Using NMR to Monitor TET-Dependent Methylcytosine Dioxygenase Activity and Regulation

• Published in: ACS chemical biology 2024-01, Vol.19 (1), p.15-21
• Main Authors: Treadway, Colton J., Boyer, Joshua A, Yang, Shiyue, Yang, Hui, Liu, Mengxi, Li, Zhijun, Cheng, Meng, Marzluff, William F., Ye, Dan, Xiong, Yue, Baldwin, Albert S., Zhang, Qi, Brown, Nicholas G.
• Format: Article
• Language: English
• Subjects: 5-Methylcytosine - metabolism; Cytosine; Dioxygenases - metabolism; DNA Methylation; DNA-Binding Proteins - metabolism; Oxidation-Reduction
• ISSN: 1554-8929; 1554-8937; 1554-8937
• DOI: 10.1021/acschembio.3c00619

The active removal of DNA methylation marks is governed by the ten-eleven translocation (TET) family of enzymes (TET1–3), which iteratively oxidize 5-methycytosine (5mC) into 5-hydroxymethycytosine (5hmC), and then 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TET proteins are frequently mutated in myeloid malignancies or inactivated in solid tumors. These methylcytosine dioxygenases are α-ketoglutarate (αKG)-dependent and are, therefore, sensitive to metabolic homeostasis. For example, TET2 is activated by vitamin C (VC) and inhibited by specific oncometabolites. However, understanding the regulation of the TET2 enzyme by different metabolites and its activity remains challenging because of limitations in the methods used to simultaneously monitor TET2 substrates, products, and cofactors during catalysis. Here, we measure TET2-dependent activity in real time using NMR. Additionally, we demonstrate that in vitro activity of TET2 is highly dependent on the presence of VC in our system and is potently inhibited by an intermediate metabolite of the TCA cycle, oxaloacetate (OAA). Despite these opposing effects on TET2 activity, the binding sites of VC and OAA on TET2 are shared with αKG. Overall, our work suggests that NMR can be effectively used to monitor TET2 catalysis and illustrates how TET activity is regulated by metabolic and cellular conditions at each oxidation step.