Significant expansion of exon-bordering protein domains during animal proteome evolution

Nucleic Acids Research

Volumn 33, Issue 1, 2005, Pages 95-105

  Liu, Mingyi ^a   Walch, Heiko ^a   Wu, Shaoping ^a   Grigoriev, Andrei ^a  

^a GPC Biotech   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; PROTEOME;

ARTICLE; CHI SQUARE TEST; GENE AMPLIFICATION; GENE DUPLICATION; INTRON; MAMMAL; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NEMATODE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; PROTEOMICS; RANK SUM TEST; ANIMAL; EXON; GENETICS; INVERTEBRATE; PROTEIN TERTIARY STRUCTURE; VERTEBRATE;

ANIMALS; EVOLUTION, MOLECULAR; EXONS; INTRONS; INVERTEBRATES; PROTEIN STRUCTURE, TERTIARY; PROTEOME; VERTEBRATES;

EID: 13744252347     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki152     Document Type: Article

References (27)

1. Ohno,S. (1970) Evolution by Gene Duplication. Springer-Verlag, Berlin.
2. Gilbert,W. (1978) Why genes in pieces?. Nature, 271 501.
3. Blake,C.C. (1978) Do genes-in-pieces imply proteins-in-pieces? Nature, 273, 267.
4. Eickbush,T. (1999) Exon shuffling in retrospect. Science 283, 1465-1467.
5. van Rijk,A. and Bloemendal,H. (2003) Molecular mechanisms of exon shuffling: illegitimate recombination. Genetica, 118, 245-249.
6. Holmes,N. and Parham,P. (1985) Exon shuffling in vivo can generate novel HLA class I molecules. EMBO J., 4, 2849-2854.
7. Maki,R., Traunecker,A., Sakano,H., Roeder,W. and Tonegawa,S. (1980) Exon shuffling generates an immunoglobulin heavy chain gene. Proc. Natl Acad. Sci. USA, 77, 2138-2142.
8. de Souza,S.J., Long,M., Klein,R.J., Roy,S., Lin,S. and Gilbert,W. (1998) Toward a resolution of the introns, early/late debate: only phase zero introns are correlated with the structure of ancient proteins. Proc. Natl Acad. Sci. USA, 95, 5094-5099.
9. de Souza,S.J., Long,M., Schoenbach,L., Roy,S.W. and Gilbert,W. (1996) Intron positions correlate with module boundaries in ancient proteins. Proc. Natl Acad. Sci. USA, 93, 14632-14636.
10. Kaessmann,H., Zollner,S., Nekrutenko,A. and Li,W.H. (2002) Signatures of domain shuffling in the human genome. Genome Res., 12, 1642-1650.
11. Long,M., Rosenberg,C. and Gilbert,W. (1995) Intron phase correlations and the evolution of the intron/exon structure of genes. Proc. Natl Acad. Sci. USA, 92, 12495-12499.
12. Patthy,L. (1999) Genome evolution and the evolution of exon-shuffling - a review. Gene, 238, 103-114.
13. Patthy,L. (1987) Intron-dependent evolution: preferred types of exons and introns. FEBS Lett., 214, 1-7.
14. Liu,M. and Grigoriev,A. (2004) Protein domains correlate strongly with exons in multiple eukaryotic genomes - evidence of exon shuffling? Trends Genet., 20, 399-403.
15. Hubbard,T., Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V., Down,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
16. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
17. Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L. (2002) The Pfam protein families database. Nucleic Acids Res., 30, 276-280.
18. Kolkman,J.A. and Stemmer,W.P. (2001) Directed evolution of proteins by exon shuffling. Nat. Biotechnol., 19, 423-428.
19. Sonnhammer,E.L., Eddy,S.R., Birney,E., Bateman,A. and Durbin,R. (1998) Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res., 26, 320-322.
20. Lynch,M. and Conery,J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science, 290, 1151-1155.
21. Looman,C., Abrink,M., Mark,C. and Hellman,L. (2002) KRAB zinc finger proteins: an analysis of the molecular mechanisms governing their increase in numbers and complexity during evolution. Mol. Biol. Evol. 19, 2118-2130.
22. Shannon,M., Hamilton,A.T., Gordon,L., Branscomb,E. and Stubbs,L. (2003) Differential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters. Genome Res. 13, 1097-1110.
23. Patthy,L. (2003) Modular assembly of genes and the evolution of new functions. Genetica, 118, 217-231.
24. Sverdlov,A.V., Rogozin,I.B., Babenko,V.N. and Koonin,E.V. (2003) Evidence of splice signal migration from exon to intron during intron evolution. Curr. Biol., 13, 2170-2174.
25. Fedorov,A., Merican,A.F. and Gilbert,W. (2002) Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc. Natl Acad. Sci. USA, 99, 16128-16133.
26. Rogozin,I.B., Wolf,Y.I., Sorokin,A.V., Mirkin,B.G. and Koonin,E.V. (2003) Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr. Biol., 13, 1512-1517.
27. Banyai,L. and Patthy,L. (2004) Evidence that human genes of modular proteins have retained significantly more ancestral introns than their fly or worm orthologues. FEBS Lett., 565, 127-132.