Linking fold, function and phylogeny: A comparative genomics view on protein (domain) evolution

Current Genomics

Volumn 9, Issue 2, 2008, Pages 88-96

  te Velthuis, Aartjan J W ^a   Bagowski, Christoph P ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

Author keywords

Alignment; Domain; Molecular evolution; Molecular modeling; MPDZ; Multiple PDZ domain protein; MUPP; PDZ; Phylogeny; Protein folding

Indexed keywords

DISHEVELLED PROTEIN; PDZ PROTEIN;

AMINO ACID SEQUENCE; COMPUTER PROGRAM; FUNCTIONAL GENOMICS; GENE FUNCTION; HUMAN; INTERNET; LIGAND BINDING; MOLECULAR EVOLUTION; MOLECULAR MODEL; MOLECULAR SYSTEMATICS; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; SYSTEMS BIOLOGY;

EID: 45849099864     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920208784139537     Document Type: Review

References (83)

1. Koonin, E.V., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Krylov, D.M., Makarova, K.S., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N. and Rao, B.S. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 2004, 5: R7.
2. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M. and Sherlock, G. Gene Ontology: tool for the unification of biology. Nat. Genet. 2000, 25: 25-29.
3. Ureta-Vidal, A., Ettwiller, L. and Birney, E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet. 2003, 4: 251-262.
4. Bin Qian, R.A.G. Distribution of indel lengths. Proteins Struct. Funct. Genet. 2001, 45: 102-104.
5. Dayhoff, M.O., Schwarz, R.M. and Orcut, B.C. A model of evolutionary change in proteins. In Atlas of protein sequence and structure, M.O. Dayhoff, ed. (Washington D.C.: National Biomedical Research Foundation), 1978, 345-352.
6. Henikoff, S. and Henikoff, J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 1992, 89: 10915-10919.
7. Felsenstein, J. PHYLIP version 3.63, Dept of Genetics, Univ of Washington, Seattle. 2004.
8. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 1997, 25: 3389-3402.
9. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. and Higgins, D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucle. Acids Res. 1997, 25: 4876-4882.
10. Pearson, W.R. Comparison of methods for searching protein sequence databases. Protein Sci. 1995, 4: 1145-1160.
11. Galperin, M.Y. and Koonin, E.V: Who's your neighbor? New computational approaches for functional genomics. Nat. Biotech. 2000, 18: 609-613.
12. Eisenberg, D., Marcotte, E.M., Xenarios, I. and Yeates, T.O. Protein function in the post-genomic era. Nature 2000, 405: 823-826.
13. Attwood, T.K. The role of pattern databases in sequence analysis. Brief Bioinformatics 2000, 1: 45-49.
14. Lerat, E., Daubin, V. and Moran, N.A. From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the gamma-Proteobacteria. PLoS Biol. 2003, 1: e19.
15. Comas, I., ntilde, aki, Moya, A., eacute, Gonz, aacute, and lez-Caudelas, F. From Phylogenetics to Phylogenomics: The Evolutionary Relationships of Insect Endosymbiotic &b.gamma;-Proteobacteria as a Test Case. Syst. Biol. 2007, 56: 1-16.
16. Zdobnov, E.M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R.R., Christophides, G.K., Thomasova, D., Holt, R.A. and Subramanian, G.M. The Interactive Fly: Comparative genome and proteome analysis of Anopheles gambiac and Drosophila melanogaster. Science 2002, 298: 149-159.
17. Zdobnov, E.M. and Bork, P. Quantification of insect genome divergence. Trends Genet. 2007, 23: 16-20.
18. Rozen, S., Skaletsky, H., Marszalek, J.D., Minx, P.J., Cordum, H.S., Waterston, R.H., Wilson, R.K. and Page D.C. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 2003, 423: 873-876.
19. Consortium, M.G.S. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420: 520-562.
20. Gavin, A, Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A., Cruciat, C., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G. and Superti-Furga, G. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415: 141-147.
21. Sheth, N., Roca, X., Hastings, M.L., Roeder, T., Krainer, A.R. and Sachidanandam, R. Comprehensive splice-site analysis using comparative genomics. Nucl. Acids Res. 2006, 34: 3955-3967.
