Mitochondrial tyrosyl-DNA phosphodiesterase 2 and its TDP2S short isoform

Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs abortive topoisomerase II cleavage complexes. Here, we identify a novel short isoform of TDP2 (TDP2(S)) expressed from an alternative transcription start site. TDP2(S) contains a mitochondrial targeting sequence, contributing to its enrichment in the mitochondria and cytosol, while full-length TDP2 contains a nuclear localization signal and the ubiquitin-associated domain in the N-terminus. Our study reveals that both TDP2 isoforms are present and active in the mitochondria. Comparison of isogenic wild-type (WT) and TDP2 knockout (TDP2(-/-/-)) DT40 cells shows that TDP2(-/-/-) cells are hypersensitive to mitochondrial-targeted doxorubicin (mtDox), and that complementing TDP2(-/-/-) cells with human TDP2 restores resistance to mtDox. Furthermore, mtDox selectively depletes mitochondrial DNA in TDP2(-/-/-) cells. Using CRISPR-engineered human cells expressing only the TDP2(S) isoform, we show that TDP2(S) also protects human cells against mtDox. Finally, lack of TDP2 in the mitochondria reduces the mitochondria transcription levels in two different human cell lines. In addition to identifying a novel TDP2(S) isoform, our report demonstrates the presence and importance of both TDP2 isoforms in the mitochondria.