Multi-step processing of replication stress-derived nascent strand DNA gaps by MRE11 and EXO1 nucleases.


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
07 10 2023
Historique:
received: 02 03 2023
accepted: 27 09 2023
medline: 23 10 2023
pubmed: 8 10 2023
entrez: 7 10 2023
Statut: epublish

Résumé

Accumulation of single stranded DNA (ssDNA) gaps in the nascent strand during DNA replication has been associated with cytotoxicity and hypersensitivity to genotoxic stress, particularly upon inactivation of the BRCA tumor suppressor pathway. However, how ssDNA gaps contribute to genotoxicity is not well understood. Here, we describe a multi-step nucleolytic processing of replication stress-induced ssDNA gaps which converts them into cytotoxic double stranded DNA breaks (DSBs). We show that ssDNA gaps are extended bidirectionally by MRE11 in the 3'-5' direction and by EXO1 in the 5'-3' direction, in a process which is suppressed by the BRCA pathway. Subsequently, the parental strand at the ssDNA gap is cleaved by the MRE11 endonuclease generating a double strand break. We also show that exposure to bisphenol A (BPA) and diethylhexyl phthalate (DEHP), which are widespread environmental contaminants due to their use in plastics manufacturing, causes nascent strand ssDNA gaps during replication. These gaps are processed through the same mechanism described above to generate DSBs. Our work sheds light on both the relevance of ssDNA gaps as major determinants of genomic instability, as well as the mechanism through which they are processed to generate genomic instability and cytotoxicity.

Identifiants

pubmed: 37805499
doi: 10.1038/s41467-023-42011-0
pii: 10.1038/s41467-023-42011-0
pmc: PMC10560291
doi:

Substances chimiques

Exodeoxyribonucleases EC 3.1.-
Endonucleases EC 3.1.-
DNA 9007-49-2
DNA, Single-Stranded 0
EXO1 protein, human EC 3.1.-
DNA Repair Enzymes EC 6.5.1.-

Types de publication

Journal Article Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

6265

Subventions

Organisme : NIGMS NIH HHS
ID : R01 GM134681
Pays : United States
Organisme : NIEHS NIH HHS
ID : R01 ES026184
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA244417
Pays : United States

Informations de copyright

© 2023. Springer Nature Limited.

