Survey of human mitochondrial diseases using new genomic/proteomic tools

Genome Biology

Volumn 2, Issue 6, 2001, Pages

  Plasterer, Thomas N ^a   Smith, Temple F ^b   Mohr, Scott C ^b  

^a BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Boston University   (United States)

Author keywords

Additional Data File; Guanidino Group; Hereditary Spastic Paraplegia; Leigh Syndrome; Thymidine Phosphorylase

Indexed keywords

MITOCHONDRIAL DNA; PROTEOME;

AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; CLASSIFICATION; DYSTONIA; GENETICS; GENOME; HEARING IMPAIRMENT; HEREDITARY MOTOR SENSORY NEUROPATHY; HEREDITARY OPTIC ATROPHY; HUMAN; IRON METABOLISM DISORDER; LEIGH DISEASE; MITOCHONDRIAL MYOPATHY; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PROTEIN TERTIARY STRUCTURE; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BAYES THEOREM; CONSERVED SEQUENCE; DEAFNESS; DNA, MITOCHONDRIAL; DYSTONIC DISORDERS; GENOME, HUMAN; HUMANS; IRON METABOLISM DISORDERS; LEIGH DISEASE; MITOCHONDRIAL MYOPATHIES; MOLECULAR SEQUENCE DATA; MUTATION; OPTIC ATROPHIES, HEREDITARY; PROTEIN STRUCTURE, TERTIARY; PROTEOME; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY, AMINO ACID; SPASTIC PARAPLEGIA, HEREDITARY;

EID: 0035229752     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2001-2-6-research0021     Document Type: Article

References (53)

