Insight into role of selection in the evolution of polyglutamine tracts in humans

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Li, Hongwei ^a   Liu, Jing ^a   Wu, Keliang ^a   Chen, Yuan ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; GLUTAMINE; GUANOSINE; POLYGLUTAMINE;

AMINO ACID SEQUENCE; ARTICLE; CODON; EVOLUTION; GENETIC CONSERVATION; HUMAN; NATURAL SELECTION; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; TANDEM REPEAT;

ANIMALS; CODON; EVOLUTION, MOLECULAR; HUMANS; MICE; PEPTIDES; RATS; REPETITIVE SEQUENCES, AMINO ACID; SEQUENCE ANALYSIS, PROTEIN;

EUKARYOTA;

EID: 84864697519     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041167     Document Type: Article

References (29)

1. Green H, Norman W, (1994) Codon reiteration and the evolution of proteins. Proc. Natl. Acad. Sci. USA 91: 4298-4302.
2. Golding GB, (1999) Simple sequence is abundant in eukaryotic proteins. Protein Science 8: 1358-1361.
3. Wright PE, Dyson HJ, (1999) Intrinsically unstructured proteins: reassessing the protein structure-function paradigm. Journal of Molecular Biology 293: 321-331.
4. Brown CJ, Takayama S, Campen AM, Vise P, Marshall TW, et al. (2002) Evolutionary rate heterogeneity in proteins with long disordered regions. Journal of Molecular Evolution 55: 104-110.
5. Simon M, Hancock JM, (2009) Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. Genome Biology 10: R59.
6. Kim MW, Chelliah Y, Kim SW, Otwinowski Z, Bezprozvanny I, (2009) Secondary structure of Huntingtin amino-terminal region. Structure 17(9): 1205-1212.
7. Fondon JM, Harold R G, (2004) Molecular origins of rapid and continuous morphological evolution. Proc Natl Acad Sci USA 101: 18058-18063.
8. Keitti A, Nobuaki Yoshida, Yuki Kataoka, Mitsuharu Sato, Hirotake Ichise, et al. (2007) Morphological change caused by loss of the taxon-specific ployalanine tract in hoxd-13. Molecular Biology and Evolution 24: 281-287.
9. Orr HT, Zoghbi HY, (2007) Trinucleotide repeat disorders. Annu.Rev.Neurosci 30: 575-621.
10. Albrecht A, Mundlos S, (2005) The other trinucleotide repeat: polyalanine expansion disorders. Current Opinion in Genetics & Development 15: 285-293.
11. Huntington's Disease Collaborative Research Group (1993) A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. Cell 72: 971-983.
12. Karlin S, Burge C, (1996) Trinucleotide repeats and long homopeptides in genes and proteins associated with nervous system disease and development. Proc Natl Acad Sci USA 93: 1560-1565.
13. Freiman RN, Tjian R, (2002) A glutamine-rich trail leads to transcription factors. Science 296: 2149-2150.
14. Dunah AW, Jeong H, Griffin A, Kim YM, Standaert DG, et al. (2002) Sp1 and TAFII130 transcriptional activity disrupted in early Huntington's disease. Science 296: 2238-2243.
15. Schaefer MH, Wanker EE, Andrade-Navarro MA, (2012) Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. Nucleic Acids Research. January 28.[Epub ahead of print] PMID.
16. Perutz MF, Johnson T, Suzuki M, Finch JT, (1994) Glutamine repeats as polar zippers: their role in inherited neurodegenerative disease. Proc. Natl. Acad. Sci. USA 91: 5335-5358.
17. Cruz F, Roux J, Robinson-Rechavi M, (2009) The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes. BMC Genomics 2009 10: 619.
18. Mularoni L, Veitia RA, Albà MM, (2007) Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats. Genomics 89: 316-325.
19. Hancock JM, Elizabeth A W, Santibanez-Koref MF, (2001) A Role for Selection in Regulating the Evolutionary Emergence of Disease-Causing and Other Coding CAG Repeats in Humans and Mice. Molecular Biology and Evolution 18: 1014-1023.
20. Mularoni L, Alice L, Toll-Riera M, Albà MM, (2010) Natural selection drives the accumulation of amino acid tandem repeats in human proteins. Genome Research 20: 745-754.
21. Albà MM, Santibanez-Koref MF, Hancock JM, (2001) The comparative genomics of polyglutamine repeats: Extreme differencein the codon organization of repeat-encoding regions between mammals and Drosophila. Journal of Molecular Evolution 52: 249-259.
22. Albà MM, Guigo R, (2004) Comparative analysis of amino acid repeats in rodents and humans. Genome Research 14: 549-554.
23. Ziheng Yang, (1994) Estimating the pattern of nucleotide substitution. Journal of Molecular Biology 39: 105-111.
24. Ziheng Yang, (1998) Likelihood Ratio Tests for Detecting Positive Selection and Application to Primate Lysozyme Evolution. Molecular Biology and Evolution 15: 568-573.
25. Ziheng Yang, (1997) Phylogenetic analysis by maximum likelihood (PAML), version 1.3. University of California, Berkeley, California, USA.
26. Ziheng Yang, Nielsen R, (2000) Estimating nonsynonymous and synonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution 17: 32-43.
27. Faux NG, Gavin AH, Khalid M, Geoffrey IW, et al. (2007) RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins. Genome Research 17: 1118-1127.
28. Albà MM, Santibanez-Koref MF, Hancock JM, (1999) Conservation of polyglutamine tract size between mice and humans depends on codon interruption. Molecular Biology and Evolution 16: 1641-1644.
29. Matteo R, Elodie M, Choumouss K, Donatella D, Ronald M, (2009) Polyglutamine Repeats Are Associated to Specific Sequence Biases That Are Conserved among Eukaryotes. PLoS ONE 7(2): e30824.