Modular assembly of genes and the evolution of new functions

Genetica

Volumn 118, Issue 2-3, 2003, Pages 217-231

  Patthy, László ^a  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

Author keywords

Exon shuffling; Extracellular signalling; Intracellular signalling; Introns; Modular protein evolution

Indexed keywords

EVOLUTION, MOLECULAR; EXONS; GENES; GENOME; INTRONS; PROTEINS;

ANIMALIA; ARCHAEA; BACTERIA (MICROORGANISMS); CHORDATA; EUKARYOTA; METAZOA; VERTEBRATA;

EID: 0038306145     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1024182432483     Document Type: Review

References (70)

1. Adami, C., C. Ofria, & T.C. Collier, 2000. Evolution of biological complexity. Proc. Natl. Acad. Sci. USA 97: 4463-4468.
2. Adams, M.D., S.E. Celniker, R.A. Holt, C.A. Evans, J.D. Gocayne et al., 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
3. Al-Sharif, W.Z., J.O. Sunyer, J.D. Lambris & L.C. Smith, 1998. Sea urchin coelomocytes specifically express a homologue of the complement component C3. J. Immunol. 160: 2983-2997.
4. Aravind, L. & G. Subramanian, 1999. Origin of multicellular eukaryotes - insights from proteome comparisons. Curr. Opin. Genet. Dev. 9: 688-694.
5. Arnold, J.M., C. Kennett & M.F. Lavin, 1997. Transient expression of a novel serine protease in the ectoderm of the ascidian Herdmania momus during development. Dev. Genes Evol. 206: 455-463.
6. Bakal, C.J. & J.E. Davies, 2000. No longer an exclusive club: eukaryotic signalling domains in bacteria. Trends Cell Biol. 10: 32-38.
7. Banfield, D.K., D.M. Irwin, D.A. Walz & R.T.A. MacGillivray, 1994. Evolution of prothrombin: isolation and characterization of the cDNAs encoding chicken and hagfish prothrombin. J. Mol. Evol. 38: 177-187.
8. Bányai, L., A. Váradi & L. Patthy, 1983. Common evolutionary origin of the fibrin-binding structures of fibronectin and tissue-type plasminogen activator. FEBS Lett. 163: 37-41.
9. Bassett Jr., D.E.. M.A. Basrai, C. Connelly, K.M. Hyland, K. Kitagawa et al., 1996. Exploiting the complete yeast genome sequence. Curr. Opin. Genet. Dev. 6: 763-766.
10. Blattner, F.R., G. Plunkett, III, C.A. Bloch, N.T. Perna, V. Burland et al., 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462.
11. Bork, P., J. Schultz & C.P. Ponting, 1997. Cytoplasmic signalling domains: the next generation. Trends Biochem. Sci. 22: 296-298.
12. Bult, C.J., O. White, G.J. Olsen, L. Zhou, R.D. Fleischmann et al., 1996. Complete genome sequence of the methanogenic Archaeon, Methanococcus jannaschii. Science 273: 1058-1073.
13. Cameron, R.A., G. Mahairas, J.P. Rast, P. Martinez, T.R. Biondi et al., 2000. A sea urchin genome project: sequence scan, virtual map, and additional resources. Proc. Natl. Acad. Sci. USA 97: 9514-9518.
14. Cavalier-Smith, T., 1985. The Evolution of Genome Size. Wiley, New York.
15. Chervitz, S.A., L. Aravind, G. Sherlock, C.A. Ball, E.V. Koonin, et al., 1998. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282: 2022-2028.
16. Claverie, J.M., 2001. Gene number. What if there are only 30,000 human genes? Science 291: 1255-1257.
17. Copley, R.R., J. Schultz, C.P. Ponting & P. Bork, 1999. Protein families in multicellular organisms. Curr. Opin. Struct. Biol. 9: 408-415.
18. de Chateau, M. & L. Bjorck, 1994. Protein PAB, a mosaic albumin-binding bacterial protein representing the first contemporary example of module shuffling. J. Biol. Chem. 269: 12147-12151.
19. de Chateau, M. & L. Bjorck, 1996. Identification of interdomain sequences promoting the intronless evolution of a bacterial protein family. Proc. Natl. Acad. Sci. USA 93: 8490-8495.
20. Dunham, I., N. Shimizu, B.A. Roe, S. Chissoe, A.R. Hunt et al., 1999. The DNA sequence of human chromosome 22. Nature 402: 489-495.
21. Duret, L., D. Mouchiroud & C. Gautier, 1995. Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol. 40: 308-317.
