Stochastic drift in mitochondrial DNA point mutations: A novel perspective ex silico

PLoS Computational Biology

Volumn 5, Issue 11, 2009, Pages

  Poovathingal, Suresh Kumar ^a   Gruber, Jan ^b   Halliwell, Barry ^b   Gunawan, Rudiyanto ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b Department of Biochemistry   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FREE RADICALS; STOCHASTIC SYSTEMS;

FREE RADICAL THEORY; INDUCED MUTATIONS; MITOCHONDRIAL DNA; POINT MUTATIONS; REACTIVE OXYGEN SPECIES; STOCHASTIC DRIFT; STOCHASTIC NATURE; STOCHASTICITY; THEORIES OF AGING; UNCERTAINTY;

TISSUE;

MITOCHONDRIAL DNA; ANTIOXIDANT; REACTIVE OXYGEN METABOLITE;

AGING; ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; DILUTION; EMBRYO; EMBRYO DEVELOPMENT; EX VIVO STUDY; HYPOTHESIS; IN VIVO STUDY; MOUSE; NONHUMAN; POINT MUTATION; STOCHASTIC MODEL; ALGORITHM; ANIMAL; BIOLOGY; CHEMISTRY; COMPUTER SIMULATION; GENETICS; METHODOLOGY; MONTE CARLO METHOD; NUCLEOTIDE SEQUENCE; OXIDATIVE STRESS; STATISTICS; TIME;

AGING; ALGORITHMS; ANIMALS; ANTIOXIDANTS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DNA MUTATIONAL ANALYSIS; DNA, MITOCHONDRIAL; MICE; MONTE CARLO METHOD; OXIDATIVE STRESS; POINT MUTATION; REACTIVE OXYGEN SPECIES; STOCHASTIC PROCESSES; TIME FACTORS;

EID: 73449083412     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000572     Document Type: Article

References (65)

