North, B. J. & Verdin, E. Protein family review Sirtuins: Sir2-related NAD-dependent protein deacetylases. Genome Biol. 5, 224 (2004).

Article  Google Scholar 

Imai, S., Armstrong, C. M., Kaeberlein, M. & Guarente, L. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403, 795–800 (2000).

CAS  Article  Google Scholar 

Tanny, J. C., Dowd, G. J., Huang, J., Hilz, H. & Moazed, D. An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing. Cell 99, 735–745 (1999).

CAS  Article  Google Scholar 

Dang, W. & Pfizer, N. C. The controversial world of sirtuins. Drug Discov. Today Technol. 12, e9–e17 (2014).

Article  Google Scholar 

Makarova, K. S., Wolf, Y. I., van der Oost, J. & Koonin, E. V. Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol. Direct 4, 29 (2009).

Article  Google Scholar 

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

Article  Google Scholar 

Ofir, G. et al. Antiviral activity of bacterial TIR domains via signaling molecules that trigger cell death. Nature 600, 116–120 (2021).

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

Lopatina, A., Tal, N. & Sorek, R. Abortive infection: Bacterial suicide as an antiviral immune strategy. Annu. Rev. Virol. 7, 371–384 (2020).

CAS  Article  Google Scholar 

Kohm, K. & Hertel, R. The life cycle of SPβ and related phages. Arch. Virol. 166, 2119–2130 (2021).

CAS  Article  Google Scholar 

Noyer-Weidner, M., Jentsch, S., Pawlek, B., Günthert, U. & Trautner, T. A. Restriction and modification in Bacillus subtilis: DNA methylation potential of the related bacteriophages Z, SPR, SP beta, phi 3T, and rho 11. J. Virol. 46, 446–453 (1983).

CAS  Article  Google Scholar 

Dragoš, A. et al. Pervasive prophage recombination occurs during evolution of spore-forming Bacilli. ISME J. 15, 1344–1358 (2021).

Article  Google Scholar 

Bernheim, A. et al. Prokaryotic viperins produce diverse antiviral molecules. Nature 589, 120–124 (2021).

CAS  Article  Google Scholar 

Freire, D. M. et al. An NAD+ phosphorylase toxin triggers mycobacterium tuberculosis cell death. Mol. Cell 73, 1282–1291.e8 (2019).

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

Skjerning, R. B., Senissar, M., Winther, K. S., Gerdes, K. & Brodersen, D. E. The RES domain toxins of RES-Xre toxin-antitoxin modules induce cell stasis by degrading NAD. Mol. Microbiol. 111, 221–236 (2019).

CAS  Article  Google Scholar 

Tang, J. Y., Bullen, N. P., Ahmad, S. & Whitney, J. C. Diverse NADase effector families mediate interbacterial antagonism via the type VI secretion system. J. Biol. Chem. 293, 1504–1514 (2018).

CAS  Article  Google Scholar 

Tal, N. et al. Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell 184, 5728–5739.e16 (2021).

CAS  Article  Google Scholar 

Millman, A. et al. Bacterial retrons function in anti-phage defense. Cell 183, 1551–1561.e12 (2020).

CAS  Article  Google Scholar 

Kaufmann, G. Anticodon nucleases. Trends Biochem. Sci. 25, 70–74 (2000).

CAS  Article  Google Scholar 

Depardieu, F. et al. A eukaryotic-like serine/threonine kinase protects staphylococci against phages. Cell Host Microbe 20, 471–481 (2016).

CAS  Article  Google Scholar 

Millman, A. et al. An expanding arsenal of immune systems that protect bacteria from phages. Preprint at bioRxiv https://doi.org/10.1101/2022.05.11.491447 (2022).

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

CAS  Article  Google Scholar 

Overkamp, W. et al. Benchmarking various green fluorescent protein variants in Bacillus subtilis, Streptococcus pneumoniae, and Lactococcus lactis for live cell imaging. Appl. Environ. Microbiol. 79, 6481–6490 (2013).

CAS  Article  Google Scholar 

Wilson, G. A. & Bott, K. F. Nutritional factors influencing the development of competence in the Bacillus subtilis transformation system. J. Bacteriol. 95, 1439–1449 (1968).

CAS  Article  Google Scholar 

Mazzocco, A., Waddell, T. E., Lingohr & E, J. R. Enumeration of bacteriophages using the small drop plaque assay system. Methods Mol. Biol. 501, 81–85 (2009).

CAS  Article  Google Scholar 

Baym, M. et al. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS ONE 10, e0128036 (2015).

Article  Google Scholar 

Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. & Korobeynikov, A. Using SPAdes De Novo Assembler. Curr. Protoc. Bioinforma. 70, 1–29 (2020).

Article  Google Scholar 

Gilchrist, C. L. M. & Chooi, Y.-H. Clinker & Clustermap.Js: automatic generation of gene cluster comparison figures. Bioinformatics 37, 2473–2475 (2021).

CAS  Article  Google Scholar 

Gabler, F. et al. Protein sequence analysis using the MPI bioinformatics toolkit. Curr. Protoc. Bioinforma. 72, 1–30 (2020).

Article  Google Scholar 

Zaremba, M. et al. Sir2-domain associated short prokaryotic Argonautes provide defence against invading mobile genetic elements through NAD+ depletion. Preprint at bioRxiv https://doi.org/10.1101/2021.12.14.472599 (2021).

Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).

CAS  Article  Google Scholar