Abstract
Mitochondrial DNA is frequently exposed to oxidative damage, as compared to nuclear DNA. Previously, we have shown that while microhomology-mediated end joining can account for DNA deletions in mitochondria, classical nonhomologous DNA end joining, the predominant double-strand break (DSB) repair pathway in nucleus, is undetectable. In the present study, we investigated the presence of homologous recombination (HR) in mitochondria to maintain its genomic integrity. Biochemical studies revealed that HR-mediated repair of DSBs is more efficient in the mitochondria of testes as compared to that of brain, kidney and spleen. Interestingly, a significant increase in the efficiency of HR was observed when a DSB was introduced. Analyses of the clones suggest that most of the recombinants were generated through reciprocal exchange, while ~ 30% of recombinants were due to gene conversion in testicular extracts. Colocalization and immunoblotting studies showed the presence of RAD51 and MRN complex proteins in the mitochondria and immunodepletion of MRE11, RAD51 or NIBRIN suppressed the HR-mediated repair. Thus, our results reveal importance of homologous recombination in the maintenance of mitochondrial genome stability.
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Drablos F, Feyzi E, Aas PA, Vaagbo CB, Kavli B, Bratlie MS, Pena-Diaz J, Otterlei M, Slupphaug G, Krokan HE (2004) Alkylation damage in DNA and RNA—repair mechanisms and medical significance. DNA Repair (Amst) 3:1389–1407. https://doi.org/10.1016/j.dnarep.2004.05.004
Gostissa M, Alt FW, Chiarle R (2011) Mechanisms that promote and suppress chromosomal translocations in lymphocytes. Annu Rev Immunol 29:319–350. https://doi.org/10.1146/annurev-immunol-031210-101329
Cooke MS, Evans MD, Dizdaroglu M, Lunec J (2003) Oxidative DNA damage: mechanisms, mutation, and disease. FASEB J 17:1195–1214. https://doi.org/10.1096/fj.02-0752rev
Barnes DE, Lindahl T (2004) Repair and genetic consequences of endogenous DNA base damage in mammalian cells. Annu Rev Genet 38:445–476. https://doi.org/10.1146/annurev.genet.38.072902.092448
Sharma S, Javadekar SM, Pandey M, Srivastava M, Kumari R, Raghavan SC (2015) Homology and enzymatic requirements of microhomology-dependent alternative end joining. Cell Death Dis 6:e1697. https://doi.org/10.1038/cddis.2015.58
Javadekar SM, Raghavan SC (2015) Snaps and mends: DNA breaks and chromosomal translocations. FEBS J 282:2627–2645. https://doi.org/10.1111/febs.13311
Jackson SP, Bartek J (2009) The DNA-damage response in human biology and disease. Nature 461:1071–1078. https://doi.org/10.1038/nature08467
Nambiar M, Raghavan SC (2011) How does DNA break during chromosomal translocations? Nucleic Acids Res 39:5813–5825. https://doi.org/10.1093/nar/gkr223
Friedberg EC, Aguilera A, Gellert M, Hanawalt PC, Hays JB, Lehmann AR, Lindahl T, Lowndes N, Sarasin A, Wood RD (2006) DNA repair: from molecular mechanism to human disease. DNA Repair (Amst) 5:986–996
Bunting SF, Nussenzweig A (2013) End-joining, translocations and cancer. Nat Rev Cancer 13:443–454. https://doi.org/10.1038/nrc3537
Ciccia A, Elledge SJ (2010) The DNA damage response: making it safe to play with knives. Mol Cell 40:179–204. https://doi.org/10.1016/j.molcel.2010.09.019
