Wang, L., Jiang, S., Deng, Z., Dedon, P. C. & Chen, S. DNA phosphorothioate modification—a new multi-functional epigenetic system in bacteria. FEMS Microbiol. Rev. 43, 109–122 (2018).
Article PubMed Central Google Scholar
Wang, L. et al. DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc. Natl Acad. Sci. USA 108, 2963–2968 (2011).
Article CAS PubMed PubMed Central Google Scholar
Wang, L. et al. Phosphorothioation of DNA in bacteria by dnd genes. Nat. Chem. Biol. 3, 709–710 (2007).
Article CAS PubMed Google Scholar
Wang, L., Tang, Y., Deng, Z. & Chen, S. DNA phosphorothioate modification systems and associated phage defense systems. Annu. Rev. Microbiol. 78, 447–462 (2024).
Article CAS PubMed Google Scholar
Jiang, S. et al. A widespread phage-encoded kinase enables evasion of multiple host antiphage defence systems. Nat. Microbiol. 9, 3226–3239 (2024).
Article CAS PubMed Google Scholar
Mueller, E. G. Trafficking in persulfides: delivering sulfur in biosynthetic pathways. Nat. Chem. Biol. 2, 185–194 (2006).
Article CAS PubMed Google Scholar
You, D., Wang, L., Yao, F., Zhou, X. & Deng, Z. A novel DNA modification by sulfur: DndA is a NifS-like cysteine desulfurase capable of assembling DndC as an iron–sulfur cluster protein in Streptomyces lividans. Biochemistry 46, 6126–6133 (2007).
Article CAS PubMed Google Scholar
Rakesh, S., Aravind, L. & Krishnan, A. Reappraisal of the DNA phosphorothioate modification machinery: uncovering neglected functional modalities and identification of new counter-invader defense systems. Nucleic Acids Res. 52, 1005–1026 (2024).
Article CAS PubMed PubMed Central Google Scholar
Pu, T. et al. An in vitro DNA phosphorothioate modification reaction. Mol. Microbiol. 113, 452–463 (2020).
Article CAS PubMed Google Scholar
Hu, W. et al. Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification. Cell Res. 22, 1203–1206 (2012).
Article CAS PubMed PubMed Central Google Scholar
Xia, S. et al. Tight control of genomic phosphorothioate modification by the ATP-modulated autoregulation and reusability of DndB. Mol. Microbiol. 111, 938–950 (2019).
Article CAS PubMed Google Scholar
Wu, X. et al. Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria. Proc. Natl Acad. Sci. USA 117, 14322–14330 (2020).
Article CAS PubMed PubMed Central Google Scholar
Chen, C. et al. Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes. Proc. Natl Acad. Sci. USA 114, 4501–4506 (2017).
Article CAS PubMed PubMed Central Google Scholar
Cao, B. et al. Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences. Nat. Commun. 5, 3951 (2014).
Article CAS PubMed Google Scholar
Tong, T. et al. Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria. Proc. Natl Acad. Sci. USA 115, E2988–E2996 (2018).
Article CAS PubMed PubMed Central Google Scholar
Xiong, L. et al. A new type of DNA phosphorothioation-based antiviral system in archaea. Nat. Commun. 10, 1688 (2019).
Article PubMed PubMed Central Google Scholar
Wei, Y. et al. Single-molecule optical mapping of the distribution of DNA phosphorothioate epigenetics. Nucleic Acids Res. 49, 3672–3680 (2021).
Article CAS PubMed PubMed Central Google Scholar
Wu, D. et al. The functional coupling between restriction and DNA phosphorothioate modification systems underlying the DndFGH restriction complex. Nat. Catal. 5, 1131–1144 (2022).
Xiong, X. et al. SspABCD–SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities. Nat. Microbiol. 5, 917–928 (2020).
Article CAS PubMed Google Scholar
Gao, H. et al. Nicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE. Nat. Commun. 13, 6773 (2022).
Article CAS PubMed PubMed Central Google Scholar
Faou, A., Rajagopal, B. S., Daniels, L. & Fauque, G. Thiosulfate, polythionates and elemental sulfur assimilation and reduction in the bacterial world. FEMS Microbiol. Lett. 75, 351–382 (1990).
Blackwood, J. K. et al. Structural and functional insights into DNA-end processing by the archaeal HerA helicase–NurA nuclease complex. Nucleic Acids Res. 40, 3183–3196 (2012).
Article CAS PubMed Google Scholar
Pu, T. et al. Phosphorothioated DNA is shielded from oxidative damage. Appl. Environ. Microbiol. 85, e00104–e00119 (2019).
Article CAS PubMed PubMed Central Google Scholar
Palenchar, P. M. Evidence that ThiI, an enzyme shared between thiamin and 4-thiouridine biosynthesis, may be a sulfurtransferase that proceeds through a persulfide intermediate. J. Biol. Chem. 275, 8283–8286 (2000).
Article CAS PubMed Google Scholar
Numata, T., Ikeuchi, Y., Fukai, S., Suzuki, T. & Nureki, O. Snapshots of tRNA sulphuration via an adenylated intermediate. Nature 442, 419–424 (2006).
Article CAS PubMed Google Scholar
Bouvier, D. et al. TtcA a new tRNA-thioltransferase with an Fe-S cluster. Nucleic Acids Res. 42, 7960–7970 (2014).
Article CAS PubMed PubMed Central Google Scholar
Kambampati, R. & Lauhon, C. T. Evidence for the transfer of sulfane sulfur from IscS to ThiI during the in vitro biosynthesis of 4-thiouridine in Escherichia coli tRNA. J. Biol. Chem. 275, 10727–10730 (2000).
Article CAS PubMed Google Scholar
You, D., Xu, T., Yao, F., Zhou, X. & Deng, Z. Direct evidence that ThiI is an ATP pyrophosphatase for the adenylation of uridine in 4-thiouridine biosynthesis. ChemBioChem 9, 1879–1882 (2008).
Article CAS PubMed Google Scholar
Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).
Article CAS PubMed PubMed Central Google Scholar
Garb, J. et al. Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion. Nat. Microbiol. 7, 1849–1856 (2022).
Article CAS PubMed Google Scholar
Liu, G. et al. Structural basis for the recognition of sulfur in phosphorothioated DNA. Nat. Commun. 9, 4689 (2018).
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