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Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems

Abstract

Cyclic-oligonucleotide-based anti-phage signalling systems (CBASS) are a family of defence systems against bacteriophages (hereafter phages) that share ancestry with the cGAS–STING innate immune pathway in animals. CBASS systems are composed of an oligonucleotide cyclase, which generates signalling cyclic oligonucleotides in response to phage infection, and an effector that is activated by the cyclic oligonucleotides and promotes cell death. Cell death occurs before phage replication is completed, therefore preventing the spread of phages to nearby cells. Here, we analysed 38,000 bacterial and archaeal genomes and identified more than 5,000 CBASS systems, which have diverse architectures with multiple signalling molecules, effectors and ancillary genes. We propose a classification system for CBASS that groups systems according to their operon organization, signalling molecules and effector function. Four major CBASS types were identified, sharing at least six effector subtypes that promote cell death by membrane impairment, DNA degradation or other means. We observed evidence of extensive gain and loss of CBASS systems, as well as shuffling of effector genes between systems. We expect that our classification and nomenclature scheme will guide future research in the developing CBASS field.

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Fig. 1: General description of CBASS systems.
Fig. 2: Phylogenetic distribution of CBASS types and effectors.
Fig. 3: Rapid gain and loss of and gene shuffling in CBASS systems.

Data availability

All genomic data that support the findings of this study are available at IMG (https://img.jgi.doe.gov/cgi-bin/mer/main.cgi). Accession codes for all data are provided in Supplementary Tables 17. PDB and Pfam databases are available at the HHsuite database page (http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/).

References

  1. 1.

    Bernheim, A. & Sorek, R. The pan-immune system of bacteria: antiviral defence as a community resource. Nat. Rev. Microbiol. 18, 113–119 (2020).

    CAS  Article  Google Scholar 

  2. 2.

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

    Article  Google Scholar 

  3. 3.

    Rostøl, J. T. & Marraffini, L. (Ph)ighting phages: how bacteria resist their parasites. Cell Host Microbe 25, 184–194 (2019).

  4. 4.

    Hampton, H. G., Watson, B. N. J. & Fineran, P. C. The arms race between bacteria and their phage foes. Nature 577, 327–336 (2020).

    CAS  Article  Google Scholar 

  5. 5.

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

    CAS  Article  Google Scholar 

  6. 6.

    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).

    CAS  Article  Google Scholar 

  7. 7.

    Severin, G. B. et al. Direct activation of a phospholipase by cyclic GMP-AMP in El Tor Vibrio cholerae. Proc. Natl Acad. Sci. USA 115, E6048–E6055 (2018).

    CAS  Article  Google Scholar 

  8. 8.

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

    CAS  Article  Google Scholar 

  9. 9.

    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).

    CAS  Article  Google Scholar 

  10. 10.

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

    CAS  Article  Google Scholar 

  11. 11.

    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).

    CAS  Article  Google Scholar 

  12. 12.

    Lowey, B. et al. CBASS immunity uses CARF-related effectors to sense 3′–5′- and 2′–5′-linked cyclic oligonucleotide signals and protect bacteria from phage infection. Cell 182, 38–49.e17 (2020).

    Article  Google Scholar 

  13. 13.

    Aravind, L. & Koonin, E. V. The HORMA domain: a common structural denominator in mitotic checkpoints, chromosome synapsis and DNA repair. Trends Biochem. Sci. 23, 284–286 (1998).

    CAS  Article  Google Scholar 

  14. 14.

    Rosenberg, S. C. & Corbett, K. D. The multifaceted roles of the HORMA domain in cellular signaling. J. Cell Biol. 211, 745–755 (2015).

    CAS  Article  Google Scholar 

  15. 15.

    Vader, G. Pch2(TRIP13): controlling cell division through regulation of HORMA domains. Chromosoma 124, 333–339 (2015).

    CAS  Article  Google Scholar 

  16. 16.

    Reader, J. S., Metzgar, D., Schimmel, P. & de Crécy-Lagard, V. Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine. J. Biol. Chem. 279, 6280–6285 (2004).

    CAS  Article  Google Scholar 

  17. 17.

    McCarty, R. M., Somogyi, A., Lin, G., Jacobsen, N. E. & Bandarian, V. The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of PreQ(0) from guanosine 5′-triphosphate in four steps. Biochemistry 48, 3847–3852 (2009).

    CAS  Article  Google Scholar 

  18. 18.

    Okada, N. et al. Novel mechanism of post-transcriptional modification of tRNA. Insertion of bases of Q precursors into tRNA by a specific tRNA transglycosylase reaction. J. Biol. Chem. 254, 3067–3073 (1979).

    CAS  PubMed  Google Scholar 

  19. 19.

    Thiaville, J. J. et al. Novel genomic island modifies DNA with 7-deazaguanine derivatives. Proc. Natl Acad. Sci. USA 113, E1452–E1459 (2016).

    CAS  Article  Google Scholar 

  20. 20.

    David, S. S., O’Shea, V. L. & Kundu, S. Base-excision repair of oxidative DNA damage. Nature 447, 941–950 (2007).

