Role of everlasting triplet expansions in protein evolution

Journal of Molecular Evolution

Volumn 72, Issue 2, 2011, Pages 232-239

  Koren, Zohar ^a   Trifonov, Edward N ^a,b  

^a UNIVERSITY OF HAIFA   (Israel)

^b MASARYK UNIVERSITY   (Czech Republic)

Author keywords

Codon usage; Evolutionary play ground; Fast adaptation; First exons; Genome inflation; Homopeptides; Selfish DNA; Tandem repeats; Triplet code; Triplet expansion disorders

Indexed keywords

OLIGOPEPTIDE; PROTEIN;

ANIMAL; ARABIDOPSIS; ARTICLE; ASPERGILLUS FUMIGATUS; CAENORHABDITIS ELEGANS; CATTLE; CHICKEN; CODON; DROSOPHILA; EXON; GENETIC DISORDER; GENETICS; HUMAN; LEISHMANIA; MOLECULAR EVOLUTION; MOUSE; SPECIES DIFFERENCE; TRINUCLEOTIDE REPEAT;

ANIMALS; ARABIDOPSIS; ASPERGILLUS FUMIGATUS; CAENORHABDITIS ELEGANS; CATTLE; CHICKENS; CODON; DROSOPHILA; EVOLUTION, MOLECULAR; EXONS; GENETIC DISEASES, INBORN; HUMANS; LEISHMANIA; MICE; OLIGOPEPTIDES; PROTEINS; SPECIES SPECIFICITY; TRINUCLEOTIDE REPEAT EXPANSION;

EUKARYOTA; GAMOCHAETA; PROKARYOTA;

EID: 79953300278     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-010-9425-0     Document Type: Article

References (40)