22. Fleischmann, R.D., M.D. Adams, O. White, R.A. Clayton, E.F. Kirkness et al., 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
23. Fraser, C.M., J.D. Gocayne, O. White, M.D. Adams, R.A. Clayton et al., 1995. The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
24. Gilbert, W., 1978. Why genes in pieces? Nature 271: 501.
25. Gerstein, M., 1997. A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure. J. Mol. Biol. 274: 562-576.
26. Gerstein, M. & M. Levitt, 1997. A structural census of the current population of protein sequences. Proc. Natl. Acad. Sci. USA 94: 11911-11916.
27. Herz, J., U. Hamann, S. Rogne, O. Myklebost, H. Gausepohl et al., 1988. Surface location and high affinity for calcium of a 500 kd liver membrane protein closely related to the LDL-receptor suggest a physiological role as lipoprotein receptor. EMBO J. 7: 4119-4127.
28. Hogenesch, J.B., K.A. Ching, S. Batalov, A.I. Su, J.R. Walker et al., 2001. A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell 106: 413-415.
29. Hutter, H., B.E. Vogel, J.D. Plenefisch, C.R. Norris, R.B. Proenca et al., 2000. Conservation and novelty in the evolution of cell adhesion and extracellular matrix genes. Science 287: 989-994.
30. Hynes, R.O. & Q. Zhao, 2000. The evolution of cell adhesion. J. Cell Biol. 150: F89-F96.
31. Jasny, B.R., 2000. The universe of Drosophila genes. Science 287: 2181.
32. Jeong, H., S.P. Mason, A.L. Barabasi & Z.N. Oltvai, 2001. Lethality and centrality in protein networks. Nature 411: 41-42.
33. Ji, X., K. Azumi, M. Sasaki & M. Nonaka. 1997. Ancient origin of the complement lectin pathway revealed by molecular cloning of mannan binding protein-associated serine protease from a urochordate, the Japanese ascidian, Halocynthia roretzi. Proc. Natl. Acad. Sci. USA 94: 6340-6345.
34. Klenk, H.P., R.A. Clayton, J.F. Tomb, O. White, K.E. Nelson et al., 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390: 364-370.
35. Kunst, F., N. Ogasawara, I. Moszer, A.M. Albertini, G. Alloni et al., 1997. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390: 248-255.
36. Kusche-Gullberg, M., K. Garrison, A.J. MacKrell, L.I. Fessler & J.H. Fessler, 1992. Laminin A chain: expression during Drosophila development and genomic sequence. EMBO J. 11: 4519-4527.
37. Lander, E.S., L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody et al., 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
38. Li, W.H., Z. Gu, H. Wang & A. Nekrutenko, 2001. Evolutionary analyses of the human genome. Nature 409: 847-849.
39. Liang, F., I. Holt, G. Pertea, S. Karamycheva, S.L. Salzberg et al., 2000. Gene index analysis of the human genome estimates approximately 120,000 genes. Nat. Genet. 25: 239-240.
40. MacKrell, A.J., M. Kusche-Gullberg & K. Garrison. 1993. Novel Drosophila laminin A chain reveals structural relationships between laminin subunits. FASEB J. 376: 375-381.
41. Miyata, T. & N. Suga, 2001. Divergence pattern of animal gene families and relationship with the Cambrian explosion. BioEssays 23: 1018-1027.
42. Nonaka, M., K. Azumi, X. Ji, C. Namikawa-Yamada, M. Sasaki et al., 1999. Opsonic complement component C3 in the solitary ascidian, Halocynthia roretzi. J. Immunol. 162: 387-391.
43. Ny, T., F. Elgh & B. Lund, 1984. The structure of human tissue-type plasminogen activator gene: correlation of intron and exon structures to functional and structural domains. Proc. Natl. Acad. Sci. USA 81: 5355-5359.
44. Ono, K., H. Suga, N. Iwabe, K. Kuma & T. Miyata, 1999. Multiple protein tyrosine phosphatases in sponges and explosive gene duplication in the early evolution of animals before the parazoan-eumetazoan split. J. Mol. Evol. 48: 654-662.
45. Patthy, L., 1985. Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules. Cell 41: 657-663.