    CAS  Article  Google Scholar 

  21. 21.

    McLennan, A. G. The Nudix hydrolase superfamily. Cell. Mol. Life Sci. 63, 123–143 (2006).

    CAS  Article  Google Scholar 

  22. 22.

    Akira, S. & Takeda, K. Toll-like receptor signalling. Nat. Rev. Immunol. 4, 499–511 (2004).

    CAS  Article  Google Scholar 

  23. 23.

    Botsford, J. L. & Harman, J. G. Cyclic AMP in prokaryotes. Microbiol. Rev. 56, 100–122 (1992).

    CAS  Article  Google Scholar 

  24. 24.

    Koonin, E. V., Makarova, K. S. & Wolf, Y. I. Evolutionary genomics of defense systems in archaea and bacteria. Annu. Rev. Microbiol. 71, 233–261 (2017).

    CAS  Article  Google Scholar 

  25. 25.

    van Houte, S., Buckling, A. & Westra, E. R. Evolutionary ecology of prokaryotic immune mechanisms. Microbiol. Mol. Biol. Rev. 80, 745–763 (2016).

    Article  Google Scholar 

  26. 26.

    Makarova, K. S. et al. Evolution and classification of the CRISPR–Cas systems. Nat. Rev. Microbiol. 9, 467–477 (2011).

    CAS  Article  Google Scholar 

  27. 27.

    Makarova, K. S. et al. An updated evolutionary classification of CRISPR–Cas systems. Nat. Rev. Microbiol. 13, 722–736 (2015).

    CAS  Article  Google Scholar 

  28. 28.

    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).

    CAS  Article  Google Scholar 

  29. 29.

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

    CAS  Article  Google Scholar 

  30. 30.

    Ofir, G. et al. DISARM is a widespread bacterial defence system with broad anti-phage activities. Nat. Microbiol. 3, 90–98 (2018).

    CAS  Article  Google Scholar 

  31. 31.

    Goldfarb, T. et al. BREX is a novel phage resistance system widespread in microbial genomes. EMBO J. 34, 169–183 (2015).

    CAS  Article  Google Scholar 

  32. 32.

    Ofir, G. & Sorek, R. Contemporary phage biology: from classic models to new insights. Cell 172, 1260–1270 (2018).

    CAS  Article  Google Scholar 

  33. 33.

    Lopatina, A., Tal, N. & Sorek, R. Abortive infection: bacterial suicide as an antiviral immune strategy. Annu. Rev. Virol. 7, 1 (2020).

    Article  Google Scholar 

  34. 34.

    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).

    CAS  Article  Google Scholar 

  35. 35.

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

    CAS  Article  Google Scholar 

  36. 36.

    Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).

    Article  Google Scholar 

  37. 37.

    Steinegger, M. et al. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinform. 20, 473 (2019).

    Article  Google Scholar 

  38. 38.

    Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000).

    CAS  Article  Google Scholar 

  39. 39.

    El-Gebali, S. et al. The Pfam protein families database in 2019. Nucleic Acids Res. 47, D427–D432 (2019).

    CAS  Article  Google Scholar 

  40. 40.

    Price, M. N., Dehal, P. S. & Arkin, A. P. Fasttree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641–1650 (2009).

    CAS  Article  Google Scholar 

  41. 41.

    Letunic, I. & Bork, P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44, W242–W245 (2016).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank the members of the Sorek laboratory for comments on earlier versions of this manuscript. A.M. was supported by a fellowship from the Ariane de Rothschild Women Doctoral Program and, in part, by the Israeli Council for Higher Education via the Weizmann Data Science Research Center. R.S. was supported in part by the Israel Science Foundation (personal grant no. 1360/16), the European Research Council (grant no. ERC-CoG 681203), the German Research Council (DFG) priority program SPP 2002 (grant no. SO 1611/1-1), the Israeli Council for Higher Education through the Weizmann Data Science Research Center, the Ernest and Bonnie Beutler Research Program of Excellence in Genomic Medicine, the Minerva Foundation with funding from the Federal German Ministry for Education and Research and the Knell Family Center for Microbiology.

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A.M. collected and analysed the data and wrote the paper. S.M. and G.A. were involved in the classification of CBASS systems. R.S. supervised the study and wrote the paper.

Corresponding author

Correspondence to Rotem Sorek.

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R.S. is a scientific cofounder and consultant of BiomX, Pantheon Bioscience and Ecophage.

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Extended data

Extended Data Fig. 1 Phylogenetic analysis of oligonucleotide cyclases (CD-NTase) and their CBASS types.

The phylogenetic tree of all cyclases, as depicted and colored in refs (5 and 8) is presented in the center. Each clade is then expanded and presented in the periphery as a circular tree to increase resolution. Outer ring depicts the effector type; middle ring depicts the system type. Numbers next to each clade represent the bootstrap value for that node in the central tree.

Supplementary information

Reporting Summary

Supplementary Tables

Supplementary Tables 1–7.

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Millman, A., Melamed, S., Amitai, G. et al. Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. Nat Microbiol 5, 1608–1615 (2020). https://doi.org/10.1038/s41564-020-0777-y

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