TIR domains are compact protein modules that sit at the heart of immune signaling across nearly every branch of life, from bacteria defending against viral invaders to plants recognizing fungal pathogens to the human immune system detecting infection. For decades, scientists viewed TIR domains mainly as adaptors that bring proteins together in signaling chains. That picture has changed dramatically. Research over the past several years has revealed that many TIR domains are enzymes capable of destroying a molecule cells cannot live without, and that this enzymatic activity is the ancient, conserved function linking immunity in organisms separated by billions of years of evolution.
What a TIR Domain Actually Does in Animal Immunity
The name “TIR” stands for Toll/interleukin-1 receptor, reflecting where the domain was first characterized: in the signaling tails of receptors that detect microbial invaders in animals. When a Toll-like receptor on a human immune cell recognizes a piece of a bacterium or virus, its intracellular TIR domain needs to pass that alarm signal deeper into the cell. It does this by linking up with other TIR-domain-containing adaptor proteins in a specific order. The adaptor called MAL (also known as TIRAP) directly contacts the TIR domain of TLR4 and then recruits a second adaptor, MyD88, through TIR-TIR interactions at three distinct surface sites on MyD88’s TIR domain.1PubMed Central. Structural basis for the multiple interactions of the MyD88 TIR domain in TLR4 signaling This chain of contact between TIR domains is what launches the inflammatory response that fights infection.
A parallel, MyD88-independent signaling branch also relies on TIR domain interactions. The adaptors TRIF and TRAM use their own TIR domains to form two-stranded filamentous structures, and these filaments are essential for triggering interferon production during certain types of infection. Cryo-electron microscopy has now resolved these filaments at near-atomic detail, revealing that the signaling mechanism is shared across all four major TLR adaptors: MyD88, MAL, TRIF, and TRAM all assemble their TIR domains into similar open-ended, filamentous scaffolds.2PubMed Central. Structural basis for TIR domain-mediated innate immune signaling by Toll-like receptor adaptors TRIF and TRAM This filament-based mechanism, sometimes called signaling by cooperative assembly formation, turns out to be a general principle of TIR domain signaling rather than a quirk of one particular adaptor.3PubMed Central. Structural characterization of TIR-domain signalosomes through a combination of structural biology approaches
The Enzymatic Surprise
The adaptor story was tidy, but it turned out to be incomplete. The game-changing discovery came from an unexpected direction: research on nerve damage. Scientists studying why severed nerve fibers degenerate found that a protein called SARM1 was the executioner. When an axon is injured, SARM1’s TIR domain activates and rapidly destroys NAD+, a molecule every cell needs to produce energy and carry out hundreds of metabolic reactions. Within minutes of SARM1 activation, NAD+ levels in the axon plummet, and the nerve fiber falls apart.4Neuron. The SARM1 TIR Domain Is an NAD+ Cleavage Enzyme that Promotes Pathological Axon Degeneration Crucially, when researchers mutated SARM1’s TIR domain to disable its enzymatic activity, injured axons survived. The enzyme was doing the killing, not just the protein-protein contact.
This discovery prompted researchers to look more broadly. It soon became clear that TIR domains from bacteria and archaea also cleave NAD+, and they do it using the same catalytic machinery, centered on a conserved glutamic acid residue.5PubMed Central. TIR Domain Proteins Are an Ancient Family of NAD+-Consuming Enzymes The enzyme activity was not a feature unique to SARM1 or to animals. It was an ancient capability shared across the tree of life. Plant TIR domains, too, were shown to cleave NAD+ in a self-association-dependent manner, and the crystal structures of both animal SARM1 and plant NLR TIR domains revealed a conserved substrate binding site for NAD+.6PubMed. NAD(+) cleavage activity by animal and plant TIR domains in cell death pathways
How Plants Use TIR Domains to Fight Pathogens
Plants lack the roaming immune cells that patrol animal bodies. Instead, each plant cell carries its own internal surveillance system built largely around intracellular receptors called NLRs. Many of these NLRs carry a TIR domain at their front end. When a pathogen injects a harmful protein into a plant cell, specific NLRs recognize the intruder, and the receptor assembles into a multi-protein complex, typically a tetramer. In this assembled state, the TIR domains become enzymatically active and start hydrolyzing NAD+. The structure of the Arabidopsis receptor RPP1 bound to a pathogen effector shows that tetramerization creates two active sites, each formed by an asymmetric pair of TIR domains working together.7PubMed. Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme
But the NAD+ cleavage in plants is not simply about draining a vital resource. The TIR domains produce specific small-molecule signals from the fragments of NAD+ and other nucleotides. These products include various isomers of cyclic ADP-ribose and a molecule called phosphoribosyl-AMP/ADP (pRib-AMP/ADP). These small molecules act as second messengers that relay the alarm downstream.8PubMed. TIR-catalyzed nucleotide signaling molecules in plant defense The relay works through a set of lipase-like proteins, most importantly EDS1 partnered with either PAD4 or SAG101. Different TIR enzymatic products selectively activate different downstream branches: one product triggers the EDS1-PAD4 complex to recruit the helper protein ADR1, while another triggers EDS1-SAG101 to recruit a different helper called NRG1.9PubMed Central. EDS1 modules as two-tiered receptor complexes for TIR-catalyzed signaling molecules to activate plant immunity The recent structural characterization of the EDS1-PAD4-ADR1 complex confirms that bacterial TIR-produced signals can also feed into this same pathway, underscoring the evolutionary overlap between plant and microbial TIR signaling.10PubMed. Activation of a helper NLR by plant and bacterial TIR immune signaling
This small-molecule relay also extends into a branch of plant immunity triggered by surface receptors. Recent work has shown that the canonical EDS1/PAD4 binding sites for phosphoribosyl-AMP/ADP, originally characterized in the context of intracellular NLR signaling, are also required for pattern-triggered immunity initiated by leucine-rich repeat receptor proteins at the cell surface.11PubMed Central. Canonical EDS1/PAD4 small-molecule binding sites are required for LRR-RP-mediated pattern-triggered immunity The TIR-generated signals, in other words, are not confined to one arm of the plant immune system but serve as a shared currency across multiple defense pathways.
Bacterial TIR Domains and the Fight Against Phages
Bacteria face relentless attack from viruses called phages, and they have evolved elaborate defense systems in response. One of the most striking is the Thoeris system, which uses a TIR-domain protein as its sensor. When a phage infects the cell, the Thoeris TIR domain produces an isomer of cyclic ADP-ribose. This small molecule then activates a second component, ThsA, which drains the cell’s NAD+ supply. With NAD+ gone, the cell dies before the phage can finish replicating, sacrificing itself to protect the wider bacterial population.12Nature. Antiviral activity of bacterial TIR domains via immune signalling molecules This strategy, called abortive infection, is brutal but effective: the phage has no surviving host cell to produce offspring, so the infection stops.
The parallels with plant immunity are striking. Plant TIR domains and bacterial Thoeris TIR domains produce overlapping sets of cyclic ADP-ribose isomers. Experimental work has demonstrated that plant TIR-produced 3’cADPR can activate the bacterial Thoeris system, showing that the chemical language is compatible across kingdoms.13PubMed Central. Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products The diversity of bacterial Thoeris systems is also much wider than initially appreciated. Systematic screening has recently identified seven new configurations of TIR-containing defense systems in bacteria, now designated Thoeris types V through XI, with 15 out of 30 tested TIR-containing operons confirmed to defend against phages.14bioRxiv. Systematic discovery of TIR-based immune signaling systems in bacteria
The Common Thread Across Kingdoms
Stepping back, the pattern that has emerged over the past decade is a remarkable case of deep evolutionary conservation. TIR domains were once defined as simple adaptors. They are now understood to be, at their core, enzymes whose activity links immunity and cell death across animals, plants, bacteria, and archaea.15PubMed. Shared TIR enzymatic functions regulate cell death and immunity across the tree of life In bacteria, TIR enzyme activity triggers abortive infection. In plants, it produces second messengers that orchestrate a programmed cell death response at the infection site. In animals, the SARM1 TIR domain destroys NAD+ to execute axon degeneration, a process that, while not classically “immune,” shares the same chemical logic of NAD+ consumption and self-destruction to limit damage.
This conservation goes beyond the general idea of “breaking down NAD+.” The catalytic residue, a glutamic acid, is the same. The structural scaffold that supports filament formation is the same. And the downstream consequence, cell or tissue destruction through metabolic collapse, is the same. What varies across kingdoms is the wiring around the TIR domain: which upstream signals activate it and which downstream effectors translate its enzymatic products into a biological outcome.
When Pathogens Weaponize TIR Domains
If TIR domains are central to immune signaling, it follows that pathogens would evolve ways to exploit them. That is exactly what happens. The bacterium Pseudomonas aeruginosa, a major cause of hospital-acquired infections, secretes a protein called PumA that contains its own TIR domain. This bacterial TIR domain physically binds to the host’s TLR adaptors TIRAP and MyD88, jamming the signaling chain that would otherwise trigger an inflammatory response. PumA simultaneously targets a protein involved in sorting receptors inside the cell (UBAP1), effectively crippling both cytokine production and receptor recycling at the same time.16PubMed Central. A Pseudomonas aeruginosa TIR effector mediates immune evasion by targeting UBAP1 and TLR adaptors PumA is essential for the bacterium’s virulence, and transferring it into a strain that normally lacks it confers the immune evasion ability, demonstrating that a single TIR-domain protein can be a potent weapon for subverting host defense.
NAD+ Depletion as a Distinct Form of Cell Death
One of the more recent and surprising findings is that the cell death caused by TIR-domain enzymatic activity in mammalian cells is not a known type of programmed cell death. It is not apoptosis, not pyroptosis, not necroptosis. Comparative testing of animal, bacterial, and plant TIR domains expressed in mammalian cells revealed that the death resulted from the sheer depletion of NAD+ rather than from the accumulation of any particular breakdown product. In other words, the cell dies because it runs out of fuel, not because a specific toxic molecule builds up.17PubMed Central. NAD(+) depletion by catalytic TIR domains triggers a distinct form of regulated necrosis in mammalian cells This finding suggests that TIR-mediated NAD+ depletion represents a form of regulated necrosis that sits outside the established categories, and it may be the primary mechanism by which bacterial TIR effectors suppress host innate immunity: kill the host cell before it can mount a proper defense.
Beyond NAD+ Cleavage
NAD+ destruction is the headline activity of TIR domains, but it may not be the only trick in the toolkit. Some bacterial TIR-domain proteins can also process a completely different type of target: RNA molecules that carry an NAD+ cap. Certain messenger RNAs in cells have an NAD+ molecule attached to their front end, and TIR proteins from bacteria including Acinetobacter baumannii and Brucella abortus can remove part of that cap, specifically the nicotinamide portion, in a reaction distinct from simple NAD+ cleavage. Mutating the catalytic glutamic acid residue knocks out both the standard NAD+ cleavage and this RNA-decapping activity, suggesting both reactions share the same active site.18PubMed Central. Toll/interleukin-1 receptor (TIR) domain-containing proteins have NAD-RNA decapping activity What this RNA-processing activity means for bacterial physiology or immunity is still being worked out, but it hints that TIR domains may regulate gene expression in ways beyond metabolite destruction.
Plant TIR domains also show catalytic versatility. Beyond NAD+, some can process ATP and other nucleic acid substrates, generating a structurally diverse set of nucleotide metabolites.8PubMed. TIR-catalyzed nucleotide signaling molecules in plant defense The full catalog of TIR enzymatic products and their downstream roles is still being mapped, making this one of the more active research frontiers in plant immunity.
