Structural Insights into the Plant Immune Receptors PRRs and NLRs

The plant immune system is composed of two classes of receptors—the membrane-anchored pattern recognition receptors (PRRs) and the intracellular nucleotide-binding and leucine-rich repeat receptors (NLRs; Jones and Dangl, 2006; Dangl et al., 2013). The PRR family consists of receptor kinases (RKs) and receptor-like proteins (RLPs) acting in the first tier of the plant immune system. PRRs contain a variable ectodomain that usually function to recognize either conserved microbial signatures known as pathogen-associated molecular patterns (PAMPs) or damage indicators known as danger-associated molecular patterns (DAMPs). PRR activation induces immune responses known as PAMP-triggered immunity (PTI) including expression of immune-related genes (Fig. 1) to ward off microbes (Macho and Zipfel, 2014). Many pathogenic microbes, however, can successfully deliver effector proteins into the plant cell to dampen PTI signaling by manipulating host targets. Plants hence have evolved NLRs as intracellular immune receptors to mediate the second level of surveillance (Fig. 1) through specific recognition of pathogen effectors (Chisholm et al., 2006). Upon perception of effectors, NLRs coordinate a rapid and robust immune signaling response termed effector-triggered immunity, which often leads to hypersensitive response (HR, local cell death at the infection site) and limitation of pathogenic microbes (Fig. 1; Jones et al., 2016). A schematic view of the two-tiered plant immune system. Recognition of PAMPs like bacterial flagellin and fungal chitin or DAMPs like secreted small peptides by PRRs induces intracellular signaling, leading to PTI. Successful pathogens deliver effector proteins (red dots) into the plant cell to dampen PTI. In some host plants, effector proteins are specifically recognized by the intracellular NLR immune receptors via different strategies, inducing effector-triggered immunity (ETI) that includes expression of immune-related genes and localized cell death referred to as HR. X, a host molecule guarded by NLRs; ID, integrated domain. A schematic view of the two-tiered plant immune system. Recognition of PAMPs like bacterial flagellin and fungal chitin or DAMPs like secreted small peptides by PRRs induces intracellular signaling, leading to PTI. Successful pathogens deliver effector proteins (red dots) into the plant cell to dampen PTI. In some host plants, effector proteins are specifically recognized by the intracellular NLR immune receptors via different strategies, inducing effector-triggered immunity (ETI) that includes expression of immune-related genes and localized cell death referred to as HR. X, a host molecule guarded by NLRs; ID, integrated domain. In the last two decades, tremendous advances have been made in functional and mechanistic dissection of plant PRRs and NLRs. There are many excellent reviews on these exciting achievements, mainly from the point view of genetics and physiology (Cui et al., 2015; Boutrot and Zipfel, 2017; Tang et al., 2017; Kourelis and van der Hoorn, 2018; Wan et al., 2019b; Zhang et al., 2017b). In this review, we highlight some of recent structural studies of PRRs and NLRs and discuss how they provided insights into their acting mechanisms. RK-PRRs contain a variable N-terminal extracellular domain (ECD), a transmembrane segment (TM), and a conserved cytoplasmic kinase domain (KD); whereas RLP-PRRs lack an obvious intracellular domain that is typically short (∼24 amino acids). Based on their ECDs, RK-PRRs can be categorized into several groups (Fig. 2A; Böhm et al., 2014; Macho and Zipfel, 2014; Zipfel, 2014). The largest one is leucine-rich repeat (LRR)-RKs and the well-known examples are FLAGELLIN-SENSITIVE2 (FLS2; Gómez-Gómez and Boller, 2000) and EF-TU RECEPTOR (Zipfel et al., 2006), sensing the PAMPs of peptide epitopes of flagellin and elongation factor, respectively. Other examples from this group include PEP RECEPTORs (PEPRs) and RLK7, which perceive the DAMPs of PLANT ELICITOR PEPTIDEs (Yamaguchi et al., 2006, 2010) and PAMP-INDUCED SECRETED PEPTIDEs (Hou et al., 2014), respectively. The Lys-motif (LysM) RK-PRRs such as CHITIN ELICITOR RECEPTOR KINASE1 (CERK1; Miya et al., 2007; Wan et al., 2008) and LYSIN MOTIF RECEPTOR KINASE5 (Cao et al., 2014) are the receptors of the polysaccharide PAMPs like chitin. WALL-ASSOCIATED KINASE1 perceiving the oligogalacturonide DAMP (Brutus et al., 2010) belongs to the epidermal growth factor-like RK-PRR. Another group of RK-PRRs contains extracellular lectin domains. Two newly identified members of this group are DOES NOT RESPOND TO NUCLEOTIDES1 (Choi et al., 2014) and LIPOOLIGOSACCHARIDE-SPECIFIC REDUCED ELICITATION (Kutschera et al., 2019), which recognize the extracellular ATP DAMP and the bacterial medium-chain 3-hydroxy fatty acids PAMP, respectively. Compared to RK-PRRs, fewer subgroups of RLP-PRRs have been characterized. One is the LRR-RLPs that usually sense PAMPs (Fig. 2A, lower). Another one is the LysM-RLPs, including the receptors of chitin, CHITIN OLIGOSACCHARIDE ELICITOR BINDING PROTEIN (CEBiP; Kaku et al., 2006) and LYSIN MOTIF DOMAIN-CONTAINING GPI-ANCHORED PROTEIN2 (LYM2; Faulkner et al., 2013). Other members from this group are LYM1 and LYM3, and LYSIN MOTIF–CONTAINING PROTEIN4 and LYSIN MOTIF–CONTAINING PROTEIN6. The former two are receptors of peptidoglycan (PGN; Willmann et al., 2011), while the latter two function to sense both PGN and chitin (Liu et al., 2012a). Plant PRRs and NLRs. A, Schematic diagrams depicting domain structures of different classes of plant PRRs. Upper, The RK-PRRs. Lower, The RLP-PRRs. The representatives in each class are shown on the right. SP, signal peptide; EGF, epidermal growth factor. B, Schematic diagrams of domain structures of different NLRs. The representatives in each class are shown on the right. Upper, Domain structures of plant NLRs based on their variable N-terminal domains. Lower, Domain structures of plant-paired NLRs and helper NLRs. Plant PRRs and NLRs. A, Schematic diagrams depicting domain structures of different classes of plant PRRs. Upper, The RK-PRRs. Lower, The RLP-PRRs. The representatives in each class are shown on the right. SP, signal peptide; EGF, epidermal growth factor. B, Schematic diagrams of domain structures of different NLRs. The representatives in each class are shown on the right. Upper, Domain structures of plant NLRs based on their variable N-terminal domains. Lower, Domain structures of plant-paired NLRs and helper NLRs. Ligand sensing by ECDs activates KDs for immune signaling. Because of the lack of KDs, RLP-PRRs generally function together with RKs. PAMP perception by single RK-PRRs such as Arabidopsis (Arabidopsis thaliana) AtCERK1 has been reported (Miya et al., 2007; Wan et al., 2008), but many RK-PRRs require a coreceptor for signaling. Several recent studies (Jaillais et al., 2011; Smakowska-Luzan et al., 2018; Xi et al., 2019) suggested that the size of ECD is crucial for ligand perception by LRR-RKs and could be used to predict whether they function as receptors or coreceptors. For instance, when the LRR-RKs containing large size of ECDs act as the ligand-binding receptors, another small LRR-RK is preferred for coreceptor, but not itself. The LRR-RK SOMATIC EMBRYOGENESIS RECEPTOR KINASE3 (SERK3, also called BRI1-ASSOCIATED KINASE1 [BAK1]) and its orthologs are commonly