Références

Mijic, S. et al. Replication fork reversal triggers fork degradation in BRCA2-defective cells. Nat. Commun. 8, 859 (2017).
pubmed: 29038466 pmcid: 5643541
Lemacon, D. et al. MRE11 and EXO1 nucleases degrade reversed forks and elicit MUS81-dependent fork rescue in BRCA2-deficient cells. Nat. Commun. 8, 860 (2017).
pubmed: 29038425 pmcid: 5643552
Kolinjivadi, A. M. et al. Smarcal1-mediated fork reversal triggers Mre11-dependent degradation of nascent DNA in the absence of Brca2 and stable Rad51 nucleofilaments. Mol. Cell 67, 867–881.e7 (2017).
pubmed: 28757209 pmcid: 5594205
Schlacher, K. et al. Double-strand break repair-independent role for BRCA2 in blocking stalled replication fork degradation by MRE11. Cell 145, 529–542 (2011).
pubmed: 21565612 pmcid: 3261725
Taglialatela, A. et al. Restoration of replication fork stability in BRCA1- and BRCA2-deficient cells by inactivation of SNF2-family fork remodelers. Mol. Cell 68, 414–430.e8 (2017).
pubmed: 29053959 pmcid: 5720682
Ray Chaudhuri, A. et al. Replication fork stability confers chemoresistance in BRCA-deficient cells. Nature 535, 382–387 (2016).
pubmed: 27443740
Guillemette, S. et al. Resistance to therapy in BRCA2 mutant cells due to loss of the nucleosome remodeling factor CHD4. Genes Dev. 29, 489–494 (2015).
pubmed: 25737278 pmcid: 4358401
Bhat, K. P. & Cortez, D. RPA and RAD51: fork reversal, fork protection, and genome stability. Nat. Struct. Mol. Biol. 25, 446–453 (2018).
pubmed: 29807999 pmcid: 6006513
Quinet, A., Lemacon, D. & Vindigni, A. Replication fork reversal: players and guardians. Mol. Cell 68, 830–833 (2017).
pubmed: 29220651 pmcid: 5895179
Thakar, T. & Moldovan, G. L. The emerging determinants of replication fork stability. Nucleic Acids Res. 49, 7224–7238 (2021).
pubmed: 33978751 pmcid: 8287955
Zellweger, R. et al. Rad51-mediated replication fork reversal is a global response to genotoxic treatments in human cells. J. Cell Biol. 208, 563–579 (2015).
pubmed: 25733714 pmcid: 4347635
Thakar, T. et al. Lagging strand gap suppression connects BRCA-mediated fork protection to nucleosome assembly through PCNA-dependent CAF-1 recycling. Nat. Commun. 13, 5323 (2022).
pubmed: 36085347 pmcid: 9463168
Quinet, A. et al. PRIMPOL-mediated adaptive response suppresses replication fork reversal in BRCA-deficient cells. Mol. Cell 77, 461–474.e9 (2020).
pubmed: 31676232 pmcid: 7007862
Tirman, S., Cybulla, E., Quinet, A., Meroni, A. & Vindigni, A. PRIMPOL ready, set, reprime! Crit. Rev. Biochem. Mol. Biol. 56, 17–30 (2021).
pubmed: 33179522
Tirman, S. et al. Temporally distinct post-replicative repair mechanisms fill PRIMPOL-dependent ssDNA gaps in human cells. Mol. Cell 81, 4026–4040.e8 (2021).
pubmed: 34624216 pmcid: 8555837
Belan, O. et al. POLQ seals post-replicative ssDNA gaps to maintain genome stability in BRCA-deficient cancer cells. Mol. Cell 82, 4664.e9–4680.e9 (2022).
Mann, A. et al. POLtheta prevents MRE11-NBS1-CtIP-dependent fork breakage in the absence of BRCA2/RAD51 by filling lagging-strand gaps. Mol. Cell 82, 4218–4231.e8 (2022).
pubmed: 36400008
Schrempf, A. et al. POLtheta processes ssDNA gaps and promotes replication fork progression in BRCA1-deficient cells. Cell Rep. 41, 111716 (2022).
pubmed: 36400033
Taglialatela, A. et al. REV1-Polzeta maintains the viability of homologous recombination-deficient cancer cells through mutagenic repair of PRIMPOL-dependent ssDNA gaps. Mol. Cell 81, 4008–4025.e7 (2021).
pubmed: 34508659 pmcid: 8500949
Hashimoto, Y., Ray Chaudhuri, A., Lopes, M. & Costanzo, V. Rad51 protects nascent DNA from Mre11-dependent degradation and promotes continuous DNA synthesis. Nat. Struct. Mol. Biol. 17, 1305–1311 (2010).
