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

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

Science ◽

10.1126/science.abd9993 ◽

2020 ◽

Vol 370 (6521) ◽

pp. eabd9993 ◽

Cited By ~ 3

Author(s):

Raoul Martin ◽

Tiancong Qi ◽

Haibo Zhang ◽

Furong Liu ◽

Miles King ◽

...

Keyword(s):

Active Site ◽

Nicotiana Benthamiana ◽

Interleukin 1 ◽

Leucine Rich Repeat ◽

Tir Domain ◽

Pathogen Effectors ◽

Cryo Electron Microscopy ◽

Pathogen Effector ◽

Tir Domains ◽

Direct Recognition

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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TIR domains of plant immune receptors are NAD+-cleaving enzymes that promote cell death

Science ◽

10.1126/science.aax1771 ◽

2019 ◽

Vol 365 (6455) ◽

pp. 799-803 ◽

Cited By ~ 69

Author(s):

Li Wan ◽

Kow Essuman ◽

Ryan G. Anderson ◽

Yo Sasaki ◽

Freddy Monteiro ◽

...

Keyword(s):

Cell Death ◽

Enzymatic Activity ◽

Interleukin 1 ◽

Adenosine Diphosphate ◽

Immune Receptors ◽

Cell Death Response ◽

A Cell ◽

Self Association ◽

Activate Cell ◽

Tir Domains

Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors activate cell death and confer disease resistance by unknown mechanisms. We demonstrate that plant Toll/interleukin-1 receptor (TIR) domains of NLRs are enzymes capable of degrading nicotinamide adenine dinucleotide in its oxidized form (NAD+). Both cell death induction and NAD+ cleavage activity of plant TIR domains require known self-association interfaces and a putative catalytic glutamic acid that is conserved in both bacterial TIR NAD+-cleaving enzymes (NADases) and the mammalian SARM1 (sterile alpha and TIR motif containing 1) NADase. We identify a variant of cyclic adenosine diphosphate ribose as a biomarker of TIR enzymatic activity. TIR enzymatic activity is induced by pathogen recognition and functions upstream of the genes enhanced disease susceptibility 1 (EDS1) and N requirement gene 1 (NRG1), which encode regulators required for TIR immune function. Thus, plant TIR-NLR receptors require NADase function to transduce recognition of pathogens into a cell death response.

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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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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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Structural Evolution of TIR-Domain Signalosomes

Frontiers in Immunology ◽

10.3389/fimmu.2021.784484 ◽

2021 ◽

Vol 12 ◽

Author(s):

Surekha Nimma ◽

Weixi Gu ◽

Natsumi Maruta ◽

Yan Li ◽

Mengqi Pan ◽

...

Keyword(s):

Cell Death ◽

Interleukin 1 ◽

Structural Evolution ◽

Functional Roles ◽

Tir Domain ◽

Cell Death Pathways ◽

System A ◽

Essential Components ◽

Self Association ◽

Tir Domains

TIR (Toll/interleukin-1 receptor/resistance protein) domains are cytoplasmic domains widely found in animals and plants, where they are essential components of the innate immune system. A key feature of TIR-domain function in signaling is weak and transient self-association and association with other TIR domains. An additional new role of TIR domains as catalytic enzymes has been established with the recent discovery of NAD+-nucleosidase activity by several TIR domains, mostly involved in cell-death pathways. Although self-association of TIR domains is necessary in both cases, the functional specificity of TIR domains is related in part to the nature of the TIR : TIR interactions in the respective signalosomes. Here, we review the well-studied TIR domain-containing proteins involved in eukaryotic immunity, focusing on the structures, interactions and their corresponding functional roles. Structurally, the signalosomes fall into two separate groups, the scaffold and enzyme TIR-domain assemblies, both of which feature open-ended complexes with two strands of TIR domains, but differ in the orientation of the two strands. We compare and contrast how TIR domains assemble and signal through distinct scaffolding and enzymatic roles, ultimately leading to distinct cellular innate-immunity and cell-death outcomes.

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Select targeting of intracellular Toll-interleukin-1 receptor resistance domains for protection against influenza-induced disease

Innate Immunity ◽

10.1177/1753425919846281 ◽

2020 ◽

Vol 26 (1) ◽

pp. 26-34

Author(s):

Kari Ann Shirey ◽

Wendy Lai ◽

Lindsey J Brown ◽

Jorge C G Blanco ◽

Robert Beadenkopf ◽

...

Keyword(s):

Immune Responses ◽

Intracellular Signaling ◽

Interleukin 1 ◽

Tir Domain ◽

Close Proximity ◽

Domain Interactions ◽

Tir Domains ◽

Molecular Patterns ◽

Lps Signaling

TLRs are a family of PRRs that respond to PAMPs or host-derived Danger-Associated Molecular Patterns (DAMPs) to initiate host inflammation and immune responses. TLR dimerization and recruitment of adapter molecules is critical for intracellular signaling and is mediated through intracellular Toll-Interleukin 1 Receptor Resistance (TIR) domain interactions. Human TIR domains, including reported structures of TIR1, TIR2, TIR6, TIR10, TIRAP, and MyD88, contain Cysteine (Cys) interactions or modifications that are disproportionally at, or near, reported biological TIR interfaces, or in close proximity to functionally important regions. Therefore, we hypothesized that intracellular TIR Cys regulation may have greater functional importance than previously appreciated. Expression of mutant TLR4-C747S or treatment of TLR4 reporter cells with a small molecule, Cys-binding inhibitor of TLR4, TAK-242, abrogated LPS signaling in vitro. Using TAK-242, mice were protected from lethal influenza challenge as previously reported for extracellular TLR4 antagonists. Molecular modeling and sequence analysis of the region surrounding TLR4-Cys747 indicate conservation of a WxxxE motif identified among bacterial and NAD+-consuming TIRs, as well as within the TIRs domains of surface TLRs 1, 2, 4, 6, and 10. Together, these data support the hypothesis that critical Cys within the TIR domain are essential for TLR4 functionality.

