Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations

The accumulation of mutant mitochondrial DNA (mtDNA) molecules in aged cells has been associated with mitochondrial dysfunction, age-related diseases and the ageing process itself. This accumulation has been shown to often occur clonally, where mutant mtDNA grow in number and overpopulate the wild-type mtDNA. However, the cell possesses quality control (QC) mechanisms that maintain mitochondrial function, in which dysfunctional mitochondria are isolated and removed by selective fusion and mitochondrial autophagy (mitophagy), respectively. The aim of this study is to elucidate the circumstances related to mitochondrial QC that allow the expansion of mutant mtDNA molecules. For the purpose of the study, we have developed a mathematical model of mitochondrial QC process by extending our previous validated model of mitochondrial turnover and fusion-fission. A global sensitivity analysis of the model suggested that the selectivity of mitophagy and fusion is the most critical QC parameter for clearing de novo mutant mtDNA molecules. We further simulated several scenarios involving perturbations of key QC parameters to gain a better understanding of their dynamic and synergistic interactions. Our model simulations showed that a higher frequency of mitochondrial fusion-fission can provide a faster clearance of mutant mtDNA, but only when mutant–rich mitochondria that are transiently created are efficiently prevented from re-fusing with other mitochondria and selectively removed. Otherwise, faster fusion-fission quickens the accumulation of mutant mtDNA. Finally, we used the insights gained from model simulations and analysis to propose a possible circumstance involving deterioration of mitochondrial QC that permits mutant mtDNA to expand with age.

[1]  Rudiyanto Gunawan,et al.  Mathematical Modeling of the Role of Mitochondrial Fusion and Fission in Mitochondrial DNA Maintenance , 2013, PloS one.

[2]  M. Hellerstein,et al.  Measurement of mitochondrial DNA synthesis in vivo using a stable isotope-mass spectrometric technique. , 2003, Journal of applied physiology.

[3]  P. Frachon,et al.  Organization and dynamics of human mitochondrial DNA , 2004, Journal of Cell Science.

[4]  J. Aiken,et al.  Mitochondrial DNA deletion mutations colocalize with segmental electron transport system abnormalities, muscle fiber atrophy, fiber splitting, and oxidative damage in sarcopenia , 2001, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[5]  R. Youle,et al.  Parkin is recruited selectively to impaired mitochondria and promotes their autophagy , 2008, The Journal of cell biology.

[6]  D. Chan,et al.  Mitochondrial dynamics–fusion, fission, movement, and mitophagy–in neurodegenerative diseases , 2009, Human molecular genetics.

[7]  G. Pastorin,et al.  Mitochondria-targeted antioxidants and metabolic modulators as pharmacological interventions to slow ageing. , 2013, Biotechnology advances.

[8]  Joel N. Meyer,et al.  Mitochondrial dynamics and autophagy aid in removal of persistent mitochondrial DNA damage in Caenorhabditis elegans , 2012, Nucleic acids research.

[9]  R. Huemer,et al.  Mitochondrial studies in senescent mice. I. Turnover of brain mitochondrial lipids. , 1971, Experimental gerontology.

[10]  Olaf Wolkenhauer,et al.  Stochastic approaches in systems biology , 2010, Wiley interdisciplinary reviews. Systems biology and medicine.

[11]  Jean-Pierre Mazat,et al.  Mitochondrial threshold effects. , 2003, The Biochemical journal.

[12]  L. Vergani,et al.  Inhibition of mitochondrial fission favours mutant over wild-type mitochondrial DNA. , 2009, Human molecular genetics.

[13]  J. Hayashi,et al.  Mitochondrial functional complementation in mitochondrial DNA-based diseases. , 2009, The international journal of biochemistry & cell biology.

[14]  J. Hayashi,et al.  Human cells are protected from mitochondrial dysfunction by complementation of DNA products in fused mitochondria , 2001, Nature Genetics.

[15]  D. Chan Fusion and fission: interlinked processes critical for mitochondrial health. , 2012, Annual review of genetics.

[16]  João Pedro de Magalhães,et al.  Meta-analysis of age-related gene expression profiles identifies common signatures of aging , 2009, Bioinform..

[17]  H. Shibasaki,et al.  Late onset mitochondrial myopathy. , 1973, Journal of the neurological sciences.

[18]  K. Nair,et al.  Decline in skeletal muscle mitochondrial function with aging in humans. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Michael T Ryan,et al.  Mitochondrial-nuclear communications. , 2007, Annual review of biochemistry.

[20]  S. Dimauro,et al.  Therapeutic prospects for mitochondrial disease. , 2010, Trends in molecular medicine.

[21]  O. Shirihai,et al.  Frequency and selectivity of mitochondrial fusion are key to its quality maintenance function. , 2009, Biophysical journal.

[22]  X. Zhuang,et al.  Whole cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution , 2008, Nature Methods.

[23]  T. Kirkwood,et al.  Transcription could be the key to the selection advantage of mitochondrial deletion mutants in aging , 2014, Proceedings of the National Academy of Sciences.

[24]  D. Turnbull,et al.  An essential guide to mtDNA maintenance , 1998, Nature Genetics.