pubmed: 20935632 pmcid: 4306207
Jackson, L. M. & Moldovan, G. L. Mechanisms of PARP1 inhibitor resistance and their implications for cancer treatment. NAR Cancer 4, zcac042 (2022).
pubmed: 36568963 pmcid: 9773381
Thakar, T. et al. Ubiquitinated-PCNA protects replication forks from DNA2-mediated degradation by regulating Okazaki fragment maturation and chromatin assembly. Nat. Commun. 11, 2147 (2020).
pubmed: 32358495 pmcid: 7195461
Cong, K. et al. Replication gaps are a key determinant of PARP inhibitor synthetic lethality with BRCA deficiency. Mol. Cell 81, 3227 (2021).
pubmed: 34358459
Panzarino, N. J. et al. Replication gaps underlie BRCA deficiency and therapy response. Cancer Res. 81, 1388–1397 (2021).
pubmed: 33184108
Paes Dias, M. et al. Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps. Mol. Cell 81, 4692–4708.e9 (2021).
pubmed: 34555355
Simoneau, A., Xiong, R. & Zou, L. The trans cell cycle effects of PARP inhibitors underlie their selectivity toward BRCA1/2-deficient cells. Genes Dev. 35, 1271–1289 (2021).
pubmed: 34385259 pmcid: 8415318
Dhoonmoon, A., Nicolae, C. M. & Moldovan, G. L. The KU-PARP14 axis differentially regulates DNA resection at stalled replication forks by MRE11 and EXO1. Nat. Commun. 13, 5063 (2022).
pubmed: 36030235 pmcid: 9420157
Feng, W. & Jasin, M. BRCA2 suppresses replication stress-induced mitotic and G1 abnormalities through homologous recombination. Nat. Commun. 8, 525 (2017).
pubmed: 28904335 pmcid: 5597640
Lim, P. X., Zaman, M. & Jasin, M. BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair. Preprint at bioRxiv https://doi.org/10.1101/2023.04.11.536470 (2023).
Cantor, S. B. Revisiting the BRCA-pathway through the lens of replication gap suppression: “gaps determine therapy response in BRCA mutant cancer”. DNA Repair 107, 103209 (2021).
pubmed: 34419699 pmcid: 9049047
Agarwal, S., Tafel, A. A. & Kanaar, R. DNA double-strand break repair and chromosome translocations. DNA Repair 5, 1075–1081 (2006).
pubmed: 16798112
Gorodetska, I., Kozeretska, I. & Dubrovska, A. BRCA genes: the role in genome stability, cancer stemness and therapy resistance. J. Cancer 10, 2109–2127 (2019).
pubmed: 31205572 pmcid: 6548160
Kripke, M. et al. Rethinking environmental carcinogenesis. Cancer Epidemiol. Biomarkers Prev 29, 1870–1875 (2020).
pubmed: 33004408
Caldwell, J. C. DEHP: genotoxicity and potential carcinogenic mechanisms-a review. Mutat. Res. 751, 82–157 (2012).
pubmed: 22484601
Dumitrascu, M. C. et al. Carcinogenic effects of bisphenol A in breast and ovarian cancers. Oncol. Lett. 20, 282 (2020).
pubmed: 33014160 pmcid: 7520752
Jalal, N., Surendranath, A. R., Pathak, J. L., Yu, S. & Chung, C. Y. Bisphenol A (BPA) the mighty and the mutagenic. Toxicol. Rep. 5, 76–84 (2018).
pubmed: 29854579
Khan, N. G. et al. A comprehensive review on the carcinogenic potential of bisphenol A: clues and evidence. Environ. Sci. Pollut. Res. Int. 28, 19643–19663 (2021).
pubmed: 33666848 pmcid: 8099816
Mokra, K., Kuzminska-Surowaniec, A., Wozniak, K. & Michalowicz, J. Evaluation of DNA-damaging potential of bisphenol A and its selected analogs in human peripheral blood mononuclear cells (in vitro study). Food Chem. Toxicol. 100, 62–69 (2017).
pubmed: 27923681
Ganesan, S. & Keating, A. F. Bisphenol A-induced ovotoxicity involves DNA damage induction to which the ovary mounts a protective response indicated by increased expression of proteins involved in DNA repair and xenobiotic biotransformation. Toxicol. Sci. 152, 169–180 (2016).
pubmed: 27208089
Li, X. et al. Di-(2-ethylhexyl) phthalate inhibits DNA replication leading to hyperPARylation, SIRT1 attenuation, and mitochondrial dysfunction in the testis. Sci. Rep. 4, 6434 (2014).
