Koonin, E. V. & Aravind, L. Origin and evolution of eukaryotic apoptosis: the bacterial connection. Cell Death Differ. 9, 394–404 (2002).
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).
Jones, J. D. G., Vance, R. E. & Dangl, J. L. Intracellular innate immune surveillance devices in plants and animals. Science 354, aaf6395 (2016).
Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084 (2020).
Gao, L. A. et al. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 377, eabm4096 (2022).
Béchon, N. et al. Diversification of molecular pattern recognition in bacterial NLR-like proteins. Nat. Commun. 15, 9860 (2024).
Robbins, L. K. et al. A bacterial NLR-related protein senses distinct phage triggers through a single interface. Preprint at bioRxiv https://doi.org/10.1101/2024.12.17.629029 (2026).
Conte, A. N. et al. DnaJ mediates phage sensing by the bacterial NLR-related protein bNACHT25. PLOS Biol. 23, e3003203 (2025).
Muralidharan, A. et al. Molecular basis for anti-jumbo phage immunity by AVAST Type 5. Mol. Cell 86, 740–756 (2026).
Kofoed, E. M. & Vance, R. E. Innate immune recognition of bacterial ligands by NAIPs determines inflammasome specificity. Nature 477, 592–595 (2011).
Zhao, Y. et al. The NLRC4 inflammasome receptors for bacterial flagellin and type III secretion apparatus. Nature 477, 596–600 (2011).
Chamaillard, M. et al. An essential role for NOD1 in host recognition of bacterial peptidoglycan containing diaminopimelic acid. Nat. Immunol. 4, 702–707 (2003).
Girardin, S. E. et al. Nod2 is a general sensor of peptidoglycan through muramyl dipeptide (MDP) detection. J. Biol. Chem. 278, 8869–8872 (2003).
Vassallo, C. N., Doering, C. R., Littlehale, M. L., Teodoro, G. I. C. & Laub, M. T. A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome. Nat. Microbiol. 7, 1568–1579 (2022).
Rousset, F. et al. Phages and their satellites encode hotspots of antiviral systems. Cell Host Microbe. 30, 740–753 (2022).
Kibby, E. M. et al. Bacterial NLR-related proteins protect against phage. Cell 186, 2410–2424 (2023).
van den Berg, D. F. et al. Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses. Cell Host Microbe 32, 1427–1443 (2024).
Rousset, F. et al. A conserved family of immune effectors cleaves cellular ATP upon viral infection. Cell 186, 3619–3631 (2023).
Makarova, K. S., Wolf, Y. I., Snir, S. & Koonin, E. V. Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J. Bacteriol. 193, 6039–6056 (2011).
Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018).
Shmakov, S. A., Makarova, K. S., Wolf, Y. I., Severinov, K. V. & Koonin, E. V. Systematic prediction of genes functionally linked to CRISPR–Cas systems by gene neighborhood analysis. Proc. Natl Acad. Sci. USA 115, E5307–E5316 (2018).
Brenes, L. R. & Laub, M. T. E. coli prophages encode an arsenal of defense systems to protect against temperate phages. Cell Host Microbe 33, 1004–1018 (2025).
Chou, W.-C., Jha, S., Linhoff, M. W. & Ting, J. P.-Y. The NLR gene family: from discovery to present day. Nat. Rev. Immunol. 23, 635–654 (2023).
Wang, J. et al. Reconstitution and structure of a plant NLR resistosome conferring immunity. Science 364, eaav5870 (2019).
Liu, F. et al. Activation of the helper NRC4 immune receptor forms a hexameric resistosome. Cell 187, 4877–4889 (2024).
Wu, Y., Sun, Y., Richet, E., Han, Z. & Chai, J. Structural basis for negative regulation of the Escherichia coli maltose system. Nat. Commun. 14, 4925 (2023).
Poon, K. K., Chu, J. C. & Wong, S. L. Roles of glucitol in the GutR-mediated transcription activation process in Bacillus subtilis: glucitol induces GutR to change its conformation and to bind ATP. J. Biol. Chem. 276, 29819–29825 (2001).
