • Han Z.
      • Wang G.
      • Qi Y.
      • Wang H.-W.
      • Zhou J.-M.
      • Chai J.
      Reconstitution and structure of a plant NLR resistosome conferring immunity.
      ,
      • Wang J.
      • Wang J.
      • Hu M.
      • Wu S.
      • Qi J.
      • Wang G.
      • Han Z.
      • Qi Y.
      • Gao N.
      • Wang H.-W.
      • Zhou J.-M.
      • Chai J.
      Ligand-triggered allosteric ADP release primes a plant NLR complex.
      RPS4 TIRTIR-NLRA. thalianaNANARRS14C6T, 4C6R,
      • Williams S.J.
      • Sohn K.H.
      • Wan L.
      • Bernoux M.
      • Sarris P.F.
      • Segonzac C.
      • Ve T.
      • Ma Y.
      • Saucet S.B.
      • Ericsson D.J.
      • Casey L.W.
      • Lonhienne T.
      • Winzor D.J.
      • Zhang X.
      • Coerdt A.
      • et al.
      Structural basis for assembly and function of a heterodimeric plant immune receptor.
      RRS1 TIRTIR-NLRA. thalianaNANARPS44C6T,4C6S
      • Williams S.J.
      • Sohn K.H.
      • Wan L.
      • Bernoux M.
      • Sarris P.F.
      • Segonzac C.
      • Ve T.
      • Ma Y.
      • Saucet S.B.
      • Ericsson D.J.
      • Casey L.W.
      • Lonhienne T.
      • Winzor D.J.
      • Zhang X.
      • Coerdt A.
      • et al.
      Structural basis for assembly and function of a heterodimeric plant immune receptor.
      SNC1 TIRTIR-NLRA. thalianaNANANA5TEC
      • Zhang X.
      • Bernoux M.
      • Bentham A.R.
      • Newman T.E.
      • Ve T.
      • Casey L.W.
      • Raaymakers T.M.
      • Hu J.
      • Croll T.I.
      • Schreiber K.J.
      • Staskawicz B.J.
      • Anderson P.A.
      • Sohn K.H.
      • Williams S.J.
      • Dodds P.N.
      • et al.
      Multiple functional self-association interfaces in plant TIR domains.
      SNC1 TIRTIR-NLRA. thalianaNANANA5H3C
      • Hyun K-G.
      • Lee Y.
      • Yoon J.
      • Yi H.
      • Song J.-J.
      Crystal structure of Arabidopsis thaliana SNC1 TIR domain.
      Sr33 CCCC-NLRAegilops tauschiiNANANA2NCG
      • Casey L.W.
      • Lavrencic P.
      • Bentham A.R.
      • Cesari S.
      • Ericsson D.J.
      • Croll T.
      • Turk D.
      • Anderson P.A.
      • Mark A.E.
      • Dodds P.N.
      • Mobli M.
      • Kobe B.
      • Williams S.J.
      The CC domain structure from the wheat stem rust resistance protein Sr33 challenges paradigms for dimerization in plant NLR proteins.
      RPP1 TIRTIR-NLRA. thalianaNANANA5TEB
      • Zhang X.
      • Bernoux M.
      • Bentham A.R.
      • Newman T.E.
      • Ve T.
      • Casey L.W.
      • Raaymakers T.M.
      • Hu J.
      • Croll T.I.
      • Schreiber K.J.
      • Staskawicz B.J.
      • Anderson P.A.
      • Sohn K.H.
      • Williams S.J.
      • Dodds P.N.
      • et al.
      Multiple functional self-association interfaces in plant TIR domains.
      NRC1 NB-ARCTIR-NLRSolanum lycopersicumNANANA6S2P
      • Steele J.F.C.
      • Hughes R.K.
      • Banfield M.J.
      Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor.
      RUN1 TIRTIR-NLRVitis rotundifoliaNANANA60OW
      • Horsefield S.
      • Burdett H.
      • Zhang X.
      • Manik M.K.
      • Shi Y.
      • Chen J.
      • Qi T.
      • Gilley J.
      • Lai J.-S.
      • Rank M.X.
      • Casey L.W.
      • Gu W.
      • Ericsson D.J.
      • Foley G.
      • Hughes R.O.
      • et al.
      NAD+ cleavage activity by animal and plant TIR domains in cell death pathways.
      Rx CCCC-NLRSolanum tuberosumNANARanGAP24M70
      • Hao W.
      • Collier S.M.
      • Moffett P.
      • Chai J.
      Structural basis for the interaction between the potato virus X resistance protein (Rx) and its cofactor Ran GTPase-activating protein 2 (RanGAP2).
      RPV1 TIRTIR-NLRVitis rotundifoliaNANANA5KU7
      • Williams S.
      • YIn L.
      • Foley G.
      • Casey L.
      • Outram M.
      • Ericsson D.
      • Lu J.
      • Boden M.
      • Dry I.
      • Kobe B.
      Structure and function of the TIR domain from the grape NLR protein RPV1.
      L6 TIRTIR-NLRLinum usitatissimummNANANA3OZI
      • Bernoux M.
      • Ve T.
      • Williams S.
      • Warren C.
      • Hatters D.
      • Valkov E.
      • Zhang X.
      • Ellis J.G.
      • Kobe B.
      • Dodds P.N.
      Structural and functional analysis of a plant resistance protein TIR domain reveals interfaces for self-association, signaling, and autoregulation.
      PtoKinaseSolanum pimpinellifoliumAvrPtoBT3SEPrf3HGK
      • Dong J.
      • Xiao F.
      • Fan F.
      • Gu L.
      • Cang H.
      • Martin G.B.
      • Chai J.
      Crystal structure of the complex between Pseudomonas effector AvrPtoB and the tomato Pto kinase reveals both a shared and a unique interface compared with AvrPto-Pto.
      a NA, not applicable.
      Figure thumbnail gr1
      Figure 1Plant immunity at a glance. Left, plants are the target of a variety of pathogens and pests that cause disease, via both their above-ground and underground structures. Right, pathogens/pests shed MAMPs or generate DAMPs that can be received by receptors to initiate cell-surface immunity. Pathogens/pests can deliver effectors to the outside (not shown here for simplicity) or inside of cells, where they can act on host systems to their benefit, including the suppression of signaling pathways downstream of cell-surface receptors. Effectors or their activities can be sensed by intracellular immune receptors (NLRs) to initiate intracellular immunity.
      There are many excellent reviews covering plant immunity and its subversion by microbial pathogens and pests published over the last ∼15 years (
      • Jones J.D.G.
      • Vance R.E.
      • Dangl J.L.
      Intracellular innate immune surveillance devices in plants and animals.
      ,
      • Kanyuka K.
      • Rudd J.J.
      Cell surface immune receptors: the guardians of the plant's extracellular spaces.
      ,
      • Jones J.D.G.
      • Dangl J.L.
      The plant immune system.
      ,
      • Chisholm S.T.
      • Coaker G.
      • Day B.
      • Staskawicz B.J.
      Host-microbe interactions: shaping the evolution of the plant immune response.
      ,
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      Resistance proteins: molecular switches of plant defence.
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      • Takken F.L.W.
      • Goverse A.
      How to build a pathogen detector: structural basis of NB-LRR function.
      ,
      • Wirthmueller L.
      • Maqbool A.
      • Banfield M.J.
      On the front line: structural insights into plant-pathogen interactions.
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      • Schellenberger R.
      • Touchard M.
      • Clément C.
      • Baillieul F.
      • Cordelier S.
      • Crouzet J.
      • Dorey S.
      Apoplastic invasion patterns triggering plant immunity: plasma membrane sensing at the frontline.
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      • van der Hoorn R.A.L.
      Defended to the nines: 25 years of resistance gene cloning identifies nine mechanisms for R protein function.
      ,
      • Tamborski J.
      • Krasileva K.V.
      Evolution of plant NLRs: from natural history to precise modifications.
      ,
      • Hogenhout S.A.
      • Van der Hoorn R.A.L.
      • Terauchi R.
      • Kamoun S.
      Emerging concepts in effector biology of plant-associated organisms.
      ). Here, as part of this JBC “Plants in the Real World” thematic series, we provide an up-to-date overview of the general concepts of plant disease resistance mechanisms, with a focus on plant immune receptor function at the molecular level. We detail how these receptors perceive pathogen signatures at the cell surface and inside host cells and how this perception is translated into an immune response. This review summarizes the general concepts of plant immunity before providing in-depth analyses of the more recent breakthroughs that have greatly expanded our understanding of plant immune receptor function. Finally, in the context of current knowledge, we discuss how plant immune receptors could be engineered to deliver novel disease resistance properties to benefit global food security.

      Effectors: Master manipulators of plant cells to promote infection

      To best understand the interplay between the pathogens/pests and the plant immune system, we must first understand effectors and their role in promoting virulence. In the broadest definition, effectors are molecules used by a diverse array of organisms (including microbes, plants, and animals) to modulate the activity of another organism. In this review, we use the term “effectors” to define protein molecules secreted by microbial pathogens and pests to promote colonization of their plant hosts (
      • Hogenhout S.A.
      • Van der Hoorn R.A.L.
      • Terauchi R.
      • Kamoun S.
      Emerging concepts in effector biology of plant-associated organisms.
      ). These effectors can be delivered to the extracellular space or deployed to the inside of host cells.
      Effector genes exist as large repertoires within pathogen genomes. They are among the most rapidly evolving genes in plant pathogens and can display high rates of nonsynonymous over synonymous mutations (
      • Dong S.
      • Raffaele S.
      • Kamoun S.
      The two-speed genomes of filamentous pathogens: waltz with plants.
      ,
      • Raffaele S.
      • Farrer R.A.
      • Cano L.M.
      • Studholme D.J.
      • MacLean D.
      • Thines M.
      • Jiang R.H.
      • Zody M.C.
      • Kunjeti S.G.
      • Donofrio N.M.
      • Meyers B.C.
      • Nusbaum C.
      • Kamoun S.
      Genome evolution following host jumps in the Irish potato famine pathogen lineage.
      ). Selection for evasion of perception by the plant immune system is a major driver for adaptation, along with selection for favorable alleles that give a fitness benefit (
      • Allen R.L.
      • Bittner-Eddy P.D.
      • Grenville-Briggs L.J.
      • Meitz J.C.
      • Rehmany A.P.
      • Rose L.E.
      • Beynon J.L.
      Host-parasite coevolutionary conflict between Arabidopsis and downy mildew.
      ). Due to their sequence diversity, it is frequently challenging to identify effectors in pathogen/pest genomes or proteomes, although many bioinformatic tools exist to establish putative effector catalogues (
      • Sperschneider J.
      Machine learning in plant–pathogen interactions: empowering biological predictions from field scale to genome scale.
      ). Functional annotation of effectors is equally challenging. Whereas some effectors are enzymes, whose putative activity can be identified from sequence or structural analysis, many do not show sequence or structural homologies to help define function (
      • Wirthmueller L.
      • Maqbool A.
      • Banfield M.J.
      On the front line: structural insights into plant-pathogen interactions.
      ,
      • Franceschetti M.
      • Maqbool A.
      • Jiménez-Dalmaroni M.J.
      • Pennington H.G.
      • Kamoun S.
      • Banfield M.J.
      Effectors of filamentous plant pathogens: commonalities amid diversity.
      ). This often necessitates significant investment in research of a single protein to establish the molecular basis of activity (
      • Varden F.A.
      • De la Concepcion J.C.
      • Maidment J.H.R.
      • Banfield M.J.
      Taking the stage: effectors in the spotlight.
      ). Such research will frequently address the host cell target of an effector, as this is often key to understanding its role in virulence. Some effectors converge on “hubs,” key components of host cell pathways, to modulate their function (
      • Weßling R.
      • Epple P.
      • Altmann S.
      • He Y.
      • Yang L.
      • Henz S.R.
      • McDonald N.
      • Wiley K.
      • Bader K.C.
      • Gläßer C.
      • Mukhtar M.S.
      • Haigis S.
      • Ghamsari L.
      • Stephens A.E.
      • Ecker J.R.
      • et al.
      Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life.
      ,
      • Mukhtar M.S.
      • Carvunis A.R.
      • Dreze M.
      • Epple P.
      • Steinbrenner J.
      • Moore J.
      • Tasan M.
      • Galli M.
      • Hao T.
      • Nishimura M.T.
      • Pevzner S.J.
      • Donovan S.E.
      • Ghamsari L.
      • Santhanam B.
      • Romero V.
      • et al.
      Independently evolved virulence effectors converge onto hubs in a plant immune system network.
      ). Such pathways include suppression of defense responses (Fig. 1) and redirection of host metabolism.
      Effectors are also an Achilles' heel for the pathogen/pest. As signatures of non-self, they can be perceived by plant immune receptors at both the cell surface and inside cells. Intracellular perception of effectors or their activities is mediated and transduced by NLRs, as described elsewhere in this review.

