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

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 Xanthomonaseuvesicatoria 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.

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Structure of the activated Roq1 resistosome directly recognizing the pathogen effector XopQ

10.1101/2020.08.13.246413 ◽

2020 ◽

Cited By ~ 4

Author(s):

Raoul Martin ◽

Tiancong Qi ◽

Haibo Zhang ◽

Furong Liu ◽

Miles King ◽

...

Keyword(s):

Immune Response ◽

Active Site ◽

Interleukin 1 ◽

Leucine Rich Repeat ◽

Tir Domain ◽

Pathogen Effectors ◽

Cryo Electron Microscopy ◽

Pathogen Effector ◽

Tir Domains ◽

Direct Recognition

AbstractPlants and animals detect pathogen infection via 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 Å resolution cryo-electron microscopy structure of the activated Roq1, an NLR native to Nicotiana benthamiana with a Toll-like interleukin-1 receptor (TIR) domain, bound to the Xanthomonas effector XopQ. 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.One Sentence SummaryVisualization of an activated plant immune receptor that triggers the immune response upon pathogen recognition.

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Integrity of the post-LRR domain is required for TNLs’ function

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-06-20-0156-r ◽

2020 ◽

Author(s):

Simon Bernard Saucet ◽

Daniel Esmenjaud ◽

Cyril Van Ghelder

Keyword(s):

Amino Acids ◽

Interleukin 1 ◽

Defense Responses ◽

Effector Proteins ◽

Domain Specificity ◽

Leucine Rich Repeat ◽

Pathogen Effector ◽

Tir Domains ◽

Conserved Amino Acids ◽

Lrr Domain

Plants trigger appropriate defense responses notably through intracellular nucleotide-binding (NB) and leucine-rich repeat (LRR) containing receptor genes (NLRs) that detect secreted pathogen effector proteins. In NLR resistance genes, the toll/interleukin-1 receptor (TIR)-NB-LRRs (TNLs) are an important subfamily out of which approximately half members carry a post-LRR (PL) domain of unknown role. We first investigated the requirement of the PL domain for TNL–mediated immune response by mutating the most conserved amino acids across PL domains of Arabidopsis thaliana TNLs. We identified several amino acids in the PL domain of RPS4 required for its ability to trigger a hypersensitive response to AvrRps4 in N. tabacum transient assay. Mutating the corresponding amino acids within the PL domain of the tobacco TNL gene N also affected its function. Consequently, our results indicate that the integrity of the PL domain at conserved positions is crucial for at least two unrelated TNLs. We then tested the PL domain specificity for function by swapping PL domains between the paralogs RPS4 and RPS4B. Our results suggest that the PL domain is involved in their TNL pair specificity, ‘off state’ stability and NLR complex activation. Considering genetically paired Arabidopsis TNLs, we finally compared the PL and TIR domains of their sensor and executor sequences, respectively. While TIR and PL domains from executors present complete motifs, sensors showed a lack of conservation with degenerated motifs. We provide here a first contribution to the functional analysis of the PL domain in order to decipher its role for TNLs’ function.

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TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death

10.1101/2021.11.09.467869 ◽

2021 ◽

Author(s):

Dongli Yu ◽

Wen Song ◽

Eddie Yong Jun Tan ◽

Li Liu ◽

Yu Cao ◽

...

Keyword(s):

Cell Death ◽

Immune Responses ◽

Interleukin 1 ◽

Structural Data ◽

Negative Regulator ◽

Synthetase Activity ◽

Leucine Rich Repeat ◽

Tir Domain ◽

Immune Receptors ◽

Tir Domains

2′,3′-cAMP is a positional isomer of the well-established second messenger 3′,5′-cAMP, but little is known on the biology of this noncanonical cyclic nucleotide monophosphate (cNMP). Toll/interleukin-1 receptor (TIR) domains of nucleotide-binding leucine-rich repeat (NLR) immune receptors have NADase function necessary but insufficient to activate plant immune responses. Here we show that plant TIR proteins, besides being NADases, act as 2′,3′-cAMP/cGMP synthetases by hydrolyzing RNA/DNA. Structural data shows that a TIR domain adopts distinct oligomers with dual and exclusive enzymatic activity. Mutations specifically disrupting the synthetase activity abrogate TIR-mediated cell death in Nicotiana benthamiana, supporting an important role for these cNMPs in TIR signaling. Furthermore, the Arabidopsis negative regulator of TIR-NLR signaling, NUDT7 displays 2′,3′-cAMP/cGMP but not 3′,5′-cAMP/cGMP phosphodiesterase activity and suppresses cell death activity of TIRs in N. benthamiana. Our study identifies a novel family of 2′,3′-cAMP/cGMP synthetase and establishes a role for the noncanonical cNMPs in plant immune responses.

