ATLANTA—The process a key enzyme uses to recognize and repair genetic damage in mammals has been described by researchers at Georgia State University.
The researchers studied thymine DNA glycosylase (TDG) – an enzyme with two principal roles in the cell: repairing damaged DNA and removing epigenetic marks from DNA, which signal changes in gene expression. The findings, published in the Proceedings of the National Academy of Sciences, provide important insights on repairing DNA abnormalities, which are often observed in diseases, specifically cancer.
From a chemical perspective, DNA is a remarkably stable molecule. Nonetheless, damage to DNA in living cells does occur because of errors in genome replication, the presence of reactive oxygen species, alkylating agents or other chemicals. Left unchecked, these processes could impair the transmission of genetic information, and threaten the integrity of the genome. Therefore, cells have evolved elaborate mechanisms for DNA repair to restore DNA to its original condition. If this repair doesn’t happen and damaged DNA gets copied, the mutation becomes permanent. DNA mutations are linked to the onset of cancer.
One repair enzyme, TDG, works as molecular scissors to cut and remove a damaged DNA base. The resulting DNA intermediate is then handed off to other enzymes that complete the repair process. Before any repair can occur, the damaged or modified base must first be located among a vast background of normal DNA and flipped out into the enzyme’s active site while ensuring no other bases get cut. The paper describes a novel mechanism for how this lesion search, base interrogation and flipping occur and explains the origin of the extraordinary specificity of TDG.
“In recent years, there has been renewed interest in TDG specifically because it has been tied to epigenetics, in addition to its role in DNA repair,” said Dr. Ivaylo Ivanov, associate professor of chemistry at Georgia State. “This study is about discovering a mechanism for how this enzyme recognizes genetic damage and epigenetic marks, including how it selects the damage and gets it to the enzyme active site where it gets cleaved.”
Scientists have recently become interested in TDG’s link to epigenetics. Changes in gene expression occur when a methyl group (one carbon atom bonded to three hydrogen atoms) is added to a certain position on cytosine, one of the four main bases found in DNA. TDG plays a central role in removing this methyl group and influences gene silencing, stem cell differentiation and alterations in normal development. TDG’s role is to remove such epigenetic modifications from DNA.
In the study, the researchers used molecular modeling to determine possible paths TDG could take to detect, force out and remove damaged DNA bases. They completed computations using the Comet machine at the San Diego Supercomputer Center. Their computed paths revealed a novel mechanism that TDG uses to detect DNA lesions and modified bases. The results also shed light on how DNA glycosylases select bases to eliminate in DNA repair and uncover universal rules for this class of enzymes.
Co-authors of the study are Kurt Martin, Bradley Kossmann, Chunli Yan and Thomas Dodd from Georgia State.
The study was funded by the National Institutes of Health (GM110387) and the National Science Foundation (MCB-119521).
To read the study, visit https://www.pnas.org/content/early/2018/05/15/1803323115.short?rss=1.
Dr. Ivaylo Ivanov
Department of Chemistry
Dr. Ivanov’s work focuses on computational biology and biophysics, molecular modeling and simulations, drug design, computational chemistry, biological assemblies and mechanisms of genome duplication and maintenance.