USP37 Prevents Premature Disassembly of Stressed Replisomes by TRAIP

Overview

Journal bioRxiv

Date 2024 Sep 16

PMID 39282314

Authors

Olga V Kochenova

Giuseppina DAlessandro

Domenic Pilger

Ernst Schmid

Sean L Richards

Marcos Rios Garcia

Satpal S Jhujh

Andrea Voigt

Vipul Gupta

Christopher J Carnie

R Alex Wu

Nadia Gueorguieva

Grant S Stewart

Johannes C Walter

Stephen P Jackson

Affiliations

Soon will be listed here.

Abstract

The E3 ubiquitin ligase TRAIP associates with the replisome and helps this molecular machine deal with replication stress. Thus, TRAIP promotes DNA inter-strand crosslink repair by triggering the disassembly of CDC45-MCM2-7-GINS (CMG) helicases that have converged on these lesions. However, disassembly of single CMGs that have stalled temporarily would be deleterious, suggesting that TRAIP must be carefully regulated. Here, we demonstrate that human cells lacking the de-ubiquitylating enzyme USP37 are hypersensitive to topoisomerase poisons and other replication stress-inducing agents. We further show that TRAIP loss rescues the hypersensitivity of knockout cells to topoisomerase inhibitors. In egg extracts depleted of USP37, TRAIP promotes premature CMG ubiquitylation and disassembly when converging replisomes stall. Finally, guided by AlphaFold-Multimer, we discovered that binding to CDC45 mediates USP37's response to topological stress. In conclusion, we propose that USP37 protects genome stability by preventing TRAIP-dependent CMG unloading when replication stress impedes timely termination.

References

Hernandez-Perez S, Cabrera E, Amoedo H, Rodriguez-Acebes S, Koundrioukoff S, Debatisse M . USP37 deubiquitinates Cdt1 and contributes to regulate DNA replication. Mol Oncol. 2016; 10(8):1196-206. PMC: 5423201. DOI: 10.1016/j.molonc.2016.05.008. View

Doench J, Fusi N, Sullender M, Hegde M, Vaimberg E, Donovan K . Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016; 34(2):184-191. PMC: 4744125. DOI: 10.1038/nbt.3437. View

Zhao Y, Tabet D, Rubio Contreras D, Lao L, Nedergaard Kousholt A, Weile J . Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens. Mol Cell. 2023; 83(15):2792-2809.e9. PMC: 10530064. DOI: 10.1016/j.molcel.2023.06.025. View

Jenkyn-Bedford M, Jones M, Baris Y, Labib K, Cannone G, Yeeles J . A conserved mechanism for regulating replisome disassembly in eukaryotes. Nature. 2021; 600(7890):743-747. PMC: 8695382. DOI: 10.1038/s41586-021-04145-3. View

Cao J, Wang X, Wang S, Chen Z, Tang J . Stabilization of estrogen receptor α by USP37 contributes to the progression of breast cancer. Cancer Sci. 2022; 114(5):2041-2052. PMC: 10154820. DOI: 10.1111/cas.15613. View

Taglialatela A, Alvarez S, Leuzzi G, Sannino V, Ranjha L, Huang J . Restoration of Replication Fork Stability in BRCA1- and BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers. Mol Cell. 2017; 68(2):414-430.e8. PMC: 5720682. DOI: 10.1016/j.molcel.2017.09.036. View

Sonneville R, Moreno S, Knebel A, Johnson C, Hastie C, Gartner A . CUL-2 and UBXN-3 drive replisome disassembly during DNA replication termination and mitosis. Nat Cell Biol. 2017; 19(5):468-479. PMC: 5410169. DOI: 10.1038/ncb3500. View

Schalbetter S, Mansoubi S, Chambers A, Downs J, Baxter J . Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability. Proc Natl Acad Sci U S A. 2015; 112(33):E4565-70. PMC: 4547287. DOI: 10.1073/pnas.1505356112. View

Bryant P, Pozzati G, Elofsson A . Improved prediction of protein-protein interactions using AlphaFold2. Nat Commun. 2022; 13(1):1265. PMC: 8913741. DOI: 10.1038/s41467-022-28865-w. View

10.

Xiao Z, Chang L, Kim J, Zhang P, Hang Q, Yap S . USP37 is a SNAI1 deubiquitinase. Am J Cancer Res. 2020; 9(12):2749-2759. PMC: 6943346. View

11.

Wu R, Pellman D, Walter J . The Ubiquitin Ligase TRAIP: Double-Edged Sword at the Replisome. Trends Cell Biol. 2020; 31(2):75-85. PMC: 7856240. DOI: 10.1016/j.tcb.2020.11.007. View

12.

Dewar J, Walter J . Mechanisms of DNA replication termination. Nat Rev Mol Cell Biol. 2017; 18(8):507-516. PMC: 6386472. DOI: 10.1038/nrm.2017.42. View

13.

Harrigan J, Jacq X, Martin N, Jackson S . Deubiquitylating enzymes and drug discovery: emerging opportunities. Nat Rev Drug Discov. 2017; 17(1):57-78. PMC: 7097658. DOI: 10.1038/nrd.2017.152. View

14.

Deegan T, Baxter J, Ortiz Bazan M, Yeeles J, Labib K . Pif1-Family Helicases Support Fork Convergence during DNA Replication Termination in Eukaryotes. Mol Cell. 2019; 74(2):231-244.e9. PMC: 6477153. DOI: 10.1016/j.molcel.2019.01.040. View

15.

Cai J, Li M, Wang X, Li L, Li Q, Hou Z . USP37 Promotes Lung Cancer Cell Migration by Stabilizing Snail Protein Deubiquitination. Front Genet. 2020; 10:1324. PMC: 6967296. DOI: 10.3389/fgene.2019.01324. View

16.

Campos L, Van Ravenstein S, Vontalge E, Greer B, Heintzman D, Kavlashvili T . RTEL1 and MCM10 overcome topological stress during vertebrate replication termination. Cell Rep. 2023; 42(2):112109. PMC: 10432576. DOI: 10.1016/j.celrep.2023.112109. View

17.

Deng L, Wu R, Sonneville R, Kochenova O, Labib K, Pellman D . Mitotic CDK Promotes Replisome Disassembly, Fork Breakage, and Complex DNA Rearrangements. Mol Cell. 2019; 73(5):915-929.e6. PMC: 6410736. DOI: 10.1016/j.molcel.2018.12.021. View

18.

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

19.

Steinegger M, Soding J . MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017; 35(11):1026-1028. DOI: 10.1038/nbt.3988. View

20.

Dewson G, Eichhorn P, Komander D . Deubiquitinases in cancer. Nat Rev Cancer. 2023; 23(12):842-862. DOI: 10.1038/s41568-023-00633-y. View