Understanding base and backbone contributions of phosphorothioate DNA for molecular recognition with SBD proteins†

Bacterial DNA phosphorothioate (PT) modification provides a specific anchoring site for sulfur-binding proteins (SBDs). Besides, their recognition patterns include phosphate links and bases neighboring the PT-modified site, thereby bringing about genome sequence-dependent properties in PT-related epigenetics. Here, we analyze the contributions of the DNA backbone (phosphates and deoxyribose) and bases bound with two SBD proteins in Streptomyces pristinaespiralis and coelicolor (SBDSco and SBDSpr). The chalcogen–hydrophobic interactions remained constantly at the anchoring site while the adjacent bases formed conditional and distinctive non-covalent interactions. More importantly, SBD/PT–DNA interactions were not limited within the traditional “4-bp core” range from 5′-I to 3′-III but extended to upstream 5′-II and 5′-III bases and even 5′′-I to 5′′-III at the non-PT-modified complementary strand. From the epigenetic viewpoint, bases 3′-II, 5′′-I, and 5′′-III of SBDSpr and 3′-II, 5′′-II, and 5′′-III of SBDSco present remarkable differentiations in the molecular recognitions. From the protein viewpoint, H102 in SBDSpr and R191 in SBDSco contribute significantly while proline residues at the PT-bound site are strictly conserved for the PT-chalcogen bond. The mutual and make-up mutations are proposed to alter the SBD/PT–DNA recognition pattern, besides additional chiral phosphorothioate modifications on phosphates 5′-II, 5′-II, 3′-I, and 3′-II.