Antiviral activity of bacterial TIR domains via immune signalling molecules

Abstract

The 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..

Viruses inhibit TIR gcADPR signaling to overcome bacterial defense

“…Whereas TIR domains in animals mainly transfer the signal by protein-protein interactions 3 , in plants and bacteria these domains produce an immune signaling molecule, which has the same mass as cyclic ADP-ribose (cADPR), but whose molecular and chemical structure remains elusive 1,4,5 . The mechanism of action of TIR-mediated immune signaling was recently deciphered for a bacterial anti-phage immune system called Thoeris 1 . This system comprises two core proteins, one of which (named ThsB) has a TIR domain and serves as the sensor for phage infection.…”

Chemical structures of cyclic ADP ribose (cADPR) isomers and the molecular basis of their production and signaling

“…Bacterial lysates containing cADPR isomers produced by bacterial ThsB or plant TIR domains have recently been shown to activate the ThsA NADase (Fig. 5a) of the Bacillus cereus MSX-D12 Thoeris antiphage defence system ( 34 ). To test if our purified cADPR isomers can directly activate ThsA, we produced and purified 4 different ThsA proteins (37-46% sequence identity) from Bacilus cereus MSX-D12 (BcThsA), Acinetobacter baumannii (AbThsA), Enterococcus faecium (EfThsA) and Streptococcus equi (SeThsA), and monitored the NAD + -cleavage activity of each in the absence and presence of ADPR, cADPR, v-cADPR (2’cADPR) and v2-cADPR (3’cADPR), using our NMR-based NADase assay (Fig.…”

“…v-cADPR (2’cADPR) can also trigger the NADase activity of ThsA (Fig. 5b and ( 34 )), but as it is a significantly weaker binder than v2-cADPR (3’cADPR) (Fig. 6), a much higher concentration of v-cADPR (2’cADPR) is needed to activate ThsA.…”

“…The first gene, thsA, encodes a protein that contains sirtuin-like or macro domain that bind NAD + or its metabolites, and a SLOG-like domain suggested as a sensor for nucleotide-related ligands (21,35). The second gene, thsB, encodes a TIR-domain-containing protein (ThsB) (21,(34)(35)(36)(37). Upon phage infection, ThsB cleaves NAD + and produces a cADPR isomer, which activates ThsA (34), causing further NAD + depletion and cell death.…”

Bacterial threat assessment of bacteriophage infection is mediated by intracellular polyamine accumulation and Gac/Rsm signaling

“…Examples of phage defense systems include restriction modification (Kruger and Bickle, 1983), CRISPR-Cas systems (Wiedenheft et al, 2012), and abortive infection systems that kill or inhibit the bacterial host before the phage can complete its lifecycle (Bernheim and Sorek, 2019; Cohen et al, 2019; Doron et al, 2018). Recent comparative immunological studies reveal some bacterial abortive infection systems share evolutionary roots with eukaryotic antiviral immune pathways (Cohen et al ., 2019; Ofir et al, 2021). Bacterial and eukaryotic immune systems share other conceptually analogous characteristics, such as the ability to detect molecules that are indicative of cellular damage.…”