A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Smith, Anthony C ^a   Robinson, Alan J ^a  

^a MEDICAL RESEARCH COUNCIL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

FUMARATE HYDRATASE; OXOGLUTARATE DEHYDROGENASE; SUCCINATE DEHYDROGENASE;

ARTICLE; BIOLOGICAL MODEL; CITRIC ACID CYCLE; DISORDERS OF MITOCHONDRIAL FUNCTIONS; ENZYMOLOGY; HEART MUSCLE CELL; HUMAN; METABOLISM; MITOCHONDRION; PATHOLOGY;

CITRIC ACID CYCLE; FUMARATE HYDRATASE; HUMANS; KETOGLUTARATE DEHYDROGENASE COMPLEX; MITOCHONDRIA; MITOCHONDRIAL DISEASES; MODELS, BIOLOGICAL; MYOCYTES, CARDIAC; SUCCINATE DEHYDROGENASE;

EID: 79959664729     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-102     Document Type: Article

References (61)

1. Schapira AH. Mitochondrial disease. Lancet 2006, 368:70-82. 10.1016/S0140-6736(06)68970-8, 16815381.
2. Thiele I, Price ND, Vo TD, Palsson BO. Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J Biol Chem 2005, 280:11683-11695. 10.1074/jbc.M409072200, 15572364.
3. Vo TD, Greenberg HJ, Palsson BO. Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J Biol Chem 2004, 279:39532-39540. 10.1074/jbc.M403782200, 15205464.
4. Yugi K, Tomita M. A general computational model of mitochondrial metabolism in a whole organelle scale. Bioinformatics 2004, 20:1795-1796. 10.1093/bioinformatics/bth125, 14962921.
5. Ramakrishna R, Edwards JS, McCulloch A, Palsson BO. Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. Am J Physiol Regul Integr Comp Physiol 2001, 280:R695-704.
6. Smith AC, Robinson AJ. MitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data. Mol Cell Proteomics 2009, 8:1324-1337. 10.1074/mcp.M800373-MCP200, 2690483, 19208617.
7. Orth JD, Thiele I, Palsson BO. What is flux balance analysis?. Nat Biotechnol 2010, 28:245-248. 10.1038/nbt.1614, 3108565, 20212490.
8. Varma A, Palsson BO. Metabolic Flux Balancing - Basic Concepts, Scientific and Practical Use. Bio-Technology 1994, 12:994-998.
9. Watt IN, Montgomery MG, Runswick MJ, Leslie AG, Walker JE. Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria. Proc Natl Acad Sci USA 2010, 107:16823-16827. 10.1073/pnas.1011099107, 2947889, 20847295.
10. Phillips TM, Gibson JB, Ellison DA. Fumarate hydratase deficiency in monozygotic twins. Pediatr Neurol 2006, 35:150-153. 10.1016/j.pediatrneurol.2006.02.005, 16876016.
11. Whelan DT, Hill RE, McClorry S. Fumaric aciduria: a new organic aciduria, associated with mental retardation and speech impairment. Clin Chim Acta 1983, 132:301-308. 10.1016/0009-8981(83)90008-6, 6616883.
12. Kerrigan JF, Aleck KA, Tarby TJ, Bird CR, Heidenreich RA. Fumaric aciduria: clinical and imaging features. Ann Neurol 2000, 47:583-588. 10.1002/1531-8249(200005)47:5<583::AID-ANA5>3.0.CO;2-Y, 10805328.
13. Bourgeron T, Chretien D, Poggi-Bach J, Doonan S, Rabier D, Letouze P, Munnich A, Rotig A, Landrieu P, Rustin P. Mutation of the fumarase gene in two siblings with progressive encephalopathy and fumarase deficiency. J Clin Invest 1994, 93:2514-2518. 10.1172/JCI117261, 294471, 8200987.
14. Remes AM, Rantala H, Hiltunen JK, Leisti J, Ruokonen A. Fumarase deficiency: two siblings with enlarged cerebral ventricles and polyhydramnios in utero. Pediatrics 1992, 89:730-734.
15. Brockmann K, Bjornstad A, Dechent P, Korenke CG, Smeitink J, Trijbels JM, Athanassopoulos S, Villagran R, Skjeldal OH, Wilichowski E, et al. Succinate in dystrophic white matter: a proton magnetic resonance spectroscopy finding characteristic for complex II deficiency. Ann Neurol 2002, 52:38-46. 10.1002/ana.10232, 12112045.
16. Bourgeron T, Rustin P, Chretien D, Birch-Machin M, Bourgeois M, Viegas-Pequignot E, Munnich A, Rotig A. Mutation of a nuclear succinate dehydrogenase gene results in mitochondrial respiratory chain deficiency. Nat Genet 1995, 11:144-149. 10.1038/ng1095-144, 7550341.
17. Birch-Machin MA, Marsac C, Ponsot G, Parfait B, Taylor RW, Rustin P, Munnich A. Biochemical investigations and immunoblot analyses of two unrelated patients with an isolated deficiency in complex II of the mitochondrial respiratory chain. Biochem Biophys Res Commun 1996, 220:57-62. 10.1006/bbrc.1996.0356, 8602857.