      Cell-surface immunity

      Two major components of cell-surface immunity in plants are membrane-localized receptor-like kinases (RLKs) and receptor-like proteins (RLPs) that detect signatures of non-self as signs of infection (
      • Jones J.D.G.
      • Dangl J.L.
      The plant immune system.
      ). RLKs/RLPs also have other roles in plants, regulating self-incompatibility, growth and development, reproduction, response to abiotic stress, and symbiosis (
      • Jones J.D.G.
      • Dangl J.L.
      The plant immune system.
      ,
      • Sanabria N.
      • Goring D.
      • Nürnberger T.
      • Dubery I.
      Self/nonself perception and recognition mechanisms in plants: a comparison of self-incompatibility and innate immunity.
      ,
      • Antolín-Llovera M.
      • Petutsching E.K.
      • Ried M.K.
      • Lipka V.
      • Nürnberger T.
      • Robatzek S.
      • Parniske M.
      Knowing your friends and foes—plant receptor-like kinases as initiators of symbiosis or defence.
      ,
      • Jamieson P.A.
      • Shan L.
      • He P.
      Plant cell surface molecular cypher: receptor-like proteins and their roles in immunity and development.
      ). Also known as pattern recognition receptors (PRRs), cell-surface immune receptors monitor the extracellular environment for pathogen/pest invasion patterns (ligands known as MAMPs (microbial-associated molecular patterns) or DAMPs (damage-associated molecular patterns)) (
      • Boller T.
      • Felix G.
      A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors.
      ,
      • Saijo Y.
      • Loo E.P-I.
      • Yasuda S.
      Pattern recognition receptors and signaling in plant–microbe interactions.
      ). Frequently, ligand-sensing cell-surface receptors require co-receptors to transduce perception of non-self into a response (
      • Böhm H.
      • Albert I.
      • Fan L.
      • Reinhard A.
      • Nürnberger T.
      Immune receptor complexes at the plant cell surface.
      ,
      • Macho A.P.
      • Zipfel C.
      Plant PRRs and the activation of innate immune signaling.
      ). Although proteinaceous receptors represent the major players in cell-surface immunity of plants, recent studies have highlighted an emerging role of membrane lipids in sensing infection (
      • Schellenberger R.
      • Touchard M.
      • Clément C.
      • Baillieul F.
      • Cordelier S.
      • Crouzet J.
      • Dorey S.
      Apoplastic invasion patterns triggering plant immunity: plasma membrane sensing at the frontline.
      ).
      Irrespective of their origin, invasion patterns recognized by cell-surface immune receptors tend to be evolutionarily constrained ligands derived from components essential to the fitness of the pathogen/pest. These essential components range from cell wall constituents or subunits of bacterial flagellin, to molecules secreted into the apoplast, to secreted proteins intended for the host cytosol (
      • Kanyuka K.
      • Rudd J.J.
      Cell surface immune receptors: the guardians of the plant's extracellular spaces.
      ). These specific ligands are perceived by cell-surface receptors at nanomolar concentrations and initiate signaling cascades, including production of reactive oxygen species (ROS), cytosolic Ca2+ bursts, activation of MAPKs, and changes in expression of various defense-related genes (
      • Boller T.
      • Felix G.
      A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors.
      ,
      • Macho A.P.
      • Zipfel C.
      Plant PRRs and the activation of innate immune signaling.
      ,
      • Dodds P.N.
      • Rathjen J.P.
      Plant immunity: towards an integrated view of plant–pathogen interactions.
      ). Generally, cell-surface immune responses are considered less volatile when compared with intracellular immunity and do not result in host cell death to restrict infection. However, they constitute an effective host strategy against infection, leading to broad-spectrum resistance (
      • Boutrot F.
      • Zipfel C.
      Function, discovery, and exploitation of plant pattern recognition receptors for broad-spectrum disease resistance.
      ). This review focuses on the mechanisms of immune activation rather than the downstream effects of extracellular and intracellular immunity; for readers interested in the physiological effects of immune activation, we recommend relevant reviews (
      • Lamb C.
      • Dixon R.A.
      The oxidative burst in plant disease resistance.
      ,
      • Balint-Kurti P.
      The plant hypersensitive response: concepts, control and consequences.
      ,
      • Greenberg J.T.
      Programmed cell death in plant-pathogen interactions.
      ).
      Signaling cascades downstream of cell-surface immune receptors are major targets of pathogen/pest effector proteins, which interfere with these processes to benefit infection. It is also worth noting that many MAMPs are shared between pathogens and mutualistic microbes (
      • Antolín-Llovera M.
      • Petutsching E.K.
      • Ried M.K.
      • Lipka V.
      • Nürnberger T.
      • Robatzek S.
      • Parniske M.
      Knowing your friends and foes—plant receptor-like kinases as initiators of symbiosis or defence.
      ,
      • Zipfel C.
      • Oldroyd G.E.
      Plant signalling in symbiosis and immunity.
      ), and as such it is important to understand how plants use extracellular immune receptors to distinguish between pathogens/pests and mutualists. In this review, we cover MAMP recognition from a pathogen/pest-detection perspective and would direct readers interested in plant-mutualist interaction to relevant reviews (
      • Antolín-Llovera M.
      • Petutsching E.K.
      • Ried M.K.
      • Lipka V.
      • Nürnberger T.
      • Robatzek S.
      • Parniske M.
      Knowing your friends and foes—plant receptor-like kinases as initiators of symbiosis or defence.
      ,
      • Zipfel C.
      • Oldroyd G.E.
      Plant signalling in symbiosis and immunity.
      ).

      Structural and functional diversity of ligand recognition by cell-surface receptors

      RLKs contain a variable extracellular domain that mediates ligand recognition, a single-pass transmembrane domain, and an intracellular KD that transduces the signal to downstream immune components (
      • Wang J.
      • Chai J.
      Structural insights into the plant immune receptors PRRs and NLRs.
      ) (Fig. 2). Most plant RLKs identified belong to the family of non-RD kinases (defined by the absence of conserved arginine in the catalytic loop) and often associate in dynamic complexes with membrane-bound RLKs that are functional RD kinases (such as BAK1 (BRASSINOSTEROID-INSENSITIVE 1–associated receptor kinase 1) and SERKs), which operate as co-receptors for perception to initiate immune signaling (
      • Dardick C.
      • Schwessinger B.
      • Ronald P.
      Non-arginine-aspartate (non-RD) kinases are associated with innate immune receptors that recognize conserved microbial signatures.
      ,
      • Ma X.
      • Xu G.
      • He P.
      • Shan L.
      SERKing coreceptors for receptors.
      ,
      • Gao X.
      • Ruan X.
      • Sun Y.
      • Wang X.
      • Feng B.
      BAKing up to survive a battle: functional dynamics of BAK1 in plant programmed cell death.
      ). Whereas RLPs exhibit a similar overall structure to RLKs, they only contain a short intracellular tail, lacking a kinase domain, and require a partner co-receptor to signal (
      • Jamieson P.A.
      • Shan L.
      • He P.
      Plant cell surface molecular cypher: receptor-like proteins and their roles in immunity and development.
      ,
      • Burkart R.C.
      • Stahl Y.
      Dynamic complexity: plant receptor complexes at the plasma membrane.
      ).
      Figure thumbnail gr2
      Figure 2Diversity of cell-surface immune receptors. A schematic representation depicts the domain architecture of different classes of plant RLKs/RLPs. Surface representations are shown for those ECDs for which crystal structures are available. LRR, crystal structure of the ECD of Arabidopsis RLK FLS2, PDB entry 4MNA (green); LysM, crystal structure of the ECD of Arabidopsis RLK–CERK1, PDB entry 4EBY (purple).
      Based on the type of ECD, RLKs and RLPs can be clustered into distinct subfamilies, including leucine-rich repeat (LRR), lysin motif (LysM), lectin, and epidermal growth factor (EGF) domain–containing receptors (
      • Böhm H.
      • Albert I.
      • Fan L.
      • Reinhard A.
      • Nürnberger T.
      Immune receptor complexes at the plant cell surface.
      ,
      • Wu Y.
      • Zhou J.-M.
      Receptor-like kinases in plant innate immunity.
      ,
      • Zipfel C.
      Plant pattern-recognition receptors.
      ) (Fig. 2). The type of ECD mainly defines the nature of the ligand perceived by the RLK/RLPs; however, a few anomalies persist. Among the best-characterized cell-surface immune receptors are the Arabidopsis LRR-type RLKs, FLS2 (flagellin-sensitive 2) and EFR (elongation factor Tu (EF-Tu) receptor) (
      • Kunze G.
      • Zipfel C.
      • Robatzek S.
      • Niehaus K.
      • Boller T.
      • Felix G.
      The N terminus of bacterial elongation factor Tu elicits innate immunity in Arabidopsis plants.
      ,
      • Chinchilla D.
      • Zipfel C.
      • Robatzek S.
      • Kemmerling B.
      • Nürnberger T.
      • Jones J.D.G.
      • Felix G.
      • Boller T.
      A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence.
      ), and the LysM-type RLKs LYK5 (lysin motif receptor kinase 5) and CERK1 (chitin elicitor receptor kinase 1) (
      • Miya A.
      • Albert P.
      • Shinya T.
      • Desaki Y.
      • Ichimura K.
      • Shirasu K.
      • Narusaka Y.
      • Kawakami N.
      • Kaku H.
      • Shibuya N.
      CERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in Arabidopsis.
      ,
      • Cao Y.
      • Liang Y.
      • Tanaka K.
      • Nguyen C.T.
      • Jedrzejczak R.P.
      • Joachimiak A.
      • Stacey G.
      The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1.
      ). FLS2 (Fig. 3) and EFR recognize peptide epitopes from the N termini of bacterial flagellin (flg22) and bacterial EF-Tu (elf18), respectively (
      • Zipfel C.
      • Kunze G.
      • Chinchilla D.
      • Caniard A.
      • Jones J.D.G.
      • Boller T.
      • Felix G.
      Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation.
      ), whereas LYK5 and CERK1 bind fungal chitin oligomers (
      • Cao Y.
      • Liang Y.
      • Tanaka K.
      • Nguyen C.T.
      • Jedrzejczak R.P.
      • Joachimiak A.
      • Stacey G.
      The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1.
      ).
      Figure thumbnail gr3
      Figure 3A mechanistic view of flg22 sensing by FLS2. flg22 (light green) stabilizes the heterodimerization of FLS2 (dark green, PDB entries 4NMA and 4NM8) with BAK1 (purple, PDB entries 3ULZ and 4NM8) (
      • Chinchilla D.
      • Zipfel C.
      • Robatzek S.
      • Kemmerling B.
      • Nürnberger T.
      • Jones J.D.G.
      • Felix G.
      • Boller T.
      A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence.
      ,
      • Schulze B.
      • Mentzel T.
      • Jehle A.K.
      • Mueller K.
      • Beeler S.
      • Boller T.
      • Felix G.
      • Chinchilla D.
      Rapid heteromerization and phosphorylation of ligand-activated plant transmembrane receptors and their associated kinase BAK1.
      ,
      • Heese A.
      • Hann D.R.
      • Gimenez-Ibanez S.
      • Jones A.M.E.
      • He K.
      • Li J.
      • Schroeder J.I.
      • Peck S.C.
      • Rathjen J.P.
      The receptor-like kinase SERK3/BAK1 is a central regulator of innate immunity in plants.
      ). Ligand perception leads to activation and phosphorylation of BIK1 (orange, PDB entry 5TOS) by BAK1 (
      • Lu D.
      • Wu S.
      • Gao X.
      • Zhang Y.
      • Shan L.
      • He P.
      A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity.
      ,
      • Zhang J.
      • Li W.
      • Xiang T.
      • Liu Z.
      • Laluk K.
      • Ding X.
      • Zou Y.
      • Gao M.
      • Zhang X.
      • Chen S.
      • Mengiste T.
      • Zhang Y.
      • Zhou J.-M.
      Receptor-like cytoplasmic kinases integrate signaling from multiple plant immune receptors and are targeted by a Pseudomonas syringae effector.
      ). Following phosphorylation, BIK1 is monoubiquitinated (Ub) by the E3 ligases RHA3A/B. Monoubiquitinated BIK1 is then released from the FLS2–BAK1 complex and initiates ROS production and Ca2+ signaling through phosphorylation of plasma membrane–localized NADPH oxidases and cyclic nucleotide–gated channels (
      • Ma X.
      • Claus L.A.N.
      • Leslie M.E.
      • Tao K.
      • Wu Z.
      • Liu J.
      • Yu X.
      • Li B.
      • Zhou J.
      • Savatin D.V.
      • Peng J.
      • Tyler B.M.
      • Heese A.
      • Russinova E.
      • He P.
      • et al.
      Ligand-induced monoubiquitination of BIK1 regulates plant immunity.
      ). The bidirectional arrow indicates that both BIK1 and BAK1 can trans-phosphorylate each other.

      Recognition of peptide/protein ligands

      LRR-RLKs are a large subfamily of cell-surface receptors that preferentially bind peptides or proteins as ligands (
      • Albert M.
      Peptides as triggers of plant defence.
      ,
      • Mott G.A.
      • Middleton M.A.
      • Desveaux D.
      • Guttman D.S.
      Peptides and small molecules of the plant-pathogen apoplastic arena.
      ,
      • Smakowska-Luzan E.
      • Mott G.A.
      • Parys K.
      • Stegmann M.
      • Howton T.C.
      • Layeghifard M.
      • Neuhold J.
      • Lehner A.
      • Kong J.
      • Grünwald K.
      • Weinberger N.
      • Satbhai S.B.
      • Mayer D.
      • Busch W.
      • Madalinski M.
      • et al.
      An extracellular network of Arabidopsis leucine-rich repeat receptor kinases.
      ). In addition to the Arabidopsis FLS2 and EFR, LRR-RLKs from rice and solanaceous plants have been characterized. The rice cell-surface receptor Xa21 binds RaxX21-sY (a sulfated, 21-amino acid synthetic RaxX peptide), a tyrosine-sulfated protein from bacteria (
      • Pruitt R.N.
      • Schwessinger B.
      • Joe A.
      • Thomas N.
      • Liu F.
      • Albert M.
      • Robinson M.R.
      • Chan L.J.G.
      • Luu D.D.
      • Chen H.
      • Bahar O.
      • Daudi A.
      • De Vleesschauwer D.
      • Caddell D.
      • Zhang W.
      • et al.
      The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium.
      ). Cell-surface receptors from tomato (CORE) and tobacco (NbCSPR) bind to conserved epitopes derived from bacterial cold shock protein (
      • Felix G.
      • Boller T.
      Molecular sensing of bacteria in plants: the highly conserved RNA-binding motif RNP-1 of bacterial cold shock proteins is recognized as an elicitor signal in tobacco.
      ,
      • Wang L.
      • Albert M.
      • Einig E.
      • Fürst U.
      • Krust D.
      • Felix G.
      The pattern-recognition receptor CORE of Solanaceae detects bacterial cold-shock protein.
      ,
      • Wei Y.
      • Caceres-Moreno C.
      • Jimenez-Gongora T.
      • Wang K.
      • Sang Y.
      • Lozano-Duran R.
      • Macho A.P.
      The Ralstonia solanacearum csp22 peptide, but not flagellin-derived peptides, is perceived by plants from the Solanaceae family.
      ). Likewise, Arabidopsis RLP23 binds the epitope nlp-20, a conserved peptide derived from ethylene-inducing peptide 1–like proteins of bacterial and filamentous pathogens (
      • Albert I.
      • Böhm H.
      • Albert M.
      • Feiler C.E.
      • Imkampe J.
      • Wallmeroth N.
      • Brancato C.
      • Raaymakers T.M.
      • Oome S.
      • Zhang H.
      • Krol E.
      • Grefen C.
      • Gust A.A.
      • Chai J.
      • Hedrich R.
      • et al.
      An RLP23–SOBIR1–BAK1 complex mediates NLP-triggered immunity.
      ).
      Although not an LRR-RLK, the Arabidopsis cell-surface receptor FERONIA (FER) uses a tandem malectin-like ECD to perceive RALF1 (rapid alkalinization factor 1) peptides. RALF peptides are cysteine-rich peptides prevalent in the plant kingdom that regulate many aspects of plant life, such as reproduction, growth, responses to environment, and immunity (
      • Haruta M.
      • Sabat G.
      • Stecker K.
      • Minkoff B.B.
      • Sussman M.R.
      A peptide hormone and its receptor protein kinase regulate plant cell expansion.
      ,
      • Xiao Y.
      • Stegmann M.
      • Han Z.
      • DeFalco T.A.
      • Parys K.
      • Xu L.
      • Belkhadir Y.
      • Zipfel C.
      • Chai J.
      Mechanisms of RALF peptide perception by a heterotypic receptor complex.
      ). Intriguingly, some functionally active RALF-like peptides have been characterized from fungal pathogens; however, the role of these RALF-like peptides in pathogenesis is unknown (
      • Thynne E.
      • Saur I.M.L.
      • Simbaqueba J.
      • Ogilvie H.A.
      • Gonzalez-Cendales Y.
      • Mead O.
      • Taranto A.
      • Catanzariti A.-M.
      • McDonald M.C.
      • Schwessinger B.
      • Jones D.A.
      • Rathjen J.P.
      • Solomon P.S.
      Fungal phytopathogens encode functional homologues of plant rapid alkalinization factor (RALF) peptides.
      ). In addition to MAMP ligands, some LRR-RLKs perceive proteinaceous DAMPs, such as Atpeps (plant elicitor peptides) and PIPs (PAMP-induced secreted peptides), respectively (
      • Krol E.
      • Mentzel T.
      • Chinchilla D.
      • Boller T.
      • Felix G.
      • Kemmerling B.
      • Postel S.
      • Arents M.
      • Jeworutzki E.
      • Al-Rasheid K.A.S.
      • Becker D.
      • Hedrich R.
      Perception of the Arabidopsis danger signal peptide 1 involves the pattern recognition receptor AtPEPR1 and its close homologue AtPEPR2.
      ,
      • Yamaguchi Y.
      • Huffaker A.
      • Bryan A.C.
      • Tax F.E.
      • Ryan C.A.
      PEPR2 is a second receptor for the Pep1 and Pep2 peptides and contributes to defense responses in Arabidopsis.
      ,
      • Hou S.
      • Wang X.
      • Chen D.
      • Yang X.
      • Wang M.
      • Turrà D.
      • Di Pietro A.
      • Zhang W.
      The secreted peptide PIP1 amplifies immunity through receptor-like kinase 7.
      ,
      • Hou S.
      • Liu Z.
      • Shen H.
      • Wu D.
      Damage-associated molecular pattern-triggered immunity in plants.
      ). Like LRR-RLKs, LRR-RLPs can also sense extracellular short peptide ligands; however, they can also sense larger extracellular proteinaceous ligands, such as apoplastic effectors. In tomato, the LRR-RLPs Cf-2/4/9 perceive apoplastic effectors Avr2, Avr4, and Avr9 from Cladosporium fulvum, respectively (
      • Dixon M.S.
      • Jones D.A.
      • Keddie J.S.
      • Thomas C.M.
      • Harrison K.
      • Jones J.D.G.
      The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat proteins.
      ,
      • Dixon M.S.
      • Hatzixanthis K.
      • Jones D.A.
      • Harrison K.
      • Jones J.D.G.
      The tomato Cf-5 disease resistance gene and six homologs show pronounced allelic variation in leucine-rich repeat copy number.
      ,
      • Krüger J.
      • Thomas C.M.
      • Golstein C.
      • Dixon M.S.
      • Smoker M.
      • Tang S.
      • Mulder L.
      • Jones J.D.G.
      A tomato cysteine protease required for Cf-2-dependent disease resistance and suppression of autonecrosis.
      ,
      • Luderer R.
      • Takken F.L.W.
      • Wit P.J.G.M.D.
      • Joosten M.H.A.J.
      Cladosporium fulvum overcomes Cf-2-mediated resistance by producing truncated AVR2 elicitor proteins.
      ,
      • Rooney H.C.E.
      • van T.
      • Klooster J.W.
      • van der Hoorn R.A.L.
      • Joosten M.H.A.J.
      • Jones J.D.G.
      • de Wit P.J.G.M.
      Cladosporium Avr2 inhibits tomato Rcr3 protease required for Cf-2-dependent disease resistance.
      ).

