Mitochondrial function and mitochondrial DNA maintenance with advancing age

Biogerontology

Volumn 15, Issue 5, 2014, Pages 417-438

  Gaziev, Azhub I ^a   Abdullaev, Serzh ^a   Podlutsky, Andrej ^b  

^a INSTITUTE OF THEORETICAL AND EXPERIMENTAL BIOPHYSICS   (Russian Federation)

^b UNIVERSITY OF ALASKA FAIRBANKS   (United States)

Author keywords

Aging; Mitochondrial biogenesis; Mitochondrial DNA (mtDNA); Mitochondrial dynamics; Mitophagy

Indexed keywords

DNA BASE; MITOCHONDRIAL DNA; NITROGEN DERIVATIVE; REACTIVE OXYGEN METABOLITE; ANTIOXIDANT; REACTIVE NITROGEN SPECIES;

AGE; AGING; BIOGENESIS; DNA DAMAGE; DNA DEGRADATION; DNA PACKAGING; DNA REPAIR; EXCISION REPAIR; GENE CONTROL; GENE DOSAGE; GENOMIC INSTABILITY; HUMAN; MITOCHONDRIAL DNA REPLICATION; MITOCHONDRIAL DYNAMICS; MITOCHONDRION; MITOPHAGY; MUTAGENESIS; MUTATION RATE; OXIDATIVE PHOSPHORYLATION; OXIDATIVE STRESS; PRIORITY JOURNAL; REVIEW; ANIMAL; AUTOPHAGY; GENETICS; METABOLISM; PATHOLOGY;

AGING; ANIMALS; ANTIOXIDANTS; AUTOPHAGY; DNA DAMAGE; DNA PACKAGING; DNA REPAIR; DNA, MITOCHONDRIAL; HUMANS; MITOCHONDRIA; MITOCHONDRIAL DEGRADATION; MUTAGENESIS; REACTIVE NITROGEN SPECIES; REACTIVE OXYGEN SPECIES;

EID: 84906937543     PISSN: 13895729     EISSN: 15736768     Source Type: Journal    
DOI: 10.1007/s10522-014-9515-2     Document Type: Review

References (254)

1. Abdullaev SA, Antipova VN, Gaziev AI (2009) Extracellular mutant mitochondrial DNA content is sharply elevated in the blood plasma of irradiated mice. Mol Biol (Mosk) 43:1063-1069
2. Akbari M, Keijzers G, Maynard S et al (2014) Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair. DNA Repair (Amst) 16:44-53
3. Alexeyev MF (2009) Is there more to aging than mitochondrial DNA and reactive oxygen species? FEBS J 276:5768-5787
4. Ameur A, Stewart JB, Freyer C et al (2011) Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins. PLoS Genet 7(3):e1002028. doi:10.1371/journal.pgen.1002028
5. Anand R, Langer T, Baker MJ (2013) Proteolytic control of mitochondrial function and morphogenesis. Biochim Biophys Acta 1833:195-204
6. Anisimov VN, Bartke A (2013) The key role of growth hormone-insulin-IGF-1 signaling in aging and cancer. Crit Rev Oncol Hematol 87:201-223
7. Anisimov VN, Zabezhinski MA, Popovich IG et al (2011) Rapamycin increases lifespan and inhibits spontaneous tumorigenesis in inbred female mice. Cell Cycle 10:4230-4236
8. Anson RM, Senturker S, Dizdaroglu M, Bohr VA (1999) Measurement of oxidatively induced base lesions in liver from Wistar rats of different ages. Free Radic Boil Med 27:456-462 (Pubitemid 29395441)
9. Antico AVG, Elguero ME, Poderoso JJ, Carreras MC (2012) Mitochondrial regulation of cell cycle and proliferation. Antioxid Redox Signal 16:1150-1180
10. Ashrafi G, Schwarz TL (2013) The pathways of mitophagy for quality control and clearance of mitochondria. Cell Death Differ 20:31-42
11. Ayer A, Tan SX, Grant CM et al (2010) The critical role of glutathione in maintenance of the mitochondrial genome. Free Radic Biol Med 49:1956-1968
12. Azzam EI, Jay-Gerin JP, Pain D (2012) Ionizing radiation-induced metabolic oxidative stress and prolonged cell injury. Cancer Lett 327(1-2):48-60. doi:10.1016/j.canlet.2011.12.012
13. Babbar M, Sheikh MS (2013) Metabolic stress and disorders related to alterations in mitochondrial fission or fusion. Mol Cell Pharmacol 5(3):109-133
14. Barja G (2013) Updating the mitochondrial free radical theory of aging: an integrated view, key aspects, and confounding concepts. Antioxid Redox Signal 19:1420-1445
15. Barja G, Herrero A (2000) Oxidative damage to mitochondrial DNA is inversely related to maximum life span in the heart and brain of mammals. FASEB J 14:312-318 (Pubitemid 30086068)
16. Barnes DE, Lindahl T (2004) Repair and genetic consequences of endogenous DNA base damage in mammalian cells. Annu Rev Genet 38:445-476 (Pubitemid 40013735)
17. Bartoletti-Stella A, Mariani E, Kurelac I et al (2013) Gamma rays induce a p53-independent mitochondrial biogenesis that is counter-regulated by HIF1a. Cell Death Dis 4:e663. doi:10.1038/cddis.2013.187
18. Bender A, Krishnan KJ, Morris CM et al (2006) High levels of mitochondrial DNA deletions in substantia nigra neurons in aging and Parkinson disease. Nat Genet 38:515-517
19. Bereiter-Hahn J, Jendrach M (2010) Mitochondrial dynamics. Int Rev Cell Mol Biol 284:1-65
20. Bilal E, Rabadan R, Alexe G et al (2008) Mitochondrial DNA haplogroup D4a Is a marker for extreme longevity in Japan. PLoS One 3(6):e2421. doi:10.1371/journal.pone.0002421
21. Bjelakovic G, Nikolova D, Gluud LL et al (2012) Antioxidant supplements for prevention of mortality in healthy participants and patients with various diseases. Cochrane Database Syst Rev 14(3):CD007176
22. Blagosklonny MV, Campisi J, Sinclair DA et al (2010) Impact papers on aging in 2009. Aging (Albany NY) 2:111-121
23. Bogenhagen DF (2012) Mitochondrial DNA nucleoid structure. Biochim Biophys Acta 1819:914-920
24. Borrás C, Gómez-Cabrera MC, Viña J (2011) The dual role of p53: DNA protection and antioxidant. Free Radic Res 45:643-652
25. Bradley MO, Kohn KW (1979) X-ray induced DNA double strand break production and repair in mammalian cells as measured by neutral filter elution. Nucleic Acids Res 7:793-804
