Broz, P. & Dixit, V. M. Inflammasomes: mechanism of assembly, regulation and signalling. Nat. Rev. Immunol. 16, 407–420 (2016).
Man, S. M. & Kanneganti, T.-D. Converging roles of caspases in inflammasome activation, cell death and innate immunity. Nat. Rev. Immunol. 16, 7–21 (2016).
Wong, S., Alattas, H. & Slavcev, R. A. A snapshot of the λ T4rII exclusion (Rex) phenotype in Escherichia coli. Curr. Genet. 67, 739–745 (2021).
Jorgensen, I., Rayamajhi, M. & Miao, E. A. Programmed cell death as a defence against infection. Nat. Rev. Immunol. 17, 151–164 (2017).
Broz, P., Pelegrín, P. & Shao, F. The gasdermins, a protein family executing cell death and inflammation. Nat. Rev. Immunol. 20, 143–157 (2020).
Jones, J. D. G., Vance, R. E. & Dangl, J. L. Intracellular innate immune surveillance devices in plants and animals. Science 354, aaf6395 (2016).
Ma, S. et al. Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme. Science 370, eabe3069 (2020).
Liu, X. et al. Inflammasome-activated gasdermin D causes pyroptosis by forming membrane pores. Nature 535, 153–158 (2016).
Ruan, J., Xia, S., Liu, X., Lieberman, J. & Wu, H. Cryo-EM structure of the gasdermin A3 membrane pore. Nature 557, 62–67 (2018).
Lieberman, J., Wu, H. & Kagan, J. C. Gasdermin D activity in inflammation and host defense. Sci. Immunol. 4, eaav1447 (2019).
Johnson, A. G. et al. Bacterial gasdermins reveal an ancient mechanism of cell death. Science 375, 221–225 (2022).
Lopatina, A., Tal, N. & Sorek, R. Abortive infection: bacterial suicide as anantiviral immune strategy. Annu. Rev. Virol. 7, 371–384 (2020).
Kibby, E. M. et al. Bacterial NLR-related proteins protect against phage. Cell 186, 2410–2424 (2023).
Leipe, D. D., Koonin, E. V. & Aravind, L. STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer. J. Mol. Biol. 343, 1–28 (2004).
Gao, L. A. et al. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 377, eabm4096 (2022).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Park, H. H. et al. The Death domain superfamily in intracellular signaling of apoptosis and inflammation. Annu. Rev. Immunol. 25, 561–586 (2007).
Werts, C., Girardin, S. E. & Philpott, D. J. TIR, CARD and PYRIN: three domains for an antimicrobial triad. Cell Death Differ. 13, 798–815 (2006).
Wu, H. & Lo, Y.-C. Structures, domains and functions in cell death (DD, DED, CARD, PYD). eLS https://doi.org/10.1002/9780470015902.a0021579 (2009).
Davis, B. K., Wen, H. & Ting, J. P.-Y. The inflammasome NLRs in immunity, inflammation, and associated diseases. Annu. Rev. Immunol. 29, 707–735 (2011).
Holm, L. Dali server: structural unification of protein families. Nucleic Acids Res. 50, W210–W215 (2022).
Matyszewski, M. et al. Cryo-EM structure of the NLRC4CARD filament provides insights into how symmetric and asymmetric supramolecular structures drive inflammasome assembly. J. Biol. Chem. 293, 20240–20248 (2018).
Humke, E. W., Shriver, S. K., Starovasnik, M. A., Fairbrother, W. J. & Dixit, V. M. ICEBERG: a novel inhibitor of interleukin-1β generation. Cell 103, 99–111 (2000).
Pinheiro, A. S. et al. Three-dimensional structure of the NLRP7 pyrin domain: Insight into pyrin-pyrin-mediated effector domain signaling in innate immunity. J. Biol. Chem. 285, 27402–27410 (2010).
Eibl, C. et al. Structural and functional analysis of the NLRP4 pyrin domain. Biochemistry 51, 7330–7341 (2012).
Hou, X. & Niu, X. The NMR solution structure of AIM2 PYD domain from Mus musculus reveals a distinct α2–α3 helix conformation from its human homologues. Biochem. Biophys. Res. Commun. 461, 396–400 (2015).
Rousset, F. & Sorek, R. The evolutionary success of regulated cell death in bacterial immunity. Curr. Opin. Microbiol. 74, 102312 (2023).
van Kempen, M. et al. Fast and accurate protein structure search with Foldseek. Nat. Biotechnol. 42, 243–246 (2024).
Suzek, B. E. et al. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31, 926–932 (2015).
Stokar-Avihail, A. et al. Discovery of phage determinants that confer sensitivity to bacterial immune systems. Cell 186, 1863–1876 (2023).
Cook, R. et al. INfrastructure for a PHAge REference Database: identification of large-scale biases in the current collection of cultured phage genomes. Phage 2, 214–223 (2021).