      Recognition of carbohydrate/non-proteinaceous ligands

      There are several different classes of receptor that are capable of sensing different carbohydrate ligands. LysM-RLKs/LysM-RLPs perceive carbohydrate MAMPs such as bacterial peptidoglycan (PGN), lipopolysaccharide (LPS), and fungal chitin (
      • Liu T.
      • Liu Z.
      • Song C.
      • Hu Y.
      • Han Z.
      • She J.
      • Fan F.
      • Wang J.
      • Jin C.
      • Chang J.
      • Zhou J.-M.
      • Chai J.
      Chitin-induced dimerization activates a plant immune receptor.
      ,
      • Miya A.
      • Albert P.
      • Shinya T.
      • Desaki Y.
      • Ichimura K.
      • Shirasu K.
      • Narusaka Y.
      • Kawakami N.
      • Kaku H.
      • Shibuya N.
      CERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in Arabidopsis.
      ,
      • Cao Y.
      • Liang Y.
      • Tanaka K.
      • Nguyen C.T.
      • Jedrzejczak R.P.
      • Joachimiak A.
      • Stacey G.
      The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1.
      ,
      • Wan J.
      • Zhang X.-C.
      • Neece D.
      • Ramonell K.M.
      • Clough S.
      • Kim S.-Y.
      • Stacey M.G.
      • Stacey G.
      A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis.
      ,
      • Gust A.A.
      Peptidoglycan perception in plants.
      ). The ECD of the cell wall-associated kinase family (WAKs) comprise repeated EGF-like domains (
      • Verica J.A.
      • He Z.-H.
      The cell wall-associated kinase (WAK) and WAK-like kinase gene family.
      ,
      • Brutus A.
      • Sicilia F.
      • Macone A.
      • Cervone F.
      • De Lorenzo G.
      A domain swap approach reveals a role of the plant wall-associated kinase 1 (WAK1) as a receptor of oligogalacturonides.
      ,
      • Kohorn B.D.
      Cell wall-associated kinases and pectin perception.
      ,
      • Souza C.D.A.
      • Li S.
      • Lin A.Z.
      • Boutrot F.
      • Grossmann G.
      • Zipfel C.
      • Somerville S.C.
      Cellulose-derived oligomers act as damage-associated molecular patterns and trigger defense-like responses.
      ) that bind various types of pectins including pathogen/wound-induced short oligogalacturonic acid fragments (OG) as well as cell wall- associated longer pectins (
      • Souza C.D.A.
      • Li S.
      • Lin A.Z.
      • Boutrot F.
      • Grossmann G.
      • Zipfel C.
      • Somerville S.C.
      Cellulose-derived oligomers act as damage-associated molecular patterns and trigger defense-like responses.
      ,
      • Kohorn B.D.
      • Kohorn S.L.
      The cell wall-associated kinases, WAKs, as pectin receptors.
      ). Intriguingly, lectin RLKs including structurally distinct lectin receptors - LORE (G-type lectins) and DORN1 (L-type lectins) senses non-carbohydrate ligands like low complexity bacterial metabolites such as bacterial medium-chain 3-hydroxy fatty acid (mc-3-OH-FA) (
      • Kutschera A.
      • Dawid C.
      • Gisch N.
      • Schmid C.
      • Raasch L.
      • Gerster T.
      • Schäffer M.
      • Smakowska-Luzan E.
      • Belkhadir Y.
      • Vlot A.C.
      • Chandler C.E.
      • Schellenberger R.
      • Schwudke D.
      • Ernst R.K.
      • Dorey S.
      • et al.
      Bacterial medium-chain 3-hydroxy fatty acid metabolites trigger immunity in Arabidopsis plants.
      ) and extracellular ATP (e-ATP- as a DAMP signal) (
      • Choi J.
      • Tanaka K.
      • Cao Y.
      • Qi Y.
      • Qiu J.
      • Liang Y.
      • Lee S.Y.
      • Stacey G.
      Identification of a plant receptor for extracellular ATP.
      ,
      • Tanaka K.
      • Choi J.
      • Cao Y.
      • Stacey G.
      Extracellular ATP acts as a damage-associated molecular pattern (DAMP) signal in plants.
      ) respectively, to trigger immune responses.

      Ligand-induced homo/heterodimerization of cell-surface receptors

      Plant cell-surface immune receptors function in complex with co-receptors and intracellular kinases to activate defense (
      • Saijo Y.
      • Loo E.P-I.
      • Yasuda S.
      Pattern recognition receptors and signaling in plant–microbe interactions.
      ,
      • Böhm H.
      • Albert I.
      • Fan L.
      • Reinhard A.
      • Nürnberger T.
      Immune receptor complexes at the plant cell surface.
      ,
      • Burkart R.C.
      • Stahl Y.
      Dynamic complexity: plant receptor complexes at the plasma membrane.
      ). The LRR-RLK BAK1 is the best-characterized co-receptor to date (
      • Tang J.
      • Han Z.
      • Sun Y.
      • Zhang H.
      • Gong X.
      • Chai J.
      Structural basis for recognition of an endogenous peptide by the plant receptor kinase PEPR1.
      ,
      • Gao X.
      • Ruan X.
      • Sun Y.
      • Wang X.
      • Feng B.
      BAKing up to survive a battle: functional dynamics of BAK1 in plant programmed cell death.
      ,
      • Yasuda S.
      • Okada K.
      • Saijo Y.
      A look at plant immunity through the window of the multitasking coreceptor BAK1.
      ). BAK1 forms heterocomplexes with peptide-binding immunity-related LRR-RLKs, including FLS2 (Fig. 3), EFR, and PEPR1 (perception of the Arabidopsis danger signal peptide), and is required for immune signaling (
      • Sun Y.
      • Li L.
      • Macho A.P.
      • Han Z.
      • Hu Z.
      • Zipfel C.
      • Zhou J.-M.
      • Chai J.
      Structural Basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex.
      ,
      • Tang J.
      • Han Z.
      • Sun Y.
      • Zhang H.
      • Gong X.
      • Chai J.
      Structural basis for recognition of an endogenous peptide by the plant receptor kinase PEPR1.
      ,
      • Schulze B.
      • Mentzel T.
      • Jehle A.K.
      • Mueller K.
      • Beeler S.
      • Boller T.
      • Felix G.
      • Chinchilla D.
      Rapid heteromerization and phosphorylation of ligand-activated plant transmembrane receptors and their associated kinase BAK1.
      ,
      • Yasuda S.
      • Okada K.
      • Saijo Y.
      A look at plant immunity through the window of the multitasking coreceptor BAK1.
      ,
      • Chinchilla D.
      • Shan L.
      • He P.
      • de Vries S.
      • Kemmerling B.
      One for all: the receptor-associated kinase BAK1.
      ). Like BAK1, SOBIR1 (suppressor of Bir 1-1) is a regulatory LRR-RLK that serves as an adaptor for certain LRR-RLPs to trigger defense (
      • Gust A.A.
      • Felix G.
      Receptor like proteins associate with SOBIR1-type of adaptors to form bimolecular receptor kinases.
      ,
      • Liebrand T.W.H.
      • van den Burg H.A.
      • Joosten M.H.A.J.
      Two for all: receptor-associated kinases SOBIR1 and BAK1.
      ,
      • van der Burgh A.M.
      • Postma J.
      • Robatzek S.
      • Joosten M.H.A.J.
      Kinase activity of SOBIR1 and BAK1 is required for immune signalling.
      ). Similar to LRR-RLKs, these RLP/adaptor complexes recruit BAK1 or other SERKs for signal transduction (
      • Tör M.
      • Lotze M.T.
      • Holton N.
      Receptor-mediated signalling in plants: molecular patterns and programmes.
      ,
      • Postma J.
      • Liebrand T.W.H.
      • Bi G.
      • Evrard A.
      • Bye R.R.
      • Mbengue M.
      • Kuhn H.
      • Joosten M.H.A.J.
      • Robatzek S.
      Avr4 promotes Cf-4 receptor-like protein association with the BAK1/SERK3 receptor-like kinase to initiate receptor endocytosis and plant immunity.
      ,
      • Domazakis E.
      • Wouters D.
      • Visser R.G.F.
      • Kamoun S.
      • Joosten M.H.A.J.
      • Vleeshouwers V.G.A.A.
      The ELR-SOBIR1 complex functions as a two-component receptor-like kinase to mount defense against Phytophthora infestans.
      ).
      By contrast, the Arabidopsis carbohydrate-binding LysM-RLK CERK1 forms chitin-bridged homodimers (
      • Liu T.
      • Liu Z.
      • Song C.
      • Hu Y.
      • Han Z.
      • She J.
      • Fan F.
      • Wang J.
      • Jin C.
      • Chang J.
      • Zhou J.-M.
      • Chai J.
      Chitin-induced dimerization activates a plant immune receptor.
      ). Homodimeric association has also been reported for the chitin-binding rice LysM-RLP CEBiP (
      • Shimizu T.
      • Nakano T.
      • Takamizawa D.
      • Desaki Y.
      • Ishii-Minami N.
      • Nishizawa Y.
      • Minami E.
      • Okada K.
      • Yamane H.
      • Kaku H.
      • Shibuya N.
      Two LysM receptor molecules, CEBiP and OsCERK1, cooperatively regulate chitin elicitor signaling in rice.
      ,
      • Squeglia F.
      • Berisio R.
      • Shibuya N.
      • Kaku H.
      Defense against pathogens: structural insights into the mechanism of chitin induced activation of innate immunity.
      ), but the rice CEBiP can also form heterodimers with rice CERK1 (
      • Liu T.
      • Liu Z.
      • Song C.
      • Hu Y.
      • Han Z.
      • She J.
      • Fan F.
      • Wang J.
      • Jin C.
      • Chang J.
      • Zhou J.-M.
      • Chai J.
      Chitin-induced dimerization activates a plant immune receptor.
      ,
      • Kaku H.
      • Nishizawa Y.
      • Ishii-Minami N.
      • Akimoto-Tomiyama C.
      • Dohmae N.
      • Takio K.
      • Minami E.
      • Shibuya N.
      Plant cells recognize chitin fragments for defense signaling through a plasma membrane receptor.
      ). Although oligomerization is important, the precise role of homo- or heterointeractions of LysM-RLK/RLPs in signaling recognition of chitin remains unclear (
      • Shimizu T.
      • Nakano T.
      • Takamizawa D.
      • Desaki Y.
      • Ishii-Minami N.
      • Nishizawa Y.
      • Minami E.
      • Okada K.
      • Yamane H.
      • Kaku H.
      • Shibuya N.
      Two LysM receptor molecules, CEBiP and OsCERK1, cooperatively regulate chitin elicitor signaling in rice.
      ).

