Phosphorothioate (PT) modification by the dnd gene cluster is the first identified DNA backbone modification and constitute an epigenetic system with multiple functions, including antioxidant ability, restriction modification, and virus resistance. Despite these advantages for hosting dnd systems, they are surprisingly distributed sporadically among contemporary prokaryotic genomes. To address this ecological paradox, we systematically investigate the occurrence and phylogeny of dnd systems, and they are suggested to have originated in ancient Cyanobacteria after the Great Oxygenation Event. Interestingly, the occurrence of dnd systems and prophages is significantly negatively correlated. Further, we experimentally confirm that PT modification activates the filamentous phage SW1 by altering the binding affinity of repressor and the transcription level of its encoding gene. Competition assays, concurrent epigenomic and transcriptomic sequencing subsequently show that PT modification affects the expression of a variety of metabolic genes, which reduces the competitive fitness of the marine bacterium Shewanella piezotolerans WP3. Our findings strongly suggest that a series of negative effects on microorganisms caused by dnd systems limit horizontal gene transfer, thus leading to their sporadic distribution. Overall, our study reveals putative evolutionary scenario of the dnd system and provides novel insights into the physiological and ecological influences of PT modification.

dnd基因簇的硫代磷酸酯（PT）修饰是第一个被识别的DNA主链修饰，并构成具有多种功能的表观遗传系统，包括抗氧化能力、限制性修饰和病毒抗性。尽管宿主dnd系统具有这些优势，但令人惊讶的是，它们在当代原核生物基因组中零星分布。为了解决这一生态悖论，我们系统地研究了dnd系统的发生和系统发育，并认为它们起源于大氧化事件后的古代蓝藻。有趣的是， dnd系统和原噬菌体的出现呈显着负相关。此外，我们通过实验证实，PT 修饰通过改变阻遏物的结合亲和力及其编码基因的转录水平来激活丝状噬菌体 SW1。随后的竞争分析、并发表观基因组和转录组测序表明，PT 修饰影响多种代谢基因的表达，从而降低了海洋细菌Shewanella piezotolerans WP3 的竞争适应性。我们的研究结果强烈表明， dnd系统对微生物造成的一系列负面影响限制了水平基因转移，从而导致其零星分布。总的来说，我们的研究揭示了dnd系统的假定进化场景，并为 PT 修饰的生理和生态影响提供了新的见解。