Wang, Y. et al. Structural and functional characterization of AfsR, an SARP family transcriptional activator of antibiotic biosynthesis in Streptomyces. PLOS Biol. 22, e3002528 (2024).
Koonin, E. V. & Aravind, L. The NACHT family—a new group of predicted NTPases implicated in apoptosis and MHC transcription activation. Trends Biochem. Sci. 25, 223–224 (2000).
Legrand, A. et al. Evolutionary characterization of antiviral SAMD9/9L across kingdoms supports ancient convergence and lineage-specific adaptations. Nat. Ecol. Evol. 9, 2206–2222 (2025).
Zhou, M. et al. Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1. Genes Dev. 29, 2349–2361 (2015).
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).
Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).
Furano, A. V. Content of elongation factor Tu in Escherichia coli. Proc. Natl Acad. Sci. USA 72, 4780–4784 (1975).
Hu, Z. et al. Structural and biochemical basis for induced self-propagation of NLRC4. Science 350, 399–404 (2015).
Duda, R. L. & Teschke, C. M. The amazing HK97 fold: versatile results of modest differences. Curr. Opin. Virol. 36, 9–16 (2019).
Loveland, A. B., Demo, G. & Korostelev, A. A. Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading. Nature 584, 640–645 (2020).
Song, H., Parsons, M. R., Rowsell, S., Leonard, G. & Phillips, S. E. Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A resolution. J. Mol. Biol. 285, 1245–1256 (1999).
Veesler, D. & Cambillau, C. A common evolutionary origin for tailed-bacteriophage functional modules and bacterial machineries. Microbiol. Mol. Biol. Rev. 75, 423–433 (2011).
Nagy, T. A., Gersabeck, G. W., Conte, A. N. & Whiteley, A. T. A phage protein screen identifies triggers of the bacterial innate immune system. Nat. Microbiol. 11, 597–609 (2026).
Iyer, L. M., Koonin, E. V. & Aravind, L. Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52. BMC Genomics 3, 8 (2002).
Zinke, M., Schröder, G. F. & Lange, A. Major tail proteins of bacteriophages of the order Caudovirales. J. Biol. Chem. 298, 101472 (2022).
Xu, J., Hendrix, R. W. & Duda, R. L. Chaperone-protein interactions that mediate assembly of the bacteriophage lambda tail to the correct length. J. Mol. Biol. 426, 1004–1018 (2014).
Pei, J., Kim, B.-H. & Grishin, N. V. PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res. 36, 2295–2300 (2008).
Leipe, D. D., Aravind, L., Grishin, N. V. & Koonin, E. V. The bacterial replicative helicase DnaB evolved from a RecA duplication. Genome Res. 10, 5–16 (2000).
Georgiou, T. et al. Specific peptide-activated proteolytic cleavage of Escherichia coli elongation factor Tu. Proc. Natl Acad. Sci. USA 95, 2891–2895 (1998).
Bingham, R., Ekunwe, S. I., Falk, S., Snyder, L. & Kleanthous, C. The major head protein of bacteriophage T4 binds specifically to elongation factor Tu. J. Biol. Chem. 275, 23219–23226 (2000).
Zhang, T. et al. Direct activation of a bacterial innate immune system by a viral capsid protein. Nature 612, 132–140 (2022).
Bouchard, J. D. & Moineau, S. Lactococcal phage genes involved in sensitivity to AbiK and their relation to single-strand annealing proteins. J. Bacteriol. 186, 3649–3652 (2004).
Yasui, R., Washizaki, A., Furihata, Y., Yonesaki, T. & Otsuka, Y. AbpA and AbpB provide anti-phage activity in Escherichia coli. Genes Genet. Syst. 89, 51–60 (2014).
Depardieu, F. et al. A eukaryotic-like serine/threonine kinase protects staphylococci against phages. Cell Host Microbe 20, 471–481 (2016).
Stokar-Avihail, A. et al. Discovery of phage determinants that confer sensitivity to bacterial immune systems. Cell 186, 1863–1876 (2023).
Tuck, O. T. et al. Genome integrity sensing by the broad-spectrum Hachiman antiphage defense complex. Cell 187, 6914–6928 (2024).
