Millman, A. et al. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 30, 1556–1569 (2022).
Garb, J. et al. Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion. Nat. Microbiol. 7, 1849–1856 (2022).
Ofir, G. et al. Antiviral activity of bacterial TIR domains via immune signalling molecules. Nature 600, 116–120 (2021).
Zaremba, M. et al. Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion. Nat. Microbiol. 7, 1857–1869 (2022).
Gao, L. A. et al. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 377, eabm4096 (2022).
Morehouse, B. R. et al. STING cyclic dinucleotide sensing originated in bacteria. Nature 586, 429–433 (2020).
Tal, N. et al. Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell 184, 5728–5739 (2021).
Chen, Y. et al. From bacteria to biomedicine: developing therapies exploiting NAD+ metabolism. Bioorg. Chem. 142, 106974 (2024).
Erhardt, H. et al. Organization of the Escherichia coli aerobic enzyme complexes of oxidative phosphorylation in dynamic domains within the cytoplasmic membrane. MicrobiologyOpen 3, 316–326 (2014).
Rodionova, I. A. et al. Metabolic and bactericidal effects of targeted suppression of NadD and NadE enzymes in mycobacteria. mBio 5, e00747-13 (2014).
Mikolcevic, P., Hlousek-Kasun, A., Ahel, I. & Mikoc, A. ADP-ribosylation systems in bacteria and viruses. Comput. Struct. Biotechnol. J. 19, 2366–2383 (2021).
Wilkinson, A., Day, J. & Bowater, R. Bacterial DNA ligases. Mol. Microbiol. 40, 1241–1248 (2001).
Rousset, F. et al. A conserved family of immune effectors cleaves cellular ATP upon viral infection. Cell 186, 3619–3631 (2023).
Maffei, E. et al. Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection. PLoS Biol. 19, e3001424 (2021).
Iyer, L. M., Burroughs, A. M., Anantharaman, V. & Aravind, L. Apprehending the NAD+–ADPr-dependent systems in the virus world. Viruses 14, 1977 (2022).
Gazzaniga, F., Stebbins, R., Chang, S. Z., McPeek, M. A. & Brenner, C. Microbial NAD metabolism: lessons from comparative genomics. Microbiol. Mol. Biol. Rev. 73, 529–541 (2009).
Tang, D. et al. Multiple enzymatic activities of a Sir2-HerA system cooperate for anti-phage defense. Mol. Cell 83, 4600–4613 (2023).
Galeazzi, L. et al. Identification of nicotinamide mononucleotide deamidase of the bacterial pyridine nucleotide cycle reveals a novel broadly conserved amidohydrolase family. J. Biol. Chem. 286, 40365–40375 (2011).
Raffaelli, N. et al. The Escherichia coli NadR regulator is endowed with nicotinamide mononucleotide adenylyltransferase activity. J. Bacteriol. 181, 5509–5511 (1999).
Khorana, H. G., Fernandes, J. F. & Kornberg, A. Pyrophosphorylation of ribose 5-phosphate in the enzymatic synthesis of 5-phosphorylribose 1-pyrophosphate. J. Biol. Chem. 230, 941–948 (1958).
Yirmiya, E. et al. Phages overcome bacterial immunity via diverse anti-defence proteins. Nature 625, 352–359 (2024).
Revollo, J. R., Grimm, A. A. & Imai, S. The NAD biosynthesis pathway mediated by nicotinamide phosphoribosyltransferase regulates Sir2 activity in mammalian cells. J. Biol. Chem. 279, 50754–50763 (2004).
Hove-Jensen, B. et al. Phosphoribosyl diphosphate (PRPP): biosynthesis, enzymology, utilization, and metabolic significance. Microbiol Mol Biol Rev 81, e00040-16 (2017).
Sabonis, D. et al. TIR domains produce histidine-ADPR conjugates as immune signaling molecules in bacteria. Preprint at bioRxiv https://www.biorxiv.org/content/10.1101/2024.01.03.573942v1 (2024).
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).
Lee, J. Y., Li, Z. & Miller, E. S. Vibrio phage KVP40 encodes a functional NAD+ salvage pathway. J. Bacteriol. 199, e00855-16 (2017).
Gao, Z. & Feng, Y. Bacteriophage strategies for overcoming host antiviral immunity. Front. Microbiol. 14, 1211793 (2023).
Mayo-Munoz, D., Pinilla-Redondo, R., Camara-Wilpert, S., Birkholz, N. & Fineran, P. C. Inhibitors of bacterial immune systems: discovery, mechanisms and applications. Nat. Rev. Genet. 25, 237–254 (2024).
Zhang, F., Song, G. & Tian, Y. Anti-CRISPRs: the natural inhibitors for CRISPR-Cas systems. Animal Model. Exp. Med. 2, 69–75 (2019).
Hobbs, S. J. et al. Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity. Nature 605, 522–526 (2022).
Huang, N. et al. Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure 17, 939–951 (2009).
Rodionov, D. A. et al. Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators. Nucleic Acids Res. 36, 2047–2059 (2008).
Tal, N. et al. Bacteria deplete deoxynucleotides to defend against bacteriophage infection. Nat. Microbiol. 7, 1200–1209 (2022).
Goldstone, D. C. et al. HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Nature 480, 379–382 (2011).
Heer, C. D. et al. Coronavirus infection and PARP expression dysregulate the NAD metabolome: an actionable component of innate immunity. J. Biol. Chem. 295, 17986–17996 (2020).
Brenner, C. Viral infection as an NAD+ battlefield. Nat. Metab. 4, 2–3 (2022).
Minh, B. Q., Nguyen, M. A. & von Haeseler, A. Ultrafast approximation for phylogenetic bootstrap. Mol. Biol. Evol. 30, 1188–1195 (2013).
Chung, C. T., Niemela, S. L. & Miller, R. H. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc. Natl Acad. Sci. USA 86, 2172–2175 (1989).
Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018).
Hove-Jensen, B., Bentsen, A. K. & Harlow, K. W. Catalytic residues Lys197 and Arg199 of Bacillus subtilis phosphoribosyl diphosphate synthase. Alanine-scanning mutagenesis of the flexible catalytic loop. FEBS J. 272, 3631–3639 (2005).
Eriksen, T. A., Kadziola, A., Bentsen, A. K., Harlow, K. W. & Larsen, S. Structural basis for the function of Bacillus subtilis phosphoribosyl-pyrophosphate synthetase. Nat. Struct. Biol. 7, 303–308 (2000).
Adler, B. A. et al. Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing. Nat. Microbiol. 7, 1967–1979 (2022).
Leavitt, A. et al. Viruses inhibit TIR gcADPR signalling to overcome bacterial defence. Nature 611, 326–331 (2022).
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).
Thomason, L. C., Costantino, N. & Court, D. L. E. coli genome manipulation by P1 transduction. Curr. Protoc. Mol. Biol. 79, 1.17.1–1.17.8 (2007).
Mazzocco, A., Waddell, T. E., Lingohr, E. & Johnson, R. P. Enumeration of bacteriophages using the small drop plaque assay system. Methods Mol. Biol. 501, 81–85 (2009).
Kitaoka, M. Automatic calculation of the kinetic parameters of enzymatic reactions with their standard errors using Microsoft Excel. J. Appl. Glycosci. 70, 33–37 (2023).
Zheng, L. et al. Fumarate induces redox-dependent senescence by modifying glutathione metabolism. Nat. Commun. 6, 6001 (2015).
Steinegger, M. & Soding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
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) v4: recent updates and new developments. Nucleic Acids Res. 47, W256–W259 (2019).