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Induced proximity of a TIR signaling domain on a plant-mammalian NLR chimera activates defense in plants

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2001185117 ◽

2020 ◽

Vol 117 (31) ◽

pp. 18832-18839 ◽

Cited By ~ 9

Author(s):

Zane Duxbury ◽

Shanshan Wang ◽

Craig I. MacKenzie ◽

Jeannette L. Tenthorey ◽

Xiaoxiao Zhang ◽

...

Keyword(s):

Plant Defense ◽

Interleukin 1 ◽

Coiled Coil ◽

Leucine Rich Repeat ◽

In Planta ◽

Tir Domain ◽

Signaling Mechanisms ◽

Signaling Domain ◽

Resistance Protein ◽

Signaling Domains

Plant and animal intracellular nucleotide-binding, leucine-rich repeat (NLR) immune receptors detect pathogen-derived molecules and activate defense. Plant NLRs can be divided into several classes based upon their N-terminal signaling domains, including TIR (Toll-like, Interleukin-1 receptor, Resistance protein)- and CC (coiled-coil)-NLRs. Upon ligand detection, mammalian NAIP and NLRC4 NLRs oligomerize, forming an inflammasome that induces proximity of its N-terminal signaling domains. Recently, a plant CC-NLR was revealed to form an inflammasome-like hetero-oligomer. To further investigate plant NLR signaling mechanisms, we fused the N-terminal TIR domain of several plant NLRs to the N terminus of NLRC4. Inflammasome-dependent induced proximity of the TIR domain in planta initiated defense signaling. Thus, induced proximity of a plant TIR domain imposed by oligomerization of a mammalian inflammasome is sufficient to activate authentic plant defense. Ligand detection and inflammasome formation is maintained when the known components of the NLRC4 inflammasome is transferred across kingdoms, indicating that NLRC4 complex can robustly function without any additional mammalian proteins. Additionally, we found NADase activity of a plant TIR domain is necessary for plant defense activation, but NADase activity of a mammalian or a bacterial TIR is not sufficient to activate defense in plants.

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NAD+ cleavage activity by animal and plant TIR domains in cell death pathways

Science ◽

10.1126/science.aax1911 ◽

2019 ◽

Vol 365 (6455) ◽

pp. 793-799 ◽

Cited By ~ 79

Author(s):

Shane Horsefield ◽

Hayden Burdett ◽

Xiaoxiao Zhang ◽

Mohammad K. Manik ◽

Yun Shi ◽

...

Keyword(s):

Cell Death ◽

Nicotinamide Adenine Dinucleotide ◽

Interleukin 1 ◽

Nicotinamide Adenine Dinucleotide Phosphate ◽

Effector Proteins ◽

Nicotinamide Adenine ◽

Cleavage Activity ◽

Pathogen Effector ◽

Cell Death Signaling ◽

Tir Domains

SARM1 (sterile alpha and TIR motif containing 1) is responsible for depletion of nicotinamide adenine dinucleotide in its oxidized form (NAD+) during Wallerian degeneration associated with neuropathies. Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors recognize pathogen effector proteins and trigger localized cell death to restrict pathogen infection. Both processes depend on closely related Toll/interleukin-1 receptor (TIR) domains in these proteins, which, as we show, feature self-association–dependent NAD+ cleavage activity associated with cell death signaling. We further show that SARM1 SAM (sterile alpha motif) domains form an octamer essential for axon degeneration that contributes to TIR domain enzymatic activity. The crystal structures of ribose and NADP+ (the oxidized form of nicotinamide adenine dinucleotide phosphate) complexes of SARM1 and plant NLR RUN1 TIR domains, respectively, reveal a conserved substrate binding site. NAD+ cleavage by TIR domains is therefore a conserved feature of animal and plant cell death signaling pathways.

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Peptide-mediated Interference of TIR Domain Dimerization in MyD88 Inhibits Interleukin-1-dependent Activation of NF-κB

Journal of Biological Chemistry ◽

10.1074/jbc.c400613200 ◽

2005 ◽

Vol 280 (16) ◽

pp. 15809-15814 ◽

Cited By ~ 128

Author(s):

Maria Loiarro ◽

Claudio Sette ◽

Grazia Gallo ◽

Andrea Ciacci ◽

Nicola Fantò ◽

...

