메뉴 건너뛰기




Volumn 7, Issue 11, 2011, Pages

Replication pauses of the Wild-Type and mutant mitochondrial DNA polymerase gamma: A simulation study

Author keywords

[No Author keywords available]

Indexed keywords

DNA; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

EID: 81355132946     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002287     Document Type: Article
Times cited : (3)

References (49)
  • 1
    • 33644635644 scopus 로고    scopus 로고
    • DNA polymerase gamma in mitochondrial DNA replication and repair
    • Graziewicz MA, Longley MJ, Copeland WC, (2006) DNA polymerase gamma in mitochondrial DNA replication and repair. Chem Rev 106: 383-405.
    • (2006) Chem Rev , vol.106 , pp. 383-405
    • Graziewicz, M.A.1    Longley, M.J.2    Copeland, W.C.3
  • 2
  • 3
    • 0035851098 scopus 로고    scopus 로고
    • Exonuclease proofreading by human mitochondrial DNA polymerase
    • Johnson AA, Johnson KA, (2001) Exonuclease proofreading by human mitochondrial DNA polymerase. J Biol Chem 276: 38097-38107.
    • (2001) J Biol Chem , vol.276 , pp. 38097-38107
    • Johnson, A.A.1    Johnson, K.A.2
  • 4
    • 0035851134 scopus 로고    scopus 로고
    • Fidelity of nucleotide incorporation by human mitochondrial DNA polymerase
    • Johnson AA, Johnson KA, (2001) Fidelity of nucleotide incorporation by human mitochondrial DNA polymerase. J Biol Chem 276: 38090-38096.
    • (2001) J Biol Chem , vol.276 , pp. 38090-38096
    • Johnson, A.A.1    Johnson, K.A.2
  • 6
    • 0033621374 scopus 로고    scopus 로고
    • The mitochondrial p55 accessory subunit of human DNA polymerase gamma enhances DNA binding, promotes processive DNA synthesis, and confers N-ethylmaleimide resistance
    • Lim SE, Longley MJ, Copeland WC, (1999) The mitochondrial p55 accessory subunit of human DNA polymerase gamma enhances DNA binding, promotes processive DNA synthesis, and confers N-ethylmaleimide resistance. J Biol Chem 274: 38197-38203.
    • (1999) J Biol Chem , vol.274 , pp. 38197-38203
    • Lim, S.E.1    Longley, M.J.2    Copeland, W.C.3
  • 7
    • 0030920779 scopus 로고    scopus 로고
    • Mitochondrial DNA maintenance in vertebrates
    • Shadel GS, Clayton DA, (1997) Mitochondrial DNA maintenance in vertebrates. Annu Rev Biochem 66: 409-435.
    • (1997) Annu Rev Biochem , vol.66 , pp. 409-435
    • Shadel, G.S.1    Clayton, D.A.2
  • 8
    • 26944500840 scopus 로고    scopus 로고
    • Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism
    • Brown TA, Cecconi C, Tkachuk AN, Bustamante C, Clayton DA, (2005) Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism. Genes Dev 19: 2466-2476.
    • (2005) Genes Dev , vol.19 , pp. 2466-2476
    • Brown, T.A.1    Cecconi, C.2    Tkachuk, A.N.3    Bustamante, C.4    Clayton, D.A.5
  • 9
    • 0034598918 scopus 로고    scopus 로고
    • Coupled leading- and lagging-strand synthesis of mammalian mitochondrial DNA
    • Holt IJ, Lorimer HE, Jacobs HT, (2000) Coupled leading- and lagging-strand synthesis of mammalian mitochondrial DNA. Cell 100: 515-524.
    • (2000) Cell , vol.100 , pp. 515-524
    • Holt, I.J.1    Lorimer, H.E.2    Jacobs, H.T.3
  • 11
    • 39649120348 scopus 로고    scopus 로고
    • Inherited mitochondrial diseases of DNA replication
    • Copeland WC, (2008) Inherited mitochondrial diseases of DNA replication. Annu Rev Med 59: 131-146.
    • (2008) Annu Rev Med , vol.59 , pp. 131-146
    • Copeland, W.C.1
  • 12
    • 33749001168 scopus 로고    scopus 로고
    • Mitochondrial DNA polymerase-gamma and human disease
    • Hudson G, Chinnery PF, (2006) Mitochondrial DNA polymerase-gamma and human disease. Hum Mol Genet 15: R244-R252.