26. Bratic A, Larsson NG (2013) The role of mitochondria in aging. J Clin Invest 123:951-957
27. Broderick S, Rehmet K, Concannon C, Nasheuer HP (2010) Eukaryotic single-stranded DNA binding proteins: central factors in genome stability. Subcell Biochem 50:143-163
28. Bua E, Johnson J, Herbst A et al (2006) Mitochondrial DNA-deletion mutations accumulate intracellularly to detrimental levels in aged human skeletal muscle fibers. Am J Hum Genet 79:469-480 (Pubitemid 44384256)
29. Burbulla LF, Fitzgerald JC, Stegen K et al (2014) Mitochondrial proteolytic stress induced by loss of mortalin function is rescued by Parkin and PINK1. Cell Death Dis 5:e1180. doi:10.1038/cddis.2014.103
30. Calvo SE, Mootha VK (2010) The mitochondrial proteome and human disease. Annu Rev Genomics Hum Genet 11:25-44. doi:10.1146/annurev-genom-082509-141720
31. Campbell CT, Kolesar JE, Kaufman BA (2012) Mitochondrial transcription factor A regulates mitochondrial transcription initiation, DNA packaging, and genome copy number. Biochim Biophys Acta 1819:921-929
32. Candas D, Fan M, Nantajit D et al (2013) CyclinB1/Cdk1 phosphorylates mitochondrial antioxidant MnSOD in cell adaptive response to radiation stress. J Mol Cell Biol 5:166-175
33. Caron F, Jacq C, Rouviere-Yaniv J (1979) Characterization of a histone-like protein extracted from yeast mitochondria. Proc Natl Acad Sci USA 76:4265-4269 (Pubitemid 9256542)
34. Carraway MS, Suliman HB, Kliment C et al (2008) Mitochondrial biogenesis in the pulmonary vasculature during inhalational lung injury and fibrosis. Antioxid Redox Signal 10:269-275
35. Cavallini G, Donati A, Capasso B et al (2014) Effects of stimulation of autophagy on the urinary excretion of biomarkers of the oxidative status. Aging Clin Exp Res 26:13-18. doi:10.1007/s40520-013-0116-8
36. Chan DC (2012) Fusion and fission: interlinked processes critical for mitochondrial health. Annu Rev Genet 46:265-287
37. Chauhan A, Vera J, Wolkenhauer O (2014) The systems biology of mitochondrial fission and fusion and implications for disease and aging. Biogerontology 15(1):1-12
38. Chen Y, Dorn II GW (2013) PINK1-phosphorylated mitofusin 2 is a Parkin receptor for culling damaged mitochondria. Science 340:471-475
39. Chen D, Cao G, Hastings T et al (2002) Age-dependent decline of DNA repair activity for oxidative lesions in rat brain mitochondria. J Neurochem 81:1273-1284 (Pubitemid 34809261)
40. Chen JQ, Cammarata PR, Baines CP, Yager JD (2009) Regulation of mitochondrial respiratory chain biogenesis by estrogens/estrogen receptors and physiological, pathological and pharmacological implications. Biochim Biophys Acta 1793:1540-1570
41. Chinnery PF, Hudson G (2013) Mitochondrial genetics. Br Med Bull 106:135-159
42. Choi YS, Hoon JJ, Min HK et al (2011) Shot-gun proteomic analysis of mitochondrial D-loop DNA binding proteins: identification of mitochondrial histones. Mol BioSyst 7:1523-1536
43. Chu CT, Ji J, Dagda RK et al (2013) Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells. Nature Cell Biol 15:1197-1205
44. Civitarese AE, Carling S, Heilbronn LK et al (2007) Calorie restriction increases muscle mitochondrial biogenesis in healthy humans. PLoS Med. 4(3):e76
45. Clayton DA (2003) Mitochondrial DNA replication: what we know. IUBMB Life 55:213-217
46. Clayton DA, Doda JN, Friedberg EC (1974) The absence of a pyrimidine dimer repair mechanism in mammalian mitochondria. Proc Natl Acad Sci USA 71:2777-2781
47. Copeland WC (2012) Defects in mitochondrial DNA replication and human disease. Crit Rev Biochem Mol Biol 47:64-74
48. Crane JD, Abadi A, Hettinga BP et al (2013) Elevated mitochondrial oxidative stress impairs metabolic adaptations to exercise in skeletal muscle. PLoS One 8(12):e81879. doi:10.1371/journal.pone.0081879
49. Crawford DR, Abramova NE, Davies KJ (1998) Oxidative stress causes a general, calcium- dependent degradation of mitochondrial polynucleotides. Free Radic Biol Med 25:1106-1111 (Pubitemid 28558338)
50. Cuervo AM (2008) Autophagy and aging: keeping that old broom working. Trends Genet 24:604-612
51. Dahm-Daphi J, Sass C, Alberti W (2000) Comparison of biological effects of DNA damage induced by ionizing radiation and hydrogen peroxide in CHO cells. Int J Radiat Biol 76:67-75 (Pubitemid 30048028)
52. Dai Y, Zheng K, Clark J, Swerdlow RH et al (2014) Rapamycin drives selection against a pathogenic heteroplasmic mitochondrial DNA mutation. Hum Mol Genet 23:637-647
53. Das S, Mitrovsky G, Vasanthi HR, Das DK (2014) Antiaging properties of a grape-derived antioxidant are regulated by mitochondrial balance of fusion and fission leading to mitophagy triggered by a signaling network of Sirt1-Sirt3-Foxo3-PINK1-PARKIN. Oxid Med Cell Longev. doi:10.1155/2014/345105
54. Deng H, Yuan L (2014) Genetic variants and animal models in SNCA and Parkinson disease. Ageing Res Rev 15:161-176
55. Derbré F, Gomez-Cabrera MC, Nascimento AL et al (2012) Age associated low mitochondrial biogenesis may be explained by lack of response of PGC-1α to exercise training. Age (Dordr) 34:669-679
56. Dillon LM, Williams SL, Hida A et al (2012) Increased mitochondrial biogenesis in muscle improves aging phenotypes in the mtDNA mutator mouse. Hum Mol Genet 21:2288-2297