Keyword(s):

Interleukin 1 ◽

Cell System ◽

Tir Domain ◽

Loop Region ◽

Good Target ◽

A Cell ◽

Tir Domains ◽

Myeloid Differentiation Factor

Myeloid differentiation factor 88 (MyD88) plays a crucial role in the signaling pathways triggered by interleukin (IL)-1 and Toll-like receptors in several steps of innate host defense. A crucial event in this signaling pathway is represented by dimerization of MyD88, which allows the recruitment of downstream kinases like IRAK-1 and IRAK-4. Herein, we have investigated the function of the Toll/IL-1 receptor (TIR) domain in MyD88 homodimerization in cell-free andin vitroexperimental settings by using epta-peptides that mimic the BB-loop region of the conserved TIR domain of different proteins. By using a pull-down assay with purified glutathioneS-transferase-MyD88 TIR or co-immunoprecipitation experiments, we found that epta-peptides derived from the TIR domain of MyD88 and IL-18R are the most effective in inhibiting homodimerization with either the isolated TIR or full-length MyD88. Moreover, we demonstrated that a cell permeable analog of MyD88 epta-peptide inhibits homodimerization of MyD88 TIR domains in anin vitrocell system and significantly reduces IL-1 signaling, as assayed by activation of the downstream transcription factor NF-κB. Our results indicate that the BB-loop in TIR domain of MyD88 is a good target for specific inhibition of MyD88-mediated signalingin vivo.

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Vaccinia virus protein A46R targets multiple Toll-like–interleukin-1 receptor adaptors and contributes to virulence

Journal of Experimental Medicine ◽

10.1084/jem.20041442 ◽

2005 ◽

Vol 201 (6) ◽

pp. 1007-1018 ◽

Cited By ~ 274

Author(s):

Julianne Stack ◽

Ismar R. Haga ◽

Martina Schröder ◽

Nathan W. Bartlett ◽

Geraldine Maloney ◽

...

Keyword(s):

Vaccinia Virus ◽

Interleukin 1 ◽

Nuclear Factor Κb ◽

Virus Protein ◽

Innate Defense ◽

Tir Domain ◽

Mitogen Activated Protein ◽

Key Aspects ◽

Tir Domains ◽

Myeloid Differentiation Factor

Viral immune evasion strategies target key aspects of the host antiviral response. Recently, it has been recognized that Toll-like receptors (TLRs) have a role in innate defense against viruses. Here, we define the function of the vaccinia virus (VV) protein A46R and show it inhibits intracellular signalling by a range of TLRs. TLR signalling is triggered by homotypic interactions between the Toll-like–interleukin-1 resistance (TIR) domains of the receptors and adaptor molecules. A46R contains a TIR domain and is the only viral TIR domain–containing protein identified to date. We demonstrate that A46R targets the host TIR adaptors myeloid differentiation factor 88 (MyD88), MyD88 adaptor-like, TIR domain–containing adaptor inducing IFN-β (TRIF), and the TRIF-related adaptor molecule and thereby interferes with downstream activation of mitogen-activated protein kinases and nuclear factor κB. TRIF mediates activation of interferon (IFN) regulatory factor 3 (IRF3) and induction of IFN-β by TLR3 and TLR4 and suppresses VV replication in macrophages. Here, A46R disrupted TRIF-induced IRF3 activation and induction of the TRIF-dependent gene regulated on activation, normal T cell expressed and secreted. Furthermore, we show that A46R is functionally distinct from another described VV TLR inhibitor, A52R. Importantly, VV lacking the A46R gene was attenuated in a murine intranasal model, demonstrating the importance of A46R for VV virulence.

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Inhibition of Interleukin 1 Receptor/Toll-like Receptor Signaling through the Alternatively Spliced, Short Form of MyD88 Is Due to Its Failure to Recruit IRAK-4

Journal of Experimental Medicine ◽

10.1084/jem.20021790 ◽

2003 ◽

Vol 197 (2) ◽

pp. 263-268 ◽

Cited By ~ 322

Author(s):

Kimberly Burns ◽

Sophie Janssens ◽

Brian Brissoni ◽

Natalia Olivos ◽

Rudi Beyaert ◽

...