Nambiar M, Kari V, Raghavan SC (2008) Chromosomal translocations in cancer. Biochim Biophys Acta 1786:139–152. https://doi.org/10.1016/j.bbcan.2008.07.005
Corneo B, Wendland RL, Deriano L, Cui X, Klein IA, Wong SY, Arnal S, Holub AJ, Weller GR, Pancake BA, Shah S, Brandt VL, Meek K, Roth DB (2007) Rag mutations reveal robust alternative end joining. Nature 449:483–486. https://doi.org/10.1038/nature06168
Hefferin ML, Tomkinson AE (2005) Mechanism of DNA double-strand break repair by non-homologous end joining. DNA Repair (Amst) 4:639–648. https://doi.org/10.1016/j.dnarep.2004.12.005
Jazayeri A, Jackson SP (2002) Screening the yeast genome for new DNA-repair genes. Genome Biol 3:REVIEWS1009
Moore JK, Haber JE (1996) Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol 16:2164–2173
Wyman C, Kanaar R (2006) DNA double-strand break repair: all’s well that ends well. Annu Rev Genet 40:363–383. https://doi.org/10.1146/annurev.genet.40.110405.090451
Sharma S, Raghavan SC (2010) Nonhomologous DNA end joining in cell-free extracts. J Nucleic Acids. https://doi.org/10.4061/2010/389129
Wang HC, Chou WC, Shieh SY, Shen CY (2006) Ataxia telangiectasia mutated and checkpoint kinase 2 regulate BRCA1 to promote the fidelity of DNA end-joining. Cancer Res 66:1391–1400. https://doi.org/10.1158/0008-5472.CAN-05-3270
Srivastava M, Nambiar M, Sharma S, Karki SS, Goldsmith G, Hegde M, Kumar S, Pandey M, Singh RK, Ray P, Natarajan R, Kelkar M, De A, Choudhary B, Raghavan SC (2012) An inhibitor of nonhomologous end-joining abrogates double-strand break repair and impedes cancer progression. Cell 151:1474–1487. https://doi.org/10.1016/j.cell.2012.11.054
Lieber MR (2010) The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79:181–211. https://doi.org/10.1146/annurev.biochem.052308.093131
Vartak SV, Raghavan SC (2015) Inhibition of nonhomologous end joining to increase the specificity of CRISPR/Cas9 genome editing. FEBS J 282:4289–4294. https://doi.org/10.1111/febs.13416
Orthwein A, Fradet-Turcotte A, Noordermeer SM, Canny MD, Brun CM, Strecker J, Escribano-Diaz C, Durocher D (2014) Mitosis inhibits DNA double-strand break repair to guard against telomere fusions. Science 344:189–193. https://doi.org/10.1126/science.1248024
Riballo E, Kuhne M, Rief N, Doherty A, Smith GC, Recio MJ, Reis C, Dahm K, Fricke A, Krempler A, Parker AR, Jackson SP, Gennery A, Jeggo PA, Lobrich M (2004) A pathway of double-strand break rejoining dependent upon ATM, Artemis, and proteins locating to gamma-H2AX foci. Mol Cell 16:715–724. https://doi.org/10.1016/j.molcel.2004.10.029
Deriano L, Roth DB (2013) Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage. Annu Rev Genet 47:433–455. https://doi.org/10.1146/annurev-genet-110711-155540
Tadi SK, Sebastian R, Dahal S, Babu RK, Choudhary B, Raghavan SC (2016) Microhomology-mediated end joining is the principal mediator of double-strand break repair during mitochondrial DNA lesions. Mol Biol Cell 27:223–235. https://doi.org/10.1091/mbc.E15-05-0260
Holthofer H, Kretzler M, Haltia A, Solin ML, Taanman JW, Schagger H, Kriz W, Kerjaschki D, Schlondorff D (1999) Altered gene expression and functions of mitochondria in human nephrotic syndrome. FASEB J 13:523–532