57. Dominy JE, Puigserver P (2013) Mitochondrial biogenesis through activation of nuclear signaling proteins. Cold Spring Harb Perspect Biol. doi:10.1101/cshperspect.a015008
58. Donati A, Cavallini G, Paradiso C et al (2001) Age-related changes in the autophagic proteolysis of rat isolated liver cells: effects of antiaging dietary restrictions. J Gerontol A Biol Sci Med Sci 56:B375-B383 (Pubitemid 32816727)
59. Eldridge A, Fan M, Woloschak G et al (2012) Manganese superoxide dismutase interacts with a large scale of cellular and mitochondrial proteins in low-dose radiation-induced adaptive radioprotection. Free Radic Biol Med 53:1838-1847
60. Ellenberger T, Tomkinson AE (2008) Eukaryotic DNA ligases: structural and functional insights. Annu Rev Biochem 77:313-338
61. Elson JL, Samuels DC, Turnbull DM, Chinnery PF (2001) Random intracellular drift explains the clonal expansion of mitochondrial DNA mutations with age. Am J Hum Genet 68:802-806 (Pubitemid 32202775)
62. ESCODD, European Standards Committee on Oxidative DNA Damage (2003) Measurement of DNA oxidation in human cells by chromatographic and enzymic methods. Free Radic Boil Med 34:1089-1099
63. Estaquier J, Vallette F, Vayssiere JL, Mignotte B (2012) The mitochondrial pathways of apoptosis. Adv Exp Med Biol 942:157-183
64. Evans MD, Dizdaroglu M, Cooke MS (2004) Oxidative DNA damage and disease: induction, repair and significance. Mutat Res 567:1-61 (Pubitemid 39162992)
65. Evdokimovsky EV, Ushakova TE, Kudriavtcev AA, Gaziev AI (2011) Alteration of mtDNA copy number, mitochondrial gene expression and extracellular DNA content in mice after irradiation. Radiat Environ Biophys 50:181-188
66. Falkenberg M, Larsson NG, Gustafsson CM (2007) DNA replication and transcription in mammalian mitochondria. Annu Rev Biochem 76:679-699
67. Figge MT, Osiewacz HD, Reichert AS (2013) Quality control of mitochondria during aging: Is there a good and a bad side of mitochondrial dynamics? BioEssays 35:314-322
68. Finley LW, Haigis MC (2009) The coordination of nuclear and mitochondrial communication during aging and calorie restriction. Ageing Res Rev 8:173-188
69. Frahm T, Mohamed SA, Bruse P et al (2005) Lack of age-related increase of mitochondrial DNA amount in brain, skeletal muscle and human heart. Mech Ageing Dev 126:1192-1200 (Pubitemid 41356520)
70. Frank M, Duvezin-Caubet S, Koob S et al (2012) Mitophagy is triggered by mild oxidative stress in a mitochondrial fission dependent manner. Biochim Biophys Acta 1823:2297-2310
71. Furda AM, Marrangoni AM, Lokshin A, Van Houten B (2012) Oxidants and not alkylating agents induce rapid mtDNA loss and mitochondrial dysfunction. DNA Repair (Amst) 11:684-692
72. Gaweda-Walerych K, Zekanowski C (2013) Integrated pathways of Parkin control over mitochondrial maintenancerelevance to Parkinson's disease pathogenesis. Acta Neurobiol Exp (Wars) 73:199-224
73. Gaziev AI (1999) DNA damage in cells exposed to ionizing radiation. Radiat Biol Radioecol 39:630-639
74. Gaziev AI (2013) Pathways for maintenance of mitochondrial DNA integrity and mitochondrial functions in cells exposed to ionizing radiation. Radiat Biol Radioecol 53:117-136
75. Gaziev AI, Podlutsky AI (2003) Low efficiency of DNA repair system in mitochondria. Tsitologya 45:403-417
76. Gaziev AI, Shaikhaev GO (2012) Limited repair of critical DNA damage in cells exposed to low dose radiation. In: Nenoi M (ed) Current topics in ionizing radiation research. InTech, Rijeka, pp 51-80
77. Gelino S, Hansen M (2013) Autophagy-an emerging antiaging mechanism. J Clin Exp Pathol 4:1-24
78. Gilkerson RW, De Vries RL, Lebot P et al (2012) Mitochondrial autophagy in cells with mtDNA mutations results from synergistic loss of transmembrane potential and mTORC1 inhibition. Hum Mol Genet 21:978-990
79. Gilley R, Balmanno K, Cope CL, Cook SJ (2013) Adaptation to chronic mTOR inhibition in cancer and in aging. Biochem Soc Trans 41:956-961
80. Gilquin B, Taillebourg E, Cherradi N et al (2010) The AAA?ATPase ATAD3A controls mitochondrial dynamics at the interface of the inner and outer membranes. Mol Cell Biol 30:1984-1996
81. Goldman J, Taylor R, Zhang Y, Jin S (2010) Autophagy and the degradation of mitochondria. Mitochondrion 10:309-315
82. Gredilla R, Bohr VA, Stevnsner T (2010) Mitochondrial DNA repair and association with aging. Exp Gerontol 45:478-488
83. Gredilla R, Garm C, Stevnsner T (2012) Nuclear and mitochondrial DNA repair in selected eukaryotic aging model systems. Oxid Med Cell Longev. doi:10.1155/2012/282438
84. Green DR, Galluzzi L, Kroemer G (2011) Mitochondria and the autophagy-inflammation-cell death axis in organismal aging. Science 333:1109-1112
85. Gulyaeva NA, Kuznetsova EA, Gaziev AI (2006) Proteins associated with mitochondrial DNA protect it against the action of X-rays and hydrogen peroxide. Biofizika 51:692-697
86. Gulyaeva NA, Abdullaev SA, Malakhova LV et al (2009) Reduction of the number of mutant copies of mitochondrial DNA in tissues of irradiated mice in the postradiation period. Russ J Genet 45:833-839
87. Guo X, Popadin KY, Markuzon N et al (2010) Repeats, longevity and the sources of mtDNA deletions: evidence from "deletional spectra". Trends Genet 26:340-343