1. St-Pierre J, Buckingham JA, Roebuck SJ, Brand MD (2002) Topology of superoxide production from different sites in the mitochondrial electron transport chain. J Biol Chem 277: 44784-44790.
2. Halliwell B, Aruoma OI (1991) DNA damage by oxygen-derived species. Its mechanism and measurement in mammalian systems. FEBS lett 281(1-2): 9-19.
3. Harman D (1972) Free radical theory of aging: dietary implication. Am J Clin Nutr 25: 839-843.
4. Gruber J, Schaffer S, Halliwell B (2008) The mitochondrial free radical theory of ageing - Where do we stand? Front Biosci 13: 6554-6579.
5. Wiesner RJ, Zsurka G, Kunz WS (2006) Mitochondrial DNA damage and the aging process: facts and imaginations. Free Rad Res 40(12): 1284-1294.
6. Schriner SE, Linford NJ, Martin GM, Treuting P, Ogburn CE, et al. (2005) Extension of murine life span by overexpression of catalase targeted to mitochondria. Science 308: 1909-1911.
7. Vermulst M, Wanagat J, Kujoth GC, Bielas JH, Rabinovitch PS, et al. (2008) DNA deletions and clonal mutations drive premature aging in mitochondrial mutator mice. Nat Genet 40: 392-394.
8. Kujoth GC, Hiona A, Pugh TD, Someya S, Panzer K, et al. (2005) Mitochondrial DNA mutations, Oxidative stress, and Apoptosis in mammalian aging. Science 309: 481-484.
9. Trifunovic A, Wredenberg A, Falkenberg M, Spelbrink JN, Rovio AT, et al. (2004) Premature ageing in mice expressing defective mitochondrial DNA polymerase. Nature 429: 417-423.
10. Beckman KB, Ames BN (1999) Endogenous oxidative damage of mtDNA. Mutat Res 424: 51-58.
11. ESCODD (2002) Inter-laboratory validation of procedures for measuring 8-oxo-7,8-dihydroguanine/ 8-oxo-7,8-dihydro-29-deoxyguanosine in DNA. Free Radic Res 36: 239-245.
12. Vermulst M, Bielas JH, Kujoth GC, Ladiges WC, Rabinovitch PS, et al. (2007) Mitochondrial point mutations do not limit the natural lifespan of mice. Nat Genet 39(4): 540-543.
13. Hamilton ML, Van Remmen H, Drake JA, Yang H, Guo ZM, et al. (2001) Does oxidative damage to DNA increase with age? Proc Natl Acad Sci U S A 98: 10469-10474.
14. Calleja M, Pena P, Ugalde C, Ferreiro C, Marco R, et al. (1993) Mitochondrial DNA remains intact during Drosophila aging, but the levels of mitochondrial transcripts are significantly reduced. J Biol Chem 268: 18891-18897.
15. Bielas JH, Loeb LA (2005) Quantification of random genomic mutations. Nat Methods 2: 285-290.
16. McAdams HH, Arkin A (1999) It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet 15: 65-69.
17. Bender A, Krishnan KJ, Morris CM, Taylor GA, Reeve AK, et al. (2006) High levels of mitochondrial DNA deletions in substantia nigra neurons in aging and Parkinson disease. Nat Genet 38: 515-517.
18. Wanagat J, Cao Z, Pathare P, Aiken JM (2001) Mitochondrial DNA deletion mutations colocalize with segmental electron transport system abnormalities, muscle fiber atrophy, fiber splitting, and oxidative damage in sarcopenia. FASEB J 15: 322-332.
19. Herndon LA, Schmeissner PJ, Dudaronek JM, Brown PA, Listner KM, et al. (2002) Stochastic and genetic factors influence tissue-specific decline in ageing C. elegans. Nature 419: 808-814.
20. Gardiner CW (2004) Handbook of Stochastic Methods: for Physics, Chemistry and the Natural Sciences (Springer Series in Synergetics). Berlin: Springer.
21. Wiesner RJ, Ruegg JC, Morano I (1992) Counting target molecules by exponential polymerase chain reaction: copy number of mitochondrial DNA in rat tissue. Biochem Bioph Res Co 183(2): 553-559.
22. Chen H, Chan DC (2005) Emerging functions of mammalian mitochondrial fusion and fission. Hum Mol Genet 14 Spec No. 2: R283-R289.
23. Chinnery PF, Samuels DC (1999) Relaxed replication of mtDNA: A model with implications for the expression of disease. Am J Hum Genet 64: 1158-1165.
24. Liu Z, Butow RA (2006) Mitochondrial retrograde signaling. Annu Rev Genet 40: 159-185.
25. 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.
26. Clayton DA (1982) Replication of animal mitochondrial DNA. Cell 28: 693-705.
27. Montgomery DC, Runger GC (2006) Applied Statistics and Probability for Engineers. New York: Wiley.
28. Kunkel TA (1992) DNA Replication Fidelity. J Biol Chem 267(26): 18251-18254.
29. Gillespie DT (1992) A rigorous derivation of the chemical master equation. Physica A 188: 404-425.
30. Gillespie DT (1991) Markov Processes: An Introduction for Physical Scientists: Academic Press. .
31. Gillespie DT (1977) Exact Stochastic Simulation of Coupled Chemical Reactions. J Phys Chem 81: 2340-2361.
32. Steuerwald N, Barritt JA, Adler R, Malter H, Schimmel T, et al. (2000) Quantification of mtDNA in single oocytes, polar bodies and subcellular components by real-time rapid cycle fluorescence monitored PCR. Zygote 8: 209-215.
33. Elliott K, O'Connor M (1976) Embryogenesis in mammals (Ciba Foundation symposium; 40): Elsevier. .
