Antiviral activity of bacterial TIR domains via signaling molecules that trigger cell death
Posted on: 5 February 2021
Preprint posted on 6 January 2021
Article now published in Nature at http://dx.doi.org/10.1038/s41586-021-04098-7
An evolutionary arms race; Shared TIRs protect against viral infection
Selected by Jonny Coates, Connor Rosen
Categories: cell biology, evolutionary biology, immunology, plant biology
Context and background
Bacteria and phages exist in a constant arms race resulting in the development of a range of bacterial antiphage defences [1]. Many of these defence systems remain poorly characterised and understood, with a major exception being the CRISPR-Cas9 system.
The thoeris system is composed of two proteins; ThsA and ThsB. ThsA has been shown to have NAD+ cleavage activity whereas ThsB resembles TIR (Toll/interleukin-1 receptor) domain proteins (Fig. 1)[2]. TIRs are the signal-inducing components of immune receptors that recognise foreign pathogens and are found in humans, plants and prokaryotes [3]. In plants, activation of TIRs causes a form of cell death termed the hypersensitive response [4]. However, the function of TIRs in prokaryotes is not fully understood.
Figure 1. The thoeris system is composed of two proteins (ThsA and ThsB). ThsA has NAD+ binding activities whereas ThsB contains a TIR domain.
The authors of the preprint investigated the mechanism of Thoeris-mediated immunity and traced connections to eukaryotic TIRs.
Key findings
1. Thoeris leads to abortive cell death via NAD depletion
Anti-phage defense systems use a variety of mechanisms to create immunity in a bacterial population. Given the role of TIR domains in causing cell death in plant cells, the authors examined whether the Thoeris system might act through an abortive infection mechanism, wherein an infected cell kills itself before phage replication and lysis can occur, protecting the overall bacterial population. Thoeris expression did lead to an abortive infection mechanism, which they subsequently showed required the NADase activity of the Thoeris ThsA protein. This enzymatic activity was dependent on the production of a cADPR isomer produced by the TIR domain of ThsB, akin to the enzymatic activity of plant TIR domains.
2. TIR domain proteins determines specificity against phages
Genomic examination of Thoeris systems revealed that they often contain multiple ThsB TIR domain-containing proteins, but these ThsB proteins showed very little sequence homology. This suggested that they may have divergent phage recognition patterns, which converge on the common “effector” ThsA protein. Indeed, expression of various combinations of ThsA/ThsB proteins revealed that the TIR domain ThsB proteins determined the specificity of phage immunity.
Figure 2. Summary figure, adapted from figure 4 of the preprint under a CC BY-NC-ND 4.0 licence.
Why this preprint
This preprint presents a fascinating link between prokaryotic and eukaryotic immunity through the shared enzymatic activities of TIR domains and production of a cADPR-like signaling molecule.
Open questions
- The authors rightly point out the difficulties in identifying the precise identity of the cADPR isomer used in the Thoeris system, and its relationship to the v-cADPR molecule used in plant TIR domain signaling processes. It will be very interesting to see the breadth of cADPR-like molecules used throughout different Thoeris systems, and the extent to which the ThsA systems of different bacteria may be triggered by different cADPR variants or if the isomer identified here is a “universal” second messenger. Given the potential for horizontal acquisition of alternative Thoeris gene systems, would a universal second messenger facilitate the acquisition of new “sensor” TIR domains or is there some advantage to evolving a distinct signaling pathway?
- What are the phage features recognized by the ThsB proteins? Nucleic-acid-sensing bacterial immune systems, such as CRISPR systems and restriction enzymes, have been widely harnessed for molecular biology and now therapeutic purposes, and the potential utilities of new tools are easily appreciated. However, alternative mechanisms may reveal intriguing aspects of phage biology.
- Bacterial immune systems are the product of ongoing arms races between bacteria and phages, and phages often evolve resistance mechanisms to protect themselves. It will be fascinating to see what “anti-Thoeris” systems can be discovered – whether they be evasion of sensing mechanisms, enzymatic breakdown of the cADPR-isomer, inhibition of NADase enzymatic activity, or even more sophisticated resistance mechanisms. Phage-bacteria battles are the source of endless biological innovation!
References
- Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, et al. Systematic discovery of anti-phage defense systems in the microbial pan-genome. Science. 2018;359. doi:10.1126/science.aar4120
- Ka D, Oh H, Park E, Kim J-H, Bae E. Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD + degradation. Nat Commun. 2020;11: 2816. doi:10.1038/s41467-020-16703-w
- Bayless AM, Nishimura MT. Enzymatic Functions for Toll/Interleukin-1 Receptor Domain Proteins in the Plant Immune System. Front Genet. 2020;11. doi:10.3389/fgene.2020.00539
- Balint‐Kurti P. The plant hypersensitive response: concepts, control and consequences. Mol Plant Pathol. 2019;20: 1163–1178. doi:10.1111/mpp.12821
doi: https://doi.org/10.1242/prelights.27015
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