Structure of the activated ROQ1 resistosome directly recognizing the pathogen effector XopQ

Tetrameric immune receptors Nucleotide-binding/leucine-rich repeat (NLR) immune receptors detect pathogen effectors and trigger a plant's immune response. Two groups have now defined the structures of two NLRs that carry Toll-like interleukin-1 receptor (TIR) domains (TIR-NLRs) (see the Perspective by Tian and Li). Ma et al. studied the Arabidopsis thaliana TIR-NLR RPP1 (recognition of Peronospora parasitica 1) and its response to effectors from an oomycete pathogen. Martin et al. studied the Nicotiana benthamiana TIR-NLR ROQ1 (recognition of XopQ 1) and its response to the Xanthomonas effector. Both groups found that these TIR-NLRs formed tetramers that, when activated by binding to the pathogen effector, exposed the active site of a nicotinamide adenine dinucleoside (NAD) hydrolase. Thus, recognition of the pathogen effector initiates NAD hydrolysis and begins the immune response. Science, this issue p. eabe3069, p. eabd9993; see also p. 1163 The mechanism of pathogen effector recognition by plant innate immune receptors and the formation of a signaling-active complex are elucidated. INTRODUCTION Plants and animals respond to pathogen invasion through intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) that directly interact with pathogen proteins or indirectly detect pathogen-derived alterations in the host proteome. Upon recognition of pathogen invasion, NLRs trigger an immune response that resolves in a variety of ways depending on the type of NLR being activated. The overall architecture of NLRs is highly conserved, consisting of a C-terminal leucine-rich repeat (LRR) platform that determines substrate specificity and a central nucleotide-binding oligomerization domain. The N-terminal domain varies between NLRs and determines the mechanism used by the host to activate the immune response. Thus, NLRs in plants have been classified according to their N-terminal domain into Toll/interleukin 1 receptor (TIR) NLRs (TNLs), coiled-coil NLRs (CNLs), and RPW8-like coiled-coil NLRs (RNLs). Pathogen detection and oligomerization of the NLR activates these N-terminal domains by bringing them in close contact. In all three cases, association of the N-terminal domain leads to localized cell death and expression of disease resistance. The TIR domains of TNLs have been shown to have oligomerization-dependent NADase activity that is required for promoting cell death, but it is not understood how the interactions between TIR domains renders them catalytically active. RATIONALE The structure of the ROQ1 (recognition of XopQ 1)–XopQ (Xanthomonas outer protein Q) complex, an immune receptor bound to its pathogen substrate, was used as a model to study the mechanism of direct binding, oligomerization, and TIR domain activation of TNLs. ROQ1 has been shown to physically interact with the Xanthomonas effector XopQ, causing it to oligomerize and trigger a TIR-dependent hypersensitive cell death response. We coexpressed, extracted, and purified the assembled ROQ1-XopQ complex from ROQ1’s native host, Nicotiana benthamiana, and solved its structure by cryo–electron microscopy to 3.8-Å resolution. The interactions described in our structure were further confirmed by in vivo mutational analysis. RESULTS Our structure reveals that ROQ1 forms a tetrameric resistosome upon recognizing XopQ. The LRR and a post-LRR domain named the C-terminal jelly-roll/Ig-like domain (C-JID), form a horseshoe-shaped scaffold that curls around the pathogen effector, thereby recognizing multiple regions of the substrate. Binding of the ROQ1 LRR to XopQ occurs through surface-exposed residues that make up the scaffold of the domain, as well as an elongated loop between two LRRs that forms a small amphipathic α-helix at the site of interaction. The mode of substrate recognition by the C-JID is reminiscent of that used by immunoglobulins to bind their antigen. Similar to the complementary-determining regions of antibodies, interconnecting loops emerging from the C-JID β-sandwich structure make substrate-specific contacts with XopQ. In particular, an extended loop of the C-JID dives into the active-site cleft of XopQ and interacts with conserved residues required for nucleoside binding, suggesting that ROQ1 not only recognizes its substrate but also inhibits its ligand-binding function. The nucleotide-binding domain (NBD), helical domain 1 (HD1) and the winged-helix domain (WHD), termed NB-ARC because of their presence in Apaf-1, R proteins, and CED-4 (ARC), are responsible for ROQ1 oligomerization in an ATP-bound state. Individual protomers intercalate in a similar fashion as found in other NLR structures, promoting association between the N-terminal TIR domains. The TIR domains bind to each other through two distinct interfaces (called AE and BE), causing them to form a dimer of dimers. BE-interface contacts cause a conformational rearrangement in a loop, called the BB-loop, at the periphery of the TIR domain active site that exposes the putative catalytic glutamate that is suggested to cleave NAD+. These results provide a rationale for the previously determined oligomerization dependence of TIR domain NADase activity. CONCLUSION We propose a step-by-step mechanism for ROQ1 immune signaling based on our structure of the activated complex and on previous biochemical studies. The LRR and C-JID of ROQ1 recognize the pathogen effector through direct contacts with its surface and active-site residues. Detection of the substrate releases autoinhibitory contacts between the NB-ARC domain and the LRR, allowing the NB-ARC domain to transition to an ATP-bound, oligomerization-prone state. Complex assembly brings the TIR domains in close contact, leading to opening of the NADase active site in an interface-dependent manner. Cleavage of NAD+ by the TIR domain results in the release of adenosine diphosphate ribose, a signaling molecule that triggers cytosolic Ca2+ influx, a widely used chemical cue in response to various biotic and abiotic stresses, leading to downstream activation of localized cell death and disease resistance. Proposed mechanism of ROQ1 activation. The LRR and C-JID of ROQ1 recognize the pathogen effector XopQ. ROQ1 oligomerizes through the NB-ARC domain (NBD, HD1, WHD) in an ATP-bound state. TIR domain association causes a conformational rearrangement of the BB-loop and opens the NADase active site. Catalytic activity of the TIR domains further signals the immune response, resulting in cell death. Plants and animals detect pathogen infection using intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) that directly or indirectly recognize pathogen effectors and activate an immune response. How effector sensing triggers NLR activation remains poorly understood. Here we describe the 3.8-angstrom-resolution cryo–electron microscopy structure of the activated ROQ1 (recognition of XopQ 1), an NLR native to Nicotiana benthamiana with a Toll-like interleukin-1 receptor (TIR) domain bound to the Xanthomonas euvesicatoria effector XopQ (Xanthomonas outer protein Q). ROQ1 directly binds to both the predicted active site and surface residues of XopQ while forming a tetrameric resistosome that brings together the TIR domains for downstream immune signaling. Our results suggest a mechanism for the direct recognition of effectors by NLRs leading to the oligomerization-dependent activation of a plant resistosome and signaling by the TIR domain.