Flap Endonuclease 1 Repairs DNA-protein Cross-links Via ADP-ribosylation-dependent Mechanisms

Overview

Journal Sci Adv

Date 2025 Jan 10

PMID 39792662

Authors

Yilun Sun

Lisa M Jenkins

Lara H El Touny

Linying Zhu

Xi Yang

Ukhyun Jo

Lauren Escobedo

Tapan K Maity

Liton Kumar Saha

Isabel Uribe

Sourav Saha

Shunichi Takeda

Anthony K L Leung

Ken Cheng

Yves Pommier

Affiliations

Soon will be listed here.

Abstract

DNA-protein cross-links (DPCs) are among the most detrimental genomic lesions. They are ubiquitously produced by formaldehyde (FA), and failure to repair FA-induced DPCs blocks chromatin-based processes, leading to neurodegeneration and cancer. The type, structure, and repair of FA-induced DPCs remain largely unknown. Here, we profiled the proteome of FA-induced DPCs and found that flap endonuclease 1 (FEN1) resolves FA-induced DPCs. We revealed that FA also damages DNA bases adjoining the DPCs, leading to DPC-conjugated 5' flap structures via the base excision repair (BER) pathway. We also found that FEN1 repairs enzymatic topoisomerase II (TOP2)-DPCs. Furthermore, we report that both FA-induced and TOP2-DPCs are adenosine diphosphate (ADP) ribosylated by poly(ADP-ribose) polymerase 1 (PARP1). PARylation of the DPCs in association with FEN1 PARylation at residue E285 is required for the recruitment of FEN1. Our work unveils the identity of proteins forming FA-induced DPCs and a previously unrecognized PARP1-FEN1 nuclease pathway repairing both FA- and TOP2-DPCs.

References

Langelier M, Steffen J, Riccio A, McCauley M, Pascal J . Purification of DNA Damage-Dependent PARPs from E. coli for Structural and Biochemical Analysis. Methods Mol Biol. 2017; 1608:431-444. DOI: 10.1007/978-1-4939-6993-7_27. View

Vaz B, Popovic M, Newman J, Fielden J, Aitkenhead H, Halder S . Metalloprotease SPRTN/DVC1 Orchestrates Replication-Coupled DNA-Protein Crosslink Repair. Mol Cell. 2016; 64(4):704-719. PMC: 5128727. DOI: 10.1016/j.molcel.2016.09.032. View

Dokshin G, Davis G, Sawle A, Eldridge M, Nicholls P, Gourley T . GCNA Interacts with Spartan and Topoisomerase II to Regulate Genome Stability. Dev Cell. 2019; 52(1):53-68.e6. PMC: 7227305. DOI: 10.1016/j.devcel.2019.11.006. View

Sun Y, Saha S, Wang W, Saha L, Huang S, Pommier Y . Excision repair of topoisomerase DNA-protein crosslinks (TOP-DPC). DNA Repair (Amst). 2020; 89:102837. PMC: 7188568. DOI: 10.1016/j.dnarep.2020.102837. View

Ray Chaudhuri A, Nussenzweig A . The multifaceted roles of PARP1 in DNA repair and chromatin remodelling. Nat Rev Mol Cell Biol. 2017; 18(10):610-621. PMC: 6591728. DOI: 10.1038/nrm.2017.53. View

Yang F, Hu Z, Guo Z . Small-Molecule Inhibitors Targeting FEN1 for Cancer Therapy. Biomolecules. 2022; 12(7). PMC: 9312813. DOI: 10.3390/biom12071007. View

Stingele J, Bellelli R, Alte F, Hewitt G, Sarek G, Maslen S . Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN. Mol Cell. 2016; 64(4):688-703. PMC: 5128726. DOI: 10.1016/j.molcel.2016.09.031. View

Saha S, Sun Y, Huang S, Baechler S, Pongor L, Agama K . DNA and RNA Cleavage Complexes and Repair Pathway for TOP3B RNA- and DNA-Protein Crosslinks. Cell Rep. 2020; 33(13):108569. PMC: 7859927. DOI: 10.1016/j.celrep.2020.108569. View

Yip M, Bodnar N, Rapoport T . Ddi1 is a ubiquitin-dependent protease. Proc Natl Acad Sci U S A. 2020; 117(14):7776-7781. PMC: 7149228. DOI: 10.1073/pnas.1902298117. View

10.

Pommier Y, Nussenzweig A, Takeda S, Austin C . Human topoisomerases and their roles in genome stability and organization. Nat Rev Mol Cell Biol. 2022; 23(6):407-427. PMC: 8883456. DOI: 10.1038/s41580-022-00452-3. View

11.

Rallabhandi P, Hashimoto K, Mo Y, Beck W, Moitra P, DArpa P . Sumoylation of topoisomerase I is involved in its partitioning between nucleoli and nucleoplasm and its clearing from nucleoli in response to camptothecin. J Biol Chem. 2002; 277(42):40020-6. DOI: 10.1074/jbc.M200388200. View

12.

Sun Y, Chen J, Pommier Y . Real-time imaging of drug-induced trapping of cellular topoisomerases and poly(ADP-ribose) polymerase 1 at the single-molecule level. Nucleic Acids Res. 2023; 51(18):e97. PMC: 10570045. DOI: 10.1093/nar/gkad735. View

13.

Welter A, Machida Y . Functions and evolution of FAM111 serine proteases. Front Mol Biosci. 2023; 9:1081166. PMC: 9798293. DOI: 10.3389/fmolb.2022.1081166. View

14.

Subramanian D, Furbee C, Muller M . ICE bioassay. Isolating in vivo complexes of enzyme to DNA. Methods Mol Biol. 2000; 95:137-47. DOI: 10.1385/1-59259-057-8:137. View

15.

Larsen N, Gao A, Sparks J, Gallina I, Wu R, Mann M . Replication-Coupled DNA-Protein Crosslink Repair by SPRTN and the Proteasome in Xenopus Egg Extracts. Mol Cell. 2019; 73(3):574-588.e7. PMC: 6375733. DOI: 10.1016/j.molcel.2018.11.024. View

16.

Balakrishnan L, Bambara R . Flap endonuclease 1. Annu Rev Biochem. 2013; 82:119-38. PMC: 3679248. DOI: 10.1146/annurev-biochem-072511-122603. View

17.

Hudson W, Ortlund E . The structure, function and evolution of proteins that bind DNA and RNA. Nat Rev Mol Cell Biol. 2014; 15(11):749-60. PMC: 4280011. DOI: 10.1038/nrm3884. View

18.

Lambre C, Barat Baviera J, Bolognesi C, Cocconcelli P, Crebelli R, Gott D . Scientific Guidance for the submission of dossiers on Food Enzymes. EFSA J. 2021; 19(10):e06851. PMC: 8529584. DOI: 10.2903/j.efsa.2021.6851. View

19.

Stormo G, Zhao Y . Determining the specificity of protein-DNA interactions. Nat Rev Genet. 2010; 11(11):751-60. DOI: 10.1038/nrg2845. View

20.

Guo E, Ishii Y, Mueller J, Srivatsan A, Gahman T, Putnam C . FEN1 endonuclease as a therapeutic target for human cancers with defects in homologous recombination. Proc Natl Acad Sci U S A. 2020; 117(32):19415-19424. PMC: 7431096. DOI: 10.1073/pnas.2009237117. View