      RLCKs in downstream defense signaling

      Ligand perception by plant cell-surface receptors typically results in homo- or heterodimerization that stimulates cis- and/or trans-phosphorylation of intracellular kinase domains (
      • Shimizu T.
      • Nakano T.
      • Takamizawa D.
      • Desaki Y.
      • Ishii-Minami N.
      • Nishizawa Y.
      • Minami E.
      • Okada K.
      • Yamane H.
      • Kaku H.
      • Shibuya N.
      Two LysM receptor molecules, CEBiP and OsCERK1, cooperatively regulate chitin elicitor signaling in rice.
      ). In turn, the kinase domains of cell-surface immune receptors activate receptor-like cytoplasmic kinases (RLCKs) to transduce immune signals (
      • Lu D.
      • Wu S.
      • Gao X.
      • Zhang Y.
      • Shan L.
      • He P.
      A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity.
      ,
      • Lin W.
      • Ma X.
      • Shan L.
      • He P.
      Big roles of small kinases: the complex functions of receptor-like cytoplasmic kinases in plant immunity and development.
      ,
      • Liang X.
      • Zhou J.-M.
      Receptor-like cytoplasmic kinases: central players in plant receptor kinase–mediated signaling.
      ).
      The Arabidopsis RLCKs BIK1 (botrytis-induced kinase 1) and PBL (PBS1-like) proteins are substrates of distinct receptor/BAK1/CERK1 complexes at the cell surface (
      • Lu D.
      • Wu S.
      • Gao X.
      • Zhang Y.
      • Shan L.
      • He P.
      A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity.
      ,
      • Zhang J.
      • Li W.
      • Xiang T.
      • Liu Z.
      • Laluk K.
      • Ding X.
      • Zou Y.
      • Gao M.
      • Zhang X.
      • Chen S.
      • Mengiste T.
      • Zhang Y.
      • Zhou J.-M.
      Receptor-like cytoplasmic kinases integrate signaling from multiple plant immune receptors and are targeted by a Pseudomonas syringae effector.
      ,
      • Veronese P.
      • Nakagami H.
      • Bluhm B.
      • AbuQamar S.
      • Chen X.
      • Salmeron J.
      • Dietrich R.A.
      • Hirt H.
      • Mengiste T.
      The membrane-anchored BOTRYTIS-INDUCED KINASE1 plays distinct roles in Arabidopsis resistance to necrotrophic and biotrophic pathogens.
      ). For example, in the absence of ligand, BIK1 interacts with BAK1 and associated cell-surface receptor kinase domains (Fig. 3). On ligand binding, a series of cis/trans-phosphorylation events promotes BIK1 dissociation from the complex (
      • Lu D.
      • Wu S.
      • Gao X.
      • Zhang Y.
      • Shan L.
      • He P.
      A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity.
      ,
      • Zhang J.
      • Li W.
      • Xiang T.
      • Liu Z.
      • Laluk K.
      • Ding X.
      • Zou Y.
      • Gao M.
      • Zhang X.
      • Chen S.
      • Mengiste T.
      • Zhang Y.
      • Zhou J.-M.
      Receptor-like cytoplasmic kinases integrate signaling from multiple plant immune receptors and are targeted by a Pseudomonas syringae effector.
      ). BIK1 then activates various downstream immune signaling pathways, including ROS burst, Ca2+ accumulation, and mitogen-activated protein kinase pathways (
      • Ranf S.
      • Eschen-Lippold L.
      • Fröhlich K.
      • Westphal L.
      • Scheel D.
      • Lee J.
      Microbe-associated molecular pattern-induced calcium signaling requires the receptor-like cytoplasmic kinases, PBL1 and BIK1.
      ,
      • Kadota Y.
      • Shirasu K.
      • Zipfel C.
      Regulation of the NADPH oxidase RBOHD during plant immunity.
      ,
      • Monaghan J.
      • Matschi S.
      • Romeis T.
      • Zipfel C.
      The calcium-dependent protein kinase CPK28 negatively regulates the BIK1-mediated PAMP-induced calcium burst.
      ). Multiple RLCKs have been identified in plants that regulate a ROS burst by phosphorylating distinct sites in RBOHD (respiratory burst oxidase homolog protein D), a membrane-localized NADPH oxidase critical for ROS formation post-MAMP detection (
      • Lal N.K.
      • Nagalakshmi U.
      • Hurlburt N.K.
      • Flores R.
      • Bak A.
      • Sone P.
      • Ma X.
      • Song G.
      • Walley J.
      • Shan L.
      • He P.
      • Casteel C.
      • Fisher A.J.
      • Dinesh-Kumar S.P.
      The receptor-like cytoplasmic kinase BIK1 localizes to the nucleus and regulates defense hormone expression during plant innate immunity.
      ,
      • Kadota Y.
      • Shirasu K.
      • Zipfel C.
      Regulation of the NADPH oxidase RBOHD during plant immunity.
      ,
      • Li L.
      • Li M.
      • Yu L.
      • Zhou Z.
      • Liang X.
      • Liu Z.
      • Cai G.
      • Gao L.
      • Zhang X.
      • Wang Y.
      • Chen S.
      • Zhou J.-M.
      The FLS2-associated kinase BIK1 directly phosphorylates the NADPH oxidase RbohD to control plant immunity.
      ,
      • Qi J.
      • Wang J.
      • Gong Z.
      • Zhou J.-M.
      Apoplastic ROS signaling in plant immunity.
      ).

      Regulation of cell-surface immune responses

      To prevent inappropriate signaling, the activity of plant cell-surface immune receptors is tightly controlled (
      • Couto D.
      • Zipfel C.
      Regulation of pattern recognition receptor signalling in plants.
      ). Plants use various strategies to help maintain cell-surface receptors in an inactive state in the absence of ligand binding, including the regulation of phosphorylation status and ubiquitination by E3 ligases (
      • Couto D.
      • Zipfel C.
      Regulation of pattern recognition receptor signalling in plants.
      ,
      • Gómez-Gómez L.
      • Bauer Z.
      • Boller T.
      Both the extracellular leucine-rich repeat domain and the kinase activity of FLS2 are required for flagellin binding and signaling in Arabidopsis.
      ,
      • Ding Z.
      • Wang H.
      • Liang X.
      • Morris E.R.
      • Gallazzi F.
      • Pandit S.
      • Skolnick J.
      • Walker J.C.
      • Van Doren S.R.
      Phosphoprotein and phosphopeptide interactions with the FHA domain from Arabidopsis kinase-associated protein phosphatase.
      ,
      • Park C.-J.
      • Caddell D.F.
      • Ronald P.C.
      Protein phosphorylation in plant immunity: insights into the regulation of pattern recognition receptor-mediated signaling.
      ).
      Phosphorylation is central to cell-surface immunity signaling cascades and is under tight regulation. Plants use phosphatases to negatively regulate cell-surface receptors to prevent the potentially harmful effects of autoinduction. For example, Arabidopsis PP2A (protein phosphatase 2A), a serine/threonine phosphatase, dephosphorylates BAK1/EFR to control defense signaling (
      • Segonzac C.
      • Macho A.P.
      • Sanmartín M.
      • Ntoukakis V.
      • Sánchez-Serrano J.J.
      • Zipfel C.
      Negative control of BAK1 by protein phosphatase 2A during plant innate immunity.
      ,
      • Durian G.
      • Rahikainen M.
      • Alegre S.
      • Brosché M.
      • Kangasjärvi S.
      Protein phosphatase 2A in the regulatory network underlying biotic stress resistance in plants.
      ). Similarly, PP2C38 regulates ligand-induced phosphorylation of BIK1, moderating signaling by this key transducer of cell-surface immunity (
      • Couto D.
      • Zipfel C.
      Regulation of pattern recognition receptor signalling in plants.
      ). A second strategy to negatively regulate cell-surface immunity is the use of pseudokinases, such as BIR1 and BIR2, that are catalytically inactive but interact with BAK1 in its resting state, preventing the association of LRR-RLKs (
      • Halter T.
      • Imkampe J.
      • Blaum B.S.
      • Stehle T.
      • Kemmerling B.
      BIR2 affects complex formation of BAK1 with ligand binding receptors in plant defense.
      ,
      • Halter T.
      • Imkampe J.
      • Mazzotta S.
      • Wierzba M.
      • Postel S.
      • Bücherl C.
      • Kiefer C.
      • Stahl M.
      • Chinchilla D.
      • Wang X.
      • Nürnberger T.
      • Zipfel C.
      • Clouse S.
      • Borst J.W.
      • Boeren S.
      • et al.
      The leucine-rich repeat receptor kinase BIR2 is a negative regulator of BAK1 in plant immunity.
      ,
      • Liu Y.
      • Huang X.
      • Li M.
      • He P.
      • Zhang Y.
      Loss-of-function of Arabidopsis receptor-like kinase BIR1 activates cell death and defense responses mediated by BAK1 and SOBIR1.
      ). Ligand binding relieves this inhibitory interaction, leading to the formation of activated immune complexes.
      Regulation of immunity can also come from controlled degradation through ubiquitination. Two closely related E3-ubiquitin ligases, PUB25 and PUB26, together with both a calcium-dependent protein kinase CPK28 and a heterotrimeric G protein, form a regulatory module and maintain BIK1 homeostasis (
      • Wang J.
      • Grubb L.E.
      • Wang J.
      • Liang X.
      • Li L.
      • Gao C.
      • Ma M.
      • Feng F.
      • Li M.
      • Li L.
      • Zhang X.
      • Yu F.
      • Xie Q.
      • Chen S.
      • Zipfel C.
      • et al.
      A regulatory module controlling homeostasis of a plant immune kinase.
      ). Similarly, PUB12 and PUB13 polyubiquitinate and mediate degradation of ligand-bound FLS2 (
      • Robatzek S.
      • Chinchilla D.
      • Boller T.
      Ligand-induced endocytosis of the pattern recognition receptor FLS2 in Arabidopsis.
      ,
      • Lu D.
      • Lin W.
      • Gao X.
      • Wu S.
      • Cheng C.
      • Avila J.
      • Heese A.
      • Devarenne T.P.
      • He P.
      • Shan L.
      Direct ubiquitination of pattern recognition receptor FLS2 attenuates plant innate immunity.
      ,
      • Smith J.M.
      • Salamango D.J.
      • Leslie M.E.
      • Collins C.A.
      • Heese A.
      Sensitivity to Flg22 is modulated by ligand-induced degradation and de novo synthesis of the endogenous flagellin-receptor FLAGELLIN-SENSING2.
      ). Intriguingly, a recent study showed that monoubiquitination of BIK1 is necessary for its release from the FLS2/BAK1 complex and immune system activation (
      • Ma X.
      • Claus L.A.N.
      • Leslie M.E.
      • Tao K.
      • Wu Z.
      • Liu J.
      • Yu X.
      • Li B.
      • Zhou J.
      • Savatin D.V.
      • Peng J.
      • Tyler B.M.
      • Heese A.
      • Russinova E.
      • He P.
      • et al.
      Ligand-induced monoubiquitination of BIK1 regulates plant immunity.
      ). This demonstrates that a variety of post-translational modifications are important for both positive and negative regulation of cell-surface immune receptors.
      In addition to regulating the pool of ligand-bound cell-surface receptors at the plasma membrane, plants also ensure the availability of ligand-free receptors for ongoing pathogen/pest perception. Cell-trafficking components, including SCD1 (DENN domain protein) (
      • Korasick D.A.
      • McMichael C.
      • Walker K.A.
      • Anderson J.C.
      • Bednarek S.Y.
      • Heese A.
      Novel functions of stomatal cytokinesis-defective 1 (SCD1) in innate immune responses against bacteria.
      ,
      • McMichael C.M.
      • Reynolds G.D.
      • Koch L.M.
      • Wang C.
      • Jiang N.
      • Nadeau J.
      • Sack F.D.
      • Gelderman M.B.
      • Pan J.
      • Bednarek S.Y.
      Mediation of clathrin-dependent trafficking during cytokinesis and cell expansion by Arabidopsis stomatal cytokinesis defective proteins.
      ) and ESCRT-I (an endosomal sorting complex required for transport) (
      • Spallek T.
      • Beck M.
      • Ben Khaled S.
      • Salomon S.
      • Bourdais G.
      • Schellmann S.
      • Robatzek S.
      ESCRT-I mediates FLS2 endosomal sorting and plant immunity.
      ,
      • Schuh A.L.
      • Audhya A.
      The ESCRT machinery: from the plasma membrane to endosomes and back again.
      ), are involved in delivering these receptors to the cell surface. Finally, it has been proposed that sets of cell-surface receptors may gather at discrete locations on membranes, forming discrete nano- or microdomains (
      • Ben Khaled S.
      • Postma J.
      • Robatzek S.
      A moving view: subcellular trafficking processes in pattern recognition receptor–triggered plant immunity.
      ,
      • Bücherl C.A.
      • Jarsch I.K.
      • Schudoma C.
      • Segonzac C.
      • Mbengue M.
      • Robatzek S.
      • MacLean D.
      • Ott T.
      • Zipfel C.
      Plant immune and growth receptors share common signalling components but localise to distinct plasma membrane nanodomains.
      ). These nano-/microdomains are proposed to use similar downstream signaling components; however, different groupings of receptors would lead to different specificity in signal perception, resulting in different responses to stimuli. However, more work is needed to understand the specificity of these nano-/microdomains and how they are clustered into spatially distinct regions of the membrane (
      • Ben Khaled S.
      • Postma J.
      • Robatzek S.
      A moving view: subcellular trafficking processes in pattern recognition receptor–triggered plant immunity.
      ,
      • Bücherl C.A.
      • Jarsch I.K.
      • Schudoma C.
      • Segonzac C.
      • Mbengue M.
      • Robatzek S.
      • MacLean D.
      • Ott T.
      • Zipfel C.
      Plant immune and growth receptors share common signalling components but localise to distinct plasma membrane nanodomains.
      ).

      Next steps in understanding cell-surface immunity

      Although hundreds of RLKs and RLPs have been identified in many plant species, only a subset have been characterized. The biological significance of the vast majority of these receptors remains elusive, and their underlying mechanism of ligand perception remains poorly understood. Understanding how cell-surface receptors with different ECDs perceive ligands will provide a foundation for engineering broad-spectrum resistance into crop plants (
      • Dong O.X.
      • Ronald P.C.
      Genetic engineering for disease resistance in plants: recent progress and future perspectives.
      ,
      • Rodriguez-Moreno L.
      • Song Y.
      • Thomma B.P.H.J.
      Transfer and engineering of immune receptors to improve recognition capacities in crops.
      ). Further, our understanding of how RLCKs coordinate their association with different receptors and facilitate distinct signaling outputs is a key challenge for the future. We have yet to understand whether activated cell-surface receptor complexes form higher-order supramolecular signaling units at the plasma membrane, what the molecular identity of these activated immune complex might be, and how they may differ across different ligand/cell-surface receptor pairs. Beyond this, we must endeavor to understand the determinants of specificity of plant cell-surface receptors for MAMPs, as this will provide insight into how plants distinguish the MAMPs of pathogenic microbes from those of the beneficial mutualistic microbes.

      Case study 1: flg22 perception by the FLS2/BAK1 complex—an exemplar of ligand perception by cell-surface receptors

      Genetic screens in Arabidopsis identified FLS2 as the gene that recognizes a conserved 22-amino acid N-terminal epitope (flg22) of bacterial flagellin to initiate cell-surface immunity (
      • Kunze G.
      • Zipfel C.
      • Robatzek S.
      • Niehaus K.
      • Boller T.
      • Felix G.
      The N terminus of bacterial elongation factor Tu elicits innate immunity in Arabidopsis plants.
      ,
      • Chinchilla D.
      • Zipfel C.
      • Robatzek S.
      • Kemmerling B.
      • Nürnberger T.
      • Jones J.D.G.
      • Felix G.
      • Boller T.
      A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence.
      ,
      • Gómez-Gómez L.
      • Boller T.
      FLS2: an LRR receptor–like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis.
      ). FLS2 belongs to the LRR-RLK class XII subfamily and shares homology with TLR5 (Toll-like receptor 5), an LRR-containing receptor that perceives flagellin in mammals (
      • Shiu S.-H.
      • Bleecker A.B.
      Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases.
      ,
      • Hayashi F.
      • Smith K.D.
      • Ozinsky A.
      • Hawn T.R.
      • Yi E.C.
      • Goodlett D.R.
      • Eng J.K.
      • Akira S.
      • Underhill D.M.
      • Aderem A.
      The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5.
      ). Fig. 3 gives a detailed mechanistic view of how flg22 is perceived by FLS2.
      Flagellin perception in Arabidopsis requires heterodimerization of FLS2 with BAK1 (
      • Chinchilla D.
      • Zipfel C.
      • Robatzek S.
      • Kemmerling B.
      • Nürnberger T.
      • Jones J.D.G.
      • Felix G.
      • Boller T.
      A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence.
      ,
      • Schulze B.
      • Mentzel T.
      • Jehle A.K.
      • Mueller K.
      • Beeler S.
      • Boller T.
      • Felix G.
      • Chinchilla D.
      Rapid heteromerization and phosphorylation of ligand-activated plant transmembrane receptors and their associated kinase BAK1.
      ,
      • Heese A.
      • Hann D.R.
      • Gimenez-Ibanez S.
      • Jones A.M.E.
      • He K.
      • Li J.
      • Schroeder J.I.
      • Peck S.C.
      • Rathjen J.P.
      The receptor-like kinase SERK3/BAK1 is a central regulator of innate immunity in plants.
      ). The crystal structure of the ECDs of FLS2 and BAK1, in complex with flg22, revealed the structural basis of flg22 perception (
      • Sun Y.
      • Li L.
      • Macho A.P.
      • Han Z.
      • Hu Z.
      • Zipfel C.
      • Zhou J.-M.
      • Chai J.
      Structural Basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex.
      ). The flg22 peptide is bound within the concave surface of the FLS2-ECD, via the leucine-rich repeat subunits LRR3 to LRR16. flg22 interactions with FLS2 are divided into two regions, separated by a kink in the peptide. The N-terminal seven amino acids of flg22 interact with LRRs 3–6, with the C-terminal 14 amino acids binding LRRs 7–16. Numerous hydrogen-bonding, electrostatic, and hydrophobic contacts are formed between flg22 and FLS2. Interactions between the FLS2 and BAK1-ECDs are both receptor- and flg22-mediated, but the peptide acts as a “molecular glue,” stabilizing the heterodimer.
      In the absence of flg22, the Arabidopsis RLCK BIK1 can associate with the FLS2 and BAK1 kinase domains. Ligand perception leads to activation and phosphorylation of BIK1 by BAK1 (
      • Lu D.
      • Wu S.
      • Gao X.
      • Zhang Y.
      • Shan L.
      • He P.
      A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity.
      ,
      • Zhang J.
      • Li W.
      • Xiang T.
      • Liu Z.
      • Laluk K.
      • Ding X.
      • Zou Y.
      • Gao M.
      • Zhang X.
      • Chen S.
      • Mengiste T.
      • Zhang Y.
      • Zhou J.-M.
      Receptor-like cytoplasmic kinases integrate signaling from multiple plant immune receptors and are targeted by a Pseudomonas syringae effector.
      ). Following phosphorylation, BIK1 is monoubiquitinated by the E3 ligases RHA3A/B (RING-H2 FINGER A3A/B). BIK1 has an N-terminal myristoylation motif, and plasma membrane localization of BIK1 is essential for ubiquitination. Monoubiquitinated BIK1 is then released from the FLS2–BAK1 complex and initiates ROS production and Ca2+ signaling through phosphorylation of plasma membrane-localized NADPH oxidases and cyclic nucleotide–gated channels (
      • Ma X.
      • Claus L.A.N.
      • Leslie M.E.
      • Tao K.
      • Wu Z.
      • Liu J.
      • Yu X.
      • Li B.
      • Zhou J.
      • Savatin D.V.
      • Peng J.
      • Tyler B.M.
      • Heese A.
      • Russinova E.
      • He P.
      • et al.
      Ligand-induced monoubiquitination of BIK1 regulates plant immunity.
      ).

      Intracellular immunity

      Intracellular immunity in plants is conferred by nucleotide-binding, leucine-rich repeat receptor proteins (NLRs). NLRs perceive the presence and/or activities of host-translocated effectors, leading to defense responses that may result in programmed cell death to limit the spread of infection (
      • Dangl J.L.
      • Jones J.D.G.
      Plant pathogens and integrated defence responses to infection.
      ). Prior to the molecular identification of NLR receptors and effectors, the genetic basis of what we now call intracellular immunity was established as the “gene-for-gene” model. The gene-for-gene model described a requirement for plants to utilize specialized immune receptors encoded by R (resistance) genes to counteract and respond to the effectors encoded by pathogen AVR (avirulence) genes (
      • Flor H.H.
      Current status of the gene-for-gene concept.
      ).

