Structural Evolution of TIR-Domain Signalosomes

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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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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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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Common and distinct features of TIR domain function

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314097575 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C242-C242

Author(s):

Simon Williams ◽

Mohammed Alaidarous ◽

Thomas Ve ◽

Xiaoxiao Zhang ◽

Eugene Valkov ◽

...

Keyword(s):

Fungal Pathogens ◽

Paracoccus Denitrificans ◽

Brucella Melitensis ◽

Interleukin 1 ◽

Adaptor Protein ◽

Site Directed Mutagenesis ◽

Tir Domain ◽

Common Features ◽

Self Association ◽

Tir Domains

TIR (Toll/interleukin-1 receptor, resistance protein) domains feature in diverse proteins with functions in the immune system, such as animal TLRs (Toll-like receptors), plant NLRs (nucleotide binding, leucine-rich repeat) and bacterial virulence factors. It has been well established, especially through the work on TLRs, that signalling depends on regulated self-association of TIR domains. However, every single TIR domain structure has revealed a different association mode [1]. In the search for common features, we have targeted a number of TIR domains from mammals, plants and bacteria to characterize structurally. We have determined the crystal structures of the TIR domains from the human TLR adaptor protein MAL [1], the bacterial protein TcpB from Brucella melitensis [2] and the plant immune proteins L6 from flax [3] and SNC1, RPS4 and RRS1 from Arabidopsis (unpublished). In the case of the proteins RPS4 and RRS1, which work together as a protein complex to confer resistance to three different bacterial and fungal pathogens, we have determined, using linker-assisted crystallization, the first structure of a hetero-dimeric complex of TIR domains (Fig. 1). The association interface in this complex is conserved in the crystals of the TIR domains of RPS4 and RRS1 on their own, as well as in those of SNC1 and another Arabidopsis protein AT1G72930. Similarly, the dimerization interface observed in the structure of TcpB is conserved in the structure of the TIR domain-containing protein from Paracoccus denitrificans. We validated the association interfaces by site-directed mutagenesis coupled with a variety of cellular assays. As self-association is key to TIR domain function, our studies are finally revealing common features of the molecular function of TIR domains across phyla.

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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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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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The TIR Domain of TIR-NB-LRR Resistance Proteins Is a Signaling Domain Involved in Cell Death Induction

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-22-2-0157 ◽

2009 ◽

Vol 22 (2) ◽

pp. 157-165 ◽

Cited By ~ 113

Author(s):

Michal R. Swiderski ◽

Doris Birker ◽

Jonathan D. G. Jones

Keyword(s):

Cell Death ◽

Transient Expression ◽

Interleukin 1 ◽

Site Directed Mutagenesis ◽

Loss Of Function ◽

Inducible Promoters ◽

Resistance Proteins ◽

Tir Domain ◽

Signaling Domain ◽

Dependent Cell

In plants, the TIR (toll interleukin 1 receptor) domain is found almost exclusively in nucleotide-binding (NB) leucine-rich repeat resistance proteins and their truncated homologs, and has been proposed to play a signaling role during resistance responses mediated by TIR containing R proteins. Transient expression in Nicotiana benthamiana leaves of “TIR + 80”, the RPS4 truncation without the NB-ARC domain, leads to EDS1-, SGT1-, and HSP90-dependent cell death. Transgenic Arabidopsis plants expressing the RPS4 TIR+80 from either dexamethasone or estradiol-inducible promoters display inducer-dependent cell death. Cell death is also elicited by transient expression of similarly truncated constructs from two other R proteins, RPP1A and At4g19530, but is not elicited by similar constructs representing RPP2A and RPP2B proteins. Site-directed mutagenesis of the RPS4 TIR domain identified many loss-of-function mutations but also revealed several gain-of function substitutions. Lack of cell death induction by the E160A substitution suggests that amino acids outside of the TIR domain contribute to cell death signaling in addition to the TIR domain itself. This is consistent with previous observations that the TIR domain itself is insufficient to induce cell death upon transient expression.

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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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Faculty Opinions recommendation of NAD+ cleavage activity by animal and plant TIR domains in cell death pathways.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.736481329.793564520 ◽

2019 ◽

Author(s):

Gitta Coaker

Keyword(s):

Cell Death ◽

Cleavage Activity ◽

Cell Death Pathways ◽

Tir Domains

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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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