18. Rivner MH, Shamsnia M, Swift TR, Trefz J, Roesel RA, Carter AL, Yanamura W, Hommes FA. Kearns-Sayre syndrome and complex II deficiency. Neurology 1989, 39:693-696.
19. Reichmann H, Angelini C. Single muscle fibre analyses in 2 brothers with succinate dehydrogenase deficiency. Eur Neurol 1994, 34:95-98.
20. Bugiani M, Lamantea E, Invernizzi F, Moroni I, Bizzi A, Zeviani M, Uziel G. Effects of riboflavin in children with complex II deficiency. Brain Dev 2006, 28:576-581. 10.1016/j.braindev.2006.04.001, 16737791.
21. Briere JJ, Favier J, El Ghouzzi V, Djouadi F, Benit P, Gimenez AP, Rustin P. Succinate dehydrogenase deficiency in human. Cell Mol Life Sci 2005, 62:2317-2324. 10.1007/s00018-005-5237-6, 16143825.
22. Rustin P, Bourgeron T, Parfait B, Chretien D, Munnich A, Rotig A. Inborn errors of the Krebs cycle: a group of unusual mitochondrial diseases in human. Biochim Biophys Acta 1997, 1361:185-197.
23. Odievre MH, Chretien D, Munnich A, Robinson BH, Dumoulin R, Masmoudi S, Kadhom N, Rotig A, Rustin P, Bonnefont JP. A novel mutation in the dihydrolipoamide dehydrogenase E3 subunit gene (DLD) resulting in an atypical form of α-ketoglutarate dehydrogenase deficiency. Hum Mutat 2005, 25:323-324.
24. Kohlschutter A, Behbehani A, Langenbeck U, Albani M, Heidemann P, Hoffmann G, Kleineke J, Lehnert W, Wendel U. A familial progressive neurodegenerative disease with 2-oxoglutaric aciduria. Eur J Pediatr 1982, 138:32-37. 10.1007/BF00442325, 7075624.
25. Guffon N, Lopez-Mediavilla C, Dumoulin R, Mousson B, Godinot C, Carrier H, Collombet JM, Divry P, Mathieu M, Guibaud P. 2-Ketoglutarate dehydrogenase deficiency, a rare cause of primary hyperlactataemia: report of a new case. J Inherit Metab Dis 1993, 16:821-830. 10.1007/BF00714273, 8295396.
26. Bonnefont JP, Chretien D, Rustin P, Robinson B, Vassault A, Aupetit J, Charpentier C, Rabier D, Saudubray JM, Munnich A. α-ketoglutarate dehydrogenase deficiency presenting as congenital lactic acidosis. J Pediatr 1992, 121:255-258. 10.1016/S0022-3476(05)81199-0, 1640293.
27. Reed JL, Vo TD, Schilling CH, Palsson BO. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 2003, 4:R54. 10.1186/gb-2003-4-9-r54, 193654, 12952533.
28. Daum G, Vance JE. Import of lipids into mitochondria. Prog Lipid Res 1997, 36:103-130. 10.1016/S0163-7827(97)00006-4, 9624424.
29. Stanley WC, Recchia FA, Lopaschuk GD. Myocardial substrate metabolism in the normal and failing heart. Physiol Rev 2005, 85:1093-1129. 10.1152/physrev.00006.2004, 15987803.
30. Cocheme HM, Murphy MP. Complex I is the major site of mitochondrial superoxide production by paraquat. J Biol Chem 2008, 283:1786-1798.
31. Murphy MP. How mitochondria produce reactive oxygen species. Biochem J 2009, 417:1-13. 10.1042/BJ20081386, 2605959, 19061483.
32. Sherry AD, Zhao P, Wiethoff AJ, Jeffrey FM, Malloy CR. Effects of aminooxyacetate on glutamate compartmentation and TCA cycle kinetics in rat hearts. Am J Physiol 1998, 274:H591-599.
33. Nuutila P, Koivisto VA, Knuuti J, Ruotsalainen U, Teras M, Haaparanta M, Bergman J, Solin O, Voipio-Pulkki LM, Wegelius U, et al. Glucose-free fatty acid cycle operates in human heart and skeletal muscle in vivo. J Clin Invest 1992, 89:1767-1774. 10.1172/JCI115780, 295871, 1601987.
34. Belke DD, Larsen TS, Gibbs EM, Severson DL. Altered metabolism causes cardiac dysfunction in perfused hearts from diabetic (db/db) mice. Am J Physiol Endocrinol Metab 2000, 279:E1104-1113.
35. Mudge GH, Mills RM, Taegtmeyer H, Gorlin R, Lesch M. Alterations of myocardial amino acid metabolism in chronic ischemic heart disease. J Clin Invest 1976, 58:1185-1192. 10.1172/JCI108571, 333286, 993339.
36. Schroeder MA, Atherton HJ, Cochlin LE, Clarke K, Radda GK, Tyler DJ. The effect of hyperpolarized tracer concentration on myocardial uptake and metabolism. Magn Reson Med 2009, 61:1007-1014. 10.1002/mrm.21934, 19253408.
37. Thomassen AR, Nielsen TT, Bagger JP, Henningsen P. Myocardial exchanges of glutamate, alanine and citrate in controls and patients with coronary artery disease. Clin Sci (Lond) 1983, 64:33-40.
