Nucleotide Immune Signaling in CBASS, Pycsar, Thoeris, and CRISPR Antiphage Defense

Abstract

Bacteria encode an arsenal of diverse systems that defend against phage infection. A common theme uniting many prevalent antiphage defense systems is the use of specialized nucleotide signals that function as second messengers to activate downstream effector proteins and inhibit viral propagation. In this article, we review the molecular mechanisms controlling nucleotide immune signaling in four major families of antiphage defense systems: CBASS, Pycsar, Thoeris, and type III CRISPR immunity. Analyses of the individual steps connecting phage detection, nucleotide signal synthesis, and downstream effector function reveal shared core principles of signaling and uncover system-specific strategies used to augment immune defense. We compare recently discovered mechanisms used by phages to evade nucleotide immune signaling and highlight convergent strategies that shape host-virus interactions. Finally, we explain how the evolutionary connection between bacterial antiphage defense and eukaryotic antiviral immunity defines fundamental rules that govern nucleotide-based immunity across all kingdoms of life.

Keywords: CBASS; Pycsar; Thoeris; antiphage defense; nucleotide second messenger; type III CRISPR.

Figure 1 ∣. Nucleotide immune signaling pathways provide protection through abortive infection.

A. Bacterial immunity can be generally categorized into ‘direct’ pathways that accomplish phage detection and effector function with a single protein or complex, and ‘signal transduction’ pathways that use separate components dedicated to detection of incoming phages and execution of effector function. B. Relative frequencies of major nucleotide immune signaling systems in bacterial anti-phage defense. Data are derived from (112, 114).

Figure 2 ∣. Mechanisms of CBASS nucleotide immune signaling and phage evasion.

A.Overview of the mechanisms of CBASS immunity. B. Chemical structures of the cyclic dinucleotide 3′3′-cGAMP and the cyclic trinucleotide 3′3′3′-cAAA as representative CBASS nucleotide immune signals. Below each structure is a list of nucleotide immune signals that have been experimentally confirmed in CBASS immunity. C. CBASS systems are extremely diverse, with types II–IV encoding additional Cap proteins that regulate CD-NTase function. Type II and type III systems are described in the main text. Type IV systems represent ~1% of all CBASS systems and are defined by the presence of Cap9 and Cap10 genes, with some operons encoding Cap11. D. Phages evade CBASS immunity by directly targeting nucleotide immune signals. E. Cartoon representation of the protein structures of V. cholerae DncV and human cGAS, highlighting conserved structural features of the nucleotidyltransferase core.

Figure 3 ∣. Mechanisms of Pycsar nucleotide immune signaling and phage evasion.

A. Overview of the mechanisms of Pycsar immunity. B. Chemical structures of the Pycsar signaling molecules 3′,5′-cCMP and 3′,5′-cUMP. C. Phages evade Pycsar immunity by targeting nucleotide immune signals with Apyc1.

Figure 4 ∣. Mechanisms of Thoeris immune signaling and phage evasion.

A. Overview of the mechanisms of Thoeris immunity. B. Chemical structures of the Thoeris signaling molecules 1′′–3′ gcADPR and His-ADPR. C. Thoeris operons contain at least one copy of ThsB and a single copy of ThsA. D. Phages evade Thoeris immunity by directly targeting nucleotide immune signals. E. Cartoon representation of the TIR domain structures of B. cereus ThsB and human SARM1 highlighting conserved structural features.

Figure 5 ∣. Mechanisms of type III CRISPR nucleotide immune signaling and phage evasion.

A. Overview of the mechanisms of type III CRISPR immunity. B. Chemical structures of cAAAA and SAM-AMP as representative type III CRISPR nucleotide immune signals. C. Phages evade type III CRISPR immunity using diverse anti-CRISPR proteins.