A candidate complex approach to study functional mitochondrial DNA changes: Sequence variation and quaternary structure modeling of Drosophila simulans cytochrome c oxidase

Journal of Molecular Evolution

Volumn 66, Issue 3, 2008, Pages 232-242

  Melvin, Richard G ^a   Katewa, Subhash D ^a   Ballard, J William O ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

Candidate complex approach; Cytochrome c oxidase; Genetic hitchhiking

Indexed keywords

AMINO ACID; CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA;

AMINO ACID SEQUENCE; ARTICLE; DROSOPHILA SIMULANS; ENZYME ACTIVITY; EVOLUTION; GENE LOCUS; GENE SEQUENCE; GENETIC CODE; GENETIC PROCEDURES; GENETIC VARIABILITY; NONHUMAN; POPULATION GENETICS; PROTEIN QUATERNARY STRUCTURE; VALIDATION PROCESS;

ANIMALS; DNA, MITOCHONDRIAL; DROSOPHILA; ELECTRON TRANSPORT COMPLEX IV; MODELS, MOLECULAR; PROTEIN STRUCTURE, QUATERNARY; VARIATION (GENETICS);

DROSOPHILA SIMULANS;

EID: 43149124830     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-008-9078-4     Document Type: Article

References (45)

1. Avise JC (1994) Molecular markers, natural history, and evolution. Chapman and Hall, New York
2. Ballard JWO (2000) Comparative genomics of mitochondrial DNA in Drosophila simulans. J Mol Evol 51:64-75
3. Ballard JWO (2004) Sequential evolution of a symbiont inferred from the host: Wolbachia and Drosophila simulans. Mol Biol Evol 21:428-444
4. Ballard JWO, James AC (2004) Differential fitness of mitochondrial DNA in perturbation cage studies correlates with global abundance and population history in Drosophila simulans. Proc R Soc Lond B Biol Sci 271:1197-1201
5. Ballard JWO, Katewa SD, Melvin RG, Chan G (2007a) Comparative analysis of mitochondrial genotype and aging. Ann NY Acad Sci 1114:93-106
6. Ballard JWO, Melvin RG, Katewa SD, Maas K (2007b) Mitochondrial DNA variation is associated with measurable differences in life-history traits and mitochondrial metabolism in Drosophila simulans. Evolution 61:1735-1747
7. Bender E, Kadenbach B (2000) The allosteric ATP-inhibition of cytochrome c oxidase activity is reversibly switched on by cAMP-dependent phosphorylation. FEBS Lett 466:130-134
8. Capaldi RA (1990) Structure and assembly of cytochrome c oxidase. Arch Biochem Biophys 280:252-262
9. Charlesworth B, Morgan MT, Charlesworth D (1993) The effect of deleterious mutations on neutral molecular variation. Genetics 134:1289-1303
10. Claros MG, Vincens P (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241:779-786
11. Das J, Miller ST, Stern DL (2004) Comparison of diverse protein sequences of the nuclear-encoded subunits of cytochrome c oxidase suggests conservation of structure underlies evolving functional sites. Mol Biol Evol 21:1572-1582
12. Dean MD (2006) A Wolbachia-associated fitness benefit depends on genetic background in Drosophila simulans. Proc Biol Sci 273:1415-1420
13. Dean MD, Ballard JWO (2005) High divergence among Drosophila simulans mitochondrial haplogroups arose in midst of long term purifying selection. Mol Phylogenet Evol 36:328-337
14. Depaulis F, Moussett S, Veuille M (2003) Power of neutrality tests to detect bottlenecks and hitchhiking. J Mol Evol 57:S190-S200
15. de Stordeur E (1997) Nonrandom partition of mitochondria in heteroplasmic Drosophila. Heredity 79:615-623
16. Ellison CK, Burton RS (2006) Disruption of mitochondrial function in interpopulation hybrids of Tigriopus californicus. Evolution 60:1382-1391
17. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693-709
18. Guex N, Peitsch MC (1997) Swiss-Model and the Swiss-PDB Viewer: an environment for comparative protein modeling. Electrophoresis 18:2714-2723
19. Hudson RR, Turelli M (2003) Stochasticity overrules the "three-times rule": genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution 57:182-190
20. James AC, Ballard JWO (2000) Expression of cytoplasmic incompatibility in Drosophila simulans and its impact on infection frequencies and distribution of Wolbachia pipientis. Evolution 54:1661-1672