88. Guo W, Wong S, Li M et al (2012) Testosterone plus lowintensity physical training in late life improves functional performance, skeletal muscle mitochondrial biogenesis, and mitochondrial quality control in male mice. PLoS One 7(12):e51180. doi:10.1371/journal.pone.0051180
89. Handschin C, Spiegelman BM (2006) Peroxisome proliferator-activated receptor gamma coactivator 1 coactivators, energy homeostasis, and metabolism. Endocr Rev 27:728-735 (Pubitemid 44936056)
90. Harman D (1956) Aging: a theory based on free radical and radiation chemistry. J Gerontol 11:298-300
91. Harman D (1972) The biologic clock: the mitochondria? J Am Geriatr Soc 20:145-147
92. Harman D (1981) The aging process. Proc Natl Acad Sci USA 78:7124-7128
93. Harrison DE, Strong R, Sharp ZD et al (2009) Rapamycin fed late in life extends lifespan in genetically heterogeneous mice. Nature 460:392-395
94. Hartmann N, Reichwald K, Wittig I et al (2011) Mitochondrial DNA copy number and function decrease with age in the short-lived fish Nothobranchius furzeri. Aging Cell 10:824-831
95. He J, Cooper HM, Reyes A, Re MD et al (2012) Mitochondrial nucleoid interacting proteins support mitochondrial protein synthesis. Nucleic Acids Res 40:6109-6121
96. Hock MB, Kralli A (2009) Transcriptional control of mitochondrial biogenesis and function. Annu Rev Physiol 71:177-203
97. Holley AK, Bakthavatchalu V, Velez-Roman JM, Clair DK (2011) Manganese superoxide dismutase: guardian of the powerhouse. Int J Mol Sci 12:7114-7162
98. Iborra FJ, Kimura H, Cook PR (2004) The functional organization of mitochondrial genomes in human cells. BMC Biol 24:2-9
99. Islam MM, Nautiyal M, Wynn RM et al (2010) Mobley Branched-chain amino acid metabolon: interaction of glutamate dehydrogenase with the mitochondrial branched-chain aminotransferase (BCATm). J Biol Chem 285:265-276
100. Itsara LS, Kennedy SR, Fox EJ et al (2014) Oxidative stress is not a major contributor to somatic mitochondrial dna mutations. PLoS Genet 10(2):e1003974. doi:10.1371/journal.pgen.1003974
101. Jackson S, Bartek J (2009) The DNA-damage response in human biology and disease. Nature 461:1071-1078
102. Jackson CB, Gallati S, Schaller A (2012) qPCR-based mitochondrial DNA quantification: influence of template DNA fragmentation on accuracy. Biochem Biophys Res Commun 423:441-447
103. Jazwinski SM (2013) The retrograde response: When mitochondrial quality control is not enough. Biochim Biophys Acta 1833:400-409
104. John JS (2014) The control of mtDNA replication during differentiation and development. Biochim Biophys Acta 1840:1345-1354
105. Johnson SC, Rabinovitch PS, Kaeberlein M (2013) mTOR is a key modulator of ageing and age-related disease. Nature 493:338-345
106. Jones AW, Yao Z, Vicencio JM et al (2012) PGC-1 family coactivators and cell fate: roles in cancer, neurodegeneration, cardiovascular disease and retrograde mitochondria-nucleus signaling. Mitochondrion 12:86-99
107. Joseph AM, Adhihetty PJ, Buford TW et al (2012) The impact of aging on mitochondrial function and biogenesis pathways in skeletal muscle of sedentary high- and low-functioning elderly individuals. Aging Cell 11:801-809
108. Joseph AM, Adhihetty PJ, Wawrzyniak NR et al (2013) Dysregulation of mitochondrial quality control processes contribute to sarcopenia in a mouse model of premature aging. PLoS One 8(7):e69327. doi:10.1371/journal.pone.0069327
109. Kamenisch Y, Fousteri M, Knoch J et al (2010) Proteins of nucleotide and base excision repair pathways interact in mitochondria to protect from loss of subcutaneous fat, a hallmark of aging. J Exp Med 207:379-390
110. Kamileri I, Karakasilioti I, Garinis GA (2012) Nucleotide excision repair: new tricks with old bricks. Trends Genet 28:566-573
111. Kang C, Chung E, Diffee G, Ji LL (2013) Exercise training attenuates aging-associated mitochondrial dysfunction in rat skeletal muscle: role of PGC-1a. Exp Gerontol 48(11):1343-1350
112. Kanki T, Wang K, Cao Y et al (2009) Atg32 is a mitochondrial protein that confers selectivity during mitophagy. Dev Cell 17:98-109
113. Kapeller I, Milman N, Yaffe N, Shlomai J (2011) Interactions of a replication initiator with histone h1-like proteins remodel the condensed mitochondrial genome. J Biol Chem 286:40566-40574
114. Kaufman BA, Durisic N, Mativetsky JM et al (2007) The mitochondrial transcription factor TFAM coordinates the assembly of multiple DNA molecules into nucleoid-like structures. Mol Biol Cell 18:3225-3236 (Pubitemid 47378666)
115. Kaushik S, Arias E, Kwon H et al (2012) Loss of autophagy in hypothalamic POMC neurons impairs lipolysis. EMBO Rep 13:258-265
116. Kazachkova N, Ramos A, Santos C, Lima M (2013) Mitochondrial DNA damage patterns and aging: revising the evidences for humans and mice. Aging Dis 4:337-350
117. Kazak L, Reyes A, Holt IJ (2012) Minimizing the damage: repair pathways keep mitochondrial DNA intact. Nat Rev Mol Cell Biol 13:659-671
118. Kennedy SR, Salk JJ, Schmitt MW, Loeb LA (2013) Ultrasensitive sequencing reveals an age-related Increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. PLoS Genet 9(9):e1003794. doi:10.1371/journal.pgen.1003794
119. Kienhöfer J, Häussler DF, Ruckelshausen F et al (2009) Association of mitochondrial antioxidant enzymes with mitochondrial DNA as integral nucleoid constituents. FASEB J 23:2034-2044