pubmed: 25242624 pmcid: 4170195
Allard, P. & Colaiacovo, M. P. Bisphenol A impairs the double-strand break repair machinery in the germline and causes chromosome abnormalities. Proc. Natl Acad. Sci. USA 107, 20405–20410 (2010).
pubmed: 21059909 pmcid: 2996676
Atkinson, A. & Roy, D. In vivo DNA adduct formation by bisphenol A. Environ. Mol. Mutagen. 26, 60–66 (1995).
pubmed: 7641708
Cuenca, L. et al. Environmentally-relevant exposure to diethylhexyl phthalate (DEHP) alters regulation of double-strand break formation and crossover designation leading to germline dysfunction in Caenorhabditis elegans. PLoS Genet. 16, e1008529 (2020).
pubmed: 31917788 pmcid: 6952080
Hu, X. et al. Mutational signatures associated with exposure to carcinogenic microplastic compounds bisphenol A and styrene oxide. NAR Cancer 3, zcab004 (2021).
pubmed: 33718875 pmcid: 7936647
Izzotti, A., Kanitz, S., D’Agostini, F., Camoirano, A. & De Flora, S. Formation of adducts by bisphenol A, an endocrine disruptor, in DNA in vitro and in liver and mammary tissue of mice. Mutat. Res. 679, 28–32 (2009).
pubmed: 19660573
Liu, J. C. et al. Di (2-ethylhexyl) phthalate exposure impairs meiotic progression and DNA damage repair in fetal mouse oocytes in vitro. Cell Death Dis. 8, e2966 (2017).
pubmed: 28771232 pmcid: 5596541
Zhao, H., Wei, J., Xiang, L. & Cai, Z. Mass spectrometry investigation of DNA adduct formation from bisphenol A quinone metabolite and MCF-7 cell DNA. Talanta 182, 583–589 (2018).
pubmed: 29501196
Morocz, M., Gali, H., Rasko, I., Downes, C. S. & Haracska, L. Single cell analysis of human RAD18-dependent DNA post-replication repair by alkaline bromodeoxyuridine comet assay. PLoS ONE 8, e70391 (2013).
pubmed: 23936422 pmcid: 3735594
Vaitsiankova, A. et al. PARP inhibition impedes the maturation of nascent DNA strands during DNA replication. Nat. Struct. Mol. Biol. 29, 329–338 (2022).
pubmed: 35332322 pmcid: 9010290
Lim, K. S. et al. USP1 is required for replication fork protection in BRCA1-deficient tumors. Mol. Cell 72, 925–941.e4 (2018).
pubmed: 30576655
Quinet, A., Carvajal-Maldonado, D., Lemacon, D. & Vindigni, A. DNA fiber analysis: mind the gap! Methods Enzymol. 591, 55–82 (2017).
pubmed: 28645379
Roy, S., Luzwick, J. W. & Schlacher, K. SIRF: quantitative in situ analysis of protein interactions at DNA replication forks. J. Cell Biol. 217, 1521–1536 (2018).
pubmed: 29475976 pmcid: 5881507
Jones, L. P. et al. Loss of BRCA1 leads to an increased sensitivity to Bisphenol A. Toxicol. Lett. 199, 261–268 (2010).
pubmed: 20868731 pmcid: 3505996
Piberger, A. L. et al. PrimPol-dependent single-stranded gap formation mediates homologous recombination at bulky DNA adducts. Nat. Commun. 11, 5863 (2020).
pubmed: 33203852 pmcid: 7673990
Lemay, J. F. et al. A genome-wide screen identifies SCAI as a modulator of the UV-induced replicative stress response. PLoS Biol. 20, e3001543 (2022).
pubmed: 36215310 pmcid: 9584372
Foster, S. S., Balestrini, A. & Petrini, J. H. Functional interplay of the Mre11 nuclease and Ku in the response to replication-associated DNA damage. Mol. Cell. Biol. 31, 4379–4389 (2011).
pubmed: 21876003 pmcid: 3209331
Jensen, K. L. & Russell, P. Ctp1-dependent clipping and resection of DNA double-strand breaks by Mre11 endonuclease complex are not genetically separable. Nucleic Acids Res. 44, 8241–8249 (2016).
pubmed: 27325741 pmcid: 5041466
Langerak, P., Mejia-Ramirez, E., Limbo, O. & Russell, P. Release of Ku and MRN from DNA ends by Mre11 nuclease activity and Ctp1 is required for homologous recombination repair of double-strand breaks. PLoS Genet. 7, e1002271 (2011).
pubmed: 21931565 pmcid: 3169521
