Recent advances in DNA phosphorothioation modification studies

Abstract

DNA phosphorothioate (PT) modification is a sulfur modification on DNA backbone, in which a non-bridging P-O bond is changed into a non-bridging P-S bond, being the first physiological modification described on the DNA backbone. It is found that the DNA with backbone phosphoration has DNA degradation (Dnd) phenotype upon running electrophoresis in Tris buffer. Moreover, this DNA phosphorothioation belongs to a kind of post-replication modification, where sulfur is incorporated stereo-specifically (i.e., it's a chiral Rp-type modification, not Sp-type configuration) into DNA backbone at specific sequences. For example, a high frequency of GA was found to be phosphorothioated in Bermanella marisrubri RED65 and Hahella chejuensis KCTC2396, determined by using high pressure or high performance liquid chromatography (HPLC) and mass methods. DNA phosphorothioation is widespread and quantized in bacterial genomes. It was reported that this DNA PT modification is controlled by the five proteins (DndA-E) encoded by dna degradation (dnd) genes cluster (dndA-E) in a sequence found in bacteria and archaea, but the mechanism about how these five proteins function during the pathway of DNA backbone PT modification remains elusive. Among these five genes, four of them, dndA and dndC-E, are essential for the PT modification, while inactivation of dndB resulted in increased phosphorothioation and altered sequence preference. In this paper, we reviewed the discovery history, the features of DNA phosphorothioation modification, and the recent research progresses on the structures and functions of the five proteins involved in DNA backbone phosphorothioation. We also discussed the antioxidant activities of phosphorothioated DNA in biological systems. Finally, for easily understanding the research direction in DNA phosphorothioation, we summarized several questions in the future studies on DNA PT modification, which includes: (1) How sulfur is incorporated into DNA backbone in biological system? (2) How the DNA phosphorothioation is affected by the proteins DndA, DndB, DndC, DndD and DndE? (3) How to get soluble DndB, DndC and DndD in a large quantity? (4) How DndA functions as a cysteine sulfur transferase, because the active site is in a rigid β-sheet conformation? © 2013 Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences.