TIR domains are protein modules that show up across virtually all branches of life, from mammals and plants to bacteria, acting as critical hubs in immune defense and, in some cases, nerve cell survival. Named for the Toll/interleukin-1 receptor proteins where they were first identified, TIR domains were long thought to work simply by linking proteins together in signaling chains. That understanding changed dramatically in recent years with the discovery that many TIR domains are actually enzymes, capable of breaking down key cellular molecules to trigger immune responses or, in the case of nerve injury, to drive cell destruction.
A Protein Module That Spans Kingdoms
The TIR domain was originally described as a protein-protein interaction module that helps relay signals downstream of the Toll-like receptor (TLR) and interleukin-1 receptor families in animals. In that context, it works as a kind of molecular matchmaker: when a TLR detects something dangerous, the TIR domains on the receptor’s inner surface recruit adaptor proteins that also carry TIR domains. Those adaptor proteins then relay the alarm deeper into the cell. But TIR domains are not exclusive to animal immune receptors. They appear in plant immune receptors, in bacterial defense systems, and in proteins involved in neuronal health. Studies of the pro-neurodegenerative protein SARM1, plant immune receptors, and many bacterial TIR-containing proteins revealed that TIR domains have enzymatic activities and can produce diverse signaling molecules using NAD+ or nucleic acids as substrates.1Current Opinion in Microbiology. Toll/interleukin-1 receptor domains in bacterial and plant immunity
How TIR Domains Build Signaling Filaments
One of the striking structural features of TIR domains is their ability to self-assemble into long filament-like structures. In animal immune signaling, the adaptor protein MAL (also called TIRAP) contains a TIR domain that spontaneously forms filaments in the lab. These filaments consist of two parallel strands of TIR domain subunits arranged in a head-to-tail pattern, held together by a structural element called the BB-loop. MAL TIR filaments can also form co-filaments with TLR4 TIR domains and trigger the assembly of another key adaptor, MyD88.2PubMed Central. Structural basis of TIR-domain-assembly formation in MAL- and MyD88-dependent TLR4 signaling MyD88 itself forms similar two-stranded assemblies, with interactions both within and between the strands.3Nature Communications. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography
The filament formation is not just an incidental lab curiosity. MyD88 forms fibrils both in isolated form and inside cells. Multiple domains of the protein work together to drive this self-assembly, with the TIR domain synergizing in filament growth by regulating how the protein puts itself together.4Fundamental Research. MyD88 self-assembles into supramolecular filaments to amplify NF-κB signaling The result is a kind of molecular amplifier: a small initial signal from an activated receptor gets converted into a large, physically robust signaling platform.
The BB-loop, a short stretch of amino acids that forms a protruding loop on the TIR domain surface, is the linchpin of this assembly. Mutations in the BB-loop completely shut down downstream signaling, as shown in structural studies of the adaptor proteins TICAM-1 (also called TRIF) and TICAM-2 (TRAM).5PubMed Central. Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling More recent structural work on TRIF and TRAM revealed that all four major TLR signaling adaptors (MyD88, MAL, TRIF, and TRAM) use a unified mechanism, forming two-stranded parallel helical arrangements where both intrastrand interactions through the BB-loop and interstrand interactions are essential.6PubMed Central. Structural basis for TIR domain-mediated innate immune signaling by Toll-like receptor adaptors TRIF and TRAM
The Enzyme Surprise
For decades, researchers treated TIR domains as passive scaffolds. The game-changing discovery came from an unexpected direction: the study of nerve cell death. SARM1 is a protein that, when activated after nerve injury, drives the destruction of the damaged nerve fiber. In 2017, researchers showed that the SARM1 TIR domain itself is an enzyme that cleaves NAD+, a molecule cells depend on for energy and hundreds of metabolic reactions. The products of this cleavage include ADP-ribose, cyclic ADP-ribose, and nicotinamide, with nicotinamide acting as a feedback inhibitor that slows the enzyme down.7Neuron. The SARM1 TIR Domain Is an NAD+ Cleavage Enzyme that Promotes Axonal Degeneration
This was not an isolated oddity. Shortly after, two landmark studies published back-to-back demonstrated that TIR domains in plant immune receptors are also NAD+-cleaving enzymes, and that this activity depends on a conserved glutamic acid residue shared with both bacterial TIR enzymes and mammalian SARM1.8PubMed Central. TIR domains of plant immune receptors are NAD(+)-cleaving enzymes that promote cell death Another group confirmed that both animal and plant TIR domains feature self-association-dependent NAD+ cleavage activity tied to cell death signaling.9PubMed. NAD(+) cleavage activity by animal and plant TIR domains in cell death pathways The picture that emerged was that TIR domains across kingdoms of life share an ancient enzymatic function, not just a structural fold.
SARM1 and Nerve Degeneration
The enzymatic activity of SARM1’s TIR domain has direct consequences for neurological disease. After a nerve fiber is cut or exposed to toxic insults, SARM1 becomes active and rapidly depletes NAD+ inside the damaged axon. Without NAD+, the axon’s energy supply collapses, and the fiber degenerates. Researchers demonstrated this using both physical injury models and drug-induced nerve damage: the NADase activity of full-length SARM1 is required inside axons to promote NAD+ depletion and degeneration after injury.10Neuron. The SARM1 TIR Domain Is an NAD+ Cleavage Enzyme that Promotes Axonal Degeneration
SARM1 does not sit in a permanently active state, though. The protein’s armadillo repeat (ARM) domains act as a built-in brake, keeping the TIR domains apart and unable to form the assemblies needed for enzyme activity. When injury occurs, a molecule called nicotinamide mononucleotide (NMN) accumulates and binds to the ARM domains, triggering them to rotate and release the TIR domains. Freed from the brake, the TIR domains snap together into a two-stranded assembly, and active enzyme sites form at the interface between TIR molecules. A single SARM1 octamer (eight copies of the protein arranged in a ring) can generate up to six catalytically active sites through this process.11PubMed Central. Structural basis of SARM1 activation, substrate recognition, and inhibition by small molecules This activation mechanism explains why SARM1 only fires under injury conditions: in healthy axons, NMN levels are low and the brake stays on.
TIR Domains in Plant Immunity
Plants have their own large family of intracellular immune receptors called NLRs, and a major subgroup of these carries TIR domains at their front end. When a plant TIR-NLR receptor detects a pathogen protein inside the cell, it activates and its TIR domain begins cleaving NAD+ and other substrates.12PubMed. Activation of a helper NLR by plant and bacterial TIR immune signaling The products of this enzymatic activity act as second messengers, chemical signals that relay the alarm to downstream defense machinery.13PubMed. TIR-catalyzed nucleotide signaling molecules in plant defense
The downstream relay in plants is well characterized. TIR-produced signaling molecules, including specific forms of ADP-ribose, bind to a protein complex involving EDS1 and its partners (SAG101 or PAD4). This binding event causes a shape change that allows EDS1 to recruit “helper” NLR proteins such as NRG1 or ADR1.14PubMed. TIR-catalyzed ADP-ribosylation reactions produce signaling molecules for plant immunity NRG1 was shown to be essential for the immune response triggered by multiple TIR-NLR receptors but dispensable for immune responses driven by a different class of NLRs that carry coiled-coil domains instead of TIR domains.15PubMed Central. NRG1 functions downstream of EDS1 to regulate TIR-NLR-mediated plant immunity in Nicotiana benthamiana This pathway was initially mapped in dicot plants (the group that includes most broadleaf species), but recent work confirms that the signaling architecture through the EDS1-PAD4-ADR1 module is conserved in monocots as well, meaning it likely predates the split between these two major plant lineages.16PubMed. TIR-mediated immune signaling through the EDS1:PAD4:ADR1 node is conserved in monocots and dicots
The enzymatic repertoire of plant TIR domains turns out to be broader than NAD+ cleavage alone. Plant TIR proteins also act as synthetases, producing cyclic nucleotides by hydrolyzing RNA and DNA. This means they can generate signaling molecules from multiple substrate types, a versatility that was not anticipated from the animal TIR literature.17Cell. Plant TIR domains act as 2′,3′-cAMP/cGMP synthetases mediating cell death The specific cyclic ADP-ribose isomers that plant TIR domains produce also differ from those made by bacterial TIR domains, suggesting that while the core enzymatic function is shared, the signaling chemistry has diversified.18PubMed Central. Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products
Bacterial TIR Domains and Antiviral Defense
Bacteria also deploy TIR domains for immune defense, and their role came into sharp focus through study of the Thoeris antiphage system. When a bacterial virus (phage) infects a Thoeris-carrying bacterium, the TIR-domain protein in the system detects the infection and produces an isomer of cyclic ADP-ribose. This small molecule activates a second protein, ThsA, which then drains the cell of NAD+. The cell dies, but the phage infection dies with it, protecting the rest of the bacterial population through a strategy known as abortive infection.19Nature. Antiviral activity of bacterial TIR domains via immune signalling molecules
Follow-up work identified the precise chemical identity of the Thoeris signaling molecule and found that it differs subtly from the molecule produced by plant TIR domains. The bacterial version activates the ThsA effector roughly ten times more efficiently than the plant-derived variant, which hints at fine-tuned specificity between different TIR systems and their downstream effectors.20PubMed. Viruses inhibit TIR gcADPR signalling to overcome bacterial defence Phages, for their part, have evolved countermeasures: some carry proteins that specifically intercept or degrade the TIR-produced signaling molecules, blocking the bacterial suicide defense before it can take effect.
Pathogen Mimicry of TIR Domains
While some bacteria use TIR domains in their own defense systems, others have weaponized them against host immunity. Several pathogenic bacteria produce proteins containing TIR domains that structurally mimic the TIR domains of host immune adaptors. By inserting themselves into the host’s signaling chain, these mimics block the normal relay from TLRs to downstream effectors and suppress the inflammatory response.
The crystal structure of a bacterial TIR domain from Paracoccus denitrificans confirmed that it adopts a fold closely resembling active host receptor TIR domains. That structural similarity allows it to physically interact with the host adaptor MyD88, effectively hijacking a key node in the signaling pathway.21PubMed Central. Molecular mimicry in innate immunity: crystal structure of a bacterial TIR domain A well-studied example in pathogenic bacteria is TcpB from Brucella, which inhibits TLR signaling by interacting directly with the host adaptors MAL and MyD88.22Journal of Biological Chemistry. Structural and Biochemical Insights into Microbial Milk of Host Toll/IL-1 Receptor Signaling Adaptors by Brucella TcpB Brucella causes a chronic infection in livestock and humans, and this immune-evasion trick is one reason the bacterium is so difficult for the immune system to clear.
Phase Separation as an Activation Trigger
A more recent discovery adds another layer to how TIR domains activate. When plant TIR proteins encounter their substrates NAD+ and ATP, they undergo phase separation, condensing into droplet-like structures inside the cell. This condensation concentrates the enzymes and their substrates into a small volume, dramatically boosting the rate of signaling-molecule production. Researchers showed that a similar condensation occurs in living plants during pathogen infection, using a TIR protein expressed at natural levels. Mutations that prevent the condensation also impair the protein’s ability to trigger cell death.23PubMed Central. Substrate-induced condensation activates plant TIR domain proteins Phase separation provides a way for TIR-based signaling to switch from “off” to “on” in a sharp, switch-like manner rather than gradually ramping up.
Drug Development Targeting TIR Domains
The central role of TIR domains in both immune signaling and nerve degeneration makes them attractive drug targets. On the neurological side, blocking SARM1’s TIR-domain enzyme activity could slow or prevent the axon loss that characterizes traumatic nerve injuries and certain neurodegenerative diseases. Researchers identified a potent isoquinoline-based small-molecule inhibitor of SARM1 that mimics the effect of genetically deleting the protein, protecting axons from degeneration after cutting or mitochondrial damage.24Cell Reports. Development of Potent and Selective SARM1 Inhibitors for the Treatment of Traumatic and Degenerative Axonopathies Structural studies revealed that this inhibitor works through an unusual mechanism: the compound undergoes a chemical exchange reaction with NAD+ inside the SARM1 active site, and the resulting product is the actual inhibitor that locks the enzyme shut.25Molecular Cell. Mechanism of SARM1 activation by small molecules and its implication in recovery from axon degeneration
On the inflammation side, excessive TLR and IL-1 receptor signaling has been linked to rheumatoid arthritis, lupus, colitis, and certain cancers. Blocking the TIR-domain interactions that hold these signaling complexes together is one strategy for dialing down inflammation without wiping out the immune system entirely.26PubMed Central. Suppression of TLR signaling by targeting TIR domain-containing proteins Early proof-of-concept came from a small molecule dubbed compound 4a, which interferes with the interaction between MyD88 and the IL-1 receptor at their TIR domains. In animal experiments, this compound blocked IL-1-driven inflammation and reduced fever in a dose-dependent manner.27PubMed Central. A low molecular weight mimic of the Toll/IL-1 receptor/resistance domain inhibits IL-1 receptor-mediated responses Building on this approach, researchers have designed compounds based on known TIR dimerization inhibitors that can target the BB-loop region across multiple adaptor proteins, not just MyD88, potentially offering broader anti-inflammatory coverage.28PubMed. Identifying the inhibition of TIR proteins involved in TLR signalling as an anti-inflammatory strategy
Why TIR Domains Keep Surprising Researchers
The story of TIR domains is a case study in how assumptions can stall a field. For about two decades after their discovery, TIR domains were filed under “protein interaction modules” and treated as molecular Velcro. The enzymatic activity was hiding in plain sight: the conserved glutamic acid residue that turned out to be the catalytic center was noted in structures but not tested for catalysis because nobody expected a scaffolding domain to moonlight as an enzyme. Once that barrier broke with the SARM1 finding, the floodgates opened. Within a few years, NADase activity was documented in plant TIR domains, bacterial TIR domains, and further bacterial defense systems, all converging on the same fundamental chemistry.
The expanding catalog of TIR enzymatic products is itself remarkable. Beyond NAD+ cleavage, plant TIR domains generate cyclic nucleotides from RNA and DNA substrates.29Cell. Plant TIR domains act as 2′,3′-cAMP/cGMP synthetases mediating cell death The repertoire of TIR-derived signaling molecules is growing rapidly, and the overlap between bacterial and plant systems suggests common evolutionary roots rather than convergent invention.30Current Opinion in Microbiology. Toll/interleukin-1 receptor domains in bacterial and plant immunity Mammalian TLR-associated TIR domains, interestingly, have not been shown to possess this enzymatic activity. They appear to function exclusively as scaffolding elements, raising the question of whether enzymatic function was lost in the animal innate immune branch or gained independently in other lineages. That puzzle remains open.
The practical upshot of all this work is that TIR domains sit at an intersection of immunology, neuroscience, microbiology, and structural biology in a way few other protein modules do. A structural element initially cataloged as a simple interaction surface turned out to be an ancient enzyme, a drug target for nerve injury, a vulnerability that pathogens exploit, and a defense weapon that bacteria wield against viruses. Each new functional layer that has been uncovered has reshaped thinking about how immune signaling works at its most fundamental level.