Mimitou, E. P. & Symington, L. S. Ku prevents Exo1 and Sgs1-dependent resection of DNA ends in the absence of a functional MRX complex or Sae2. EMBO J. 29, 3358–3369 (2010).
pubmed: 20729809 pmcid: 2957202
Balestrini, A. et al. The Ku heterodimer and the metabolism of single-ended DNA double-strand breaks. Cell Rep. 3, 2033–2045 (2013).
pubmed: 23770241
Chanut, P., Britton, S., Coates, J., Jackson, S. P. & Calsou, P. Coordinated nuclease activities counteract Ku at single-ended DNA double-strand breaks. Nat. Commun. 7, 12889 (2016).
pubmed: 27641979 pmcid: 5031800
Reginato, G., Cannavo, E. & Cejka, P. Physiological protein blocks direct the Mre11-Rad50-Xrs2 and Sae2 nuclease complex to initiate DNA end resection. Genes Dev. 31, 2325–2330 (2017).
pubmed: 29321179 pmcid: 5795779
Wang, W., Daley, J. M., Kwon, Y., Krasner, D. S. & Sung, P. Plasticity of the Mre11-Rad50-Xrs2-Sae2 nuclease ensemble in the processing of DNA-bound obstacles. Genes Dev. 31, 2331–2336 (2017).
pubmed: 29321177 pmcid: 5795780
Wang, W. et al. A DNA nick at Ku-blocked double-strand break ends serves as an entry site for exonuclease 1 (Exo1) or Sgs1-Dna2 in long-range DNA end resection. J. Biol. Chem. 293, 17061–17069 (2018).
pubmed: 30224356 pmcid: 6222114
Shibata, A. et al. DNA double-strand break repair pathway choice is directed by distinct MRE11 nuclease activities. Mol. Cell 53, 7–18 (2014).
pubmed: 24316220
Feng, Z. et al. Rad52 inactivation is synthetically lethal with BRCA2 deficiency. Proc. Natl Acad. Sci. USA 108, 686–691 (2011).
pubmed: 21148102
Lok, B. H., Carley, A. C., Tchang, B. & Powell, S. N. RAD52 inactivation is synthetically lethal with deficiencies in BRCA1 and PALB2 in addition to BRCA2 through RAD51-mediated homologous recombination. Oncogene 32, 3552–3558 (2013).
pubmed: 22964643
Rossi, M. J., DiDomenico, S. F., Patel, M. & Mazin, A. V. RAD52: paradigm of synthetic lethality and new developments. Front. Genet. 12, 780293 (2021).
pubmed: 34887904 pmcid: 8650160
Lakind, J. S. & Naiman, D. Q. Daily intake of bisphenol A and potential sources of exposure: 2005-2006 National Health and Nutrition Examination Survey. J. Expo. Sci. Environ. Epidemiol. 21, 272–279 (2011).
pubmed: 20237498
Csanady, G. A. et al. Distribution and unspecific protein binding of the xenoestrogens bisphenol A and daidzein. Arch. Toxicol. 76, 299–305 (2002).
pubmed: 12107647
Genuis, S. J., Beesoon, S., Birkholz, D. & Lobo, R. A. Human excretion of bisphenol A: blood, urine, and sweat (BUS) study. J. Environ. Public Health 2012, 185731 (2012).
pubmed: 22253637
Vandenberg, L. N., Hunt, P. A., Myers, J. P. & Vom Saal, F. S. Human exposures to bisphenol A: mismatches between data and assumptions. Rev. Environ. Health 28, 37–58 (2013).
pubmed: 23612528
Clements, K. E. et al. Loss of E2F7 confers resistance to poly-ADP-ribose polymerase (PARP) inhibitors in BRCA2-deficient cells. Nucleic Acids Res. 46, 8898–8907 (2018).
pubmed: 30032296 pmcid: 6158596
Nicolae, C. M. et al. The ADP-ribosyltransferase PARP10/ARTD10 interacts with proliferating cell nuclear antigen (PCNA) and is required for DNA damage tolerance. J. Biol. Chem. 289, 13627–13637 (2014).
pubmed: 24695737 pmcid: 4036367

Auteurs

Anastasia Hale (A)

Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.

Ashna Dhoonmoon (A)

Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.

Joshua Straka (J)

Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.

Claudia M Nicolae (CM)

Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA. cmn14@psu.edu.

George-Lucian Moldovan (GL)

Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA. glm29@psu.edu.

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