21. James AC, Ballard JWO (2003) Mitochondrial genotype affects fitness in Drosophila simulans. Genetics 164:187-194
22. Kaplan NL, Hudson RR, Langley CH (1989) The "hitchhiking effect" revisited. Genetics 123:887-899
23. Katewa SD, Ballard JW (2007) Sympatric Drosophila simulans flies with distinct mtDNA show difference in mitochondrial respiration and electron transport. Insect Biochem Mol Biol 37:213-222
24. Kreitman M (1983) Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304:412-417
25. Liu W, Gnanasambandam R, Benjamin J, Kaur G, Getman PB, Siegel AJ, Shortridge RD, Singh S (2007) Mutations in cytochrome c oxidase subunit VIA cause neurodegeneration and motor dysfunction in Drosophila. Genetics 176:937-946
26. Ludwig B, Bender E, Arnold S, Huttemann M, Lee I, Kadenbach B (2001) Cytochrome c oxidase and the regulation of oxidative phosphorylation. Chem Biochem 2:392-403
27. Mandal S, Guptan P, Owusu-Ansah E, Banerjee U (2005) Mitochondrial regulation of cell cycle progression during development as revealed by the tenured mutation in Drosophila. Dev Cell 9:843-854
28. Martin PD, Malkowski MG, Box J, Esmon CT, Edwards BF (1997) New insights into the regulation of the blood clotting cascade derived from the X-ray crystal structure of bovine meizothrombin des F1 in complex with PPACK. Structure 5:1681-1693
29. Maynard-Smith J, Haigh J (1974) The hitch-hiking effect of a favourable gene. Genet Res 23:23-35
30. Melvin RG, Ballard JWO (2006) Intraspecific variation in survival and mitochondrial oxidative phosphorylation in wild caught Drosophila simulans. Aging Cell 5:225-233
31. Nachman MW (1998) Deleterious mutations in animal mitochondrial DNA. Genetica 103:61-69
32. Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205-217
33. Powell JR, Caccone A, Amato GD, Yoon C (1986) Rates of nucleotide substitution in Drosophila mitochondrial-DNA and nuclear-DNA are similar. Proc Natl Acad Sci USA 83:9090-9093
34. Rand DM, Haney RA, Fry AJ (2004) Cytonuclear coevolution: the genomics of cooperation. Trends Ecol Evol 19:645-653
35. Roubertoux PL, Sluyter F, Carlier M, Marcet B, Maarouf-Veray F, Cherif C, Marican C, Arrechi P, Godin F, Jamon M, Verrier B, Cohen-Salmon C (2003) Mitochondrial DNA modifies cognition in interaction with the nuclear genome and age in mice. Nat Genet 35:65-69
36. Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175
37. Ruiz-Pesini E, Lapena AC, Diez-Sanchez C, Perez-Martos A, Montoya J, Alvarez E, Diaz M, Urries A, Montoro L, Lopez-Perez MJ, Enriquez JA (2000) Human mtDNA haplogroups associated with high or reduced spermatozoa motility. Am J Hum Genet 67:682-696
38. Schizas NV, Chandler GT, Coull BC, Klosterhaus SL, Quattro JM (2001) Differential survival of three mitochondrial lineages of a marine benthic copepod exposed to a pesticide mixture Environ Sci Technol 35:535-538
39. Schmidt TR, Wu W, Goodman M, Grossman LI (2001) Evolution of nuclear- and mitochondrial-encoded subunit interaction in cytochrome c oxidase. Mol Biol Evol 18:563-569
40. Schmidt TR, Wildman DE, Uddin M, Opazo JC, Goodman M, Grossman LI (2005) Rapid electrostatic evolution at the binding site for cytochrome c on cytochrome c oxidase in anthropoid primates. Proc Natl Acad Sci USA 102:6379-6384
41. Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology modeling server. Nucleic Acids Res 31:3381-3385
42. Tajima F (1989) Statistical method for testing the neutral mutatio n hypothesis by DNA polymorphism. Genetics 123:585-595
43. Takeda K, Takahashi S, Onishi A, Hanada H, Imai H (2000) Replicative advantage and tissue-specific segregation of RR mitochondrial DNA between C57BL/6 and RR heteroplasmic mice. Genetics 155:777-783
44. Tsukihara T, Shimokata K, Katayama Y, Shimada H, Muramoto K, Aoyama H, Mochizuki M, Shinzawa-Itoh K, Yamashita E, Yao M, Ishimura Y, Yoshikawa S (2003) The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process. Proc Natl Acad Sci USA 100:15304-15309
45. Villani G, Greco M, Papa S, Attardi G (1998) Low reserve of cytochrome c oxidase capacity in vivo in the respiratory chain of a variety of human cell types. J Biol Chem 273:31829-31836