1. Abbas AK, Lichtman AH (2003) Cellular and molecular immunology, 5th edn. Saunders, Philadelphia
2. Alba MM, Guigo R (2004) Comparative analysis of amino acid repeats in rodents and humans. Genome Res 14:549-554 (Pubitemid 38500225)
3. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2007) Molecular biology of the cell, 5th edn. Garland Science, New York
4. Bacolla A, Larson JE, Collins JR, Li J, Milosavljevic A, Stenson PD, Cooper DN, Wells RD (2008) Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties. Genome Res 18:1545-1553
5. Black DL (2003) Mechanisms of alternative pre-messenger RNA splicing. Ann Rev Biochem 72:291-336
6. Brown LY, Brown SA (2004) Alanine tracts: the expanding story of human illness and trinucleotide repeats. Trends Genet 20:51-58 (Pubitemid 38032820)
7. Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601-603 (Pubitemid 10070865)
8. Faux NG, Bottomley SP, Lesk AM, Irving JA, Morrison JR, de la Banda MG, Whisstock JC (2005) Functional insights from the distribution and role of homopeptide repeat-containing proteins. Genome Res 15:537-551 (Pubitemid 41057816)
9. Faux NG, Huttley GA, Mahmood K, Webb GI, de la Banda MG, Whisstock JC (2007) RCPdb: an evolutionary classification and codon usage database for repeat-containing proteins. Genome Res 17:1118-1127 (Pubitemid 47026359)
10. Fondon JW, Garner HR (2004) Molecular origins of rapid and continuous morphological evolution. Proc Natl Acad Sci USA 101:18058-18063
11. Gogarten JP, Alireza GS, Zhaxybayeva O, Olendzenski L, Hilario E (2002) Inteins: structure, function, and evolution. Ann Rev Microbiol 56:263-287 (Pubitemid 35217456)
12. Haerty W, Golding GB (2010) Genome-wide evidence for selection acting on single amino acid repeats. Genome Res 20:755-760
13. Hamada H, Petrino MG, Kakunaga T, Seidman M, Stollar BD (1984) Enhanced gene expression by the poly(dT-dG) poly(dC-dA) sequence. Mol Cell Biol 4:2622-2630 (Pubitemid 15113599)
14. Huntley MA, Clark AG (2007) Evolutionary analysis of amino acid repeats across the genomes of 12 drosophila species. Mol Biol Evol 24:2598-2609
15. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21-123
16. Karlin S, Brocchieri L, Bergman A, Mrazek J, Gentles AJ (2002) Amino acid runs in eukaryotic proteomes and disease associations. Proc Nat Acad Sci USA 99:333-338 (Pubitemid 34060363)
17. Kashi Y, King DG (2006) Simple sequence repeats as advantageous mutators in evolution. Trends Genet 22:253-259
18. King DG (1994) Triple repeat DNA as a highly mutable regulatory mechanism. Science 263:595-596
19. Kozlowski P, de Mezer M, Krzyzosiak WJ (2010) Trinucleotide repeats in human genome and exome. Nucl Acids Res 38:4027-4039
20. Matlin AJ, Clark F, Smith CW (2005) Understanding alternative splicing: towards a cellular code. Nat Rev 6:386-398 (Pubitemid 40637856)
21. Matula M, Kypr J (1999) Nucleotide sequences flanking dinucleotide microsatellites in the human, mouse and Drosophila genomes. J Biomol Struct Dynam 17:275-280 (Pubitemid 29510985)
22. Mazrimas JA, Hatch FT (1972) Possible relationship between satellite DNA and evolution of kangaroo rat species (genus Dipodomys). Nat New Biol 240:102
23. Mirkin SM (2006) DNA structures, repeat expansions and human hereditary disorders. Curr Opin Struct Biol 16:351-358
24. Mularoni L, Ledda A, Toll-Riera M, Mar Albà M (2010) Natural selection drives the accumulation of amino acid tandem repeats in human proteins. Genome Res 20:745-754
25. Ohshima K, Kang S, Larson JE, Wells RD (1996) Cloning, characterization, and properties of seven triplet repeat DNA sequences. J Biol Chem 271:16773-16783 (Pubitemid 26239043)
26. Orgel LE, Crick FHC (1980) Selfish DNA: the ultimate parasite. Nature 284:604-607 (Pubitemid 10070866)
27. Orr HT, Zoghbi HY (2007) Trinucleotide repeat disorders. Annu Rev Neurosci 30:575-621 (Pubitemid 47218768)
28. Pearson CE, Edamura KN, Cleary JD (2005) Repeat instability: mechanisms of dynamic mutations. Nat Rev Genet 6:729-742
29. Pino S, Trifonov EN, Di Mauro E (in press) On the observable transition to living matter. Genomics Proteomics Bioinform
30. Richards RI, Sutherland GR (1997) Dynamic mutation: possible mechanisms and significance in human disease. Trends Biochem Sci 22:432-436
31. Siwach P, Pophaly SD, Ganesh S (2006) Genomic and evolutionary insights into genes encoding proteins with single amino acid repeats. Mol Biol Evol 23:1357-1369 (Pubitemid 43992337)
32. Trifonov EN (1989) The multiple codes of nucleotide sequences. Bull Math Biol 51:417-432
33. Trifonov EN (1996) Interfering contexts of regulatory sequence elements. CABIOS 12:423-429
34. Trifonov EN (2000) Consensus temporal order of amino acids and evolution of the triplet code. Gene 261:139-151
35. Trifonov EN (2004) The triplet code from first principles. J Biomol Struct Dynam 22:1-11
36. Trifonov EN (2006) Early molecular evolution. Isr J Ecol Evol 52:375-387
37. Trifonov EN (2010) Towards reconstruction of molecular origin of life. J Cosmol 10:3374-3380
38. Trifonov EN, Bettecken T (1997) Sequence fossils, triplet expansion, and reconstruction of earliest codons. Gene 205:1-6 (Pubitemid 28029594)
39. Usdin K (2008) The biological effects of simple tandem repeats: lessons from the repeat expansion diseases. Genome Res 18:1011-1019
40. Zoghbi HY, Orr HT (2000) Glutamine repeats and neurodegeneration. Ann Rev Neurosci 23:217-247 (Pubitemid 30350043)