Structural basis for MTA1c-mediated DNA N6-adenine methylation

Jiyun Chen, Rong Hu, Ying Chen, Xiaofeng Lin, Wenwen Xiang, Hong Chen, Canglin Yao and Liang Liu ()
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Jiyun Chen: Xiamen University
Rong Hu: Xiamen University
Ying Chen: Xiamen University
Xiaofeng Lin: Xiamen University
Wenwen Xiang: Xiamen University
Hong Chen: Xiamen University
Canglin Yao: University of California, San Diego
Liang Liu: Xiamen University

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract DNA N6-adenine methylation (6 mA) has recently been found to play a crucial role in epigenetic regulation in eukaryotes. MTA1c, a newly discovered 6 mA methyltransferase complex in ciliates, is composed of MTA1, MTA9, p1 and p2 subunits and specifically methylates ApT dinucleotides, yet its mechanism of action remains unknown. Here, we report the structures of Tetrahymena thermophila MTA1 (TthMTA1), Paramecium tetraurelia MTA9 (PteMTA9)-TthMTA1 binary complex, as well as the structures of TthMTA1-p1-p2 and TthMTA1-p2 complexes in apo, S-adenosyl methionine-bound and S-adenosyl homocysteine-bound states. We show that MTA1 is the catalytically active subunit, p1 and p2 are involved in the formation of substrate DNA-binding channel, and MTA9 plays a structural role in the stabilization of substrate binding. We identify that MTA1 is a cofactor-dependent catalytically active subunit, which exhibits stable SAM-binding activity only after assembly with p2. Our structures and corresponding functional studies provide a more detailed mechanistic understanding of 6 mA methylation.

Date: 2022
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DOI: 10.1038/s41467-022-31060-6

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