shared coreceptors by LRR-RKs involved in diverse signaling pathways including immunity (Ma et al., 2016). Additionally, BAK1/SERKs together with the LRR-RK SUPPRESSOR OF BIR-1 (SOBIR1) also function as coreceptors of multiple LRR-RLPs (Liebrand et al., 2014). Given their critical role in plant immunity, BAK1/SERKs are subjected to negative regulation by pathogen effectors (Ma et al., 2016) and by host components like the LRR-RK BAK1-INTERACTING RECEPTOR KINASEs (BIRs; Gao et al., 2009; Halter et al., 2014) in Arabidopsis. More recently, the Arabidopsis malectin-like RK FERONIA (FER) was shown to act as a scaffold for regulation of assembly of PRR-containing complexes (Shen et al., 2017; Stegmann et al., 2017). Chitin, a polymeric n-acetyl-glucosamine (NAG), is a well-characterized fungal PAMP. Different mechanisms are employed by Arabidopsis and rice (Oryza sativa) for perception of the PAMP. The LysM-RKs AtCERK1 (Miya et al., 2007; Wan et al., 2008; Liu et al., 2012b) and LYSIN MOTIF RECEPTOR KINASE5 (Cao et al., 2014) are direct receptors of chitin in Arabidopsis. In contrast, direct chitin recognition in rice is through the LysM-RLP OsCEBiP to activate OsCERK1 (Kaku et al., 2006; Shimizu et al., 2010; Liu et al., 2016a). The crystal structures of AtCERK1ECD and OsCEBiPECD in complex with a chito-pentamer and a chito-tetramer, respectively, revealed a conserved chitin recognition mechanism (Fig. 3, A and B; Liu et al., 2016a, 2012b). The structures of AtCERK1ECD and OsCEBiPECD are conserved in their LysMs, but only LysM2 was found to bind chitin. In the structures, chito-oligomers anchor to a shallow groove created by two loops of LysM2. Recognition of the chitin by AtCERK1 and OsCEBiP is mainly through a conserved of of LysM2 that with recognition and activation of PRRs. A, Recognition of chitin by in the is the crystal of AtCERK1ECD in complex with a chito-pentamer AtCERK1ECD is shown in chitin in the are shown in for are B, Recognition of chitin by in the is the crystal of OsCEBiPECD in complex with a as molecular to of with its coreceptor is the of the complex in The are Recognition of by its receptor The crystal of in complex with is shown in recognition and activation of PRRs. A, Recognition of chitin by in the is the crystal of AtCERK1ECD in complex with a chito-pentamer AtCERK1ECD is shown in chitin in the are shown in for are B, Recognition of chitin by in the is the crystal of OsCEBiPECD in complex with a as molecular to of with its coreceptor is the of the complex in The are Recognition of by its receptor The crystal of in complex with is shown in of the groups of chitin with AtCERK1 and OsCEBiP can the two proteins to the PAMP from Liu et al., 2016a, 2012b). in to chitin, PGN et al., and et al., also immune responses in Arabidopsis. PGN perception by AtCERK1 is through the LYM1 and LYM3, how AtCERK1 is studies suggested that also to LysM2 of AtCERK1 but with a different from the or the et al., AtCERK1 was suggested to recognize a chitin, to immune responses in Arabidopsis et al., 2010; et al., which is by a recent et al., and functional AtCERK1 for activation (Liu et al., 2012b). A chitin was to act as a which two AtCERK1 bind for known as the A of OsCEBiP suggested that of with each LysM2 in a (Liu et al., the Two suggested on One is called the two bind to one chitin from et al., 2014). of with of or to the et al., in which two AtCERK1 an groove for chitin or is a of the and an for of immunity by a of and et al., 2014). of the mechanisms is for AtCERK1 and OsCEBiP The LRR-RK PRR flagellin by its conserved N-terminal a peptide called as a coreceptor is for immune signaling et al., 2007; et al., 2013). 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