      NLRs comprise multiple domains with distinct functions

      NLRs belong to the AAA+ class of “signal-transducing ATPases with numerous domains” (STAND) ATPases that share a conserved central nucleotide-binding domain across plant, animal, and fungal kingdoms (
      • Takken F.L.W.
      • Tameling W.I.L.
      To nibble at plant resistance proteins.
      ). The STAND superfamily includes APAF1, the primary component of the mammalian apoptosome (
      • Zou H.
      • Li Y.
      • Liu X.
      • Wang X.
      An APAF-1·cytochrome c multimeric complex is a functional apoptosome that activates procaspase-9.
      ), and NLRC4 (NLR family CARD domain–containing protein 4) and NLRP3 (NLR family pyrin domain–containing 3), which are the best-characterized NLRs of the metazoan immune system (
      • Bentham A.
      • Burdett H.
      • Anderson P.A.
      • Williams S.J.
      • Kobe B.
      Animal NLRs provide structural insights into plant NLR function.
      ,
      • Duncan J.A.
      • Bergstralh D.T.
      • Wang Y.
      • Willingham S.B.
      • Ye Z.
      • Zimmermann A.G.
      • Ting J.P.-Y.
      Cryopyrin/NALP3 binds ATP/dATP, is an ATPase, and requires ATP binding to mediate inflammatory signaling.
      ,
      • Poyet J.L.
      • Srinivasula S.M.
      • Tnani M.
      • Razmara M.
      • Fernandes-Alnemri T.
      • Alnemri E.S.
      Identification of Ipaf, a human caspase-1-activating protein related to Apaf-1.
      ,
      • Sharif H.
      • Wang L.
      • Wang W.L.
      • Magupalli V.G.
      • Andreeva L.
      • Qiao Q.
      • Hauenstein A.V.
      • Wu Z.
      • Núñez G.
      • Mao Y.
      • Wu H.
      Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome.
      ,
      • Tenthorey J.L.
      • Haloupek N.
      • López-Blanco J.R.
      • Grob P.
      • Adamson E.
      • Hartenian E.
      • Lind N.A.
      • Bourgeois N.M.
      • Chacón P.
      • Nogales E.
      • Vance R.E.
      The structural basis of flagellin detection by NAIP5: a strategy to limit pathogen immune evasion.
      ,
      • Zhang L.
      • Chen S.
      • Ruan J.
      • Wu J.
      • Tong A.B.
      • Yin Q.
      • Li Y.
      • David L.
      • Lu A.
      • Wang W.L.
      • Marks C.
      • Ouyang Q.
      • Zhang X.
      • Mao Y.
      • Wu H.
      Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization.
      ).
      Classically, plant NLRs comprise a C-terminal LRR domain; a central nucleotide-binding domain known as the NB-ARC (nucleotide-binding domain shared with APAF1, R gene products and CED4 (
      • Van der Biezen E.A.
      • Jones J.D.
      Plant disease-resistance proteins and the gene-for-gene concept.
      ); and a variable N-terminal module, which is typically either a TIR (Toll/interleukin-1 receptor/resistance), CC (coiled-coil) domain, or an RPW8 (resistance to powdery mildew 8)-like CC domain (CC-RPW8) (
      • Duxbury Z.
      • Ma Y.
      • Furzer O.J.
      • Huh S.U.
      • Cevik V.
      • Jones J.D.G.
      • Sarris P.F.
      Pathogen perception by NLRs in plants and animals: parallel worlds.
      ). Interestingly, LRR domains appear in both cell-surface and intracellular immune receptors and are widely found to be ligand recognition motifs that mediate protein-protein interactions across kingdoms of life. The LRR domain has been implicated in effector recognition for some NLRs, although it is also likely to be important for autoinhibition of the receptor (
      • Bentham A.
      • Burdett H.
      • Anderson P.A.
      • Williams S.J.
      • Kobe B.
      Animal NLRs provide structural insights into plant NLR function.
      ,
      • Dodds P.N.
      • Lawrence G.J.
      • Catanzariti A.-M.
      • Ayliffe M.A.
      • Ellis J.G.
      The Melampsora lini AvrL567 avirulence genes are expressed in haustoria and their products are recognized inside plant cells.
      ,
      • Faustin B.
      • Lartigue L.
      • Bruey J.M.
      • Luciano F.
      • Sergienko E.
      • Bailly-Maitre B.
      • Volkmann N.
      • Hanein D.
      • Rouiller I.
      • Reed J.C.
      Reconstituted NALP1 inflammasome reveals two-step mechanism of caspase-1 activation.
      ). The NB-ARC domain functions as a molecular switch, with effector perception relayed through this domain via nucleotide exchange (ADP for ATP) (
      • Takken F.L.W.
      • Goverse A.
      How to build a pathogen detector: structural basis of NB-LRR function.
      ). The N-terminal domains are required for immunity and divide the NLRs into three major classes: TIR-NLRs, CC-NLRs, and RPW8-NLRs (
      • Jones J.D.G.
      • Vance R.E.
      • Dangl J.L.
      Intracellular innate immune surveillance devices in plants and animals.
      ). Transient expression assays in plants have shown that the N-terminal domains can initiate cell death autonomously and in the absence of an effector (
      • Zhang X.
      • Dodds P.N.
      • Bernoux M.
      What do we know about NOD-like receptors in plant immunity?.
      ). Recently, some NLRs have been shown to incorporate additional noncanonical domains into their architecture (
      • Cesari S.
      • Bernoux M.
      • Moncuquet P.
      • Kroj T.
      • Dodds P.N.
      A novel conserved mechanism for plant NLR protein pairs: the “integrated decoy hypothesis.
      ). Known as integrated domains (IDs), these domains can directly interact with effectors (
      • Maqbool A.
      • Saitoh H.
      • Franceschetti M.
      • Stevenson C.E.M.
      • Uemura A.
      • Kanzaki H.
      • Kamoun S.
      • Terauchi R.
      • Banfield M.J.
      Structural basis of pathogen recognition by an integrated HMA domain in a plant NLR immune receptor.
      ,
      • Zhang Z.-M.
      • Ma K.-W.
      • Gao L.
      • Hu Z.
      • Schwizer S.
      • Ma W.
      • Song J.
      Mechanism of host substrate acetylation by a YopJ family effector.
      ,
      • Cesari S.
      • Thilliez G.
      • Ribot C.
      • Chalvon V.
      • Michel C.
      • Jauneau A.
      • Rivas S.
      • Alaux L.
      • Kanzaki H.
      • Okuyama Y.
      • Morel J.B.
      • Fournier E.
      • Tharreau D.
      • Terauchi R.
      • Kroj T.
      The rice resistance protein pair RGA4/RGA5 recognizes the Magnaporthe oryzae effectors AVR-Pia and AVR1-CO39 by direct binding.
      ,
      • Sarris P.F.
      • Duxbury Z.
      • Huh S.U.
      • Ma Y.
      • Segonzac C.
      • Sklenar J.
      • Derbyshire P.
      • Cevik V.
      • Rallapalli G.
      • Saucet S.B.
      • Wirthmueller L.
      • Menke F.L.H.
      • Sohn K.H.
      • Jones J.D.G.
      A plant immune receptor detects pathogen effectors that target WRKY transcription factors.
      ,
      • Le Roux C.
      • Huet G.
      • Jauneau A.
      • Camborde L.
      • Tremousaygue D.
      • Kraut A.
      • Zhou B.
      • Levaillant M.
      • Adachi H.
      • Yoshioka H.
      • Raffaele S.
      • Berthome R.
      • Coute Y.
      • Parker J.E.
      • Deslandes L.
      A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity.
      ). Intriguingly, many NLR IDs share sequence/structural homology with established virulence-associated host targets of effectors, such as transcription factors or proteins important for cell homeostasis (
      • Cesari S.
      Multiple strategies for pathogen perception by plant immune receptors.
      ). Overall, the individual domains of plant NLRs function together to deliver an effective immune response against pathogen/pests.

      Effector detection: Direct and indirect perception of effectors by plant NLRs

      Conceptually, how plant NLRs perceive effectors has been grouped into three overarching models: the direct recognition model (non-ID), indirect recognition model (via guardees or decoys), and the integrated domain recognition model (via integration of effector targets as IDs into the NLR architecture) (Figs. 4A and 5).
      Figure thumbnail gr4
      Figure 4NLRs perceive effectors via distinct mechanisms and induce immune responses through different mechanisms. A, effector (purple) perception induces activation of the NLR (orange) via direct binding. NLRs can indirectly perceive and respond to effectors by monitoring modifications of a physiologically relevant host target (Guardee, gray) or a molecular mimic that likely resulted via gene duplication and is now only involved in immune signaling (Decoy, blue). NLRs can directly perceive and respond to effectors via NLR integrated domains (blue), which likely have their evolutionary origin in ancestral host targets of effectors. B, NLR singletons are able to initiate immune responses upon effector perception. Several sensor NLRs require downstream helper NLRs (green) to transduce effector perception into immune responses. NLRs can function in pairs or as part of interconnected networks.
      Figure thumbnail gr5
      Figure 5Incorporation of host targets in NLRs leads to the evolution of NLR with integrated domains. NLRs (orange) can sense changes in host proteins (gray) that are targeted by pathogen effector molecules (purple) and initiate defense signaling. Over time, some of these host proteins can be found integrated into the NLR core structure (blue), acting as the effector recognition domains for the NLR. Binding of an effector to the integrated domain of an NLR leads to initiation of defense responses.

      Direct recognition

      The LRR domain of NLR proteins has been implicated in direct interaction with effectors, as well as having a role in autoinhibition of receptor activity. Best-characterized in flax, this plant shows a variety of resistance phenotypes toward different strains of the flax stem rust pathogen (Melampsora lini) expressing different effector alleles (
      • Islam M.R.
      • Mayo G.M.E.
      A compendium on host genes in flax conferring resistance to flax rust.
      ). In particular, dissection of flax NLRs from the L resistance gene loci (encoding L5, L6, and L7 NLRs among others) and how they perceive alleles of the effector AVRL-567 revealed polymorphisms in the LRR region that underpin specificity (
      • Dodds P.N.
      • Lawrence G.J.
      • Catanzariti A.-M.
      • Ayliffe M.A.
      • Ellis J.G.
      The Melampsora lini AvrL567 avirulence genes are expressed in haustoria and their products are recognized inside plant cells.
      ,
      • Ellis J.G.
      • Lawrence G.J.
      • Luck J.E.
      • Dodds P.N.
      Identification of regions in alleles of the flax rust resistance gene that determine differences in gene-for-gene specificity.
      ). Similarly, polymorphisms between the flax NLR variants P and P2 within the LRR domain determine different flax stem rust resistance specificities (
      • Dodds P.N.
      • Lawrence G.J.
      • Ellis J.G.
      Six amino acid changes confined to the leucine-rich repeat β-strand/β-turn motif determine the difference between the P and P2 rust resistance specificities in flax.
      ). Although genetic and biochemical evidence for effector perception by LRR domains is established, to date, the structural basis of such interactions has yet to be determined.