    • (2006) Hum Mol Genet , vol.15 , pp. 244-252
    • Hudson, G.1    Chinnery, P.F.2
  • 13
    • 67349191588 scopus 로고    scopus 로고
    • DNA polymerase gamma and mitochondrial disease: Understanding the consequence of POLG mutations
    • Chan SSL, Copeland WC, (2009) DNA polymerase gamma and mitochondrial disease: Understanding the consequence of POLG mutations. BBA-Bioenergetics 1787: 312-319.
    • (2009) BBA-Bioenergetics , vol.1787 , pp. 312-319
    • Chan, S.S.L.1    Copeland, W.C.2
  • 15
    • 24744464580 scopus 로고    scopus 로고
    • The common A467T mutation in the human mitochondrial DNA polymerase (POLG) compromises catalytic efficiency and interaction with the accessory subunit
    • Chan SSL, Longley MJ, Copeland WC, (2005) The common A467T mutation in the human mitochondrial DNA polymerase (POLG) compromises catalytic efficiency and interaction with the accessory subunit. J Biol Chem 280: 31341-31346.
    • (2005) J Biol Chem , vol.280 , pp. 31341-31346
    • Chan, S.S.L.1    Longley, M.J.2    Copeland, W.C.3
  • 16
    • 20144388894 scopus 로고    scopus 로고
    • Infantile hepatocerebral syndromes associated with mutations in the mitochondrial DNA polymerase-gamma A
    • Ferrari G, Lamantea E, Donati A, Filosto M, Briem E, et al. (2005) Infantile hepatocerebral syndromes associated with mutations in the mitochondrial DNA polymerase-gamma A. Brain 128: 723-731.
    • (2005) Brain , vol.128 , pp. 723-731
    • Ferrari, G.1    Lamantea, E.2    Donati, A.3    Filosto, M.4    Briem, E.5
  • 17
    • 2142705756 scopus 로고    scopus 로고
    • POLG mutations associated with Alpers' syndrome and mitochondrial DNA depletion
    • Naviaux RK, Nguyen KV, (2004) POLG mutations associated with Alpers' syndrome and mitochondrial DNA depletion. Ann Neurol 55: 706-712.
    • (2004) Ann Neurol , vol.55 , pp. 706-712
    • Naviaux, R.K.1    Nguyen, K.V.2
  • 18
    • 33745713884 scopus 로고    scopus 로고
    • Phenotypic spectrum associated with mutations of the mitochondrial polymerase gamma gene
    • Horvath R, Hudson G, Ferrari G, Futterer N, Ahola S, et al. (2006) Phenotypic spectrum associated with mutations of the mitochondrial polymerase gamma gene. Brain 129: 1674-1684.
    • (2006) Brain , vol.129 , pp. 1674-1684
    • Horvath, R.1    Hudson, G.2    Ferrari, G.3    Futterer, N.4    Ahola, S.5
  • 19
    • 23944456723 scopus 로고    scopus 로고
    • Functional defects due to spacer-region mutations of human mitochondrial DNA polymerase in a family with an ataxia-myopathy syndrome
    • Luoma PT, Luo NG, Loscher WN, Farr CL, Horvath R, et al. (2005) Functional defects due to spacer-region mutations of human mitochondrial DNA polymerase in a family with an ataxia-myopathy syndrome. Hum Mol Genet 14: 1907-1920.
    • (2005) Hum Mol Genet , vol.14 , pp. 1907-1920
    • Luoma, P.T.1    Luo, N.G.2    Loscher, W.N.3    Farr, C.L.4    Horvath, R.5
  • 20
    • 0034943967 scopus 로고    scopus 로고
    • Mutation of POLG is associated with progressive external ophthalmoplegia characterized by mtDNA deletions
    • Van Goethem G, Dermaut B, Lofgren A, Martin JJ, Van Broeckhoven C, (2001) Mutation of POLG is associated with progressive external ophthalmoplegia characterized by mtDNA deletions. Nat Genet 28: 211-212.
    • (2001) Nat Genet , vol.28 , pp. 211-212
    • Van Goethem, G.1    Dermaut, B.2    Lofgren, A.3    Martin, J.J.4    Van Broeckhoven, C.5
  • 21
    • 16844382687 scopus 로고    scopus 로고
    • Autosomal recessive mitochondrial ataxic syndrome due to mitochondrial polymerase gamma mutations
    • Winterthun S, Ferrari G, He L, Taylor RW, Zeviani M, et al. (2005) Autosomal recessive mitochondrial ataxic syndrome due to mitochondrial polymerase gamma mutations. Neurology 64: 1204-1208.