46. Patthy, L., 1987. Intron-dependent evolution: preferred types of exons and introns. FEBS Lett. 214: 1-7.
47. Patthy, L., 1991. Modular exchange principles in proteins. Curr. Opin. Struct. Biol. 1: 351-361.
48. Patthy, L., 1994. Exons and introns. Curr. Opin. Struct. Biol. 4: 383-392.
49. Patthy, L., 1995. Protein evolution by exon-shuffling. Molecular Biology Intelligence Unit. R.G. Landes Company, Springer-Verlag, New York, Berlin, Heidelberg, London, Paris, Tokyo, Hong Kong, Barcelona, Budapest.
50. Patthy, L., 1996a. Evolution of human proteins by exon-shuffling, pp. 35-71 in Human Genome Evolution, edited by M. Jackson, T. Strachan & G.A. Dover, Human Molecular Genetics Series BIOS Scientific Publishers Ltd., Oxford.
51. Patthy, L., 1996b. Exon shuffling and other ways of module exchange. Matrix Biol. 15: 301-310.
52. Patthy, L., 1999a. Genome evolution and the evolution of exon-shuffling - a review. Gene 238: 103-114.
53. Patthy, L., 1999b. Protein Evolution. Blackwell Science Ltd., Oxford.
54. Pennisi, E., 2000. Human Genome Project. And the gene number is . . .? Science 288: 1146-1147.
55. Plowman, G.D., S. Sudarsanam, J. Bingham, D. Whyte & T. Hunter, 1999. The protein kinases of Caenorhabditis elegans: a model for signal transductlon in multicellular organisms. Proc. Natl. Acad. Sci. USA 96: 3603-3610.
56. Raychowdhury, R., J.L. Niles, R.T. McCluskey & J.A. Smith, 1989. Autoimmune target in Heymann Nephritis is a glycoprotein with homology to the LDL receptor. Science 244: 1163-1165.
57. Rubin, G.M., M.D. Yandell, J.R. Wortman, G.L. Gabor Miklos, C.R. Nelson et al., 2000. Comparative genomics of the eukaryotes. Science 24(287): 2204-2215.
58. Saito, A., S. Pietromonaco, A.K. Loo & M.G. Farquhar, 1994. Complete cloning and sequencing of rat gp330/'megalin', a distinctive member of the low density lipoprotein receptor gene family. Proc. Natl. Acad. Sci. USA 91: 9725-9729.
59. Sheehan, J., M. Templer, M. Gregory, R. Hanumanthaiah, D. Troyer et al., 2001. Demonstration of the extrinsic coagulation pathway in teleostei: identification of zebrafish coagulation factor VII. Proc. Natl. Acad. Sci. USA 98: 8768-8773.
60. Shimeld, S.M., 1998. Characterization of AmphiF-spondin reveals the modular evolution of chordate F-spondin genes. Mol. Biol. Evol. 15: 1218-1223.
61. Sidow, A., 1996. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6: 715-722.
62. Simmen, M.W., S. Leitgeb, V.H. Clark, S.J.M. Jones & A. Bird, 1998. Gene number in an invertebrate chordate, Ciona intestinalis. Proc. Natl. Acad. Sci. USA 95: 4437-4440.
63. Smaglik, P., 2000, Researchers take a gamble on the human genome. Nature 405: 264.
64. Smith, L.C., C.S. Shih & S.G. Dachenhausen, 1998. Coelomocytes express SpBf, a homologue of factor B, the second component in the sea urchin complement system. J. Immunol. 161: 6784-6793.
65. Szathmary, E., F. Jordan & C. Pal, 2001. Can genes explain biological complexity? Science 292: 1315-1316.
66. Suga, H., M. Koyanagi, D. Hoshiyama, K. Ono, N. Iwabe et al., 1999. Extensive gene duplication in the early evolution of animals before the parazoan-eumetazoan split demonstrated by G proteins and protein tyrosine kinases from sponge and hydra. J. Mol. Evol. 48: 646-653.
67. The Arabidopsis Genome Initiative, 1999. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
68. The C. elegans Sequencing Consortium, 1998. Genome sequence of the nematode C. elegans. A platform for investigating biology. Science 282: 2012-2018.
69. Venter, J.C., M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural et al., 2001. The sequence of the human genome. Science 291: 1304-1351.
70. Yochem, J. & I. Greenwald, 1993. A gene for a low density lipoprotein-related protein in the nematode Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 90: 4572-4576.