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Review
. 2017 Mar 1;119(5):827-702.
doi: 10.1093/aob/mcw171.

Animal NLRs Provide Structural Insights Into Plant NLR Function

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Free PMC article
Review

Animal NLRs Provide Structural Insights Into Plant NLR Function

Adam Bentham et al. Ann Bot. .
Free PMC article

Abstract

Background: The plant immune system employs intracellular NLRs (nucleotide binding [NB], leucine-rich repeat [LRR]/nucleotide-binding oligomerization domain [NOD]-like receptors) to detect effector proteins secreted into the plant cell by potential pathogens. Activated plant NLRs trigger a range of immune responses, collectively known as the hypersensitive response (HR), which culminates in death of the infected cell. Plant NLRs show structural and functional resemblance to animal NLRs involved in inflammatory and innate immune responses. Therefore, knowledge of the activation and regulation of animal NLRs can help us understand the mechanism of action of plant NLRs, and vice versa.

Scope: This review provides an overview of the innate immune pathways in plants and animals, focusing on the available structural and biochemical information available for both plant and animal NLRs. We highlight the gap in knowledge between the animal and plant systems, in particular the lack of structural information for plant NLRs, with crystal structures only available for the N-terminal domains of plant NLRs and an integrated decoy domain, in contrast to the more complete structures available for animal NLRs. We assess the similarities and differences between plant and animal NLRs, and use the structural information on the animal NLR pair NAIP/NLRC4 to derive a plausible model for plant NLR activation.

Conclusions: Signalling by cooperative assembly formation (SCAF) appears to operate in most innate immunity pathways, including plant and animal NLRs. Our proposed model of plant NLR activation includes three key steps: (1) initially, the NLR exists in an inactive auto-inhibited state; (2) a combination of binding by activating elicitor and ATP leads to a structural rearrangement of the NLR; and (3) signalling occurs through cooperative assembly of the resistosome. Further studies, structural and biochemical in particular, will be required to provide additional evidence for the different features of this model and shed light on the many existing variations, e.g. helper NLRs and NLRs containing integrated decoys.

Keywords: Avirulence protein; cryo-electron microscopy; crystal structure; effector-triggered immunity (ETI); leucine-rich repeat (LRR)/nucleotide-binding oligomerization domain (NOD)-like receptor (NLR); nucleotide binding (NB); plant pathogen effector protein; resistance protein; three-dimensional structure.