38. Khairallah M, Labarthe F, Bouchard B, Danialou G, Petrof BJ, Des Rosiers C. Profiling substrate fluxes in the isolated working mouse heart using13C-labeled substrates: focusing on the origin and fate of pyruvate and citrate carbons. Am J Physiol Heart Circ Physiol 2004, 286:H1461-1470.
39. Rennie MJ, Ahmed A, Khogali SE, Low SY, Hundal HS, Taylor PM. Glutamine metabolism and transport in skeletal muscle and heart and their clinical relevance. J Nutr 1996, 126:1142S-1149S.
40. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531. 10.1093/bioinformatics/btg015, 12611808.
41. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2009, 38:D355-360. 2808910, 19880382.
42. Ziegler A, Zaugg CE, Buser PT, Seelig J, Kunnecke B. Non-invasive measurements of myocardial carbon metabolism using in vivo 13C NMR spectroscopy. NMR Biomed 2002, 15:222-234. 10.1002/nbm.764, 11968138.
43. Kacser H, Burns JA. The molecular basis of dominance. Genetics 1981, 97:639-666. 1214416, 7297851.
44. Tillakaratne NJ, Medina-Kauwe L, Gibson KM. γ-Aminobutyric acid (GABA) metabolism in mammalian neural and nonneural tissues. Comp Biochem Physiol A Physiol 1995, 112:247-263. 10.1016/0300-9629(95)00099-2, 7584821.
45. Paradies G, Petrosillo G, Paradies V, Ruggiero FM. Role of cardiolipin peroxidation and Ca2+ in mitochondrial dysfunction and disease. Cell Calcium 2009, 45:643-650. 10.1016/j.ceca.2009.03.012, 19368971.
46. Palmieri F. The mitochondrial transporter family (SLC25): physiological and pathological implications. Pflugers Arch 2004, 447:689-709. 10.1007/s00424-003-1099-7, 14598172.
47. Kunji ER. The role and structure of mitochondrial carriers. FEBS Lett 2004, 564:239-244. 10.1016/S0014-5793(04)00242-X, 15111103.
48. UniProt-Consortium The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 2010, 38:D142-148. 2808944, 19843607, UniProt-Consortium.
49. Camon E, Barrell D, Lee V, Dimmer E, Apweiler R. The Gene Ontology Annotation (GOA) Database -- an integrated resource of GO annotations to the UniProt Knowledgebase. In Silico Biol 2004, 4:5-6.
50. Chang A, Scheer M, Grote A, Schomburg I, Schomburg D. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res 2009, 37:D588-592. 10.1093/nar/gkn820, 2686525, 18984617.
51. Abad MF, Di Benedetto G, Magalhaes PJ, Filippin L, Pozzan T. Mitochondrial pH monitored by a new engineered green fluorescent protein mutant. J Biol Chem 2004, 279:11521-11529. 10.1074/jbc.M306766200, 14701849.
52. Gellera C, Uziel G, Rimoldi M, Zeviani M, Laverda A, Carrara F, DiDonato S. Fumarase deficiency is an autosomal recessive encephalopathy affecting both the mitochondrial and the cytosolic enzymes. Neurology 1990, 40:495-499.
53. Le Novere N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 2005, 23:1509-1515. 10.1038/nbt1156, 16333295.
54. Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2007, 2:727-738. 10.1038/nprot.2007.99, 17406635.
55. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 10.1101/gr.1239303, 403769, 14597658.
56. Ma H, Zeng AP. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19:270-277. 10.1093/bioinformatics/19.2.270, 12538249.
57. Jankowski MD, Henry CS, Broadbelt LJ, Hatzimanikatis V. Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J 2008, 95:1487-1499. 10.1529/biophysj.107.124784, 2479599, 18645197.
58. Price ND, Famili I, Beard DA, Palsson BO. Extreme pathways and Kirchhoff's second law. Biophys J 2002, 83:2879-2882. 10.1016/S0006-3495(02)75297-1, 1302372, 12425318.
59. Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD. Computational prediction of human metabolic pathways from the complete human genome. Genome Biol 2005, 6:R2. 549063, 15642094.
60. Belke DD, Larsen TS, Lopaschuk GD, Severson DL. Glucose and fatty acid metabolism in the isolated working mouse heart. Am J Physiol 1999, 277:R1210-1217.
61. Petrova-Benedict R, Robinson BH, Stacey TE, Mistry J, Chalmers RA. Deficient fumarase activity in an infant with fumaricacidemia and its distribution between the different forms of the enzyme seen on isoelectric focusing. Am J Hum Genet 1987, 40:257-266. 1684096, 3578275.