1. Das S, Smith TF: Identifying nature's protein Lego set. In Advances in Protein Chemistry. Edited by Richards FM, Eisenberg DS,Kim PS. San Diego: Academic Press;. 2000, 159-183.
2. Lang BF, Burger G, O'Kelly CJ, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Gray MW: An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature. 1997, 387: 493-497. DOI: 10.1038/387493a0
3. Taanman JW: The mitochondrial genome: structure, transcription, translation and replication. Biochim Biophys Acta. 1999, 1410: 103-123. DOI: 10.1016/S0005-2728(98)00161-3
4. Leonard JV, Schapira AH: Mitochondrial respiratory chain disorders I: mitochondrial DNA defects. Lancet. 2000, 355: 299-304. DOI: 10.1016/S0140-6736(99)05225-3
5. Mitochondrial disorders. [http://www.neuro.wustl.edu/neuromuscular/mitosyn.html]
6. 2+ responses. Science. 1998, 280: 1763-1766. DOI: 10.1126/science.280.5370.1763
7. Skulachev VP: Mitochondrial filaments and clusters as intracellular power-transmitting cables. Trends Biochem Sci. 2001, 26: 23-29. DOI: 10.1016/S0968-0004(00)01735-7
8. Schapira AH: Mitochondrial disorders. Biochim Biophys Acta. 1999, 1410: 99-102. DOI: 10.1016/S0005-2728(98)00160-1
9. Hayashi J, Ohta S, Kikuchi A, Takemitsu M, Goto Y, Nonaka I: Introduction of disease-related mitochondrial DNA deletions into HeLa cells lacking mitochondrial DNA results in mitochondrial dysfunction. Proc Natl Acad Sci USA. 1991, 88: 10614-10618. DOI: 10.1073/pnas.88.23.10614
10. Chomyn A, Martinuzzi A, Yoneda M, Daga A, Hurko O, Johns D, Lai ST, Nonaka I, Angelini C, Attardi G: MELAS mutation in mtDNA binding site for transcription termination factor causes defects in protein synthesis and in respiration but no change in levels of upstream and downstream mature transcripts. Proc Natl Acad Sci USA. 1992, 89: 4221-4225. DOI: 10.1073/pnas.89.10.4221
11. Riordan-Eva P, Harding AE: Leber's hereditary optic neuropathy: the clinical relevance of different mitochondrial DNA mutations. J Med Genet. 1995, 32: 81-87. DOI: 10.1136/jmg.32.2.81
12. Brown MD, Voljavec AS, Lott MT, MacDonald I, Wallace DC: Leber's hereditary optic neuropathy: a model for mitochondrial neurodegenerative diseases. FASEB J. 1992, 6: 2791-2799.
13. Zeviani M, Bertagnolio B, Uziel G: Neurological presentations of mitochondrial diseases. J Inherit Metab Dis. 1996, 19: 504-520. DOI: 10.1007/BF01799111
14. Trounce I, Neill S, Wallace DC: Cytoplasmic transfer of the mtDNA nt 8993 T → G (ATP6) point mutation associated with Leigh syndrome into mtDNA-less cells demonstrates cosegregation with a decrease in state III respiration and ADP/O ratio. Proc Natl Acad Sci USA. 1994, 91: 8334-8338. DOI: 10.1073/pnas.91.18.8334
15. Santorelli FM, Shanske S, Macaya A, DeVivo DC, DiMauro S: The mutation at nt 8993 of mitochondrial DNA is a common cause of Leigh's syndrome. Ann Neurol. 1993, 34: 827-834. DOI: 10.1002/ana.410340612
16. Marsac C, Benelli C, Desguerre I, Diry M, Fouque F, De Meirleir L, Ponsot G, Seneca S, Poggi F, Saudubray JM, et al: Biochemical and genetic studies of four patients with pyruvate dehydrogenase E1 alpha deficiency. Hum Genet. 1997, 99: 785-792. 10.1007/s004390050449. DOI: 10.1007/s004390050449
17. Dahl H-HM: Getting to the nucleus of mitochondrial disorders: Identification of respiratory chain-enzyme genes causing Leigh syndrome. Am J Hum Genet. 1998, 63: 1594-1597. DOI: 10.1086/302169
18. Tiranti V, Hoertnagel K, Carrozzo R, Galimberti C, Munaro M, Granatiero M, Zelante L, Gasparini P, Marzella R, Rocchi M, et al: Mutations of SURF-1 in Leigh disease associated with cytochrome c oxidase deficiency. Am J Hum Genet. 1998, 63: 1609-1621. DOI: 10.1086/302150
19. Poyau A, Buchet K, Bouzidi MF, Zabot MT, Echenne B, Yao J, Shoubridge EA, Godinot C: Missense mutations in SURF1 associated with deficient cytochrome c oxidase assembly in Leigh syndrome patients. Hum Genet. 2000, 106: 194-205. 10.1007/s004390051028. DOI: 10.1007/s004390051028
20. 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. DOI: 10.1038/ng1095-144
21. Parfait B, Chretien D, Rotig A, Marsac C, Munnich A, Rustin P: Compound heterozygous mutations in the flavoprotein gene of the respiratory chain complex II in a patient with Leigh syndrome. Hum Genet. 2000, 106: 236-243. 10.1007/s004390051033. DOI: 10.1007/s004390051033
22. Nishino I, Spinazzola A, Hirano M: Thymidine phosphorylase gene mutations in MNGIE, a human mitochondrial disorder. Science. 1999, 283: 689-692. 10.1002/(SICI)1097-010X(19990601)283:7<689::AID-JEZ7>3.0.CO;2-T. DOI: 10.1126/science.283.5402.689
23. Miyadera K, Dohmae N, Takio K, Sumizawa T, Haraguchi M, Furukawa T, Yamada Y, Akiyama S: Structural characterization of thymidine phosphorylase from human placenta. Biochem Biophys Res Commun. 1995, 212: 1040-1045. 10.1006/bbrc.1995.2074. DOI: 10.1006/bbrc.1995.2074
24. Brown NS, Bicknell R: Thymidine phosphorylase, 2-deoxy-D-ribose and angiogenesis. Biochem J. 1998, 334: 1-8. DOI: 10.1042/bj3340001
25. Jin H, May M, Tranebjaerg L, Kendall E, Fontan G, Jackson J, Subramony SH, Arena F, Lubs H, Smith S, et al: A novel X-linked gene, DDP, shows mutations in families with deafness (DFN-1), dystonia, mental deficiency and blindness. Nat Genet. 1996, 14: 177-180. DOI: 10.1038/ng1096-177
