[Frontiers in Bioscience, Scholar, 7, 109-124, June 1, 2015]

Endangered species: mitochondrial DNA loss as a mechanism of human disease

Alan Herrera 1 , Iraselia Garcia 1 , Norma Gaytan 1 , Edith Jones 1 , Alicia Maldonado 2 , Robert Gilkerson 1, 2

1Departments of Biology and 2Clinical Laboratory Sciences, University of Texas-Pan American, 1201 West University Drive, Edinburg, TX 78539 USA

TABLE OF CONTENTS

1. Abstract
2. MtDNA: Composition, copy number and organization
3. Loss of mtDNA across human disease
    3.1. Diabetes and metabolic disease
    3.2. Cardiovascular disease
    3.3. Aging
4. MtDNA mutations: heteroplasmy, threshold effects, and bioenergetic function
    4.1. MtDNA mutations
    4.2. Heteroplasmy and threshold
    4.3. MtDNA depletion syndromes
5. Mechanisms of mtDNA damage and cell-wide effects
    5.1. The network is down: Impacts on organellar structure/function
    5.2. Cell-wide impacts of mtDNA loss: apoptosis and signaling
6. Concluding remarks
7. Acknowledgements
8. References

1. ABSTRACT

Human mitochondrial DNA (mtDNA) is a small maternally inherited DNA, typically present in hundreds of copies in a single human cell. Thus, despite its small size, the mitochondrial genome plays a crucial role in the metabolic homeostasis of the cell. Our understanding of mtDNA genotype-phenotype relationships is derived largely from studies of the classical mitochondrial neuromuscular diseases, in which mutations of mtDNA lead to compromised mitochondrial bioenergetic function, with devastating pathological consequences. Emerging research suggests that loss, rather than mutation, of mtDNA plays a major role across a range of prevalent human diseases, including diabetes mellitus, cardiovascular disease, and aging. Here, we examine the ‘rules’ of mitochondrial genetics and function, the clinical settings in which loss of mtDNA is an emerging pathogenic mechanism, and explore mtDNA damage and its consequences for the organellar network and cell at large. As extranuclear genetic material arrayed throughout the cell to support metabolism, mtDNA is increasingly implicated in a host of disease conditions, opening a range of exciting questions regarding mtDNA and its role in cellular homeostasis.

8. REFERENCES

1. S. Anderson, A. T. Bankier, B. G. Barrell, M. H. de Bruijn, A. R. Coulson, J. Drouin, I. C. Eperon, D. P. Nierlich, B. A. Roe, F. Sanger, P. H. Schreier, A. J. Smith, R. Staden and I. G. Young: Sequence and organization of the human mitochondrial genome. Nature, 290(5806), 457-65 (1981)
DOI: 10.1038/290457a0

2. S. DiMauro and E. A. Schon: Mitochondrial respiratory-chain diseases. New Engl. J. Med., 348(26), 2656-68 (2003)
DOI: 10.1056/NEJMra022567

3. F. Legros, F. Malka, P. Frachon, A. Lombes and M. Rojo: Organization and dynamics of human mitochondrial DNA. J. Cell Sci., 117(Pt 13), 2653-62 (2004)
DOI: 10.1242/jcs.01134

4. A. P. Rebelo, L. M. Dillon and C. T. Moraes: Mitochondrial DNA transcription regulation and nucleoid organization. J. Inherit. Metab. Dis., 34(4), 941-51 (2011)
DOI: 10.1007/s10545-011-9330-8

5. L. Sagan: On the origin of mitosing cells. J. Theoret. Biol., 14(3), 255-74 (1967)
DOI: 10.1016/0022-5193(67)90079-3

6. E. A. Schon, S. Dimauro, M. Hirano and R. W. Gilkerson: Therapeutic prospects for mitochondrial disease. Trends Mol. Med., 16, 268-276 (2010)
DOI: 10.1016/j.molmed.2010.04.007

7. S. W. Taylor, E. Fahy, B. Zhang, G. M. Glenn, D. E. Warnock, S. Wiley, A. N. Murphy, S. P. Gaucher, R. A. Capaldi, B. W. Gibson and S. S. Ghosh: Characterization of the human heart mitochondrial proteome. Nat. Biotech., 21(3), 281-6 (2003)
DOI: 10.1038/nbt793

8. D. Mokranjac and W. Neupert: Thirty years of protein translocation into mitochondria: unexpectedly complex and still puzzling. Biochim. Biophys. Acta, 1793(1), 33-41 (2009)
DOI: 10.1016/j.bbamcr.2008.06.021

9. G. S. Hotamisligil, N. S. Shargill and B. M. Spiegelman: Adipose expression of tumor necrosis factor-alpha: direct role in obesity-linked insulin resistance. Science, 259(5091), 87-91 (1993)
DOI: 10.1126/science.7678183

10. R. Feinstein, H. Kanety, M. Z. Papa, B. Lunenfeld and A. Karasik: Tumor necrosis factor-alpha suppresses insulin-induced tyrosine phosphorylation of insulin receptor and its substrates. J. Biol. Chem., 268(35), 26055-8 (1993)

11. Y. S. Lee, P. Li, J. Y. Huh, I. J. Hwang, M. Lu, J. I. Kim, M. Ham, S. Talukdar, A. Chen, W. J. Lu, G. K. Bandyopadhyay, R. Schwendener, J. Olefsky and J. B. Kim: Inflammation is necessary for long-term but not short-term high-fat diet-induced insulin resistance. Diabetes, 60(10), 2474-83 (2011)
DOI: 10.2337/db11-0194