Keyword(s):

Short Form ◽

Interleukin 1 ◽

Negative Regulator ◽

Death Domain ◽

Innate Immune Responses ◽

Tir Domain ◽

Intermediate Domain ◽

Alternatively Spliced ◽

Tir Domains ◽

Multiple Signaling

Toll-like receptors (TLRs) and members of the proinflammatory interleukin 1 receptor (IL-1R) family are dependent on the presence of MyD88 for efficient signal transduction. The bipartite nature of MyD88 (N-terminal death domain [DD] and COOH-terminal Toll/IL-1 receptor [TIR] domain) allows it to link the TIR domain of IL-1R/TLR with the DD of the Ser/Thr kinase termed IL-1R–associated kinase (IRAK)-1. This triggers IRAK-1 phosphorylation and in turn the activation of multiple signaling cascades such as activation of the transcription factor nuclear factor (NF)-κB. In contrast, expression of MyD88 short (MyD88s), an alternatively spliced form of MyD88 that lacks only the short intermediate domain separating the DD and TIR domains, leads to a shutdown of IL-1/lipopolysaccharide-induced NF-κB activation. Here, we provide the molecular explanation for this difference. MyD88 but not MyD88s strongly interacts with IRAK-4, a newly identified kinase essential for IL-1R/TLR signaling. In the presence of MyD88s, IRAK-1 is not phosphorylated and neither activates NF-κB nor is ubiquitinated. Thus, MyD88s acts as a negative regulator of IL-1R/TLR/MyD88-triggered signals, leading to a transcriptionally controlled negative regulation of innate immune responses.

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Activation of TIR signaling is required for pattern-triggered immunity

10.1101/2020.12.27.424494 ◽

2020 ◽

Author(s):

Hainan Tian ◽

Siyu Chen ◽

Zhongshou Wu ◽

Kevin Ao ◽

Hoda Yaghmaiean ◽

...

Keyword(s):

Immune Responses ◽

Interleukin 1 ◽

Defense Responses ◽

Effector Proteins ◽

Leucine Rich Repeat ◽

Number Of Genes ◽

Genes Encoding ◽

Signaling Activation ◽

Tir Domains ◽

The Relationship

AbstractPlant immune responses are mainly activated by two types of receptors. Plasma membrane-localized pattern recognition receptors (PRRs) recognize conserved features of microbes, and intracellular nucleotide-binding leucine rich repeat receptors (NLRs) recognize effector proteins from pathogens. NLRs possessing N-terminal Toll/interleukin-1 receptor (TIR) domains (TNLs) activate two parallel signaling pathways via the EDS1/PAD4/ADR1s and the EDS1/SAG101/NRG1s modules. The relationship between PRR-mediated pattern-triggered immunity (PTI) and TIR signaling is unclear. Here we report that activation of TIR signaling plays a key role in PTI. Blocking TIR signaling by knocking out components of the EDS1/PAD4/ADR1s and EDS1/SAG101/NRG1s modules results in attenuated PTI responses such as reduced salicylic acid (SA) levels and expression of defense genes, and compromised resistance against pathogens. Consistently, PTI is attenuated in transgenic plants that have reduced accumulation of NLRs. Upon treatment with PTI elicitors such as flg22 and nlp20, a large number of genes encoding TNLs or TIR domain-containing proteins are rapidly induced, likely responsible for activating TIR signaling during PTI. In support, overexpression of some of these genes results in activation of defense responses. Overall, our study reveals that TIR signaling activation is an important mechanism for boosting plant defense during PTI.

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The blast pathogen effector AVR-Pik binds and stabilizes rice heavy metal-associated (HMA) proteins to co-opt their function in immunity

10.1101/2020.12.01.406389 ◽

2020 ◽

Cited By ~ 1

Author(s):

K. Oikawa ◽

K. Fujisaki ◽

M. Shimizu ◽

T. Takeda ◽

H. Saitoh ◽

...

Keyword(s):

Heavy Metal ◽

Susceptibility Gene ◽

Leucine Rich Repeat ◽

Nucleotide Binding Domain ◽

Host Proteins ◽

Immune Receptors ◽

Pathogen Effectors ◽

Pathogen Effector ◽

Integrated Domains ◽

Complex Architecture

AbstractPlant intracellular nucleotide-binding domain and leucine-rich repeat-containing (NLR) immune receptors have a complex architecture. They can include noncanonical integrated domains that are thought to have evolved from host targets of pathogen effectors to serve as pathogen baits. However, the functions of host proteins with similarity to NLR integrated domains and the extent to which they are targeted by pathogen effectors remain largely unknown. Here, we show that the blast fungus effector AVR-Pik binds a subset of related rice proteins containing a heavy metal-associated (HMA) domain, one of the domains that has repeatedly integrated into plant NLR immune receptors. We find that AVR-Pik binding stabilizes the rice HMA proteins OsHIPP19 and OsHIPP20. Knockout of OsHIPP20 causes enhanced disease resistance towards the blast pathogen, indicating that OsHIPP20 is a susceptibility gene (S-gene). We propose that AVR-Pik has evolved to bind HMA domain proteins and co-opt their function to suppress immunity. Yet this binding carries a trade-off, it triggers immunity in plants carrying NLR receptors with integrated HMA domains.

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