120. Kim I, Lemasters JJ (2011) Mitophagy selectively degrades individual damaged mitochondria after photoirradiation. Antioxid Redox Signal 14:1919-1928
121. Kim GJ, Chandrasekaran K, Morgan WF (2006) Mitochondrial dysfunction, persistently elevated levels of reactive oxygen species and radiation-induced genomic instability: a review. Mutagenesis 21:361-367 (Pubitemid 44691124)
122. Kissova I, Deffieu M, Manon S, Camougrand N (2004) Uth1p is involved in the autophagic degradation of mitochondria. J Biol Chem 279:39068-39074 (Pubitemid 39296069)
123. Klionsky DJ (2014) Citing recent declines in the discovery of new ATG genes, some scientists now suggest that the end of autophagy research may be within sight. Autophagy 10:715-716
124. Klionsky DJ, Schulman BA (2014) Dynamic regulation of macroautophagy by distinctive ubiquitin-like proteins. Nat Struct Mol Biol 21:336-345
125. Klionsky DJ, Abdalla FC, Abeliovich H et al (2012) Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy 8:445-544
126. Kotiadis VN, Duchen MR, Osellame LD (2014) Mitochondrial quality control and communications with the nucleus are important in maintaining mitochondrial function and cell health. Biochim Biophys Acta 1840:1254-1265
127. Kraytsberg Y, Kudryavtseva E, McKee AC et al (2006) Mitochondrial DNA deletions are abundant and cause functional impairment in aged human substantia nigra neurons. Nat Genet 38:518-520
128. Kraytsberg Y, Simon DK, Turnbull DM, Khrapko K (2009) Do mtDNA deletions drive premature aging in mtDNA mutator mice? Aging Cell 4:502-506
129. Kujoth GC, Hiona A, Pugh TD et al (2005) Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging. Science 309:481-484 (Pubitemid 40994689)
130. Kukat C, Larsson NG (2013) mtDNA makes a U-turn for the mitochondrial nucleoid. Trends Cell Biol 23:457-463
131. Kukat C, Wurm CA, Spahr H et al (2011) Super-resolution microscopy reveals that mammalian mitochondrial nucleoids have a uniform size and frequently contain a single copy of mtDNA. Proc Natl Acad Sci USA 108:13534-13539
132. Kutsyi MP, Gouliaeva NA, Kuznetsova EA, Gaziev AI (2005) DNA-binding proteins of mammalian mitochondria. Mitochondrion 5:35-44 (Pubitemid 40197723)
133. Lagouge M, Larsson NG (2013) The role of mitochondrial DNA mutations and free radicals in disease and ageing. J Intern Med 273:529-543
134. Lagouge M, Argmann C, Gerhart-Hines Z et al (2006) Resveratrol improves mitochondrial function and protects against metabolic disease by activating SIRT1 and PGC-1alpha. Cell 127:1109-1122 (Pubitemid 44894520)
135. Lamming DW, Ye L, Sabatini DM, Baur JA (2013) Rapalogs and mTOR inhibitors as anti-aging therapeutics. J Clin Invest 123:980-989
136. Lanza IR, Nair KS (2010) Mitochondrial function as a determinant of life span. Eur J Physiol 459:277-289
137. Lapointe J, Hekimi S (2010) When a theory of aging ages badly. Cell Mol Life Sci 67:1-8
138. Lapucci A, Pittelli M, Rapizzi E et al (2011) Poly(ADP-ribose) polymerase-1 is a nuclear epigenetic regulator of mitochondrial DNA repair and transcription. Mol Pharmacol 79:932-940
139. Larsson NG (2010) Somatic mitochondrial DNA mutations in mammalian aging. Annu Rev Biochem 79:683-706
140. Lee HC, Wei YH (2005) Mitochondrial biogenesis and mitochondrial DNA maintenance of mammalian cells under oxidative stress. Int J Biochem Cell Biol 37:822-834
141. Lee HC, Wei YH (2012) Mitochondria and aging. Adv Exp Med Biol 942:311-327
142. Lee IH, Cao L, Mostoslavsky R et al (2008) A role for the NADdependent deacetylase Sirt1 in the regulation of autophagy. Proc Natl Acad Sci USA 105:3374-3379 (Pubitemid 351723560)
143. Lemasters JJ (2005) Selective mitochondrial autophagy, or mitophagy, as a targeted defense against oxidative stress, mitochondrial dysfunction, and aging. Rejuvenation Res 8:3-5
144. Li LY, Luo X, Wang X (2001) Endonuclease G is an apoptotic DNase when released from mitochondria. Nature 412:95-99 (Pubitemid 32851517)
145. Lim KS, Jeyaseelan K, Whiteman M et al (2005) Oxidative damage in mitochondrial DNA is not extensive. Ann N Y Acad Sci 1042:210-220 (Pubitemid 40967641)
146. Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362:709-715
147. Lionaki E, Markaki M, Tavernarakis N (2013) Autophagy and ageing: insights from invertebrate model organisms. Ageing Res Rev 12:413-428
148. Lipinski MM, Zheng B, Lu T et al (2010) Genome-wide analysis reveals mechanisms modulating autophagy in normal brain aging and in Alzheimer's disease. Proc Natl Acad Sci USA 107:14164-14169
149. López-Otín C, Blasco MA, Partridge L et al (2013) The hallmarks of aging. Cell 153:1194-1217
150. Luo X, Kraus WL (2012) On PAR with PARP: cellular stress signaling through poly(ADP-ribose) and PARP-1. Genes Dev 26:417-432
151. Ma YS, Wu SB, LeeWYet al (2009) Response to the increase of oxidative stress and mutation of mitochondrial DNA in aging. Biochim Biophys Acta 1790:1021-1029
152. Madeo F, Tavernarakis N, Kroemer G (2010) Can autophagy promote longevity? Nat Cell Biol 12:842-846
153. Margulis L (1992) Biodiversity: molecular biological domains, symbiosis and kingdom origins. Biosystems 27(1):39-51
154. Marín-García J, Akhmedov AT, Moe GW (2013) Mitochondria in heart failure: the emerging role of mitochondrial dynamics. Heart Fail Rev 18:439-456