Kren BT, Wong PY, Steer CJ (2003) Short, single-stranded oligonucleotides mediate targeted nucleotide conversion using extracts from isolated liver mitochondria. DNA Repair (Amst) 2:531–546
Sage JM, Gildemeister OS, Knight KL (2010) Discovery of a novel function for human Rad51: maintenance of the mitochondrial genome. J Biol Chem 285:18984–18990. https://doi.org/10.1074/jbc.M109.099846
Chen M, Liu B, Gao Q, Zhuo Y, Ge J (2011) Mitochondria-targeted peptide MTP-131 alleviates mitochondrial dysfunction and oxidative damage in human trabecular meshwork cells. Invest Ophthalmol Vis Sci 52:7027–7037. https://doi.org/10.1167/iovs.11-7524
Yakes FM, Van Houten B (1997) Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress. Proc Natl Acad Sci USA 94:514–519
Hudson EK, Hogue BA, Souza-Pinto NC, Croteau DL, Anson RM, Bohr VA, Hansford RG (1998) Age-associated change in mitochondrial DNA damage. Free Radic Res 29:573–579
Hudson EK, Tsuchiya N, Hansford RG (1998) Age-associated changes in mitochondrial mRNA expression and translation in the Wistar rat heart. Mech Ageing Dev 103:179–193
Michikawa Y, Mazzucchelli F, Bresolin N, Scarlato G, Attardi G (1999) Aging-dependent large accumulation of point mutations in the human mtDNA control region for replication. Science 286:774–779
Pakendorf B, Stoneking M (2005) Mitochondrial DNA and human evolution. Annu Rev Genomics Hum Genet 6:165–183. https://doi.org/10.1146/annurev.genom.6.080604.162249
Stierum RH, Croteau DL, Bohr VA (1999) Purification and characterization of a mitochondrial thymine glycol endonuclease from rat liver. J Biol Chem 274:7128–7136
Stierum RH, Dianov GL, Bohr VA (1999) Single-nucleotide patch base excision repair of uracil in DNA by mitochondrial protein extracts. Nucleic Acids Res 27:3712–3719
Mason PA, Matheson EC, Hall AG, Lightowlers RN (2003) Mismatch repair activity in mammalian mitochondria. Nucleic Acids Res 31:1052–1058
Akbari M, Visnes T, Krokan HE, Otterlei M (2008) Mitochondrial base excision repair of uracil and AP sites takes place by single-nucleotide insertion and long-patch DNA synthesis. DNA Repair (Amst) 7:605–616. https://doi.org/10.1016/j.dnarep.2008.01.002
Liu P, Qian L, Sung JS, de Souza-Pinto NC, Zheng L, Bogenhagen DF, Bohr VA, Wilson DM 3rd, Shen B, Demple B (2008) Removal of oxidative DNA damage via FEN1-dependent long-patch base excision repair in human cell mitochondria. Mol Cell Biol 28:4975–4987. https://doi.org/10.1128/MCB.00457-08
Szczesny B, Tann AW, Longley MJ, Copeland WC, Mitra S (2008) Long patch base excision repair in mammalian mitochondrial genomes. J Biol Chem 283:26349–26356. https://doi.org/10.1074/jbc.M803491200
de Souza-Pinto NC, Mason PA, Hashiguchi K, Weissman L, Tian J, Guay D, Lebel M, Stevnsner TV, Rasmussen LJ, Bohr VA (2009) Novel DNA mismatch-repair activity involving YB-1 in human mitochondria. DNA Repair (Amst) 8:704–719. https://doi.org/10.1016/j.dnarep.2009.01.021
Jacobs HT, Lehtinen SK, Spelbrink JN (2000) No sex please, we’re mitochondria: a hypothesis on the somatic unit of inheritance of mammalian mtDNA. BioEssays 22:564–572. https://doi.org/10.1002/(SICI)1521-1878(200006)22:6<564:AID-BIES9>3.0.CO;2-4
D’Aurelio M, Gajewski CD, Lin MT, Mauck WM, Shao LZ, Lenaz G, Moraes CT, Manfredi G (2004) Heterologous mitochondrial DNA recombination in human cells. Hum Mol Genet 13:3171–3179. https://doi.org/10.1093/hmg/ddh326
