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HomeNatureSingle phage proteins sequester signals from TIR and cGAS-like enzymes

Single phage proteins sequester signals from TIR and cGAS-like enzymes

  • Manik, M. K. et al. Cyclic ADP ribose isomers: production, chemical structures, and immune signaling. Science 377, eadc8969 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ofir, G. et al. Antiviral activity of bacterial TIR domains via immune signalling molecules. Nature 600, 116–120 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Cohen, D. et al. Cyclic GMP-AMP signalling protects bacteria against viral infection. Nature 574, 691–695 (2019).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Leavitt, A. et al. Viruses inhibit TIR gcADPR signaling to overcome bacterial defense. Nature 611, 326–331 (2022).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Yirmiya, E. et al. Phages overcome bacterial immunity via diverse anti-defense proteins. Nature 625, 352–359 (2024).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Huiting, E. et al. Bacteriophages inhibit and evade cGAS-like immune function in bacteria. Cell 186, 864–876 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jenson, J. M., Li, T., Du, F., Ea, C. K. & Chen, Z. J. Ubiquitin-like conjugation by bacterial cGAS enhances anti-phage defence. Nature 616, 326–331 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Cao, X. et al. Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides. Mol. Cell 84, 375–385 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Millman, A. et al. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 30, 1556–1569 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rousset, F. et al. Phages and their satellites encode hotspots of antiviral systems. Cell Host Microbe 30, 740–753 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Johnson, M. C. et al. Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems. Nucleic Acids Res. 51, 4995–5005 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stanley, S. Y. & Maxwell, K. L. Phage-encoded anti-CRISPR defenses. Annu. Rev. Genet. 52, 445–464 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, Y. & Bondy-Denomy, J. Anti-CRISPRs go viral: the infection biology of CRISPR-Cas inhibitors. Cell Host Microbe 29, 704–714 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jia, N. & Patel, D. J. Structure-based functional mechanisms and biotechnology applications of anti-CRISPR proteins. Nat. Rev. Mol. Cell Biol. 22, 563–579 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Davidson, A. R. et al. Anti-CRISPRs: protein inhibitors of CRISPR-Cas systems. Annu. Rev. Biochem. 89, 309–332 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gao, Z. & Feng, Y. Bacteriophage strategies for overcoming host antiviral immunity. Front. Microbiol. 14, 1211793 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hobbs, S. J. et al. Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity. Nature 605, 522–526 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Athukoralage, J. S. et al. An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity. Nature 577, 572–575 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Whiteley, A. T. et al. Bacterial cGAS-like enzymes synthesize diverse nucleotide signals. Nature 567, 194–199 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fatma, S., Chakravarti, A., Zeng, X. & Huang, R. H. Molecular mechanisms of the CdnG-Cap5 antiphage defense system employing 3′,2′-cGAMP as the second messenger. Nat. Commun. 12, 6381 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burroughs, A. M., Zhang, D., Schäffer, D. E., Iyer, L. M. & Aravind, L. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Nucleic Acids Res. 43, 10633–10654 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Davies, B. W., Bogard, R. W., Young, T. S. & Mekalanos, J. J. Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence. Cell 149, 358–370 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Duncan-Lowey, B., McNamara-Bordewick, N. K., Tal, N., Sorek, R. & Kranzusch, P. J. Effector-mediated membrane disruption controls cell death in CBASS antiphage defense. Mol. Cell 81, 5039–5051 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tesson, F. et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat. Commun. 13, 2561 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, Y. et al. Bacterial defense systems exhibit synergistic anti-phage activity. Cell Host Microbe 32, 557–572 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • van Beljouw, S. P. B., Sanders, J., Rodriguez-Molina, A. & Brouns, S. J. J. RNA-targeting CRISPR-Cas systems. Nat. Rev. Microbiol. 21, 21–34 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Tal, N. et al. Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell 184, 5728–5739 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Molina, R., Sofos, N. & Montoya, G. Structural basis of CRISPR-Cas type III prokaryotic defence systems. Curr. Opin. Struct. Biol. 65, 119–129 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lau, R. K. et al. Structure and mechanism of a cyclic trinucleotide-activated bacterial endonuclease mediating bacteriophage immunity. Mol. Cell 77, 723–733 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ye, Q. et al. HORMA domain proteins and a Trip13-like ATPase regulate bacterial cGAS-like enzymes to mediate bacteriophage immunity. Mol. Cell 77, 709–722 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Thomas, J. A. et al. Extensive proteolysis of head and inner body proteins by a morphogenetic protease in the giant Pseudomonas aeruginosa phage φKZ. Mol. Microbiol. 84, 324–339 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fossati, A. et al. Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping. Nat. Commun. 14, 5156 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Guan, J. et al. Bacteriophage genome engineering with CRISPR–Cas13a. Nat. Microbiol. 7, 1956–1966 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Uribe, R. V. et al. Discovery and characterization of Cas9 inhibitors disseminated across seven bacterial phyla. Cell Host Microbe 25, 233–241 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jenal, U., Reinders, A. & Lori, C. Cyclic di-GMP: second messenger extraordinaire. Nat. Rev. Microbiol. 15, 271–284 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Morehouse, B. R. et al. STING cyclic dinucleotide sensing originated in bacteria. Nature 586, 429–433 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mahendra, C. et al. Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer. Nat. Microbiol. 5, 620–629 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Slavik, K. M. et al. cGAS-like receptors sense RNA and control 3′2′-cGAMP signalling in Drosophila. Nature 597, 109–113 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cai, H. et al. The virus-induced cyclic dinucleotide 2′3′-c-di-GMP mediates STING-dependent antiviral immunity in Drosophila. Immunity 56, 1991–2005 (2023).

  • Grüschow, S., Adamson, C. S. & White, M. F. Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector. Nucleic Acids Res. 49, 13122–13134 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McMahon, S. A. et al. Structure and mechanism of a type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate. Nat. Commun. 11, 500 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Niewoehner, O. et al. Type III CRISPR–Cas systems produce cyclic oligoadenylate second messengers. Nature 548, 543–548 (2017).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Kazlauskiene, M., Kostiuk, G., Venclovas, Č., Tamulaitis, G. & Siksnys, V. A. Cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems. Science 357, 605–609 (2017).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Adams, P. D., Grosse-Kunstleve, R. W., Hung, L. W., Ioerger, T. R. & Terwilliger, T. C. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Emsley, P., Lohkamp, B., Scott, W. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).

  • Qiu, D., Damron, F. H., Mima, T., Schweizer, H. P. & Yu, H. D. PBAD-based shuttle vectors for functional analysis of toxic and highly regulated genes in Pseudomonas and Burkholderia spp. and other bacteria. Appl. Environ. Microbiol. 74, 7422–7426 (2008).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Choi, K. H. & Schweizer, H. P. Mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa. Nat. Protoc. 1, 153–161 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Choi, K. H. et al. Genetic tools for select-agent-compliant manipulation of Burkholderia pseudomallei. Appl. Environ. Microbiol. 74, 1064–1075 (2008).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Abby, S. S., Néron, B., Ménager, H., Touchon, M. & Rocha, E. P. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS ONE 9, e110726 (2014).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Katoh, K., Rozewicki, J. & Yamada, K. D. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief. Bioinform. 20, 1160–1166 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

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