155. Martin LJ (2012) Biology of mitochondria in neurodegenerative diseases. Prog Mol Biol Transl Sci 107:355-415
156. Marzetti E, Csiszar A, Dutta D et al (2013) Role of mitochondrial dysfunction and altered autophagy in cardiovascular aging and disease: from mechanisms to therapeutics. Am J Physiol Heart Circ Physiol 305:H459-H476
157. Masuyama M, Iida R, Takatsuka H et al (2005) Quantitative change in mitochondrial DNA content in various mouse tissues during aging. Biochim Biophys Acta 1723:302-308 (Pubitemid 40744699)
158. Matsushima Y, Kaguni LS (2012) Matrix proteases in mitochondrial DNA function. Biochim Biophys Acta 1819:1080-1087
159. McInnes J (2013) Insights on altered mitochondrial function and dynamics in the pathogenesis of neurodegeneration. Transl Neurodegener 2(1):12. doi:10.1186/2047-9158-2-12
160. McKinney EA, Oliveira MT (2013) Replicating animal mitochondrial DNA. Genet Mol Biol 36(3):308-315
161. Melser S, Chatelain EH, Lavie J et al (2013) Rheb regulates mitophagy induced by mitochondrial energetic status. Cell Metab 17:719-730
162. Menshikova EV, Ritov VB, Fairfull L et al (2006) Effects of exercise on mitochondrial content and function in aging human skeletal muscle. J Gerontol A 61:534-540
163. Merksamer PI, Liu Y, He W et al (2013) The sirtuins, oxidative stress and aging: an emerging link. Aging (Albany NY) 5:144-150
164. Meyer JN, Bess AS (2012) Involvement of autophagy and mitochondrial dynamics in determining the fate and effects of irreparable mitochondrial DNA damage. Autophagy 8:822-1823
165. Miller FJ, Rosenfeldt FL, Zhang C et al (2003) Precise determination of mitochondrial DNA copy number in human skeletal and cardiac muscle by a PCR-based assay: lack of change of copy number with age. Nucleic Acids Res 31(11):e61
166. Mitra S, Izumi T, Boldogh I et al (2007) Intracellular trafficking and regulation of mammalian AP-endonuclease 1 (APE1), an essential DNA repair protein. DNA Repair (Amst) 6:461-469 (Pubitemid 46357051)
167. Miyaki M, Yatagai K, Ono T (1977) Strand breaks of mammalian mitochondrial DNA induced by carcinogens. Chem Biol Interact 17:321-329 (Pubitemid 8138818)
168. Miyamoto Y, Kitamura N, Nakamura Y et al (2011) Possible existence of lysosome-like organella within mitochondria and its role in mitochondrial quality control. PLoS One 6(1):e16054. doi:10.1371/journal.pone.0016054
169. Montier LC, Deng JJ, Bai Y (2009) Number matters: control of mammalian mitochondrial DNA copy number. J.Genet Genomics 36:125-131
170. Muftuoglu M, Mori MP, de Souza-Pinto NC (2014) Formation and repair of oxidative damage in the mitochondrial DNA. Mitochondrion. doi:10.1016/j.mito. 2014.03.007
171. Murphy MP (2009) How mitochondria produce reactive oxygen species. Biochem J 417:1-13
172. Murphy MP, Holmgren A, Larsson NG et al (2011) Unraveling the biological roles of reactive oxygen species. Cell Metab 13:361-365
173. Nakada K, Sato A, Hayashi J (2009) Mitochondrial functional complementation in mitochondrial DNA-based diseases. Int J Biochem Cell Biol 41:1907-1913
174. Narendra DP, Youle RJ (2014) Targeting mitochondrial dysfunction: role for PINK1 and Parkin in mitochondrial quality control. Antioxid Redox Signal 14:1929-1938
175. Narendra DP, Walker JE, Youle R (2012) Mitochondrial quality control mediated by PINK1 and Parkin: links to parkinsonism. Cold Spring Harb Perspect Biol 4:a011338
176. Nisoli E, Tonello C, Cardile A et al (2005) Calorie restriction promotes mitochondrial biogenesis by inducing the expression of eNOS. Science 310:314-317 (Pubitemid 41457197)
177. Okamoto K, Kondo-Okamoto N (2012) Mitochondria and autophagy: critical interplay between the two homeostats. Biochim Biophys Acta 1820:595-600
178. Okamoto K, Kondo-Okamoto N, Ohsumi Y (2009) Mitochondria-anchored receptor Atg32 mediates degradation of mitochondria via selective autophagy. Dev Cell 17:87-97
179. Orvedahl A, Sumpter R Jr, Xiao G et al (2011) Image-based genome-wide siRNA screen identifies selective autophagy factors. Nature 480:113-117
180. Otera H, Ishihara N, Mihara K (2013) New insights into the function and regulation of mitochondrial fission. Biochim Biophys Acta 1833:1256-1268
181. Owusu-Ansah E, Yavari A, Mandal S, Banerjee U (2008) Distinct mitochondrial retrograde signals control the G1-S cell cycle checkpoint. Nat Genet 40:356-361 (Pubitemid 351311760)
182. Pagliarini DJ, Calvo SE, Chang B et al (2008a) A mitochondrial protein compendium elucidates complex I disease biology. Cell 134:112-123 (Pubitemid 351916708)
183. Pagliarini DJ, Calvo SE, Chang B et al (2008b) A mitochondrial protein compendium elucidates complex I disease biology. Cell 134:112-123 (Pubitemid 351916708)
184. Palikaras K, Tavernarakis N (2014) Mitochondrial homeostasis: the interplay between mitophagy and mitochondrial biogenesis. Exp Gerontol. doi:10.1016/j.exger.01.021
185. Pani G, Galeotti T (2011) Role of MnSOD and p66shc in mitochondrial response to p53. Antioxid Redox Signal 15:1715-1727
186. Pankotai E, Lacza Z, Muranyi M, Szabo C (2009) Intra-mitochondrial poly(ADP-ribosyl)ation: potential role for alphaketoglutarate dehydrogenase. Mitochondrion 9:159-164
187. Parrish J, Li L, Klotz K et al (2001) Mitochondrial endonuclease G is important for apoptosis in C. elegans. Nature 412:90-94 (Pubitemid 32851516)