12. A. M. Johnson and J. M. Olefsky: The origins and drivers of insulin resistance. Cell, 152(4), 673-84 (2013)
DOI: 10.1016/j.cell.2013.01.041

13. V. B. Ritov, E. V. Menshikova, K. Azuma, R. Wood, F. G. Toledo, B. H. Goodpaster, N. B. Ruderman and D. E. Kelley: Deficiency of electron transport chain in human skeletal muscle mitochondria in type 2 diabetes mellitus and obesity. Am. J. Phys., 298(1), E49-58 (2010)

14. V. K. Mootha, C. M. Lindgren, K. F. Eriksson, A. Subramanian, S. Sihag, J. Lehar, P. Puigserver, E. Carlsson, M. Ridderstrale, E. Laurila, N. Houstis, M. J. Daly, N. Patterson, J. P. Mesirov, T. R. Golub, P. Tamayo, B. Spiegelman, E. S. Lander, J. N. Hirschhorn, D. Altshuler and L. C. Groop: PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet., 34(3), 267-73 (2003)
DOI: 10.1038/ng1180

15. T. Kadowaki, H. Kadowaki, Y. Mori, K. Tobe, R. Sakuta, Y. Suzuki, Y. Tanabe, H. Sakura, T. Awata, Y. Goto and et al.: A subtype of diabetes mellitus associated with a mutation of mitochondrial DNA. New Engl. J. Med., 330(14), 962-8 (1994)
DOI: 10.1056/NEJM199404073301403

16. M. M. Lindroos, R. Borra, N. Mononen, T. Lehtimaki, K. A. Virtanen, V. Lepomaki, L. Guiducci, P. Iozzo, K. Majamaa and P. Nuutila: Mitochondrial diabetes is associated with insulin resistance in subcutaneous adipose tissue but not with increased liver fat content. J. Inherit. Metab. Dis., 34(6), 1205-12 (2011)
DOI: 10.1007/s10545-011-9338-0

17. D. F. Bogenhagen, D. Rousseau and S. Burke: The layered structure of human mitochondrial DNA nucleoids. J. Biol. Chem., 283(6), 3665-75 (2008)
DOI: 10.1074/jbc.M708444200

18. T. F. Gianotti, S. Sookoian, G. Dieuzeide, S. I. Garcia, C. Gemma, C. D. Gonzalez and C. J. Pirola: A decreased mitochondrial DNA content is related to insulin resistance in adolescents. Obesity, 16(7), 1591-5 (2008)
DOI: 10.1038/oby.2008.253

19. C. J. Hsieh, S. W. Weng, C. W. Liou, T. K. Lin, J. B. Chen, M. M. Tiao, Y. T. Hung, I. Y. Chen, W. T. Huang and P. W. Wang: Tissue-specific differences in mitochondrial DNA content in type 2 diabetes. Diab. Res. Clin. Pract., 92(1), 106-10 (2011)
DOI: 10.1016/j.diabres.2011.01.010

20. M. Wang, X. C. Wang, Z. Y. Zhang, B. Mou and R. M. Hu: Impaired mitochondrial oxidative phosphorylation in multiple insulin-sensitive tissues of humans with type 2 diabetes mellitus. J. Int. Med. Res., 38(3), 769-81 (2010)

21. J. Hakansson, B. Eliasson, U. Smith and S. Enerback: Adipocyte mitochondrial genes and the forkhead factor FOXC2 are decreased in type 2 diabetes patients and normalized in response to rosiglitazone. Diabet. Metab. Syndr., 3, 32 (2011)
DOI: 10.1186/1758-5996-3-32

22. H. K. Lee, J. H. Song, C. S. Shin, D. J. Park, K. S. Park, K. U. Lee and C. S. Koh: Decreased mitochondrial DNA content in peripheral blood precedes the development of non-insulin-dependent diabetes mellitus. Diab. Res. Clin. Pract., 42(3), 161-7 (1998)
DOI: 10.1016/S0168-8227(98)00110-7

23. C. D. Mathers and D. Loncar: Projections of global mortality and burden of disease from 2002 to 2030. PLoS Med, 3(11), e442 (2006
DOI: 10.1371/journal.pmed.0030442

24. K. D. Kochanek, J. Xu, S. L. Murphy, A. M. Minino and H. C. Kung: Deaths: final data for 2009. Natl Vital Stat Rep, 60(3), 1-116 (2011)

25. H. Lemieux and C. L. Hoppel: Mitochondria in the human heart. J Bioenerg Biomembr, 41(2), 99-106 (2009)
DOI: 10.1007/s10863-009-9211-0

26. A. Dorner and H. P. Schultheiss: The myocardial expression of the adenine nucleotide translocator isoforms is specifically altered in dilated cardiomyopathy. Herz, 25(3), 176-80 (2000)
DOI: 10.1007/s000590050004

27. Y. Tang, C. Mi, J. Liu, F. Gao and J. Long: Compromised mitochondrial remodeling in compensatory hypertrophied myocardium of spontaneously hypertensive rat. Cardiovasc Pathol, 23(2), 101-6 (2014)

28. K. Schwarz, N. Siddiqi, S. Singh, C. J. Neil, D. K. Dawson and M. P. Frenneaux: The breathing heart - mitochondrial respiratory chain dysfunction in cardiac disease. Int J Cardiol, 171(2), 134-43 (2014)
DOI: 10.1016/j.ijcard.2013.12.014

