Mutational bias plays an important role in shaping longevity-related amino acid content in mammalian mtDNA-encoded proteins

Journal of Molecular Evolution

Volumn 74, Issue 5-6, 2012, Pages 332-341

  Aledo, Juan Carlos ^a   Valverde, Héctor ^a   De Magalhães, João Pedro ^b  

^a UNIVERSITY OF MÁLAGA   (Spain)

^b UNIVERSITY OF LIVERPOOL   (United Kingdom)

Author keywords

Evolution; Longevity; Methionine Cysteine; Mitochondria; Oxidative stress; Threonine

Indexed keywords

AMINO ACID; MITOCHONDRIAL DNA; MITOCHONDRIAL PROTEIN; NUCLEOTIDE;

ANIMAL; ARTICLE; GENETICS; LONGEVITY; MAMMAL; MUTATION;

AMINO ACIDS; ANIMALS; DNA, MITOCHONDRIAL; LONGEVITY; MAMMALS; MITOCHONDRIAL PROTEINS; MUTATION; NUCLEOTIDES;

MAMMALIA;

EID: 84865798412     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-012-9510-7     Document Type: Article

References (38)

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, 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
3. Balaban RS, Nemoto S, Finkel T (2005) Mitochondria, oxidants, and aging. Cell 120:483-495
4. Barja G (1998) Mitochondrial free radical production and aging in mammals and birds. Ann N Y Acad Sci 854:224-238
5. Bender A, Hajieva P, Moosmann B (2008) Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria. Proc Natl Acad Sci USA 105:16496-16501
6. Berlett BS, Stadtman ER (1997) Protein oxidation in aging, disease, and oxidative stress. J Biol Chem 272:20313-20316
7. Brand MD (2000) Uncoupling to survive? The role of mitochondrial inefficiency in ageing. Exp Gerontol 35:811-820
8. Collins D, Jukes T (1993) Relationship between G ? C in silent sites of codons and amino acid composition of human proteins. J Mol Evol 36:201-213
9. D'Onofrio G, Mouchiroud D, Aïssani B, Gautier C, Bernardi G (1991) Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J Mol Evol 32:504-510
10. de Magalhães JP, Costa J (2009) A database of vertebrate longevity records and their relation to other life-history traits. J Evol Biol 22:1770-1774
11. de Magalhães JP, Costa J, Church GM (2007) An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts. J Gerontol A 62:149-160
12. Fonseca MM, Posada D, Harris DJ (2008) Inverted replication of vertebrate mitochondria. Mol Biol Evol 25:805-808
13. Foster PG, Jermiin LS, Hickey DA (1997) Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol 44:282-288
14. Harman D (2006) Free radical theory of aging: an update: increasing the functional life span. Ann N Y Acad Sci 1067:10-21
15. Jia W, Higgs PG (2008) Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol Biol Evol 25:339-351
16. Jobson RW, Dehne-Garcia A, Galtier N (2010) Apparent longevityrelated adaptation of mitochondrial amino acid content is due to nucleotide compositional shifts. Mitochondrion 10:540-547
17. Kitazoe Y, Kishino H, Hasegawa M, Nakajima N, Thorne JL, Tanaka M (2008) Adaptive threonine increase in transmembrane regions of mitochondrial proteins in higher primates. PLoS ONE 3:e3343
18. Kitazoe Y, Kishino H, Hasegawa M, Matsui A, Lane N, Tanaka M (2011) Stability of mitochondrial membrane proteins in terrestrial vertebrates predicts aerobic capacity and longevity. Genome Biol Evol 3:1233-1244
19. Lambert AJ, Boysen HM, Buckingham JA, Yang T, Podlutsky A, Austad SN, Kunz TH, Buffenstein R, Brand MD (2007) Low rates of hydrogen peroxide production by isolated heart mitochondria associate with long maximum lifespan in vertebrate homeotherms. Aging Cell 6:607-618
20. Lambert AJ, Buckingham JA, Boysen HM, Brand MD (2010) Low complex I content explains the low hydrogen peroxide production rate of heart mitochondria from the long-lived pigeon, Columba livia. Aging Cell 9:78-91
21. Levine RL, Mosoni L, Berlett BS, Stadtman ER (1996) Methionine residues as endogenous antioxidants in proteins. Proc Natl Acad Sci USA 93:15036-15040
22. Min XJ, Hickey DA (2007) DNA asymmetric strand bias affects the amino acid composition of mitochondrial proteins. DNA Res 14:201-206
23. Moosmann B, Behl C (2008) Mitochondrially encoded cysteine predicts animal lifespan. Aging Cell 7:32-46
24. Nabholz B, Glémin S, Galtier N (2008) Strong variations of mitochondrial mutation rate across mammals - the longevity hypothesis. Mol Biol Evol 25:120-130
25. Nikolaou C, Almirantis Y (2006) Deviations from Chargaff's second parity rule in organellar DNA insights into the evolution of organellar genomes. Gene 381:34-41
26. Pamplona R (2011) Mitochondrial DNA damage and animal longevity: insights from comparative studies. J Aging Res 2011:807108
27. Pamplona R, Barja G (2011) An evolutionary comparative scan for longevity-related oxidative stress resistance mechanisms in homeotherms. Biogerontology 12:409-435
28. Pamplona R, Costantini D (2011) Molecular and structural antioxidant defenses against oxidative stress in animals. AJP Regul Integr Comp Physiol 301:R843-R863
29. Pamplona R, Portero-Otín M, Riba D, Ruíz C, Prat J, Bellmunt MJ, Barja G (1998) Mitochondrial membrane peroxidizability index is inversely related to maximum life span in mammals. J Lipid Res 39:1989-1994
30. Pamplona R, Portero-Otín M, Sanz A, Ayala V, Vasileva E, Barja G (2005) Protein and lipid oxidative damage and complex I content are lower in the brain of budgerigars and canaries than in mice. Relation to aging rate. Age 27:267-280
31. Ruiz MC, Ayala V, Portero-Otín M, Requena JR, Barja G, Pamplona R (2005) Protein methionine content and MDA-lysine adducts are inversely related to maximum life span in the heart of mammals. Mech Ageing Dev 126:1106-1114
32. Samuels DC (2005) Life span is related to the free energy of mitochondrial DNA. Mech Ageing Dev 126:1123-1129
33. 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
34. Singer GA, Hickey DA (2000) Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol Biol Evol 17:1581-1588
35. Speakman JR, Talbot DA, Selman C, Snart S, McLaren JS, Redman P, Krol E, Jackson DM, Johnson MS, Brand MD (2004) Uncoupled and surviving: individual mice with high metabolism have greater mitochondrial uncoupling and live longer. Aging Cell 3:87-95
36. Stadtman ER, Van Remmen H, Richardson A, Wehr NB, Levine RL (2005) Methionine oxidation and aging. Biochim Biophys Acta 1703:135-140
37. Sueoka N (1961) Compositional correlation between deoxyribonucleic acid and protein. Cold Spring Harbor symposium on quantitative biology
38. Wang H-C, Singer GAC, Hickey DA (2004) Mutational bias affects protein evolution in flowering plants. Mol Biol Evol 21:90-96