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Antiviral activity of bacterial TIR domains via signaling molecules that trigger cell death

10.1101/2021.01.06.425286 ◽

2021 ◽

Author(s):

Gal Ofir ◽

Ehud Herbst ◽

Maya Baroz ◽

Daniel Cohen ◽

Adi Millman ◽

...

Keyword(s):

Cell Death ◽

Intracellular Signaling ◽

Interleukin 1 ◽

Signaling Molecules ◽

Immune Systems ◽

Tir Domain ◽

Cyclic Adp Ribose ◽

Molecular Signal ◽

Tir Domains ◽

Intracellular Signaling Molecules

AbstractThe Toll/interleukin-1 receptor (TIR) domain is a canonical component of animal and plant immune systems. In plants, intracellular pathogen sensing by immune receptors triggers their TIR domains to generate a molecule which is a variant of cyclic ADP-ribose (v-cADPR). This molecule is hypothesized to activate plant cell death via a yet unresolved pathway. TIR domains were recently also shown to be involved in a bacterial anti-phage defense system called Thoeris, but the mechanism of Thoeris defense remained unknown. In this study we report that phage infection triggers Thoeris TIR-domain proteins to produce an isomer of cyclic ADP-ribose. This molecular signal activates a second protein, ThsA, which then depletes the cell of the essential molecule nicotinamide adenine dinucleotide (NAD) and leads to abortive infection and cell death. We further show that similar to eukaryotic innate immune systems, bacterial TIR-domain proteins determine the immunological specificity to the invading pathogen. Our results describe a new antiviral signaling pathway in bacteria, and suggest that generation of intracellular signaling molecules is an ancient immunological function of TIR domains conserved in both plant and bacterial immunity.

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Multiple functional self-association interfaces in plant TIR domains

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1621248114 ◽

2017 ◽

Vol 114 (10) ◽

pp. E2046-E2052 ◽

Cited By ~ 55

Author(s):

Xiaoxiao Zhang ◽

Maud Bernoux ◽

Adam R. Bentham ◽

Toby E. Newman ◽

Thomas Ve ◽

...

Keyword(s):

Crystal Structure ◽

Cell Death ◽

Interleukin 1 ◽

Tir Domain ◽

Disease Resistance Protein ◽

Resistance Protein ◽

Cell Death Signaling ◽

Self Association ◽

Tir Domains ◽

Diverse Plant

The self-association of Toll/interleukin-1 receptor/resistance protein (TIR) domains has been implicated in signaling in plant and animal immunity receptors. Structure-based studies identified different TIR-domain dimerization interfaces required for signaling of the plant nucleotide-binding oligomerization domain-like receptors (NLRs) L6 from flax and disease resistance protein RPS4 fromArabidopsis. Here we show that the crystal structure of the TIR domain from theArabidopsisNLR suppressor of npr1-1, constitutive 1 (SNC1) contains both an L6-like interface involving helices αD and αE (DE interface) and an RPS4-like interface involving helices αA and αE (AE interface). Mutations in either the AE- or DE-interface region disrupt cell-death signaling activity of SNC1, L6, and RPS4 TIR domains and full-length L6 and RPS4. Self-association of L6 and RPS4 TIR domains is affected by mutations in either region, whereas only AE-interface mutations affect SNC1 TIR-domain self-association. We further show two similar interfaces in the crystal structure of the TIR domain from theArabidopsisNLR recognition ofPeronospora parasitica1 (RPP1). These data demonstrate that both the AE and DE self-association interfaces are simultaneously required for self-association and cell-death signaling in diverse plant NLRs.

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Toll9 from Bombyx mori functions as a pattern recognition receptor that shares features with Toll-like receptor 4 from mammals

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2103021118 ◽

2021 ◽

Vol 118 (19) ◽

pp. e2103021118

Author(s):

Ruonan Zhang ◽

Xiaofeng Li ◽

Jie Zhang ◽

Yanjun Li ◽

Yuan Wang ◽

...

Keyword(s):

Pattern Recognition ◽

Bombyx Mori ◽

Interleukin 1 ◽

Structural Data ◽

Pattern Recognition Receptor ◽

Inflammatory Factors ◽

Microbial Infection ◽

Mammalian Tlrs ◽

Tir Domains ◽

Recognition Receptor

Toll/Toll-like receptors (TLRs) are key regulators of the innate immune system in both invertebrates and vertebrates. However, while mammalian TLRs directly recognize pathogen-associated molecular patterns, the insect Toll pathway is thought to be primarily activated by binding Spätzle cytokines that are processed from inactive precursors in response to microbial infection. Phylogenetic and structural data generated in this study supported earlier results showing that Toll9 members differ from other insect Tolls by clustering with the mammalian TLR4 group, which recognizes lipopolysaccharide (LPS) through interaction with myeloid differentiation-2 (MD-2)–like proteins. Functional experiments showed that BmToll9 from the silkmoth Bombyx mori also recognized LPS through interaction with two MD-2–like proteins, previously named BmEsr16 and BmPP, that we refer to in this study as BmMD-2A and BmMD-2B, respectively. A chimeric BmToll9–TLR4 receptor consisting of the BmToll9 ectodomain and mouse TLR4 transmembrane and Toll/interleukin-1 (TIR) domains also activated LPS-induced release of inflammatory factors in murine cells but only in the presence of BmMD-2A or BmMD-2B. Overall, our results indicate that BmToll9 is a pattern recognition receptor for LPS that shares conserved features with the mammalian TLR4–MD-2–LPS pathway.

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