26. Koehler CM, Leuenberger D, Merchant S, Renold A, Junne T, Schatz G: Human deafness dystonia syndrome is a mitochondrial disease. Proc Natl Acad Sci USA. 1999, 96: 2141-2146. DOI: 10.1073/pnas.96.5.2141
27. Tranebjaerg L, Hamel BC, Gabreels FJ, Renier WO, Van Ghelue M: A de novo missense mutation in a critical domain of the X-linked DDP gene causes the typical deafness-dystonia-optic atrophy syndrome. Eur J Hum Genet. 2000, 8: 464-467. DOI: 10.1038/sj.ejhg.5200483
28. Koehler CM, Merchant S, Schatz G: How membrane proteins travel across the mitochondrial intermembrane space. Trends Biochem Sci. 1999, 24: 428-432. DOI: 10.1016/S0968-0004(99)01462-0
29. Leuenberger D, Bally NA, Schatz G, Koehler CM: Different import pathways through the mitochondrial intermembrane space for inner membrane proteins. EMBO J. 1999, 18: 4816-4822. DOI: 10.1093/emboj/18.17.4816
30. Rotig A, de Lonlay P, Chretien D, Foury F, Koenig M, Sidi D, Munnich A, Rustin P: Aconitase and mitochondrial iron-sulphur protein deficiency in Friedreich ataxia. Nat Genet. 1997, 17: 215-217. DOI: 10.1038/ng1097-215
31. Delatycki MB, Williamson R, Forrest SM: Friedreich ataxia: an overview. J Med Genet. 2000, 37: 1-8. DOI: 10.1136/jmg.37.1.1
32. Sakamoto N, Chastain PD, Parniewski P, Ohshima K, Pandolfo M, Griffith JD, Wells RD: Sticky DNA: self-association properties of long GAA.TTC repeats in R.R.Y Triplex structures from Friedreich's ataxia. Mol Cell. 1999, 3: 465-475. DOI: 10.1016/S1097-2765(00)80474-8
33. Branda SS, Yang ZY, Chew A, Isaya G: Mitochondrial intermediate peptidase and the yeast frataxin homolog together maintain mitochondrial iron homeostasis in Saccharomyces cerevisiae. Hum Mol Genet. 1999, 8: 1099-1110. DOI: 10.1093/hmg/8.6.1099
34. Allikmets R, Raskind WH, Hutchinson A, Schueck ND, Dean M, Koeller DM: Mutation of a putative mitochondrial iron transporter gene (ABC7) in X-linked sideroblastic anemia and ataxia (XLSA/A). Hum Mol Genet. 1999, 8: 743-749. DOI: 10.1093/hmg/8.5.743
35. Stultz CM, White JV, Smith TF: Structural analysis based on state-space modeling. Protein Sci. 1993, 2: 305-314. DOI: 10.1002/pro.5560020302
36. White JV, Stultz CM, Smith TF: Protein classification by stochastic modeling and optimal filtering of amino acid sequences. Math Biosci. 1994, 119: 35-75. DOI: 10.1016/0025-5564(94)90004-3
37. Casari G, De Fusco M, Ciarmatori S, Zeviani M, Mora M, Fernandez P, De Michele G, Filla A, Cocozza S, Marconi R, et al: Spastic paraplegia and OXPHOS impairment caused by mutations in paraplegin, a nuclear-encoded mitochondrial metallopro-tease. Cell. 1998, 93: 973-983. DOI: 10.1016/S0092-8674(00)81203-9
38. Steglich G, Neupert W, Langer T: Prohibitins regulate membrane protein degradation by the m-AAA protease in mitochondria. Mol Cell Biol. 1999, 19: 3435-3442. DOI: 10.1128/MCB.19.5.3435
39. Online Mendelian Inheritance in Man. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM]
40. Mitochondrial Project. [http://www.mips.biochem.mpg.de/proj/medgen/mitop/]
41. Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, et al: Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Res. 1999, 27: 74-78. DOI: 10.1093/nar/27.1.74
42. Mewes HW, Frishman D, Gruber C, Geier B, Haase D, Kaps A, Lemcke K, Mannhaupt G, Pfeiffer F, Schuller C, et al: MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 2000, 28: 37-40. DOI: 10.1093/nar/28.1.37
43. Hodges PE, McKee AH, Davis BP, Payne WE, Garrels JI: The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. Nucleic Acids Res. 1999, 27: 69-73. DOI: 10.1093/nar/27.1.69
44. de Pinto B, Malladi SB, Altamura N: MitBASE pilot: a database on nuclear genes involved in mitochondrial biogenesis and its regulation in Saccharomyces cerevisiae. Nucleic Acids Res. 1999, 27: 147-149. DOI: 10.1093/nar/27.1.147
45. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. 10.1006/jmbi.1990.9999. DOI: 10.1016/S0022-2836(05)80360-2
46. Bairoch A, Apweiler R: The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res. 1999, 27: 49-54. DOI: 10.1093/nar/27.1.49
47. Wootton JC, Federhen S: Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 1996, 266: 554-571. DOI: 10.1016/S0076-6879(96)66035-2
48. Smith RF, Smith TF: Automatic generation of primary sequence patterns from sets of related protein sequences. Proc Natl Acad Sci USA. 1990, 87: 118-122. DOI: 10.1073/pnas.87.1.118
49. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000, 28: 235-242. DOI: 10.1093/nar/28.1.235
50. Sayle RA, Milner-White EJ: RASMOL: biomolecular graphics for all. Trends Biochem Sci. 1995, 20: 374- DOI: 10.1016/S0968-0004(00)89080-5
51. Kraulis PJ: MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr. 1991, 24: 946-950. 10.1107/S0021889891004399. DOI: 10.1107/S0021889891004399
52. Merritt E, Bacon D: Raster3D: photorealistic molecular graphics. Methods Enzymol. 1997, 277: 505-524. DOI: 10.1016/S0076-6879(97)77028-9
53. Amino acid classes. [http://bmerc-www.bu.edu/description/aaclasses.html]