34. Piko L, Taylor KD (1987) Amounts of mitochondrial DNA and abundance of some mitochondrial gene transcripts in early mouse embryos. Dev Biol 123: 364-374.
35. Larsson NG, Clayton DA (1995) Molecular genetic aspects of human mitochondrial disorders. Annu Rev Genet 29: 151-178.
36. Turnbull DM, Lightowlers RN (1998) An essential guide to mtDNA maintenance. Nat Genet 18: 199-200.
37. Larsson NG, Wang J, Wilhelmsson H, Oldfors A, Rustin P, et al. (1998) Mitochondrial transcription factor A is necessary for mtDNA maintenance and embryogenesis in mice. Nat Genet 18: 231-236.
38. Moraes CT (2001) What regulates mitochondrial DNA copy number in animal cells? Trends Genet 17(4): 199-205.
39. Sissman NJ (1970) Developmental Landmarks in Cardiac Morphogenesis: Comparative Chronology. Am J Cardiol 25: 141-148.
40. Karatza C, Stein WD, Shall S (1984) Kinetics of in vitro ageing of mouse embryo fibroblasts. J Cell Sci 65: 163-175.
41. Cervantes RB, Stringer JR, Shao C, Tischfield JA, Stambrook PJ (2002) Embryonic stem cells and somatic cells differ in mutation frequency and type. Proc Natl Acad Sci USA 99(6): 3586-3590.
42. Shadel GS, Clayton DA (1997) Mitochondrial DNA Maintenance in vertebrates. Ann Rev Biochem 66: 409-435.
43. Zhang D, Mott JL, Chang SW, Denniger G, Feng Z, et al. (2000) Construction of Transgenic Mice with Tissue-Specific Acceleration of Mitochondrial DNA Mutagenesis. Genomics 69: 151-161.
44. Terman A, Brunk UT (2005) Autophagy in cardiac myocyte homeostasis, aging, and pathology. Cardiovasc Res 68: 355-365.
45. Collins ML, Eng S, Hoh R, Hellerstein MK (2003) Measurement of mitochondrial DNA synthesis in vivo using a stable isotope-mass spectrometric technique. J Appl Physiol 94: 2203-2211.
46. Gross NJ, Getz GS, Rabionowitz M (1969) Apparent turnover of mitochondrial Deoxyribonucleic acid and mitochondrial phospholipids in the tissues of the rat. J Biol Chem 244(6): 1552-1562.
47. Michalopoulos GK, DeFrances MC (1997) Liver regeneration. Science 276: 60-66.
48. Chanda S, Mehendale HM (1996) Hepatic cell division and tissue repair: a key to survival after liver injury. Mol Med Today 2: 82-89.
49. Korr H, Kurz C, Seidler TO, Sommer D, Schmitz C (1998) Mitochondrial DNA synthesis studied autoradiographically in various cell types in vivo. Braz J Med Biol Res 31: 289-298.
50. Menzies RA, Gold PH (1971) The turnover of mitochondria in a variety of tissues of young adult and aged rats. J Biol Chem 246: 2425-2429.
51. Miwa S, Lawless C, von Zglinicki T (2008) Mitochondrial turnover in liver is fast in vivo and is accelerated by dietary restriction: application of a simple dynamic model. Aging Cell 7: 920-923.
52. Rossigol R, Faustin B, Rocher C, Malgat M, Mazat J-P, et al. (2003) Mitochondrial threshold effects. Biochem J 370: 751-762.
53. Davis AF, Clayton DA (1996) In Situ Localization of Mitochondrial DNA Replication in Intact Mammalian Cells. J Cell Biol 135: 883-893.
54. Cadet ARJ, Cadet J, Moller L, Poulsen HE, Vina J (2004) Are we sure we know how to measure 8-oxo-7,8-dihydroguanine in DNA from human cells? Arch Biochem Biophys 423(1): 57-65.
55. on Oxidative DNA Damage) ESCODD (2002) Comparative analysis of baseline 8-oxo-7,8-dihydroguanine in mammalian cell DNA, by different methods in different laboratories: an approach to consensus. Carcinogenesis 23: 2129-2133.
56. Wang D, Kreutzer DA, Essigmann JM (1998) Mutagenicity and repair of oxidative DNA damage: insights from studies using defined lesions. Mutat Res 400: 99-115.
57. Lim KS, Jeyaseelan K, Whiteman M, Jenner A, Halliwell B (2005) Oxidative damage in mitochondrial DNA is not extensive. Ann N Y Acad Sci 1042: 210-220.
58. Halliwell B (2007) Oxidative stress and cancer: have we moved forward? Biochem J 401: 1-11.
59. Kowald A, Kirkwood TB (1993) Mitochondrial mutations, cellular instability and ageing: modelling the population dynamics of mitochondria. Mutat Res 295: 93-103.
60. Kowald A, Kirkwood TBL (2000) Accumulation of Defective Mitochondria through delayed degradation of damaged organelles and its possible role in the ageing of post-mitotic and dividing cells. J Theor Biol 202: 145-160.
61. Limson M, Jackson CM (1931) Changes in the weights of various organs and systems of young rats maintained on a low-protein diet. J Nutr 5(2): 163-174.
62. Trifunovic A, Hansson A, Wredenberg A, Rovio AT, Dufour E, et al. (2005) Somatic mtDNA mutations cause aging phenotypes without affecting reactive oxygen species production. Proc Natl Acad Sci U S A 102: 17993-17998.
63. Grey ADNJ (2004) Mitochondrial mutations in mammalian aging: An overhasty about-turn. Rejuv Res 7(3): 171-174.
64. Piko L, Taylor D (1987) Amounts of Mitochondrial DNA and Abundance of Some Mitochondrial Gene Transcripts in Early Mouse Embryos. Dev Bio 123: 364-374.
65. Weiss JN (1997) The Hill equation revisited: uses and misuses. FASEB 11: 835-841.