Yu, Y. T. & Snyder, L. Translation elongation factor Tu cleaved by a phage-exclusion system. Proc. Natl Acad. Sci. USA 91, 802–806 (1994).
Rousset, F. et al. TIR signaling activates caspase-like immunity in bacteria. Science 387, 510–516 (2025).
Schmitz, M., Querques, I., Oberli, S., Chanez, C. & Jinek, M. Structural basis for the assembly of the type V CRISPR-associated transposon complex. Cell 185, 4999–5010 (2022).
Kidmose, R. T., Vasiliev, N. N., Chetverin, A. B., Andersen, G. R. & Knudsen, C. R. Structure of the Qbeta replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins. Proc. Natl Acad. Sci. USA 107, 10884–10889 (2010).
Harvey, K. L., Jarocki, V. M., Charles, I. G. & Djordjevic, S. P. The diverse functional roles of Elongation Factor Tu (EF-Tu) in microbial pathogenesis. Front. Microbiol. 10, 2351 (2019).
Sharif, H. et al. Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome. Nature 570, 338–343 (2019).
Zhang, T. et al. A bacterial immunity protein directly senses two disparate phage proteins. Nature 635, 728–735 (2024).
Schäffer, A. A. et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29, 2994–3005 (2001).
Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).
Edgar, R. C. Muscle5: high-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. Nat. Commun. 13, 6968 (2022).
Esterman, E. S., Wolf, Y. I., Kogay, R., Koonin, E. V. & Zhaxybayeva, O. Evolution of DNA packaging in gene transfer agents. Virus Evol. 7, veab015 (2021).
Deorowicz, S., Debudaj-Grabysz, A. & Gudyś, A. FAMSA: Fast and accurate multiple sequence alignment of huge protein families. Sci. Rep. 6, 33964 (2016).
Lefort, V., Desper, R. & Gascuel, O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol. Biol. Evol. 32, 2798–2800 (2015).
Marchler-Bauer, A. et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 45, D200–D203 (2017).
Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T. T.-Y. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 8, 28–36 (2017).
Tesson, F. et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat. Commun. 13, 2561 (2022).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Varadi, M. et al. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Res. 52, D368–D375 (2024).
van Kempen, M. et al. Fast and accurate protein structure search with Foldseek. Nat. Biotechnol. 42, 243–246 (2023).
Wishart, D. S. et al. PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res. 51, W443–W450 (2023).
Katoh, K., Misawa, K., Kuma, K.-I. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
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).
Zimmermann, L. et al. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J. Mol. Biol. 430, 2237–2243 (2018).
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).
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Picelli, S. et al. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res. 24, 2033–2040 (2014).
Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).
Li, J. et al. TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples. Nat. Methods 17, 399–404 (2020).
McAlister, G. C. et al. MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes. Anal. Chem. 86, 7150–7158 (2014).
Eng, J. K., Jahan, T. A. & Hoopmann, M. R. Comet: an open-source MS/MS sequence database search tool. Proteomics 13, 22–24 (2013).
Huttlin, E. L. et al. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 143, 1174–1189 (2010).
Elias, J. E. & Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207–214 (2007).
Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J. & Gygi, S. P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2, 43–50 (2003).
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Comput. Biol. 13, e1005595 (2017).
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Bouras, G. et al. Pharokka: a fast scalable bacteriophage annotation tool. Bioinformatics 39, btac776 (2023).
Bouras, G. et al. Protein structure-informed bacteriophage genome annotation with Phold. Nucleic Acids Res. 54, gkaf1448 (2026).
Grigson, S. R., Giles, S. K., Edwards, R. A. & Papudeshi, B. Knowing and naming: phage annotation and nomenclature for phage therapy. Clin. Infect. Dis. 77, S352–S359 (2023).
Adriaenssens, E. & Brister, J. R. How to name and classify your phage: an informal guide. Viruses 9, 70 (2017).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
Chen, M. Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks. Commun. Biol. 8, 798 (2025).
Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).
Kim, W. et al. Rapid and sensitive protein complex alignment with Foldseek-Multimer. Nat. Methods 22, 469–472 (2025).
