Phosphorothioate (PT) DNA modifications—in which a nonbonding phosphate oxygen is replaced with sulfur—represent a widespread, horizontally transferred epigenetic system in prokaryotes and have a highly unusual property of occupying only a small fraction of available consensus sequences in a genome. Using Salmonella enterica as a model, we asked a question of fundamental importance: How do the PT-modifying DndA-E proteins select their G_PSAAC/G_PSTTC targets? Here, we applied innovative analytical, sequencing, and computational tools to discover a novel behavior for DNA-binding proteins: The Dnd proteins are “parked” at the G^6mATC Dam methyltransferase consensus sequence instead of the expected GAAC/GTTC motif, with removal of the ^6mA permitting extensive PT modification of GATC sites. This shift in modification sites further revealed a surprising constancy in the density of PT modifications across the genome. Computational analysis showed that GAAC, GTTC, and GATC share common features of DNA shape, which suggests that PT epigenetics are regulated in a density-dependent manner partly by DNA shape-driven target selection in the genome.

硫代磷酸酯（PT）DNA修饰（其中一个非键合的磷酸氧被硫代替）代表了原核生物中一种广泛的，水平转移的表观遗传系统，并且具有非常不寻常的特性，即仅占据基因组中一小部分可用的共有序列。我们以肠沙门氏菌为模型，提出了一个至关重要的问题：修饰PT的DndA-E蛋白如何选择其G _PS AAC / G _PS TTC目标？在这里，我们应用了创新的分析，测序和计算工具来发现DNA结合蛋白的新行为：将Dnd蛋白“停在” G ^6m ATC Dam甲基转移酶共有序列上，而不是预期的GAAC / GTTC基序，将其去除的^6m A允许对GATC站点进行广泛的PT修改。修饰位点的这种变化进一步揭示了整个基因组中PT修饰密度的令人惊讶的恒定性。计算分析表明，GAAC，GTTC和GATC具有DNA形状的共同特征，这表明PT表观遗传学受密度依赖的方式部分地受基因组中DNA形状驱动的靶标选择的调控。