Figures

F<sc>ig</sc>. 1.
Fig. 1.
Domain architecture of representative plant and animal NLR and STAND proteins. A tripartite ‘signalling domain-NOD-sensor domain’ architecture is conserved throughout most proteins of the NLR family. Variability is often observed for the N-terminal signalling domains, with a suite of different protein-interaction domains occupying this region. In the animal NLRs, we typically see two classes, NLRC (NLR family, containing caspase recruitment domain [CARD]) and NLRP (NLR family containing pyrin domain [PYD]), and additionally the NLR-family apoptosis-inhibitory proteins (NAIPs), in which the N-terminal domain consists of one or more tandem baculovirus inhibitor-of-apoptosis repeat (BIR) domains (Inohara and Nunez, 2003). Plant NLRs are divided into two classes based on their N-terminal signalling domains: coiled-coiled (CC) domains (CNL proteins) or Toll/interleukin-1 receptor/resistance (TIR) domains (TNL proteins). Some variability exists in the NACHT/NB-ARC NOD modules between species; the second helical domain (HD2) found in animal NLRs, which connects the winged-helix (WHD) domain and C-terminal sensor domain, has not yet been identified in plant NLRs. Notably, the apoptotic response proteins APAF-1 (apoptotic protease-activating factor 1) and CED-4 differ from NLRs in the sensor domain; APAF-1 contains WD/WD40 repeats, whereas CED-4 uses separate sensor proteins to detect stimuli (Fairlie et al., 2006). Some NLRs incorporate additional domains to assist with function, e.g. the HMA domains of the rice NLRs RGA5 and Pik (Okuyama et al., 2011; Maqbool et al., 2015), the WRKY domain in the Arabidopsis NLR RRS1 (Deslandes et al., 2003), the CARD in NOD2 (Bertin et al., 1999) and PYD in DEFCAP (Chu et al., 2001; Hlaing et al., 2001).
F<sc>ig</sc>. 2.
Fig. 2.
Simplified signal transduction pathway diagrams for representative NLRs and STAND proteins. Signalling of NLR proteins is complex and occurs in a family-dependent manner. One of the earliest-characterized NLRs, NOD1 (nucleotide oligomerization domain protein 1), directly interacts with MAMPs such as LPS and activates the transcription factor NF-κB, resulting in the of release pro-inflammatory cytokines (Inohara et al., 1999; Ogura et al., 2001). The NLRC (NLR family, CARD containing) and NLRP (NLR family, PYD containing) family members have also been demonstrated to release pro-inflammatory cytokines through the activation of caspase-1, mediated by CARD/PYD domain interactions directly with caspase-1 or through the ASC (apoptosis-associated speck-like protein containing a CARD) adaptor protein (Dowds et al., 2003; Masumoto et al., 2003). However, there is a large body of evidence suggesting there is no direct interaction between these proteins and their stimuli. Members of the NAIP family of NLRs function as sensors in cooperation with NLRC proteins, which act as adaptors (Lightfield et al., 2008; Halff et al., 2012; Lu et al., 2014). The cooperation of NAIP proteins with NLRP proteins is yet to be determined, but has been speculated (Yin et al., 2015). NLRP and NLRC proteins have been implicated in the activation of pyroptosis through ASC-dependent and independent caapase-1 activation (Fink et al., 2008; Bergsbaken et al., 2009; Schroder and Tschopp, 2010). Activation of NLRP and NLRC proteins results in the formation of large oligomeric assemblies termed inflammasomes (Gross et al., 2009; Halff et al., 2012; Lu et al., 2014; Hu et al., 2015; Zhang et al., 2015). The NOD-containing apoptotic protease-activating factor 1 (APAF-1) has been demonstrated to activate caspase-9-mediated apoptosis through direct interaction with cytosolic cytochrome c, released from a disrupted mitochondrial matrix (Zou et al., 1997; Benedict et al., 2000). Like NLRC proteins, activated APAF-1 forms a large oligomeric assembly, the apoptosome, but in a 1:1 stoichiometry with cytochrome c (Zou et al., 1999; Reubold et al., 2011). Little is known about the signalling pathways of plant NLRs in comparison with their animal counterparts. What is clear is that stimulus detection can occur in a direct or indirect manner, and that self-association of N-terminal signalling domains is vital for NLR signalling (Bernoux et al., ; Maekawa et al., 2011a; Williams et al., 2014,). However, upstream and downstream signalling partners for most plant NLRs remain elusive.
F<sc>ig</sc>. 3.
Fig. 3.
Structural studies of N-terminal signalling domains of plant NLRs. Structures are displayed in cartoon representation with transparent surface. All protein structure figures were prepared using Pymol (DeLano Scientific LLC). (A) Crystal structure of flax L6 TIR domain (green; Protein Data Bank [PDB] ID 3OZI) (Bernoux et al., 2011b). (B) Crystal structure of the complex of TIR domains from Arabidopsis RPS4 and RRS1 in blue and magenta, respectively (PDB ID 4C6T) (Williams et al., 2014). (C) Crystal structure of the CC domain of barley MLA10 (the two molecules in the dimer are shown in yellow and lime; PDB ID 3QFL) (Maekawa et al., 2011a). (D) Structure of the CC domain of potato Rx (orange) in complex with the WPP domain of RanGAP2 in grey (PDB ID 4M70) (Hao et al., 2013).
F<sc>ig</sc>. 4.
Fig. 4.
Structure-based model of NAIP/NLRC4 activation. (A) NLRC4 is maintained in an auto-inhibited state through ADP binding and NACHT:LRR domain interactions. Interactions between NLRC4 and NAIP2 bound to PrgJ leads to disassociation of ADP and conformational changes in the protein, leading to the release of the NACHT domain from the LRR and the binding of ATP. (B) Activated NLRC4 molecules are able to trigger activation of inactive NLRC4 molecules, leading to a disc-like assembly. The structures are shown in cartoon and surface representations, based on the structures of inactive NLRC4 (PDB ID 4KXF) (Hu et al., 2013) and activated NLRC4 without the N-terminal CARD (PDB ID 3JBL) (Hu et al., 2015). In each protein chain, the colour changes continuously from the N-terminus (NOD, blue) to the C-terminus (LRR domain, red).
F<sc>ig</sc>. 5.
Fig. 5.
Model for signalling by cooperative assembly formation (SCAF) of plant NLRs. When unchallenged by pathogen effectors, plant NLRs exist in equilibrium between a closed inactive conformation (stabilized by ADP binding) and an open activated conformation, with the equilibrium strongly skewed towards the former. Both ATP and effector (or effector-induced elicitor in the case of indirect effector recognition) binding stabilize the active conformation, but only when both ATP and effector are bound, the equilibrium shifts sufficiently towards the active conformation to cause downstream events to take place. The active conformer presents new interfaces supporting oligomerization, and the NLRs are able to oligomerize. In analogy with NAIP/NLRC4, a small proportion of active NLRs can seed the conformational transition of further inactive NLRs to the active conformation and allow them to participate in the oligomerization, leading to a cooperative assembly of the resistosome. The downstream adaptors and ‘effector enzymes’ have not been identified in plant systems at this stage.

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