188. Payne BI, Wilson IJ, Wai-Man PY et al (2013) Universal heteroplasmy of human mitochondrial DNA. Hum Mol Genet 22:384-390
189. Pérez VI, Bokov A, Van Remmen H et al (2009) Is the oxidative stress theory of aging dead? Biochim Biophys Acta 1790:1005-1014
190. Peterson CM, Johannsen DL, Ravussin E (2012) Skeletal muscle mitochondria and aging: a review. J Aging Res 2012:194821. doi:10.1155/2012/194821
191. Poovathingal SK, Gruber J, Lakshmanan L et al (2012) Is mitochondrial DNA turnover slower than commonly assumed? Biogerontology 13:557-564
192. Powers SK, Jackson MJ (2008) Exercise-induced oxidative stress: cellular mechanisms and impact on muscle force production. Physiol Rev 88:1243-1276
193. Raimundo N (2014) Mitochondrial pathology: stress signals from the energy factory. Trends Mol Med. doi:10.1016/j.molmed.2014.01.005
194. Ranieri M, Brajkovic S, Riboldi G et al (2013) Mitochondrial fusion proteins and human diseases. Neurol Res Int 2013:293893. doi:10.1155/2013/293893
195. Ravikumar B, Sarkar S, Davies JE et al (2010) Regulation of mammalian autophagy in physiology and pathophysiology. Physiol Rev 90:1383-1435
196. Reyes A, He J, Mao CC et al (2011) Actin and myosin contribute to mammalian mitochondrial DNA maintenance. Nucleic Acids Res 39:5098-5108
197. Reznick RM, Zong H, Li J et al (2007) Aging-associated reductions in AMP-activated protein kinase activity and mitochondrial biogenesis. Cell Metab 5:151-156 (Pubitemid 46172924)
198. Richter C, Park JW, Ames BN (1988) Normal oxidative damage to mitochondrial and nuclear DNA is extensive. Proc Natl Acad Sci USA 85:6465-6467
199. Ristow M, Schmeisser S (2011) Extending life span by increasing oxidative stress. Free Radic Biol Med 51:327-336
200. Ristow M, Zarse K (2010) How increased oxidative stress promotes longevity and metabolic health: the concept of mitochondrial hormesis (mitohormesis). Exp Gerontol 45:410-418
201. Ristow M, Zarse K, Oberbach A et al (2009) Antioxidants prevent health-promoting effects of physical exercise in humans. Proc Natl Acad Sci USA 106:8665-8670
202. Ross JM, Stewart JB, Hagström E et al (2013) Germline mitochondrial DNA mutations aggravate ageing and can impair brain development. Nature 501:412-415
203. Rossi MN, Carbone M, Mostocotto C et al (2009) Mitochondrial localization of PARP-1 requires interaction with mitofilin and is involved in the maintenance of mitochondrial DNA integrity. J Biol Chem 284:31616-31624
204. Rossignol R, Faustin B, Rocher C et al (2003) Mitochondrial threshold effects. Biochem J 370:751-762 (Pubitemid 36399067)
205. Rubinsztein DC, Marino G, Kroemer G (2011) Autophagy and Aging. Cell 146:682-695
206. Sablina AA, Budanov AV, Ilyinskaya GV et al (2005) The antioxidant function of the p53 tumor suppressor. Nat Med 11:1306-1313 (Pubitemid 41752911)
207. Safdar A, Bourgeois JM, Ogborn DI et al (2011) Endurance exercise rescues progeroid aging and induces systemic mitochondrial rejuvenation in mtDNA mutator mice. Proc Natl Acad Sci USA 108:4135-4140
208. Sato A, Kono T, Nakada K et al (2005) Gene therapy for progeny of mito-mice carrying pathogenic mtDNA by nuclear transplantation. Proc Natl Acad Sci USA 102:16765-16770 (Pubitemid 41688851)
209. Scarffe LA, Stevens DA, Dawson VL, Dawson TM (2014) Parkin and PINK1: much more than mitophagy. Trends Neurosci 37:315-324
210. Scarpulla RC (2008) Transcriptional paradigms in mammalian mitochondrial biogenesis and function. Physiol Rev 88:611-638
211. Schiavi A, Ventura N (2014) The interplay between mitochondria and autophagy and its role in the aging process. Exp Gerontol. doi:10.1016/j.exger. 2014.02.015
212. Schroeder EA, Raimundo N, Shadel GS (2013) Epigenetic silencing mediates mitochondria stress-induced longevity. Cell Metab 17:954-964
213. Seo AY, Joseph AM, Dutta D et al (2010) New insights into the role of mitochondria in aging: mitochondrial dynamics and more. J Cell Sci 123:2533-2542
214. Shadel GS, Clayton DA (1997) Mitochondrial DNA maintenance in vertebrates. Annu Rev Biochem 66:409-435
215. Shokolenko I, Venediktova N, Bochkareva A et al (2009) Oxidative stress induces degradation of mitochondrial DNA. Nucleic Acids Res 37:2539-2548
216. Short KR, Bigelow ML, Kahl J et al (2005) Decline in skeletal muscle mitochondrial function with aging in humans. Proc Natl Acad Sci USA 102:5618-5623 (Pubitemid 40530306)
217. Skulachev MV, Antonenko YN, Anisimov VN et al (2011) Mitochondrial- targeted plastoquinone derivatives. Effect on senescence and acute age-related pathologies. Curr Drug Targets 12:800-826
218. Song S, Pursell ZF, Copeland WC et al (2005) DNA precursor asymmetries in mammalian tissue mitochondria and possible contribution to mutagenesis through reduced replication fidelity. Proc Natl Acad Sci USA 102:4990-4995
219. Spees JL, Olson SD, Whitney MJ, Prockop DJ (2006) Mitochondrial transfer between cells can rescue aerobic respiration. Proc Natl Acad Sci USA 103:1283-1288 (Pubitemid 43191157)
220. Springer W, Kahle PJ (2011) Regulation of PINK1-Parkin-mediated mitophagy. Autophagy 7:266-278
221. Stetler RA, Leak RK, Gao Y, Chen J (2013) The dynamics of the mitochondrial organelle as a potential therapeutic target. J Cereb Blood Flow Metab 33:22-32