    • (2005) Neurology , vol.64 , pp. 1204-1208
    • Winterthun, S.1    Ferrari, G.2    He, L.3    Taylor, R.W.4    Zeviani, M.5
  • 22
    • 81355137450 scopus 로고    scopus 로고
    • Clinical course of a boy with Alpers syndrome due to homozygosity for A467T mutation in POLG gene
    • Utzig N, Burtzlaff C, Vogelgesang S, Warzok RW, Horvath R, et al. (2007) Clinical course of a boy with Alpers syndrome due to homozygosity for A467T mutation in POLG gene. Acta Neuropathol 114: 71.
    • (2007) Acta Neuropathol , vol.114 , pp. 71
    • Utzig, N.1    Burtzlaff, C.2    Vogelgesang, S.3    Warzok, R.W.4    Horvath, R.5
  • 23
    • 61349156086 scopus 로고    scopus 로고
    • Proof of progression over time: Finally fulminant brain, muscle, and liver affection in Alpers syndrome associated with the A467T POLG1 mutation
    • Boes M, Bauer J, Urbach H, Elger CE, Frank S, et al. (2009) Proof of progression over time: Finally fulminant brain, muscle, and liver affection in Alpers syndrome associated with the A467T POLG1 mutation. Seizure-Eur J Epilep 18: 232-234.
    • (2009) Seizure-Eur J Epilep , vol.18 , pp. 232-234
    • Boes, M.1    Bauer, J.2    Urbach, H.3    Elger, C.E.4    Frank, S.5
  • 24
    • 76649083564 scopus 로고    scopus 로고
    • Sensory ataxic neuropathy dysarthria and ophthalmoparesis (sando) in a sibling pair with a homozygous p.A467T POLG mutation
    • McHugh JC, Lonergan R, Howley R, O'Rourke K, Taylor RW, et al. (2010) Sensory ataxic neuropathy dysarthria and ophthalmoparesis (sando) in a sibling pair with a homozygous p.A467T POLG mutation. Muscle Nerve 41: 265-269.
    • (2010) Muscle Nerve , vol.41 , pp. 265-269
    • McHugh, J.C.1    Lonergan, R.2    Howley, R.3    O'Rourke, K.4    Taylor, R.W.5
  • 25
    • 2642580016 scopus 로고    scopus 로고
    • Premature ageing in mice expressing defective mitochondrial DNA polymerase
    • 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.
    • (2004) Nature , vol.429 , pp. 417-423
    • Trifunovic, A.1    Wredenberg, A.2    Falkenberg, M.3    Spelbrink, J.N.4    Rovio, A.T.5
  • 26
    • 22344456832 scopus 로고    scopus 로고
    • Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging
    • 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.
    • (2005) Science , vol.309 , pp. 481-484
    • Kujoth, G.C.1    Hiona, A.2    Pugh, T.D.3    Someya, S.4    Panzer, K.5
  • 27
    • 65549121567 scopus 로고    scopus 로고
    • Mice expressing an error-prone DNA polymerase in mitochondria display elevated replication pausing and chromosomal breakage at fragile sites of mitochondrial DNA
    • Bailey LJ, Cluett TJ, Reyes A, Prolla TA, Poulton J, et al. (2009) Mice expressing an error-prone DNA polymerase in mitochondria display elevated replication pausing and chromosomal breakage at fragile sites of mitochondrial DNA. Nucleic Acids Res 37: 2327-2335.
    • (2009) Nucleic Acids Res , vol.37 , pp. 2327-2335
    • Bailey, L.J.1    Cluett, T.J.2    Reyes, A.3    Prolla, T.A.4    Poulton, J.5
  • 28
    • 79953735503 scopus 로고    scopus 로고
    • Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins
    • Ameur A, Stewart JB, Freyer C, Hagstro E, Ingman M, et al. (2011) Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins. PLoS Genet 7: 1-9.
    • (2011) PLoS Genet , vol.7 , pp. 1-9
    • Ameur, A.1    Stewart, J.B.2    Freyer, C.3    Hagstro, E.4    Ingman, M.5
  • 29
    • 78649499624 scopus 로고    scopus 로고
    • The mtDNA mutation spectrum of the progeroid Polg mutator mouse includes abundant control region multimers
    • Williams SL, Huang J, Edwards YJ, Ulloa RH, Dillon LM, et al. (2010) The mtDNA mutation spectrum of the progeroid Polg mutator mouse includes abundant control region multimers. Cell Metab 12: 675-682.