[25]  K. Khrapko,et al.  Mutation and intracellular clonal expansion of mitochondrial genomes: two synergistic components of the aging process? , 2003, Mechanisms of Ageing and Development.

[26]  R. A. Butow,et al.  Mitochondrial retrograde signaling. , 2006, Annual review of genetics.

[27]  A. Lombès,et al.  Organization, dynamics and transmission of mitochondrial DNA: focus on vertebrate nucleoids. , 2006, Biochimica et biophysica acta.

[28]  Min Wu,et al.  Fission and selective fusion govern mitochondrial segregation and elimination by autophagy , 2008, The EMBO journal.

[29]  I. Struewing,et al.  Lithium increases PGC‐1α expression and mitochondrial biogenesis in primary bovine aortic endothelial cells , 2007, The FEBS journal.

[30]  N. Bulleid Disulfide bond formation in the mammalian endoplasmic reticulum. , 2012, Cold Spring Harbor perspectives in biology.

[31]  Suresh Kumar Poovathingal,et al.  Stochastic Drift in Mitochondrial DNA Point Mutations: A Novel Perspective Ex Silico , 2009, PLoS Comput. Biol..

[32]  Fernando J. Pineda,et al.  Mitochondrial fission and fusion dynamics: the long and short of it , 2008, Cell Death and Differentiation.

[33]  Saltelli Andrea,et al.  Global Sensitivity Analysis: The Primer , 2008 .

[34]  C. Moraes,et al.  Mechanisms of human mitochondrial DNA maintenance: the determining role of primary sequence and length over function. , 1999, Molecular biology of the cell.

[35]  T. Schwarz,et al.  The pathways of mitophagy for quality control and clearance of mitochondria , 2012, Cell Death and Differentiation.

[36]  Glyn Nelson,et al.  Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions , 2014, PLoS Comput. Biol..

[37]  T. Prolla,et al.  Mitochondrial Fusion Is Required for mtDNA Stability in Skeletal Muscle and Tolerance of mtDNA Mutations , 2010, Cell.

[38]  E. Doria,et al.  Relationship between Human Aging Muscle and Oxidative System Pathway , 2012, Oxidative medicine and cellular longevity.

[39]  T. Kuroiwa,et al.  Organization of multiple nucleoids and DNA molecules in mitochondria of a human cell. , 1991, Experimental cell research.

[40]  P. Chinnery,et al.  Normal levels of wild-type mitochondrial DNA maintain cytochrome c oxidase activity for two pathogenic mitochondrial DNA mutations but not for m.3243A-->G. , 2007, American journal of human genetics.

[41]  C. Lawless,et al.  Mitochondrial turnover in liver is fast in vivo and is accelerated by dietary restriction: application of a simple dynamic model , 2008, Aging cell.

[42]  N. Gross,et al.  Apparent turnover of mitochondrial deoxyribonucleic acid and mitochondrial phospholipids in the tissues of the rat. , 1969, The Journal of biological chemistry.

[43]  David C Samuels,et al.  A model of the nuclear control of mitochondrial DNA replication. , 2003, Journal of theoretical biology.

[44]  S. Dimauro,et al.  Molecular analysis of the muscle pathology associated with mitochondrial DNA deletions , 1992, Nature Genetics.

[45]  M. Bayona-Bafaluy,et al.  Human mitochondrial DNA with large deletions repopulates organelles faster than full-length genomes under relaxed copy number control. , 2002, Nucleic acids research.

[46]  E. Robin,et al.  Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells , 1988, Journal of cellular physiology.

[47]  G. Love,et al.  Stochastically determined directed movement explains the dominant small‐scale mitochondrial movements within non‐neuronal tissue culture cells , 2009, FEBS letters.

[48]  H. Fukui,et al.  Mechanisms of formation and accumulation of mitochondrial DNA deletions in aging neurons. , 2009, Human molecular genetics.

[49]  T. Prolla,et al.  Increased mitochondrial biogenesis in muscle improves aging phenotypes in the mtDNA mutator mouse. , 2012, Human molecular genetics.

[50]  Rudiyanto Gunawan,et al.  Effects of lithium on age-related decline in mitochondrial turnover and function in Caenorhabditis elegans. , 2014, The journals of gerontology. Series A, Biological sciences and medical sciences.

[51]  Alison S. Tomlin,et al.  GUI-HDMR - A software tool for global sensitivity analysis of complex models , 2009, Environ. Model. Softw..

[52]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[53]  Laura C. Greaves,et al.  Mitochondrial DNA mutations and ageing. , 2009, Biochimica et biophysica acta.

[54]  B. Roelofsen,et al.  Molecular membrane biology: editor J. A. Lucy, Taylor and Francis, £45.00 (individual); £89.00 (institutional) , 1995 .

[55]  P. Hammerstein,et al.  Morpho-dynamic changes of mitochondria during ageing of human endothelial cells , 2005, Mechanisms of Ageing and Development.

[56]  Michael Meyer-Hermann,et al.  Deceleration of Fusion–Fission Cycles Improves Mitochondrial Quality Control during Aging , 2012, PLoS Comput. Biol..