Gilkerson R, Bravo L, Garcia I, Gaytan N, Herrera A, Maldonado A, Quintanilla B (2013) The mitochondrial nucleoid: integrating mitochondrial DNA into cellular homeostasis. Cold Spring Harb Perspect Biol 5:a011080. https://doi.org/10.1101/cshperspect.a011080
Gilkerson RW, Schon EA, Hernandez E, Davidson MM (2008) Mitochondrial nucleoids maintain genetic autonomy but allow for functional complementation. J Cell Biol 181:1117–1128. https://doi.org/10.1083/jcb.200712101
Phillips AF, Millet AR, Tigano M, Dubois SM, Crimmins H, Babin L, Charpentier M, Piganeau M, Brunet E, Sfeir A (2017) Single-molecule analysis of mtDNA replication uncovers the basis of the common deletion. Mol Cell 65(527–538):e6. https://doi.org/10.1016/j.molcel.2016.12.014
Oppliger T, Wurgler FE, Sengstag C (1993) A plasmid system to monitor gene conversion and reciprocal recombination in vitro. Mutat Res 291:181–192
Raghavan SC, Raman MJ (2004) Nonhomologous end joining of complementary and noncomplementary DNA termini in mouse testicular extracts. DNA Repair (Amst) 3:1297–1310. https://doi.org/10.1016/j.dnarep.2004.04.007
Sathees CR, Raman MJ (1999) Mouse testicular extracts process DNA double-strand breaks efficiently by DNA end-to-end joining. Mutat Res 433:1–13
Maianski NA, Geissler J, Srinivasula SM, Alnemri ES, Roos D, Kuijpers TW (2004) Functional characterization of mitochondria in neutrophils: a role restricted to apoptosis. Cell Death Differ 11:143–153. https://doi.org/10.1038/sj.cdd.4401320
Chiruvella KK, Sebastian R, Sharma S, Karande AA, Choudhary B, Raghavan SC (2012) Time-dependent predominance of nonhomologous DNA end-joining pathways during embryonic development in mice. J Mol Biol 417:197–211. https://doi.org/10.1016/j.jmb.2012.01.029
Baumann P, West SC (1998) DNA end-joining catalyzed by human cell-free extracts. Proc Natl Acad Sci USA 95:14066–14070
Srivastava N, Raman MJ (2007) Homologous recombination-mediated double-strand break repair in mouse testicular extracts and comparison with different germ cell stages. Cell Biochem Funct 25:75–86. https://doi.org/10.1002/cbf.1375
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning a laboratory manual. Cold Spring Harbor Laboratory Press, New York
Sharma S, Choudhary B, Raghavan SC (2011) Efficiency of nonhomologous DNA end joining varies among somatic tissues, despite similarity in mechanism. Cell Mol Life Sci 68:661–676. https://doi.org/10.1007/s00018-010-0472-x
Kumar TS, Kari V, Choudhary B, Nambiar M, Akila TS, Raghavan SC (2010) Anti-apoptotic protein BCL2 down-regulates DNA end joining in cancer cells. J Biol Chem 285:32657–32670. https://doi.org/10.1074/jbc.M110.140350
Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM (1994) Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 58:401–465
Szostak JW, Orr-Weaver TL, Rothstein RJ, Stahl FW (1983) The double-strand-break repair model for recombination. Cell 33:25–35
Wallace DC (2005) The mitochondrial genome in human adaptive radiation and disease: on the road to therapeutics and performance enhancement. Gene 354:169–180. https://doi.org/10.1016/j.gene.2005.05.001
Wallace DC (2005) A mitochondrial paradigm of metabolic and degenerative diseases, aging, and cancer: a dawn for evolutionary medicine. Annu Rev Genet 39:359–407. https://doi.org/10.1146/annurev.genet.39.110304.095751