      Indirect recognition

      NLRs can act as “guards” for host proteins targeted by effectors (known as guardees (
      • Cesari S.
      Multiple strategies for pathogen perception by plant immune receptors.
      )). Guard/guardee interactions can be divided into two models. In both models, the NLR monitors the biochemical status of the guardee (e.g. detecting post-translational modification or cleavage/degradation). In the guard model, the guardee is important for host cell function, whereas in the decoy model, the guardee is a mimic of an effector target but does not have a function outside of immunity.
      RIN4 (RPM1 (resistance to Pseudomonas syringae pv. maculicola 1)-interacting protein 4) is a plasma membrane–localized negative regulator of plant immunity (
      • Mackey D.
      • Holt 3rd, B.F.
      • Wiig A.
      • Dangl J.L.
      RIN4 interacts with Pseudomonas syringae type III effector molecules and is required for RPM1-mediated resistance in Arabidopsis.
      ). This protein is a classic example of an effector “hub,” a host protein that is targeted by multiple effectors from different pathogens, and as a consequence, it is guarded by multiple NLRs (
      • Mukhtar M.S.
      • Carvunis A.R.
      • Dreze M.
      • Epple P.
      • Steinbrenner J.
      • Moore J.
      • Tasan M.
      • Galli M.
      • Hao T.
      • Nishimura M.T.
      • Pevzner S.J.
      • Donovan S.E.
      • Ghamsari L.
      • Santhanam B.
      • Romero V.
      • et al.
      Independently evolved virulence effectors converge onto hubs in a plant immune system network.
      ). The Arabidopsis NLRs RPM1 and RPS2 (resistance to P. syringae 2) monitor the biochemical status of RIN4, detecting modifications, such as phosphorylation and degradation, that lead to activation of immunity (
      • Mackey D.
      • Holt 3rd, B.F.
      • Wiig A.
      • Dangl J.L.
      RIN4 interacts with Pseudomonas syringae type III effector molecules and is required for RPM1-mediated resistance in Arabidopsis.
      ,
      • Mackey D.
      • Belkhadir Y.
      • Alonso J.M.
      • Ecker J.R.
      • Dangl J.L.
      Arabidopsis RIN4 is a target of the type III virulence effector AvrRpt2 and modulates RPS2-mediated resistance.
      ).
      In tomato, Pto is a protein kinase that directly interacts with the NLR Prf (
      • Mucyn T.S.
      • Clemente A.
      • Andriotis V.M.E.
      • Balmuth A.L.
      • Oldroyd G.E.D.
      • Staskawicz B.J.
      • Rathjen J.P.
      The tomato NBARC-LRR protein Prf interacts with Pto kinase in vivo to regulate specific plant immunity.
      ,
      • Mucyn T.S.
      • Wu A.-J.
      • Balmuth A.L.
      • Arasteh J.M.
      • Rathjen J.P.
      Regulation of tomato Prf by Pto-like protein kinases.
      ). Pto is a decoy that mimics the intracellular domains of cell-surface immune receptors (
      • Mucyn T.S.
      • Clemente A.
      • Andriotis V.M.E.
      • Balmuth A.L.
      • Oldroyd G.E.D.
      • Staskawicz B.J.
      • Rathjen J.P.
      The tomato NBARC-LRR protein Prf interacts with Pto kinase in vivo to regulate specific plant immunity.
      ,
      • Mucyn T.S.
      • Wu A.-J.
      • Balmuth A.L.
      • Arasteh J.M.
      • Rathjen J.P.
      Regulation of tomato Prf by Pto-like protein kinases.
      ) and acts as a trap for effectors that pathogens have delivered to interfere with receptor signaling. Pto has no known function outside of this bait activity (
      • Ntoukakis V.
      • Saur I.M.
      • Conlan B.
      • Rathjen J.P.
      The changing of the guard: the Pto/Prf receptor complex of tomato and pathogen recognition.
      ). Direct interactions between effectors and Pto lead to oligomerization of Prf and immune activation (
      • Mucyn T.S.
      • Wu A.-J.
      • Balmuth A.L.
      • Arasteh J.M.
      • Rathjen J.P.
      Regulation of tomato Prf by Pto-like protein kinases.
      ,
      • Ntoukakis V.
      • Saur I.M.
      • Conlan B.
      • Rathjen J.P.
      The changing of the guard: the Pto/Prf receptor complex of tomato and pathogen recognition.
      ).

      Integrated domain model

      The integrated domain model is an evolutionary innovation in plant NLRs where a domain that mimics an effector target is positioned in an NLR architecture, serving as a sensor domain by directly interacting with effectors (Figs. 4A and 5). A well-studied example of NLR IDs are the heavy metal–associated (HMA) domains of rice receptor proteins Pik-1 (Pyricularia oryzae resistance-k) and the Pia sensor NLR (RGA5; R-gene analog 5), which directly bind effectors of the fungal pathogen Magnaporthe oryzae (
      • Maqbool A.
      • Saitoh H.
      • Franceschetti M.
      • Stevenson C.E.M.
      • Uemura A.
      • Kanzaki H.
      • Kamoun S.
      • Terauchi R.
      • Banfield M.J.
      Structural basis of pathogen recognition by an integrated HMA domain in a plant NLR immune receptor.
      ,
      • Cesari S.
      • Thilliez G.
      • Ribot C.
      • Chalvon V.
      • Michel C.
      • Jauneau A.
      • Rivas S.
      • Alaux L.
      • Kanzaki H.
      • Okuyama Y.
      • Morel J.B.
      • Fournier E.
      • Tharreau D.
      • Terauchi R.
      • Kroj T.
      The rice resistance protein pair RGA4/RGA5 recognizes the Magnaporthe oryzae effectors AVR-Pia and AVR1-CO39 by direct binding.
      ). Biochemical, structural, and in planta studies have shown how these HMA domains interact with pathogen effectors and demonstrate how different NLR variants perceive different alleles of the effectors (
      • Maqbool A.
      • Saitoh H.
      • Franceschetti M.
      • Stevenson C.E.M.
      • Uemura A.
      • Kanzaki H.
      • Kamoun S.
      • Terauchi R.
      • Banfield M.J.
      Structural basis of pathogen recognition by an integrated HMA domain in a plant NLR immune receptor.
      ,
      • De la Concepcion J.C.
      • Franceschetti M.
      • Maqbool A.
      • Saitoh H.
      • Terauchi R.
      • Kamoun S.
      • Banfield M.J.
      Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen.
      ,
      • Guo L.
      • Cesari S.
      • de Guillen K.
      • Chalvon V.
      • Mammri L.
      • Ma M.
      • Meusnier I.
      • Bonnot F.
      • Padilla A.
      • Peng Y.-L.
      • Liu J.
      • Kroj T.
      Specific recognition of two MAX effectors by integrated HMA domains in plant immune receptors involves distinct binding surfaces.
      ,
      • Ortiz D.
      • de Guillen K.
      • Cesari S.
      • Chalvon V.
      • Gracy J.
      • Padilla A.
      • Kroj T.
      Recognition of the Magnaporthe oryzae effector AVR-Pia by the decoy domain of the rice NLR immune receptor RGA5.
      ). Interestingly, a single integrated domain in an NLR can perceive multiple effectors. For example, the WRKY transcription factor–like domain of the Arabidopsis NLR RRS1 (resistance to Ralstonia solanacearum 1) interacts with two sequence-divergent and structurally divergent effectors (
      • Narusaka M.
      • Shirasu K.
      • Noutoshi Y.
      • Kubo Y.
      • Shiraishi T.
      • Iwabuchi M.
      • Narusaka Y.
      RRS1 and RPS4 provide a dual Resistance-gene system against fungal and bacterial pathogens.
      ). One of these effectors adopts a helix-loop-helix fold with an unknown virulence function (AvrRps4 (resistance to P. syringae 4); presumed to be a protein-protein interaction module) (
      • Zhang Z.-M.
      • Ma K.-W.
      • Gao L.
      • Hu Z.
      • Schwizer S.
      • Ma W.
      • Song J.
      Mechanism of host substrate acetylation by a YopJ family effector.
      ,
      • Sohn K.H.
      • Hughes R.K.
      • Piquerez S.J.
      • Jones J.D.G.
      • Banfield M.J.
      Distinct regions of the Pseudomonas syringae coiled-coil effector AvrRps4 are required for activation of immunity.
      ), whereas a second is an acetyltransferase (PopP2) that acetylates both WRKY transcription factors and the RRS1-WRKY (
      • Zhang Z.-M.
      • Ma K.-W.
      • Gao L.
      • Hu Z.
      • Schwizer S.
      • Ma W.
      • Song J.
      Mechanism of host substrate acetylation by a YopJ family effector.
      ,
      • Sohn K.H.
      • Hughes R.K.
      • Piquerez S.J.
      • Jones J.D.G.
      • Banfield M.J.
      Distinct regions of the Pseudomonas syringae coiled-coil effector AvrRps4 are required for activation of immunity.
      ). The structural basis of interaction between the RRS1-WRKY and PopP2 has been elucidated (
      • Zhang Z.-M.
      • Ma K.-W.
      • Gao L.
      • Hu Z.
      • Schwizer S.
      • Ma W.
      • Song J.
      Mechanism of host substrate acetylation by a YopJ family effector.
      ,
      • Sohn K.H.
      • Hughes R.K.
      • Piquerez S.J.
      • Jones J.D.G.
      • Banfield M.J.
      Distinct regions of the Pseudomonas syringae coiled-coil effector AvrRps4 are required for activation of immunity.
      ), but the equivalent structure with AvrRps4 remains to be determined. The RRS1-WRKY case demonstrates the versatility of effector perception that integrated domains deliver to NLRs and suggests their utility for receptor engineering.

      Case study 2: Integrated HMA domains—exemplars of integrated domains in NLRs

      Many different types of proteins have been found as IDs in plant NLRs, and likely function in direct perception of effectors (
      • Steuernagel B.
      • Witek K.
      • Krattinger S.G.
      • Ramirez-Gonzalez R.H.
      • Schoonbeek H-J.
      • Yu G.
      • Baggs E.
      • Witek A.
      • Yadav I.
      • Krasileva K.V.
      • Jones J.D.
      • Uauy C.
      • Keller B.
      • Ridout C.J.
      • Wulff B.B.
      The NLR-Annotator tool enables annotation of the intracellular immune receptor repertoire.
      ,
      • Bailey P.C.
      • Schudoma C.
      • Jackson W.
      • Baggs E.
      • Dagdas G.
      • Haerty W.
      • Moscou M.
      • Krasileva K.V.
      Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions.
      ,
      • Sarris P.F.
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      Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread.