TIR Domain Proteins Are an Ancient Family of NAD+-Consuming Enzymes

Abstract

The Toll/interleukin-1 receptor (TIR) domain is the signature signaling domain of Toll-like receptors (TLRs) and their adaptors, serving as a scaffold for the assembly of protein complexes for innate immune signaling [1, 2]. TIR domain proteins are also expressed in plants, where they mediate disease resistance [3, 4], and in bacteria, where they have been associated with virulence [5-9]. In pursuing our work on axon degeneration [10], we made the surprising discovery that the TIR domain of SARM1 (sterile alpha and TIR motif containing 1), a TLR adaptor protein, has enzymatic activity [11]. Upon axon injury, the SARM1 TIR domain cleaves nicotinamide adenine dinucleotide (NAD), destroying this essential metabolic co-factor to trigger axon destruction [11, 12]. Whereas current studies of TIR domains focus on their scaffolding function, our findings with SARM1 inspired us to ask whether this enzymatic activity is the primordial function of the TIR domain. Here we show that ancestral prokaryotic TIR domains constitute a new family of NADase enzymes. Using purified proteins from a cell-free translation system, we find that TIR domain proteins from both bacteria and archaea cleave NAD into nicotinamide and ADP-ribose (ADPR), with catalytic cleavage executed by a conserved glutamic acid. A subset of bacterial and archaeal TIR domains generates a non-canonical variant cyclic ADPR (cADPR) molecule, and the full-length TIR domain protein from pathogenic Staphylococcus aureus induces NAD loss in mammalian cells. These findings suggest that the primordial function of the TIR domain is the enzymatic cleavage of NAD and establish TIR domain proteins as a new class of metabolic regulatory enzymes.

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical spongeIanthella basta

“…Four types of ELPs are found in Ca . N. ianthellae: Proteins with tetratricopeptide repeats (TPR), the Toll‐interleukin‐1 receptor (TIR)–like domain PF08937 (DUF1863; Cort et al ., ; Essuman et al ., ), immunoglobulin‐like (Ig‐like) domains (DUF5011; Shigeno‐Nakazawa et al ., ), and hyaline repeats (HYR; Callebaut et al ., ) and an extensive discussion of these ELPs is provided in the Supporting Information.…”

Structure-function analysis of ZAR1 immune receptor reveals key molecular interactions for activity

“…TIR domains in NLRs have commonly been thought of as scaffolding proteins (Vajjhala et al, 2017). However, TIR domains in bacteria and Archaea were recently shown to act as NADase enzymes (Essuman et al, 2018). CC domains have no homology to proteins with known enzymatic activity.…”

Evolutionary model of protein secondary structure capable of revealing new biological relationships

“…TIR domains function as a homotypic interaction motif, and the molecular basis of interactions has recently been characterized for TLR4 signalling assembly with MyD88 and MAL (Ve et al, 2017). The TIR domains from the mammalian protein SARM1 and some bacterial proteins have also been shown to have NAD + -cleavage activity (Essuman et al, 2017(Essuman et al, , 2018; this finding suggests there may be evolutionary, rather than merely structural links with bacterial enzymes such as the CMP hydrolase MilB. We therefore considered that an evolutionary analysis could provide insights into the functions of TIR domains and structurally similar proteins.…”