    • (2010) Cell Metab , vol.12 , pp. 675-682
    • Williams, S.L.1    Huang, J.2    Edwards, Y.J.3    Ulloa, R.H.4    Dillon, L.M.5
  • 30
    • 41349087783 scopus 로고    scopus 로고
    • DNA deletions and clonal mutations drive premature aging in mitochondrial mutator mice
    • 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.
    • (2008) Nat Genet , vol.40 , pp. 392-394
    • Vermulst, M.1    Wanagat, J.2    Kujoth, G.C.3    Bielas, J.H.4    Rabinovitch, P.S.5
  • 31
    • 70450121949 scopus 로고    scopus 로고
    • On Mitochondria, Mutations, and Methodology
    • Vermulst M, Wanagat J, Loeb LA, (2009) On Mitochondria, Mutations, and Methodology. Cell Metab 10: 437-437.
    • (2009) Cell Metab , vol.10 , pp. 437
    • Vermulst, M.1    Wanagat, J.2    Loeb, L.A.3
  • 32
    • 77955268966 scopus 로고    scopus 로고
    • Analysis of enzyme kinetic data for mtDNA replication
    • Song Z, Samuels DC, (2010) Analysis of enzyme kinetic data for mtDNA replication. Methods 51: 385-391.
    • (2010) Methods , vol.51 , pp. 385-391
    • Song, Z.1    Samuels, D.C.2
  • 33
    • 59149086519 scopus 로고    scopus 로고
    • An analysis of enzyme kinetics data for mitochondrial DNA strand termination by nucleoside reverse transcription inhibitors
    • Wendelsdorf KV, Song Z, Cao Y, Samuels DC, (2009) An analysis of enzyme kinetics data for mitochondrial DNA strand termination by nucleoside reverse transcription inhibitors. PLoS Comput Biol 5: 11.
    • (2009) PLoS Comput Biol , vol.5 , pp. 11
    • Wendelsdorf, K.V.1    Song, Z.2    Cao, Y.3    Samuels, D.C.4
  • 34
    • 0017030517 scopus 로고
    • General method for numerically simulating stochastic time evolution of coupled chemical-reactions
    • Gillespie DT, (1976) General method for numerically simulating stochastic time evolution of coupled chemical-reactions. J Comput Phys 22: 403-434.
    • (1976) J Comput Phys , vol.22 , pp. 403-434
    • Gillespie, D.T.1
  • 35
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical-reactions
    • Gillespie DT, (1977) Exact stochastic simulation of coupled chemical-reactions. J Phys Chem 81: 2340-2361.
    • (1977) J Phys Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 37
    • 20844442462 scopus 로고    scopus 로고
    • POLG mutations in neurodegenerative disorders with ataxia but no muscle involvement
    • Van Goethem G, Luoma P, Rantamaki M, Al Memar A, Kaakkola S, et al. (2004) POLG mutations in neurodegenerative disorders with ataxia but no muscle involvement. Neurology 63: 1251-1257.
    • (2004) Neurology , vol.63 , pp. 1251-1257
    • Van Goethem, G.1    Luoma, P.2    Rantamaki, M.3    Al Memar, A.4    Kaakkola, S.5
  • 38
    • 0019978703 scopus 로고
    • Replication of animal mitochondrial-DNA
    • Clayton DA, (1982) Replication of animal mitochondrial-DNA. Cell 28: 693-705.
    • (1982) Cell , vol.28 , pp. 693-705
    • Clayton, D.A.1
  • 39
    • 0034701029 scopus 로고    scopus 로고
    • Human mitochondrial DNA polymerase holoenzyme: Reconstitution and characterization
    • Johnson AA, Tsai YC, Graves SW, Johnson KA, (2000) Human mitochondrial DNA polymerase holoenzyme: Reconstitution and characterization. Biochemistry 39: 1702-1708.
    • (2000) Biochemistry , vol.39 , pp. 1702-1708
    • Johnson, A.A.1    Tsai, Y.C.2    Graves, S.W.3    Johnson, K.A.4
  • 40
    • 33646085120 scopus 로고    scopus 로고
    • A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase
    • Fan L, Kim S, Farr CL, Schaefer KT, Randolph KM, et al. (2006) A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase. J Mol Biol 358: 1229-1243.