29. J. Wang, J. P. Silva, C. M. Gustafsson, P. Rustin and N. G. Larsson: Increased in vivo apoptosis in cells lacking mitochondrial DNA gene expression. Proc. Natl. Acad. Sci. USA, 98(7), 4038-43 (2001)
DOI: 10.1016/j.nutres.2013.02.005

30. T. Ide, H. Tsutsui, S. Hayashidani, D. Kang, N. Suematsu, K. Nakamura, H. Utsumi, N. Hamasaki and A. Takeshita: Mitochondrial DNA damage and dysfunction associated with oxidative stress in failing hearts after myocardial infarction. Circ. Res., 88(5), 529-35 (2001)
DOI: 10.1073/pnas.061038798

31. J. Liu and S. G. Lloyd: High-fat, low-carbohydrate diet alters myocardial oxidative stress and impairs recovery of cardiac function after ischemia and reperfusion in obese rats. Nutr. Res., 33(4), 311-21 (2013)
DOI: 10.1161/01.RES.88.5.529

32. G. Karamanlidis, L. Nascimben, G. S. Couper, P. S. Shekar, F. del Monte and R. Tian: Defective DNA replication impairs mitochondrial biogenesis in human failing hearts. Circ. Res., 106(9), 1541-8 (2010)
DOI: 10.1161/CIRCRESAHA.109.212753

33. A. Garnier, J. Zoll, D. Fortin, B. N’Guessan, F. Lefebvre, B. Geny, B. Mettauer, V. Veksler and R. Ventura-Clapier: Control by circulating factors of mitochondrial function and transcription cascade in heart failure: a role for endothelin-1 and angiotensin II. Circ. Heart Fail., 2(4), 342-50 (2009)
DOI: 10.1161/CIRCHEARTFAILURE.108.812099

34. R. W. Nesto and S. Zarich: Acute myocardial infarction in diabetes mellitus: lessons learned from ACE inhibition. Circulation, 97(1), 12-5 (1998)
DOI: 10.1161/01.CIR.97.1.12

35. F. M. Yakes and B. Van Houten: Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress. Proc Natl Acad Sci U S A, 94(2), 514-9 (1997)
DOI: 10.1073/pnas.94.2.514

36. D. Harman: Aging: a theory based on free radical and radiation chemistry. J Gerontol, 11(3), 298-300 (1956)
DOI: 10.1093/geronj/11.3.298

37. D. Harman: Free radical theory of aging: dietary implications. Am. J. Clin. Nutr., 25(8), 839-43 (1972)

38. C. Richter, J. W. Park and B. N. Ames: Normal oxidative damage to mitochondrial and nuclear DNA is extensive. Proc Natl Acad Sci U S A, 85(17), 6465-7 (1988)
DOI: 10.1073/pnas.85.17.6465

39. A. M. Furda, A. S. Bess, J. N. Meyer and B. Van Houten: Analysis of DNA damage and repair in nuclear and mitochondrial DNA of animal cells using quantitative PCR. Methods Mol Biol, 920, 111-32 (2012)
DOI: 10.1007/978-1-61779-998-3_9

40. R. Barazzoni, K. R. Short and K. S. Nair: Effects of aging on mitochondrial DNA copy number and cytochrome c oxidase gene expression in rat skeletal muscle, liver, and heart. J Biol Chem, 275(5), 3343-7 (2000)
DOI: 10.1074/jbc.275.5.3343

41. N. Hartmann, K. Reichwald, I. Wittig, S. Drose, S. Schmeisser, C. Luck, C. Hahn, M. Graf, U. Gausmann, E. Terzibasi, A. Cellerino, M. Ristow, U. Brandt, M. Platzer and C. Englert: Mitochondrial DNA copy number and function decrease with age in the short-lived fish Nothobranchius furzeri. Aging Cell, 10(5), 824-31 (2011)
DOI: 10.1111/j.1474-9726.2011.00723.x

42. L. M. Cree, S. K. Patel, A. Pyle, S. Lynn, D. M. Turnbull, P. F. Chinnery and M. Walker: Age-related decline in mitochondrial DNA copy number in isolated human pancreatic islets. Diabetologia, 51(8), 1440-3 (2008)
DOI: 10.1007/s00125-008-1054-4

43. K. R. Short, M. L. Bigelow, J. Kahl, R. Singh, J. Coenen-Schimke, S. Raghavakaimal and K. S. Nair: Decline in skeletal muscle mitochondrial function with aging in humans. Proc Natl Acad Sci U S A, 102(15), 5618-23 (2005)
DOI: 10.1073/pnas.0501559102

44. O. E. Rooyackers, D. B. Adey, P. A. Ades and K. S. Nair: Effect of age on in vivo rates of mitochondrial protein synthesis in human skeletal muscle. Proc Natl Acad Sci U S A, 93(26), 15364-9 (1996)
DOI: 10.1073/pnas.93.26.15364

45. D. C. Wallace, G. Singh, M. T. Lott, J. A. Hodge, T. G. Schurr, A. M. Lezza, L. J. Elsas, 2nd and E. K. Nikoskelainen: Mitochondrial DNA mutation associated with Leber’s hereditary optic neuropathy. Science, 242(4884), 1427-30 (1988)
DOI: 10.1126/science.3201231