[57]  R. Scarpulla,et al.  Transcriptional regulatory circuits controlling mitochondrial biogenesis and function. , 2004, Genes & development.

[58]  Sarah Sonnay,et al.  Parkin promotes the ubiquitination and degradation of the mitochondrial fusion factor mitofusin 1 , 2011, Journal of neurochemistry.

[59]  F. Sanger,et al.  Sequence and organization of the human mitochondrial genome , 1981, Nature.

[60]  D. Chan,et al.  Disruption of Fusion Results in Mitochondrial Heterogeneity and Dysfunction* , 2005, Journal of Biological Chemistry.

[61]  O. Shirihai,et al.  Mitochondrial fusion, fission and autophagy as a quality control axis: the bioenergetic view. , 2008, Biochimica et biophysica acta.

[62]  D. Turnbull,et al.  Accumulation of mitochondrial DNA mutations in ageing, cancer, and mitochondrial disease: is there a common mechanism? , 2002, The Lancet.

[63]  A. Terman,et al.  Inhibition of autophagy with 3-methyladenine results in impaired turnover of lysosomes and accumulation of lipofuscin-like material. , 2004, European journal of cell biology.

[64]  E. Schon,et al.  Mitochondrial nucleoids maintain genetic autonomy but allow for functional complementation , 2008, The Journal of cell biology.

[65]  C. Schmitz,et al.  Mitochondrial DNA synthesis studied autoradiographically in various cell types in vivo. , 1998, Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas.

[66]  J. Bereiter-Hahn,et al.  Mitochondrial dynamics generate equal distribution but patchwork localization of respiratory Complex I , 2006, Molecular membrane biology.

[67]  F. Benes,et al.  Gene expression profiling of substantia nigra dopamine neurons: further insights into Parkinson's disease pathology. , 2009, Brain : a journal of neurology.

[68]  A. Godzik,et al.  Mitochondrial fission in apoptosis, neurodegeneration and aging. , 2003, Current opinion in cell biology.

[69]  R. Youle,et al.  Mitochondrial quality control mediated by PINK1 and Parkin: links to parkinsonism. , 2012, Cold Spring Harbor perspectives in biology.

[70]  P. Chinnery,et al.  Relaxed replication of mtDNA: A model with implications for the expression of disease. , 1999, American journal of human genetics.

[71]  Yidong Bai,et al.  Number matters: control of mammalian mitochondrial DNA copy number. , 2009, Journal of genetics and genomics = Yi chuan xue bao.

[72]  E. Feldman,et al.  Mechanisms of Disease: mitochondria as new therapeutic targets in diabetic neuropathy , 2006, Nature Clinical Practice Neurology.

[73]  E. Shoubridge,et al.  Late‐onset mitochondrial myopathy , 1995, Annals of neurology.

[74]  C. Leeuwenburgh,et al.  Upregulated autophagy protects cardiomyocytes from oxidative stress-induced toxicity , 2013, Autophagy.

[75]  Jeong W. Pak,et al.  Accumulation of mitochondrial DNA deletion mutations in aged muscle fibers: evidence for a causal role in muscle fiber loss. , 2007, The journals of gerontology. Series A, Biological sciences and medical sciences.

[76]  Shin-ichi Arimura,et al.  Frequent fusion and fission of plant mitochondria with unequal nucleoid distribution. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[77]  E. Schon,et al.  Mitochondrial autophagy in cells with mtDNA mutations results from synergistic loss of transmembrane potential and mTORC1 inhibition. , 2012, Human molecular genetics.

[78]  G. Dorn,et al.  PINK1-Phosphorylated Mitofusin 2 Is a Parkin Receptor for Culling Damaged Mitochondria , 2013, Science.

[79]  I. Nonaka,et al.  Single muscle fiber analysis of mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke‐like episodes (MELAS) , 1994, Annals of neurology.

[80]  O. Shirihai,et al.  Mitochondrial ‘kiss‐and‐run’: interplay between mitochondrial motility and fusion–fission dynamics , 2009, The EMBO journal.

[81]  C. Moraes What regulates mitochondrial DNA copy number in animal cells? , 2001, Trends in genetics : TIG.

[82]  B. Spiegelman,et al.  Activation of the PPAR/PGC-1alpha pathway prevents a bioenergetic deficit and effectively improves a mitochondrial myopathy phenotype. , 2008, Cell metabolism.

[83]  Kerwyn Casey Huang,et al.  Optimal Dynamics for Quality Control in Spatially Distributed Mitochondrial Networks , 2013, PLoS Comput. Biol..

[84]  Hiroshi Kimura,et al.  The functional organization of mitochondrial genomes in human cells , 2004, BMC Biology.

[85]  J. Hayashi,et al.  Inter-mitochondrial complementation: Mitochondria-specific system preventing mice from expression of disease phenotypes by mutant mtDNA , 2001, Nature Medicine.

[86]  N. Larsson Somatic mitochondrial DNA mutations in mammalian aging. , 2010, Annual review of biochemistry.

[87]  Rudiyanto Gunawan,et al.  Is mitochondrial DNA turnover slower than commonly assumed? , 2012, Biogerontology.