    • (2006) J Mol Biol , vol.358 , pp. 1229-1243
    • Fan, L.1    Kim, S.2    Farr, C.L.3    Schaefer, K.T.4    Randolph, K.M.5
  • 42
    • 0037013234 scopus 로고    scopus 로고
    • Active site mutation in DNA polymerase gamma associated with progressive external ophthalmoplegia causes error-prone DNA synthesis
    • Ponamarev MV, Longley MJ, Nguyen D, Kunkel TA, Copeland WC, (2002) Active site mutation in DNA polymerase gamma associated with progressive external ophthalmoplegia causes error-prone DNA synthesis. J Biol Chem 277: 15225-15228.
    • (2002) J Biol Chem , vol.277 , pp. 15225-15228
    • Ponamarev, M.V.1    Longley, M.J.2    Nguyen, D.3    Kunkel, T.A.4    Copeland, W.C.5
  • 44
    • 79952034603 scopus 로고    scopus 로고
    • Sequence-specific stalling of DNA polymerase gamma and the effects of mutations causing progressive ophthalmoplegia
    • Atanassova N, M. FJ, Wanrooij S, Macao B, Goffart S, et al. (2011) Sequence-specific stalling of DNA polymerase gamma and the effects of mutations causing progressive ophthalmoplegia. Hum Mol Genet 20: 1212-1223.
    • (2011) Hum Mol Genet , vol.20 , pp. 1212-1223
    • Atanassova, N.M.F.J.1    Wanrooij, S.2    Macao, B.3    Goffart, S.4
  • 45
    • 79960481596 scopus 로고    scopus 로고
    • Effect of the Y955C Mutation on Mitochondrial DNA Polymerase Nucleotide Incorporation Efficiency and Fidelity
    • Estep PA, Johnson KA, (2011) Effect of the Y955C Mutation on Mitochondrial DNA Polymerase Nucleotide Incorporation Efficiency and Fidelity. Biochemistry 50: 6376-6386.
    • (2011) Biochemistry , vol.50 , pp. 6376-6386
    • Estep, P.A.1    Johnson, K.A.2
  • 46
    • 33846026386 scopus 로고    scopus 로고
    • Fidelity of the human mitochondrial DNA polymerase
    • Lee HR, Johnson KA, (2006) Fidelity of the human mitochondrial DNA polymerase. J Biol Chem 281: 36236-36240.
    • (2006) J Biol Chem , vol.281 , pp. 36236-36240
    • Lee, H.R.1    Johnson, K.A.2
  • 47
    • 73449089818 scopus 로고    scopus 로고
    • DNA Polymerase Fidelity: Comparing Direct Competition of Right and Wrong dNTP Substrates with Steady State and Pre-Steady State Kinetics
    • Bertram JG, Oertell K, Petruska J, Goodman MF, (2010) DNA Polymerase Fidelity: Comparing Direct Competition of Right and Wrong dNTP Substrates with Steady State and Pre-Steady State Kinetics. Biochemistry 49: 20-28.
    • (2010) Biochemistry , vol.49 , pp. 20-28
    • Bertram, J.G.1    Oertell, K.2    Petruska, J.3    Goodman, M.F.4
  • 48
    • 21644445569 scopus 로고    scopus 로고
    • Mitochondrial deoxynucleotide pools in quiescent fibroblasts - A possible model for mitochondrial neurogastrointestinal encephalomyopathy (MNGIE)
    • Ferraro P, Pontarin G, Crocco L, Fabris S, Reichard P, et al. (2005) Mitochondrial deoxynucleotide pools in quiescent fibroblasts- A possible model for mitochondrial neurogastrointestinal encephalomyopathy (MNGIE). J Biol Chem 280: 24472-24480.
    • (2005) J Biol Chem , vol.280 , pp. 24472-24480
    • Ferraro, P.1    Pontarin, G.2    Crocco, L.3    Fabris, S.4    Reichard, P.5
  • 49
    • 0014787124 scopus 로고
    • The isolation by isopycnic density-gradient centrifugation of two mitochondrial populations from livers of embryonic and fed and starved adult rats
    • Pollak JK, Munn EA, (1970) The isolation by isopycnic density-gradient centrifugation of two mitochondrial populations from livers of embryonic and fed and starved adult rats. Biochem J 117: 913-919.
    • (1970) Biochem J , vol.117 , pp. 913-919
    • Pollak, J.K.1    Munn, E.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.