Thermodynamic stability explains the differential evolutionary dynamics of cytochrome b and COX I in mammals

Journal of Molecular Evolution

Volumn 74, Issue 1-2, 2012, Pages 69-80

  Aledo, Juan Carlos ^a   Valverde, Héctor ^a   Ruíz Camacho, Manuel ^a  

^a UNIVERSITY OF MÁLAGA   (Spain)

Author keywords

COX I; Cytochrome b; Evolvability; MtDNA; Natural selection; Protein evolution

Indexed keywords

CYTOCHROME B; CYTOCHROME C OXIDASE;

ANIMAL; ARTICLE; COMPARATIVE STUDY; ENTROPY; GENETIC SELECTION; GENETICS; MAMMAL; MOLECULAR EVOLUTION; MUTATION; PHYLOGENY; PROTEIN STABILITY; SPECIES DIFFERENCE;

ANIMALS; CYTOCHROMES B; ELECTRON TRANSPORT COMPLEX IV; ENTROPY; EVOLUTION, MOLECULAR; MAMMALS; MUTATION; PHYLOGENY; PROTEIN STABILITY; SELECTION, GENETIC; SPECIES SPECIFICITY;

MAMMALIA;

EID: 84862640504     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-012-9489-0     Document Type: Article

References (37)

1. Albu M, Min XJ, Hickey D, Golding B (2008) Uncorrected nucleotide bias in mtDNA can mimic the effects of positive Darwinian selection. Mol Biol Evol 25:2521-2524
2. Aledo JC (2004) Glutamine breakdown in rapidly dividing cells: waste or investment? Bioessays 26:778-785 (Pubitemid 38987611)
3. Aledo JC, Li Y, de Magalhães JP, Ruíz-Camacho M, Pérez-Claros JA (2011) Mitochondrially encoded methionine is inversely related to longevity in mammals. Aging Cell 10:198-207
4. Bielawski JP, Gold JR (1996) Unequal synonymous substitution rates within and between two protein-coding mitochondrial genes. Mol Biol Evol 13:889-892 (Pubitemid 26240093)
5. Bloom JD, Drummond DA, Arnold FH, Wilke CO (2006a) Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol 23:1751-1761 (Pubitemid 44309769)
6. Bloom JD, Labthavikul ST, Otey CR, Arnold FH (2006b) Protein stability promotes evolvability. Proc Natl Acad Sci USA 103:5869-5874
7. Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J, Schwede T (2009) Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc 4:1-13
8. Brown WM, George M, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA 76:1967-1971 (Pubitemid 9207037)
9. Bustamante CD, Townsend JP, Hartl DL (2000) Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Mol Biol Evol 17:301-308 (Pubitemid 30075599)
10. Conant GC (2009) Neutral evolution on mammalian protein surfaces. Trends Genet 25:377-381
11. Conant GC, Stadler PF (2009) Solvent exposure imparts similar selective pressures across a range of yeast proteins. Mol Biol Evol 26:1155-1161
12. Conant GC, Wagner GP, Stadler PF (2007) Modeling amino acid substitution patterns in orthologous and paralogous genes. Mol Phylogenet Evol 42:298-307 (Pubitemid 44751513)
13. DiMauro S, Schon EA (2008) Mitochondrial disorders in the nervous system. Annu Rev Neurosci 31:91-123
14. Eilers M, Shekar SC, Shieh T, Smith SO, Fleming PJ (2000) Internal packing of helical membrane proteins. Proc Natl Acad Sci USA 97:5796-5801 (Pubitemid 30367478)
15. Faith JJ, Pollock DD (2003) Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics 165:735-745 (Pubitemid 37337639)
16. Franzosa EA, Xia Y (2009) Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol 26:2387-2395
17. Gallardo ME, Moreno-Loshuertos R, López C, Casqueiro M, Silva J, Bonilla F et al (2006) m.6267G[A: a recurrent mutation in the human mitochondrial DNA that reduces cytochrome c oxidase activity and is associated with tumors. Hum Mutat 27:575-582 (Pubitemid 43865731)
18. Guerois R, Nielsen JE, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320:369-387 (Pubitemid 34722226)
19. Kimura M (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267: 275-276 (Pubitemid 8095610)
20. Lin Y, Hsu W, Hwang J, Li W (2007) Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. Mol Biol Evol 24:1005-1011 (Pubitemid 46536711)
21. Miller S, Janin J, Lesk AM, Chothia C (1987) Interior and surface of monomeric proteins. J Mol Biol 196:641-656
22. Mirny L, Shakhnovich E (2001) Evolutionary conservation of the folding nucleus. J Mol Biol 308:123-129 (Pubitemid 33043560)
23. Navarro A, Boveris A (2007) The mitochondrial energy transduction system and the aging process. Am J Physiol 292:C670-C686
24. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418-426 (Pubitemid 16010523)
25. Pál C, Papp B, Lercher MJ (2006) An integrated view of protein evolution. Nat Rev Genet 7:337-348
26. Popot JL, Engelman D (2000) Helical membrane protein folding, stability, and evolution. Annu Rev Biochem 69:881-922
27. Reyes A, Gissi C, Pesole G, Saccone C (1998) Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol Biol Evol 15:957-966 (Pubitemid 28364449)
28. Scharfe C, Lu HH, Neuenburg JK, Allen EA, Li G, Klopstock T et al (2009) Mapping gene associations in human mitochondria using clinical disease phenotypes. PLoS Comput Biol 5(4):e1000374
29. 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 (Pubitemid 32268009)
30. Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L (2005) The FoldX web server: an online force field. Nucleic Acids Res 33:W382-W388 (Pubitemid 44529948)
31. Thompson MJ, Goldstein RA (1996) Constructing amino acid residue substitution classes maximally indicative of local protein structure. Proteins 25:28-37 (Pubitemid 26156339)
32. Tokuriki N, Tawfik DS (2009) Stability effects of mutations and protein evolvability. Curr Opin Struct Biol 19:596-604
33. Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS (2007) The stability effects of protein mutations appear to be universally distributed. J Mol Biol 369:1318-1332 (Pubitemid 46770766)
34. Tsodikov OV, Record MT, Sergeev YV (2002) Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J Comput Chem 23:600-609 (Pubitemid 34312083)
35. Warnecke T, Weber CC, Hurst LD (2009) Why there is more to protein evolution than protein function: splicing, nucleosomes and dual-coding sequence. Biochem Soc Trans 37:756-761
36. Welch JJ, Bininda-Emonds ORP, Bromham L (2008) Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evol Biol 8:53
37. Zhang J, He X (2005) Significant impact of protein dispensability on the instantaneous rate of protein evolution. Mol Biol Evol 22:1147-1155 (Pubitemid 40471427)