Millman, A., Melamed, S., Amitai, G. & Sorek, R. Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. Nat. Microbiol. 5, 1608–1615 (2020).
Miller, E. S. et al. Bacteriophage T4 genome. Microbiol. Mol. Biol. Rev. 67, 86–156 (2003).
Shinedling, S., Parma, D. & Gold, L. Wild-type bacteriophage T4 is restricted by the lambda rex genes. J. Virol. 61, 3790–3794 (1987).
Landsmann, J., Kroger, M. & Hobom, G. The rex region of bacteriophage lambda: two genes under three-way control. Gene 20, 11–24 (1982).
Rousset, F. et al. Phages and their satellites encode hotspots of antiviral systems. Cell Host Microbe 30, 740–753 (2022).
Isaev, A. et al. Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence. Nucleic Acids Res. 48, 5397–5406 (2020).
Bedoui, S., Herold, M. J. & Strasser, A. Emerging connectivity of programmed cell death pathways and its physiological implications. Nat. Rev. Mol. Cell Biol. 21, 678–695 (2020).
Hofmann, K. The evolutionary origins of programmed cell death signaling. Cold Spring Harb. Perspect. Biol. 12, a036442 (2020).
Wein, T. & Sorek, R. Bacterial origins of human cell-autonomous innate immune mechanisms. Nat. Rev. Immunol. 22, 629–638 (2022).
Kaur, G., Iyer, L. M., Burroughs, A. M. & Aravind, L. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. eLife 10, e70394 (2021).
Kaur, G., Burroughs, A. M., Iyer, L. M. & Aravind, L. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. eLife 9, e52696 (2020).
Mitchell, P. S., Sandstrom, A. & Vance, R. E. The NLRP1 inflammasome: new mechanistic insights and unresolved mysteries. Curr. Opin. Immunol. 60, 37–45 (2019).
Shi, J. et al. Inflammatory caspases are innate immune receptors for intracellular LPS. Nature 514, 187–192 (2014).
Tesson, F. et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat. Commun. 13, 2561 (2022).
Jones, J. D. G. & Dangl, J. L. The plant immune system. Nature 444, 323–329 (2006).
Adachi, H., Derevnina, L. & Kamoun, S. NLR singletons, pairs, and networks: evolution, assembly, and regulation of the intracellular immunoreceptor circuitry of plants. Curr. Opin. Plant Biol. 50, 121–131 (2019).
Remick, B. C., Gaidt, M. M. & Vance, R. E. Effector-triggered immunity. Annu. Rev. Immunol. 41, 453–481 (2023).
Sandstrom, A. et al. Functional degradation: a mechanism of NLRP1 inflammasome activation by diverse pathogen enzymes. Science 364, eaau1330 (2019).
Robinson, K. S. et al. Enteroviral 3C protease activates the human NLRP1 inflammasome in airway epithelia. Science 370, eaay2002 (2020).
Johnston, J. B. et al. A poxvirus-encoded pyrin domain protein interacts with ASC-1 to inhibit host inflammatory and apoptotic responses to infection. Immunity 23, 587–598 (2005).
Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018).
Millman, A. et al. Bacterial retrons function in anti-phage defense. Cell 183, 1551–1561 (2020).
Bernheim, A. et al. Prokaryotic viperins produce diverse antiviral molecules. Nature 589, 120–124 (2021).
Lee, T. S. et al. BglBrick vectors and datasheets: a synthetic biology platform for gene expression. J. Biol. Eng. 5, 12 (2011).
Mazzocco, A., Waddell, T. E., Lingohr, E. & Johnson, R. P. In Bacteriophages: Methods and Protocols (eds Kropinski, A. M. & Cloike, M. R. J.) 81–85 (Humana Press, 2009).
Kropinski, A. M., Mazzocco, A., Waddell, T. E., Lingohr, E. & Johnson, R. P. In Bacteriophages: Methods and Protocols (eds Kropinski, A. M. & Cloike, M. R. J.) 69–76 (Humana Press, 2009).
Baym, M. et al. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS ONE 10, e0128036 (2015).
Deatherage, D. E. & Barrick, J. E. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. (Clifton, NJ) 1151, 165–188 (2014).
Chung, C. T. & Miller, R. H. In Methods in Enzymology Vol. 218 (ed. Wu, R.) 621–627 (Academic Press, 1993).
Frey, S. & Görlich, D. A new set of highly efficient, tag-cleaving proteases for purifying recombinant proteins. J. Chromatogr. A 1337, 95–105 (2014).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018).
Zhou, W. et al. Structure of the human cGAS–DNA complex reveals enhanced control of immune surveillance. Cell 174, 300–311 (2018).
Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. Sect. Struct. Biol. 75, 861–877 (2019).
Chen, I.-M. A. et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 47, D666–D677 (2019).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).
Cretin, G. et al. SWORD2: hierarchical analysis of protein 3D structures. Nucleic Acids Res. 50, W732–W738 (2022).
Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).
Millman, A. et al. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 30, 1556–1569 (2022).
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).