Bohr VA (2002) Repair of oxidative DNA damage in nuclear and mitochondrial DNA, and some changes with aging in mammalian cells. Free Radic Biol Med 32:804–812
Sykora P, Croteau DL, Bohr VA, Wilson DM 3rd (2011) Aprataxin localizes to mitochondria and preserves mitochondrial function. Proc Natl Acad Sci USA 108:7437–7442. https://doi.org/10.1073/pnas.1100084108
Thyagarajan B, Campbell C (1997) Elevated homologous recombination activity in fanconi anemia fibroblasts. J Biol Chem 272:23328–23333
Dmitrieva NI, Malide D, Burg MB (2011) Mre11 is expressed in mammalian mitochondria where it binds to mitochondrial DNA. Am J Physiol Regul Integr Comp Physiol 301:R632–R640. https://doi.org/10.1152/ajpregu.00853.2010
Kalifa L, Quintana DF, Schiraldi LK, Phadnis N, Coles GL, Sia RA, Sia EA (2012) Mitochondrial genome maintenance: roles for nuclear nonhomologous end-joining proteins in Saccharomyces cerevisiae. Genetics 190:951–964. https://doi.org/10.1534/genetics.111.138214
Lakshmipathy U, Campbell C (1999) The human DNA ligase III gene encodes nuclear and mitochondrial proteins. Mol Cell Biol 19:3869–3876
Chacinska A, Pfannschmidt S, Wiedemann N, Kozjak V, Sanjuan Szklarz LK, Schulze-Specking A, Truscott KN, Guiard B, Meisinger C, Pfanner N (2004) Essential role of Mia40 in import and assembly of mitochondrial intermembrane space proteins. EMBO J 23:3735–3746. https://doi.org/10.1038/sj.emboj.7600389
Barchiesi A, Wasilewski M, Chacinska A, Tell G, Vascotto C (2015) Mitochondrial translocation of APE1 relies on the MIA pathway. Nucleic Acids Res 43:5451–5464. https://doi.org/10.1093/nar/gkv433
Lu L-Y, Yu X (2015) Double-strand break repair on sex chromosomes: challenges during male meiotic prophase. Cell Cycle 14(4):516–525. https://doi.org/10.1080/15384101.2014.998070
Johnson RD, Jasin M (2000) Sister chromatid gene conversion is a prominent double-strand break repair pathway in mammalian cells. EMBO J 19:3398–3407. https://doi.org/10.1093/emboj/19.13.3398
Jain S, Sugawara N, Haber JE (2016) Role of double-strand break end-tethering during gene conversion in Saccharomyces cerevisiae. PLoS Genet 12:e1005976. https://doi.org/10.1371/journal.pgen.1005976
Acknowledgements
We thank Prof. Mercy J. Raman, Dr. Mridula Nambiar, Dr. Monica Pandey, Dr. Supriya Vartak, Dipayan Ghosh and SCR Lab members for critical reading of the manuscript. We would like to thank Dr. Umesh Varshney, IISc for providing us Tg1 bacterial strain. We also would like to thank Dr. Ganesh Nagaraju, IISc for providing us with the TFAM antibody. We thank the Central Animal and Confocal facilities of the Indian Institute of Science for the help. Financial assistance from CSIR, New Delhi (37(1579)/13/EMR-II) and from IISc-DBT partnership programme [DBT/BF/PR/INS/2011-12/IISc] for SCR is acknowledged. SD is supported by fellowship from IISc, Bangalore (India).
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Dahal, S., Dubey, S. & Raghavan, S.C. Homologous recombination-mediated repair of DNA double-strand breaks operates in mammalian mitochondria. Cell. Mol. Life Sci. 75, 1641–1655 (2018). https://doi.org/10.1007/s00018-017-2702-y
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DOI: https://doi.org/10.1007/s00018-017-2702-y