46. I. J. Holt, A. E. Harding and J. A. Morgan-Hughes: Deletions of muscle mitochondrial DNA in patients with mitochondrial myopathies. Nature, 331(6158), 717-9 (1988)
DOI: 10.1038/331717a0

47. R. Rossignol, B. Faustin, C. Rocher, M. Malgat, J. P. Mazat and T. Letellier: Mitochondrial threshold effects. The Biochem J, 370(Pt 3), 751-62 (2003)
DOI: 10.1042/BJ20021594

48. Y. Tatuch, J. Christodoulou, A. Feigenbaum, J. T. Clarke, J. Wherret, C. Smith, N. Rudd, R. Petrova-Benedict and B. H. Robinson: Heteroplasmic mtDNA mutation (T----G) at 8993 can cause Leigh disease when the percentage of abnormal mtDNA is high. Am J Hum Genet, 50(4), 852-8 (1992)

49. M. Sciacco, E. Bonilla, E. A. Schon, S. DiMauro and C. T. Moraes: Distribution of wild-type and common deletion forms of mtDNA in normal and respiration-deficient muscle fibers from patients with mitochondrial myopathy. Hum Mol Genet, 3(1), 13-9 (1994)
DOI: 10.1093/hmg/3.1.13

50. J. Hayashi, S. Ohta, A. Kikuchi, M. Takemitsu, Y. Goto and I. Nonaka: Introduction of disease-related mitochondrial DNA deletions into HeLa cells lacking mitochondrial DNA results in mitochondrial dysfunction. Proc Natl Acad Sci USA, 88(23), 10614-8 (1991)
DOI: 10.1073/pnas.88.23.10614

51. W. K. Porteous, A. M. James, P. W. Sheard, C. M. Porteous, M. A. Packer, S. J. Hyslop, J. V. Melton, C. Y. Pang, Y. H. Wei and M. P. Murphy: Bioenergetic consequences of accumulating the common 4977-bp mitochondrial DNA deletion. European journal of biochemistry / FEBS, 257(1), 192-201 (1998)

52. A. W. El-Hattab and F. Scaglia: Mitochondrial DNA depletion syndromes: review and updates of genetic basis, manifestations, and therapeutic options. Neurotherap, 10(2), 186-98 (2013)
DOI: 10.1007/s13311-013-0177-6

53. A. Trifunovic, A. Wredenberg, M. Falkenberg, J. N. Spelbrink, A. T. Rovio, C. E. Bruder, Y. M. Bohlooly, S. Gidlof, A. Oldfors, R. Wibom, J. Tornell, H. T. Jacobs and N. G. Larsson: Premature ageing in mice expressing defective mitochondrial DNA polymerase. Nature, 429(6990), 417-23 (2004)
DOI: 10.1007/s13311-013-0177-6

54. R. W. Gilkerson, E. A. Schon, E. Hernandez and M. M. Davidson: Mitochondrial nucleoids maintain genetic autonomy but allow for functional complementation. J Cell Biol. 181(7), 1117-28 (2008)
DOI: 10.1083/jcb.200712101

55. F. Pallotti, A. Baracca, E. Hernandez-Rosa, W. F. Walker, G. Solaini, G. Lenaz, G. V. Melzi D’Eril, S. Dimauro, E. A. Schon and M. M. Davidson: Biochemical analysis of respiratory function in cybrid cell lines harbouring mitochondrial DNA mutations. Biochem J., 384(Pt 2), 287-93 (2004)
DOI: 10.1042/BJ20040561

56. S. Bannwarth, V. Procaccio, A. S. Lebre, C. Jardel, A. Chaussenot, C. Hoarau, H. Maoulida, N. Charrier, X. Gai, H. M. Xie, M. Ferre, K. Fragaki, G. Hardy, B. Mousson de Camaret, S. Marlin, C. M. Dhaenens, A. Slama, C. Rocher, J. Paul Bonnefont, A. Rotig, N. Aoutil, M. Gilleron, V. Desquiret-Dumas, P. Reynier, J. Ceresuela, L. Jonard, A. Devos, C. Espil-Taris, D. Martinez, P. Gaignard, K. H. Le Quan Sang, P. Amati-Bonneau, M. J. Falk, C. Florentz, B. Chabrol, I. Durand-Zaleski and V. Paquis-Flucklinger: Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders. J Med Genet, 50(10), 704-14 (2013)
DOI: 10.1136/jmedgenet-2013-101604

57. S. Bannwarth, V. Procaccio, A. S. Lebre, C. Jardel, A. Chaussenot, C. Hoarau, H. Maoulida, N. Charrier, X. Gai, H. M. Xie, M. Ferre, K. Fragaki, G. Hardy, B. Mousson de Camaret, S. Marlin, C. M. Dhaenens, A. Slama, C. Rocher, J. Paul Bonnefont, A. Rotig, N. Aoutil, M. Gilleron, V. Desquiret-Dumas, P. Reynier, J. Ceresuela, L. Jonard, A. Devos, C. Espil-Taris, D. Martinez, P. Gaignard, K. H. Le Quan Sang, P. Amati-Bonneau, M. J. Falk, C. Florentz, B. Chabrol, I. Durand-Zaleski and V. Paquis-Flucklinger: Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders. J Med Genet, 50(10), 704-14 (2013)
DOI: 10.1136/jmedgenet-2013-101604