SARM1 and the Nerve Damage Connection
The SARM1 protein occupies a unique niche among TIR-domain proteins because its primary role is not in classical immunity but in nervous system biology. After an axon is cut or exposed to certain toxins (including the chemotherapy drug vincristine), SARM1’s TIR domain activates, and the resulting NAD+ depletion causes the axon to self-destruct.19PubMed Central. The SARM1 Toll/Interleukin-1 Receptor Domain Possesses Intrinsic NAD+ Cleavage Activity that Promotes Pathological Axonal Degeneration This process, called Wallerian degeneration, happens in traumatic brain injuries, peripheral neuropathies, and chemotherapy-induced nerve damage.
SARM1 activation depends on its TIR domain forming dimers, and a specialized motif called the SARM1-specific loop is essential for both NAD+ consumption and axon destruction. The same mechanism operates in the worm Caenorhabditis elegans, where the SARM1 equivalent (called TIR-1) also destroys NAD+ upon TIR domain dimerization, causing neuronal death.20PubMed Central. SARM1-specific motifs in the TIR domain enable NAD+ loss and regulate injury-induced SARM1 activation This conservation across hundreds of millions of years of animal evolution suggests that controlled self-destruction of damaged nerve fibers is an important biological function, possibly to clear debris and allow regrowth, though in many disease contexts the destruction is pathological rather than helpful.
Therapeutic Prospects and Pitfalls
Because SARM1’s TIR domain drives axon degeneration across so many conditions, it has become a high-profile drug target. One approach uses small molecules that undergo a base-exchange reaction with NAD+ inside SARM1’s active site, generating an inhibitor in situ. One such compound, DSRM-3716, blocks SARM1 at remarkably low concentrations and protects axons from degeneration caused by both physical injury and mitochondrial dysfunction.21Molecular Cell. Mechanism of SARM1 activation and inhibition by small molecules The idea is appealing: block the enzyme, save the nerve.
However, this class of inhibitors has a serious catch. At doses below the threshold needed for full inhibition, these base-exchange inhibitors paradoxically activate SARM1, worsening cell death and neuronal damage rather than preventing it. In a mouse model of autoimmune-driven neurodegeneration, a low dose of one such compound made the disease worse.22PubMed Central. SARM1 base-exchange inhibitors induce SARM1 activation and neurodegeneration at low doses This dose-dependent flip between protection and harm complicates clinical development considerably. Getting the dose precisely right is not just a matter of efficacy but of safety, since underdosing could actively accelerate the disease the drug is meant to treat.
On the other side of TIR biology, researchers have also targeted the adaptor interactions in TLR signaling. A decoy peptide modeled on the surface of the MAL adaptor, called MIP2, blocks both MyD88-dependent and TRIF-dependent signaling downstream of TLR4 and has shown therapeutic promise in animal models of psoriasis, lupus, fatty liver disease, and sepsis.23PubMed. The αC helix of TIRAP holds therapeutic potential in TLR-mediated autoimmune diseases The idea here is to intercept the protein-protein interaction side of TIR biology to dampen overactive inflammation without shutting down the enzymatic branch entirely.
How Plant NLRs Are Fine-Tuned
Given that TIR-domain NLR receptors in plants can trigger cell death and scorched-earth immune responses, keeping them tightly controlled is critical. Unregulated NLR activation would be as dangerous as the pathogen itself, leading to widespread tissue death. Recent work has highlighted the role of post-translational modifications in maintaining this balance. Phosphorylation, ubiquitination, lipidation, acetylation, and SUMOylation all regulate NLR stability, activation thresholds, and signaling output. The enzymes responsible, including kinases and E3 ubiquitin ligases, control the conformational dynamics that determine whether an NLR stays dormant or fires.24Trends in Biochemical Sciences. Post-translational regulation of plant NLR immune receptors This regulatory layer adds nuance to the picture: TIR enzymatic activity is powerful, but the cell has multiple checkpoints to ensure it only fires when genuinely needed.