Cyclic ADP ribose isomers: Production, chemical structures, and immune signaling

Abstract

Cyclic ADP ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via NAD + hydrolysis. We show that v-cADPR (2′cADPR) and v2-cADPR (3′cADPR) isomers are cyclized by O -glycosidic bond formation between the ribose moieties in ADPR. Structures of 2′cADPR-producing TIR domains reveal conformational changes leading to an active assembly that resembles those of Toll-like receptor adaptor TIR domains. Mutagenesis reveals a conserved tryptophan essential for cyclization. We show that 3′cADPR is an activator of ThsA effector proteins from bacterial anti-phage defense systems termed Thoeris, and a suppressor of plant immunity when produced by the effector HopAM1. Collectively, our results reveal the molecular basis of cADPR isomer production and establish 3′cADPR in bacteria as an antiviral and plant immunity-suppressing signaling molecule.

Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products

“…The discovery that the human TIR protein, SARM1, executes axonal degeneration via NAD + -hydrolase activity was pivotal to understanding TIR-immunity in plants and prokaryotes (Gerdts et al, 2015; Essuman et al, 2017; Essuman et al, 2022). Indeed, TIR-immune proteins of both plants and prokaryotes are now known to be enzymes which consume and/or modify nucleotides (including NAD + ) or nucleic acids, and this enzymatic function is required for immune signaling across the tree of life (Horsefield et al, 2019; Wan et al, 2019; Essuman et al, 2022; Huang et al, 2022; Jia et al, 2022; Manik et al, 2022; Yu et al, 2022). The number and type of identified small molecules produced by enzymatic TIRs is expanding rapidly (Eastman et al, 2022a; Essuman et al, 2022; Lapin et al, 2022).…”

“…Certain mechanistic features of enzymatic TIRs are conserved even across very distant phyla (Essuman et al, 2018; Wan et al, 2019; Essuman et al, 2022). For instance, all examined prokaryotic and eukaryotic TIRs require a conserved glutamate (E) residue for catalysis (Essuman et al, 2017; Horsefield et al, 2019; Ofir et al, 2021; Essuman et al, 2022; Manik et al, 2022). Additionally, enzymatic TIRs contain a flexible loop, termed the BB-loop, which lays over the catalytic pocket and has been proposed to regulate substrate access (Ma et al, 2020; Martin et al, 2020; Manik et al, 2022; Shi et al, 2022).…”

“…For instance, all examined prokaryotic and eukaryotic TIRs require a conserved glutamate (E) residue for catalysis (Essuman et al, 2017; Horsefield et al, 2019; Ofir et al, 2021; Essuman et al, 2022; Manik et al, 2022). Additionally, enzymatic TIRs contain a flexible loop, termed the BB-loop, which lays over the catalytic pocket and has been proposed to regulate substrate access (Ma et al, 2020; Martin et al, 2020; Manik et al, 2022; Shi et al, 2022). Enzymatic TIR-domains also require self-association via TIR-TIR interfaces to engage in catalysis (Horsefield et al, 2019; Wan et al, 2019; Manik et al, 2022; Shi et al, 2022).…”

“…Additionally, enzymatic TIRs contain a flexible loop, termed the BB-loop, which lays over the catalytic pocket and has been proposed to regulate substrate access (Ma et al, 2020; Martin et al, 2020; Manik et al, 2022; Shi et al, 2022). Enzymatic TIR-domains also require self-association via TIR-TIR interfaces to engage in catalysis (Horsefield et al, 2019; Wan et al, 2019; Manik et al, 2022; Shi et al, 2022). Cryo-EM studies have provided key insights into how oligomerization and self-association promote the activation of plant TIR-NLRs, as well as CC-NLRs (Wang et al, 2019a; Wang et al, 2019b; Ma et al, 2020; Martin et al, 2020).…”

“…SARM1 NADase activity produces ADPR and canonical cyclic ADPR (cADPR), which are both secondary messengers that can trigger intracellular Ca 2+ -signaling cascades within animal cells (Fliegert et al, 2020; Eastman et al, 2022a; Li et al, 2022). Intriguingly, the TIR-domains of plants and prokaryotes produce non-canonical cADPR-isomers from NAD + , such as 3’cADPR or 2’cADPR (Essuman et al, 2018; Wan et al, 2019; Essuman et al, 2022; Manik et al, 2022; Weagley et al, 2022). 3’cADPR is the NADase product of the HopAM1 TIR-protein - a virulence factor encoded by the plant pathogen Pseudomonas syringae DC3000 (Eastman et al, 2022b).…”