58. C. Richter, J. W. Park and B. N. Ames: Normal oxidative damage to mitochondrial and nuclear DNA is extensive. Proc. Natl. Acad. Sci. USA, 85(17), 6465-7 (1988)
DOI: 10.1073/pnas.85.17.6465

59. G. C. Kujoth, A. Hiona, T. D. Pugh, S. Someya, K. Panzer, S. E. Wohlgemuth, T. Hofer, A. Y. Seo, R. Sullivan, W. A. Jobling, J. D. Morrow, H. Van Remmen, J. M. Sedivy, T. Yamasoba, M. Tanokura, R. Weindruch, C. Leeuwenburgh and T. A. Prolla: Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging. Science, 309(5733), 481-4 (2005)
DOI: 10.1126/science.1112125

60. I. Shokolenko, N. Venediktova, A. Bochkareva, G. L. Wilson and M. F. Alexeyev: Oxidative stress induces degradation of mitochondrial DNA. Nucl Acids Res, 37(8), 2539-48 (2009)
DOI: 10.1093/nar/gkp100

61. Y. Kraytsberg, E. Kudryavtseva, A. C. McKee, C. Geula, N. W. Kowall and K. Khrapko: Mitochondrial DNA deletions are abundant and cause functional impairment in aged human substantia nigra neurons. Nat Genet, 38(5), 518-20 (2006)
DOI: 10.1038/ng1778

62. A. Bender, K. J. Krishnan, C. M. Morris, G. A. Taylor, A. K. Reeve, R. H. Perry, E. Jaros, J. S. Hersheson, J. Betts, T. Klopstock, R. W. Taylor and D. M. Turnbull: High levels of mitochondrial DNA deletions in substantia nigra neurons in aging and Parkinson disease. Nat Genet, 38(5), 515-7 (2006)
DOI: 10.1038/ng1769

63. G. R. Campbell, Y. Kraytsberg, K. J. Krishnan, N. Ohno, I. Ziabreva, A. Reeve, B. D. Trapp, J. Newcombe, R. Reynolds, H. Lassmann, K. Khrapko, D. M. Turnbull and D. J. Mahad: Clonally expanded mitochondrial DNA deletions within the choroid plexus in multiple sclerosis. Acta Neuropathol, 124(2), 209-20 (2012)
DOI: 10.1007/s00401-012-1001-9

64. H. Fukui and C. T. Moraes: Mechanisms of formation and accumulation of mitochondrial DNA deletions in aging neurons. Hum Mol Genet, 18(6), 1028-36 (2009) doi:10.1.093/hmg/ddn437
DOI: 10.1093/hmg/ddn437

65. B. A. Kaufman, N. Durisic, J. M. Mativetsky, S. Costantino, M. A. Hancock, P. Grutter and E. A. Shoubridge: The mitochondrial transcription factor TFAM coordinates the assembly of multiple DNA molecules into nucleoid-like structures. Mol Biol Cell, 18(9), 3225-36 (2007)
DOI: 10.1091/mbc.E07-05-0404

66. T. Kanki, K. Ohgaki, M. Gaspari, C. M. Gustafsson, A. Fukuoh, N. Sasaki, N. Hamasaki and D. Kang: Architectural role of mitochondrial transcription factor A in maintenance of human mitochondrial DNA. Mol Cell Biol, 24(22), 9823-34 (2004)
DOI: 10.1128/MCB.24.22.9823-9834.2004

67. Y. Matsushima, Y. Goto and L. S. Kaguni: Mitochondrial Lon protease regulates mitochondrial DNA copy number and transcription by selective degradation of mitochondrial transcription factor A (TFAM). Proc Natl Acad Sci USA, 107(43), 18410-5 (2010)
DOI: 10.1073/pnas.1008924107

68. N. Vadrot, S. Ghanem, F. Braut, L. Gavrilescu, N. Pilard, A. Mansouri, R. Moreau and F. Reyl-Desmars: Mitochondrial DNA maintenance is regulated in human hepatoma cells by glycogen synthase kinase 3beta and p53 in response to tumor necrosis factor alpha. PloS one, 7(7), e40879 (2012)
DOI: 10.1371/journal.pone.0040879

69. H. B. Suliman, K. E. Welty-Wolf, M. S. Carraway, D. A. Schwartz, J. W. Hollingsworth and C. A. Piantadosi: Toll-like receptor 4 mediates mitochondrial DNA damage and biogenic responses after heat-inactivated E. coli. FASEB J, 19(11), 1531-3 (2005)

70. A. Mathew, T. A. Lindsley, A. Sheridan, D. L. Bhoiwala, S. F. Hushmendy, E. J. Yager, E. A. Ruggiero and D. R. Crawford: Degraded mitochondrial DNA is a newly identified subtype of the damage associated molecular pattern (DAMP) family and possible trigger of neurodegeneration. Journal of Alzheimer’s disease : JAD, 30(3), 617-27 (2012)

71. W. W. Chaung, R. Wu, Y. Ji, W. Dong and P. Wang: Mitochondrial transcription factor A is a proinflammatory mediator in hemorrhagic shock. Int J Mol Med, 30(1), 199-203 (2012)

72. V. P. Skulachev, L. E. Bakeeva, B. V. Chernyak, L. V. Domnina, A. A. Minin, O. Y. Pletjushkina, V. B. Saprunova, I. V. Skulachev, V. G. Tsyplenkova, J. M. Vasiliev, L. S. Yaguzhinsky and D. B. Zorov: Thread-grain transition of mitochondrial reticulum as a step of mitoptosis and apoptosis. Mol Cell Biochem, 256-257(1-2), 341-58 (2004)
DOI: 10.1023/B:MCBI.0000009880.94044.49