222. Stuart JA, Bourque BM, de Souza-Pinto NC, Bohr VA (2005) No evidence of mitochondrial respiratory dysfunction in OGG1-null mice deficient in removal of 8-oxodeoxyguanine from mitochondrial DNA. Free Radic Biol Med 38:737-745 (Pubitemid 40249744)
223. Suen D, Narendra DP, Tanaka A et al (2010) Parkin overexpression selects against a deleterious mtDNA mutation in heteroplasmic cybrid cells. Proc Natl Acad Sci USA 107:11835-11840
224. Szczesny B, Tann AW, Mitra S (2010) Age- and tissue-specific changes in mitochondrial and nuclear DNA base excision repair activity in mice: susceptibility of skeletal muscles to oxidative injury. Mech Ageing Dev 131:330-337
225. Tao R, Coleman MC, Pennington JD et al (2010) Sirt3-mediated deacetylation of evolutionarily conserved lysine 122 regulates MnSOD activity in response to stress. Mol Cell 40:893-904
226. Taylor RW, Turnbull DM (2005) Mitochondrial DNA mutations in human disease. Nat Rev Genet 6:389-402 (Pubitemid 40577182)
227. Terman A (1995) The effect of age on formation and elimination of autophagic vacuoles in mouse hepatocytes. Gerontology 41(2):319-326
228. Terman A, Kurz T, Navratil M et al (2010) Mitochondrial turnover and aging of long-lived postmitotic cells: the mitochondrial-lysosomal axis theory of aging. Antioxid Redox Signal 12:503-535
229. Tokarz P, Kaarniranta K, Blasiak J (2013) Role of antioxidant enzymes and small molecular weight antioxidants in the pathogenesis of age-related macular degeneration (AMD). Biogerontology 14:461-482
230. Tranah GJ (2011) Mitochondrial-nuclear epistasis: implications for human aging and longevity. Ageing Res Rev 10:238-252
231. Trifunovic A, Wredenberg A, Falkenberg M et al (2004) Premature aging in mice expressing defective mitochondrial DNA polymerase. Nature 429:417-423 (Pubitemid 38715133)
232. Tseng AH, Shieh SS, Wang DL (2013) SIRT3 deacetylates Foxo3 to protect mitochondria against oxidative damage. Free Radic Biol Med 63:222-234
233. Van Laar VS, Berman SB (2013) The interplay of neuronal mitochondrial dynamics and bioenergetics: implications for Parkinson's disease. Neurobiol Dis 51:43-55
234. Van Remmen H, Ikeno Y, Hamilton M et al (2003) Life-long reduction in MnSOD activity results in increased DNA damage and higher incidence of cancer but does not accelerate aging. Physiol Genomics 16:29-37 (Pubitemid 38420018)
235. Veal E, Day A (2011) Hydrogen peroxide as a signaling molecule. Antioxid Redox Signal 15:147-151
236. Vermulst M, Bielas JH, Kujoth GC et al (2007) Mitochondrial point mutations do not limit the natural lifespan of mice. Nat Genet 39:540-543 (Pubitemid 46514771)
237. Vermulst M, Wanagat J, Kujoth GC et al (2008) DNA deletions and clonal mutations drive premature aging in mitochondrial mutator mice. Nat Genet 40:392-394 (Pubitemid 351450885)
238. Vijg J, Suh Y (2013) Genome Instability and Aging. Annu Rev Physiol 75:645-668
239. Vincow ES, Merrihew G, Thomas RE et al (2013) The PINK1-Parkin pathway promotes both mitophagyand selective respiratory chain turnover in vivo. Proc Natl Acad Sci USA 110:6400-6405
240. Vives-Bauza C, Zhou C, Huang Y et al (2010) PINK1-dependent recruitment of Parkin to mitochondria in mitophagy. Proc Natl Acad Sci USA 107:378-383
241. 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
242. Wallace DC, Fan W (2010) Energetics, epigenetics, mitochondrial genetics. Mitochondrion 10:12-31
243. Wang Y, Kim NS, Haince JF et al (2011) Poly(ADP-ribose) (PAR) binding to apoptosis- inducing factor is critical for PAR polymerase-1-dependent cell death (parthanatos). Sci Signal 4(167):ra20. doi:10.1126/scisignal.2000902
244. Wang CH, Wu SB, Wu YT, Wei YH (2013) Oxidative stress response elicited by mitochondrial dysfunction: implication in the pathophysiology of aging. Exp Biol Med (Maywood) 238:450-460
245. Weichhart T (2012) Mammalian target of rapamycin: a signaling kinase for every aspect of cellular life. Methods Mol Biol 821:1-14
246. Wenz T (2013) Regulation of mitochondrial biogenesis and PGC-1α under cellular stress. Mitochondrion 13:134-142
247. Westermann B (2010) Mitochondrial fusion and fission in cell life and death. Nat Rev Mol Cell Biol 11:872-884
248. Wu S, Zhou F, Zhang Z, Xing D (2011) Mitochondrial oxidative stress causes mitochondrial fragmentation via differential modulation of mitochondrial fission-fusion proteins. FEBS J 278:941-954
249. Youle RJ, van der Bliek AM (2012) Mitochondrial fission, fusion, and stress. Science 337:1062-1065
250. Zanin MB, Donohue JM, Everitt BA (2010) Evidence that core histone H3 is targeted to the mitochondria in Brassica oleracea. Cell Biol Int 34:997-1003
251. Zelko IN, Mariani TJ, Folz RJ (2002) Superoxide dismutase multigene family: a comparison of the CuZn-SOD (SOD1), Mn-SOD (SOD2), and EC-SOD (SOD3) gene structures, evolution, and expression. Free Radic Biol Med 33:337-349 (Pubitemid 34790245)
252. Zhang C, Cuervo AM (2008) Restoration of chaperone-mediated autophagy in aging liver improves cellular maintenance and hepatic function. Nat Med 14:959-965
253. Zhang Q, Wu Y, Zhang P et al (2012) Exercise induces mitochondrial biogenesis after brain ischemia in rats. Neuroscience 205:10-17
254. Zhao J, Lendahl U, Nister M (2013) Regulation of mitochondrial dynamics: convergences and divergences between yeast and vertebrates. Cell Mol Life Sci 70:951-976