73. Y. Yoon, E. W. Krueger, B. J. Oswald and M. A. McNiven: The mitochondrial protein hFis1 regulates mitochondrial fission in mammalian cells through an interaction with the dynamin-like protein DLP1. Mol Cell Biol, 23(15), 5409-20 (2003)
DOI: 10.1128/MCB.23.15.5409-5420.2003

74. S. Gandre-Babbe and A. M. van der Bliek: The novel tail-anchored membrane protein Mff controls mitochondrial and peroxisomal fission in mammalian cells. Mol Biol Cell, 19(6), 2402-12 (2008)
DOI: 10.1091/mbc.E07-12-1287

75. H. Chen, A. Chomyn and D. C. Chan: Disruption of fusion results in mitochondrial heterogeneity and dysfunction. J Biol Chem, 280(28), 26185-92 (2005)
DOI: 10.1074/jbc.M503062200

76. A. Olichon, L. Baricault, N. Gas, E. Guillou, A. Valette, P. Belenguer and G. Lenaers: Loss of OPA1 perturbates the mitochondrial inner membrane structure and integrity, leading to cytochrome c release and apoptosis. J Biol Chem, 278(10), 7743-6 (2003)
DOI: 10.1074/jbc.C200677200

77. L. Griparic, N. N. van der Wel, I. J. Orozco, P. J. Peters and A. M. van der Bliek: Loss of the intermembrane space protein Mgm1/OPA1 induces swelling and localized constrictions along the lengths of mitochondria. J Biol Chem, 279(18), 18792-8 (2004)
DOI: 10.1074/jbc.M400920200

78. D. H. Margineantu, W. Gregory Cox, L. Sundell, S. W. Sherwood, J. M. Beechem and R. A. Capaldi: Cell cycle dependent morphology changes and associated mitochondrial DNA redistribution in mitochondria of human cell lines. Mitochondrion, 1(5), 425-35 (2002)
DOI: 10.1074/jbc.M400920200

79. F. J. Iborra, H. Kimura and P. R. Cook: The functional organization of mitochondrial genomes in human cells. BMC Biol, 2, 9 (2004)
DOI: 10.1186/1741-7007-2-9

80. R. Ban-Ishihara, T. Ishihara, N. Sasaki, K. Mihara and N. Ishihara: Dynamics of nucleoid structure regulated by mitochondrial fission contributes to cristae reformation and release of cytochrome c. Proc Natl Acad Sci USA, 110(29), 11863-8 (2013)
DOI: 10.1073/pnas.1301951110

81. J. He, H. M. Cooper, A. Reyes, M. Di Re, H. Sembongi, T. R. Litwin, J. Gao, K. C. Neuman, I. M. Fearnley, A. Spinazzola, J. E. Walker and I. J. Holt: Mitochondrial nucleoid interacting proteins support mitochondrial protein synthesis. Nucl Acids Res, 40(13), 6109-21 (2012)
DOI: 10.1093/nar/gks266

82. R. W. Gilkerson, D. H. Margineantu, R. A. Capaldi and J. M. Selker: Mitochondrial DNA depletion causes morphological changes in the mitochondrial reticulum of cultured human cells. FEBS letters, 474(1), 1-4 (2000)
DOI: 10.1016/S0014-5793(00)01527-1

83. M. Karbowski, C. Kurono, M. Wozniak, M. Ostrowski, M. Teranishi, Y. Nishizawa, J. Usukura, T. Soji and T. Wakabayashi: Free radical-induced megamitochondria formation and apoptosis. Free Radic Biol Med, 26(3-4), 396-409 (1999)
DOI: 10.1016/S0891-5849(98)00209-3

84. L. Griparic, T. Kanazawa and A. M. van der Bliek: Regulation of the mitochondrial dynamin-like protein Opa1 by proteolytic cleavage. J Cell Biol, 178(5), 757-64 (2007)
DOI: 10.1083/jcb.200704112

85. B. Head, L. Griparic, M. Amiri, S. Gandre-Babbe and A. M. van der Bliek: Inducible proteolytic inactivation of OPA1 mediated by the OMA1 protease in mammalian cells. J Cell Biol, 187(7), 959-66 (2009)
DOI: 10.1083/jcb.200906083

86. S. Ehses, I. Raschke, G. Mancuso, A. Bernacchia, S. Geimer, D. Tondera, J. C. Martinou, B. Westermann, E. I. Rugarli and T. Langer: Regulation of OPA1 processing and mitochondrial fusion by m-AAA protease isoenzymes and OMA1. J Cell Biol, 187(7), 1023-36 (2009)
DOI: 10.1083/jcb.200906084

87. M. P. King and G. Attardi: Human cells lacking mtDNA: repopulation with exogenous mitochondria by complementation. Science, 246(4929), 500-3 (1989)
DOI: 10.1126/science.2814477

88. W. Qian and B. Van Houten: Alterations in bioenergetics due to changes in mitochondrial DNA copy number. Methods, 51(4), 452-7 (2010)
DOI: 10.1016/j.ymeth.2010.03.006

89. M. F. Marusich, B. H. Robinson, J. W. Taanman, S. J. Kim, R. Schillace, J. L. Smith and R. A. Capaldi: Expression of mtDNA and nDNA encoded respiratory chain proteins in chemically and genetically-derived Rho0 human fibroblasts: a comparison of subunit proteins in normal fibroblasts treated with ethidium bromide and fibroblasts from a patient with mtDNA depletion syndrome. Biochim Biophys Acta, 1362(2-3), 145-59 (1997)
DOI: 10.1016/S0925-4439(97)00061-6

90. R. W. Gilkerson, R. L. De Vries, P. Lebot, J. D. Wikstrom, E. Torgyekes, O. S. Shirihai, S. Przedborski and E. A. Schon: Mitochondrial autophagy in cells with mtDNA mutations results from synergistic loss of transmembrane potential and mTORC1 inhibition. Hum. Mol. Genet., 21(5), 978-90 (2012)
DOI: 10.1093/hmg/ddr529

91. K. Buchet and C. Godinot: Functional F1-ATPase essential in maintaining growth and membrane potential of human mitochondrial DNA-depleted rho degrees cells. J Biol Chem, 273(36), 22983-9 (1998)
DOI: 10.1074/jbc.273.36.22983

92. J. F. Kerr, A. H. Wyllie and A. R. Currie: Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics. Br J Cancer, 26(4), 239-57 (1972)
DOI: 10.1038/bjc.1972.33

93. M. D. Jacobson, M. Weil and M. C. Raff: Programmed cell death in animal development. Cell, 88(3), 347-54 (1997)
DOI: 10.1016/S0092-8674(00)81873-5

94. D. R. Green: ‘Tit-for-tat’ in cell biology. Nat Rev Mol Cell Biol, 12(2), 73 (2011)
DOI: 10.1038/nrm3054

95. C. J. Norbury and I. D. Hickson: Cellular responses to DNA damage. Annu Rev Pharmacol Toxicol, 41, 367-401 (2001)
DOI: 10.1146/annurev.pharmtox.41.1.367

96. K. F. Ferri and G. Kroemer: Mitochondria--the suicide organelles. Bioessays, 23(2), 111-5 (2001)

97. M. Enari, H. Sakahira, H. Yokoyama, K. Okawa, A. Iwamatsu and S. Nagata: A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD. Nature, 391(6662), 43-50 (1998)
DOI: 10.1038/34112

98. M. Peltz, T. T. He, G. A. t. Adams, R. Y. Chao and M. E. Jessen: Myocardial oxygen demand and redox state affect fatty acid oxidation in the potassium-arrested heart. Surgery, 136(2), 150-9 (2004)
DOI: 10.1016/j.surg.2004.04.007

99. P. Juo, C. J. Kuo, J. Yuan and J. Blenis: Essential requirement for caspase-8/FLICE in the initiation of the Fas-induced apoptotic cascade. Curr Biol, 8(18), 1001-8 (1998)

100. D. Brenner and T. W. Mak: Mitochondrial cell death effectors. Curr Opin Cell Biol, 21(6), 871-7 (2009)
DOI: 10.1016/j.ceb.2009.09.004

101. E. N. Shiozaki, J. Chai and Y. Shi: Oligomerization and activation of caspase-9, induced by Apaf-1 CARD. Proc Natl Acad Sci U S A, 99(7), 4197-202 (2002)
DOI: 10.1073/pnas.072544399

102. D. R. Green: Means to an end. Cold Spring Harbor Laboratory Press, Cold Spring Harbor (2011)

103. D. Acehan, X. Jiang, D. G. Morgan, J. E. Heuser, X. Wang and C. W. Akey: Three-dimensional structure of the apoptosome: implications for assembly, procaspase-9 binding, and activation. Mol Cell, 9(2), 423-32 (2002)
DOI: 10.1016/S1097-2765(02)00442-2

104. G. Kroemer, N. Zamzami and S. A. Susin: Mitochondrial control of apoptosis. Immunol Today, 18(1), 44-51 (1997)
DOI: 10.1016/S0167-5699(97)80014-X

105. J. Collins, C. Schadi, K. Young, J. Vesely and M. Willingham: Major DNA Fragmentation Is a Late Event in Apoptosis. J. Histochem. Cytochem., 45(7) (1997)

106. E. Bossy-Wetzel, D. D. Newmeyer and D. R. Green: Mitochondrial cytochrome c release in apoptosis occurs upstream of DEVD-specific caspase activation and independently of mitochondrial transmembrane depolarization. EMBO J, 17(1), 37-49 (1998)
DOI: 10.1093/emboj/17.1.37

107. S. Jiang, J. Cai, D. C. Wallace and D. P. Jones: Cytochrome c-mediated apoptosis in cells lacking mitochondrial DNA. Signaling pathway involving release and caspase 3 activation is conserved. J Biol Chem, 274(42), 29905-11 (1999)
DOI: 10.1074/jbc.274.42.29905

108. M. Marella, B. B. Seo, A. Matsuno-Yagi and T. Yagi: Mechanism of cell death caused by complex I defects in a rat dopaminergic cell line. J Biol Chem, 282(33), 24146-56 (2007)
DOI: 10.1074/jbc.M701819200

109. A. H. Remels, H. R. Gosker, P. Schrauwen, P. P. Hommelberg, P. Sliwinski, M. Polkey, J. Galdiz, E. F. Wouters, R. C. Langen and A. M. Schols: TNF-alpha impairs regulation of muscle oxidative phenotype: implications for cachexia? FASEB J., 24(12), 5052-62 (2010)

110. A. Nechushtan, C. L. Smith, I. Lamensdorf, S. H. Yoon and R. J. Youle: Bax and Bak coalesce into novel mitochondria-associated clusters during apoptosis. J Cell Biol, 153(6), 1265-76 (2001)
DOI: 10.1083/jcb.153.6.1265

111. X. Liu, C. N. Kim, J. Yang, R. Jemmerson and X. Wang: Induction of apoptotic program in cell-free extracts: requirement for dATP and cytochrome c. Cell, 86(1), 147-57 (1996)
DOI: 10.1016/S0092-8674(00)80085-9

112. C. Du, M. Fang, Y. Li, L. Li and X. Wang: Smac, a mitochondrial protein that promotes cytochrome c-dependent caspase activation by eliminating IAP inhibition. Cell, 102(1), 33-42 (2000)
DOI: 10.1016/S0092-8674(00)00008-8

113. S. A. Susin, H. K. Lorenzo, N. Zamzami, I. Marzo, B. E. Snow, G. M. Brothers, J. Mangion, E. Jacotot, P. Costantini, M. Loeffler, N. Larochette, D. R. Goodlett, R. Aebersold, D. P. Siderovski, J. M. Penninger and G. Kroemer: Molecular characterization of mitochondrial apoptosis-inducing factor. Nature, 397(6718), 441-6 (1999)
DOI: 10.1038/17135

114. L. Y. Li, X. Luo and X. Wang: Endonuclease G is an apoptotic DNase when released from mitochondria. Nature, 412(6842), 95-9 (2001)
DOI: 10.1038/35083620
DOI: 10.1038/35084037

115. B. Baliga and S. Kumar: Apaf-1/cytochrome c apoptosome: an essential initiator of caspase activation or just a sideshow? Cell Death Differ, 10(1), 16-8 (2003)
DOI: 10.1038/sj.cdd.4401166

116. A. W. Tann, I. Boldogh, G. Meiss, W. Qian, B. Van Houten, S. Mitra and B. Szczesny: Apoptosis Induced by Persistent Single-strand Breaks in Mitochondrial Genome: CRITICAL ROLE OF EXOG (5’-EXO/ENDONUCLEASE) IN THEIR REPAIR. J. Biol. Chem., 286(37), 31975-83 (2011)
DOI: 10.1074/jbc.M110.215715

117. M. D. Jacobson, J. F. Burne, M. P. King, T. Miyashita, J. C. Reed and M. C. Raff: Bcl-2 blocks apoptosis in cells lacking mitochondrial DNA. Nature, 361(6410), 365-9 (1993)
DOI: 10.1038/361365a0

118. J. Q. Kwong, M. S. Henning, A. A. Starkov and G. Manfredi: The mitochondrial respiratory chain is a modulator of apoptosis. J. Cell Biol., 179(6), 1163-77 (2007)
DOI: 10.1038/361365a0

119. P. A. Parone, D. I. James, S. Da Cruz, Y. Mattenberger, O. Donze, F. Barja and J. C. Martinou: Inhibiting the mitochondrial fission machinery does not prevent Bax/Bak-dependent apoptosis. Mol Cell Biol, 26(20), 7397-408 (2006)
DOI: 10.1128/MCB.02282-05

120. S. Wasiak, R. Zunino and H. M. McBride: Bax/Bak promote sumoylation of DRP1 and its stable association with mitochondria during apoptotic cell death. J Cell Biol, 177(3), 439-50 (2007)
DOI: 10.1083/jcb.200610042

121. M. Germain, J. P. Mathai, H. M. McBride and G. C. Shore: Endoplasmic reticulum BIK initiates DRP1-regulated remodelling of mitochondrial cristae during apoptosis. EMBO J, 24(8), 1546-56 (2005)
DOI: 10.1038/sj.emboj.7600592

122. S. Frank, B. Gaume, E. S. Bergmann-Leitner, W. W. Leitner, E. G. Robert, F. Catez, C. L. Smith and R. J. Youle: The role of dynamin-related protein 1, a mediator of mitochondrial fission, in apoptosis. Dev Cell, 1(4), 515-25 (2001)
DOI: 10.1016/S1534-5807(01)00055-7

123. S. Montessuit, S. P. Somasekharan, O. Terrones, S. Lucken-Ardjomande, S. Herzig, R. Schwarzenbacher, D. J. Manstein, E. Bossy-Wetzel, G. Basanez, P. Meda and J. C. Martinou: Membrane remodeling induced by the dynamin-related protein Drp1 stimulates Bax oligomerization. Cell, 142(6), 889-901 (2010)
DOI: 10.1016/j.cell.2010.08.017

124. Y. E. Kushnareva, A. A. Gerencser, B. Bossy, W. K. Ju, A. D. White, J. Waggoner, M. H. Ellisman, G. Perkins and E. Bossy-Wetzel: Loss of OPA1 disturbs cellular calcium homeostasis and sensitizes for excitotoxicity. Cell Death Diff., 20(2), 353-65 (2013)
DOI: 10.1038/cdd.2012.128

125. E. Owusu-Ansah, A. Yavari, S. Mandal and U. Banerjee: Distinct mitochondrial retrograde signals control the G1-S cell cycle checkpoint. Nature genetics, 40(3), 356-61 (2008)
DOI: 10.1038/ng.2007.50