22. Parkinson, J., Mitreva, M., Whitton, C., Thomson, M., Daub, J., Martin, J., Schmid, R., Hall, N., Barrell, B., Waterston, R.H., McCarter, J.P. and Blaxter, M.L. A transcriptomic analysis of the phylum Nematoda. Nat. Genet. 2004, 36: 1259-1267.
23. Wang, Q., Prabhakar, S., Chanan, S., Cheng, J., Rubin, E. and Boffelli, D. Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons. Genome Biol. 2007, 8: R1.
24. Price, M., Dehal, P. and Arkin, A. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol. 2008, 9: R4.
25. Price, M.N., Dehal, P.S. and Arkin, A.P. Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Comput. Biol. 2007, 3: 1739-1750.
26. Lercher, M.J. and Pal, C. Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years. Mol. Biol. Evol. 2007: msm283.
27. Wyder, S., Kriventseva, E., Schroder, R., Kadowaki, T. and Zdobnov, E. Quantification of ortholog losses in insects and vertebrates, Genome Biol. 2007, 8: R242.
28. Wang, X., Grus, W.E. and Zhang, J. Gene losses during human origins. PLoS Biol. 2006, 4: e52.
29. Chen, S.L., Hung, C.-S., Xu, J., Reigstad, C.S., Magrini, V., Sabo, A., Blasiar, D., Bieri, T., Meyer, R.R., Ozersky, P., Armstrong, J.R., Fulton, R.S., Latreille, J.P., Spieth, J., Hooton, T.M., Mardis, E.R., Hultgren, S.J. and Gordon, J.I. Identification of genes subject to positive selection in uropathogenic strains off Escherichia coli: A comparative genomics approach. Proc. Natl. Acad. Sci. USA 2006, 103: 5977-5982.
30. Thomas, J.W., Touchman, J.W., Blakesley, R.W., Bouffard, G.G., Beckstrom-Sternberg, S.M., Margulies, E.H., Blanchette, M., Siepel, A.C., Thomas, P.J., McDowell, J.C., Maskeri, B., Hansen, N.F., Schwartz, M.S., Weber.R.J., Kent, W.J., Karolchik, D., Bruen, T.C., Bevan, R., Cutler, D.J., Schwartz, S., Elnitski, L., Idol, J.R., Prasad, A.B., Lee-Lin, S.Q., Maduro, V.V.B., Summers, T.J., Portnoy, M.E., Dietrich, N.L., Akhter, N., Ayele, K., Benjamin, B., Cariaga, K., Brinkley, C.P., Brooks, S.Y., Granite, S.,. Guan, X., Gupta, J., Haghighi, P., Ho, S.L., Huang, M.C., Karlins, E., Laric, P.L., Legaspi, R., Lim, M.J., Maduro, Q.L., Masiello, C.A., Mastrian, S.D., McCloskey, J.C., Pearson, R., Stantripop, S., Tiongson, E.E., Tran, J.T., Tsurgeon, C., Vogt, J.L., Walker, M.A., Wetherby, K.D., Wiggins, L.S., Young, A.C., Zhang, L.H., Osoegawa, K., Zhu, B., Zhao, B., Shu: C.L., De Jong, P.J., Lawrence, C.E., Smit, A.F., Chakravarti, A., Haussler, D., Green, P., Miller, W. and Green, E.D. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 2003, 424: 788-793.
31. Premzl, M., Gready J.E., Jermiin, L.S., Simonic, T. and Marshall Graves, J.A. Evolution of Vertebrate Genes Related to Prion and Shadoo Proteins - Clues from Comparative Genomic Analysis. Mol. Biol. Evol. 2004, 21: 2210-2231.
32. Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A.S., Hou, M., Rösenbloom, K., Clawson, H., Spieth, J., Hillier, L.W. and Richards, S. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005, 15: 1034-1050.
33. Ullmer, C., Schmuck, K., Figge, A. and Lübbert, H. Cloning and characterization of MUPP1, a novel PDZ domain protein. FEBS Lett. 1998, 424: 63-68.
34. Klingensmith, J., Nusse, R. and Perrimon, N. The Drosophila segment polarity gene dishevelled encodes a novel protein required for response to the wingless signal. Genes Dev. 1994, 8: 118-130.
35. Ackermann, F., Zitranski, N., Heydecke, D., Wilhelm, B., Gudermann, T. and Boekhoff, I. The Multi-PDZ domain protein MUPP1 as a lipid raft-associated scaffolding protein controlling the acrosome reaction in mammalian spermatozoa. J. Cell. Physiol. 2008, 214: 757-768.
36. Coyne, C.B., Voelker, T., Pichla, S.L. and Bergelson, J.M. The coxsackievirus and adenovirus receptor interacts with the multi-PDZ domain protein-1I (MUPP-1) within the tight junction. J. Biol. Chem. 2004, 279:48079-48084.
37. Martin, T.A., Watkins, G., Mansel, R.E. and Jiang, W.G. Loss of tight junction plaque molecules in breast cancer tissues is associated with a poor prognosis in patients with breast cancer. Eur. J. Cancer 2004, 40: 2717-2725.
38. Wharton, Jr., K.A. Runnin' with the Dvl: proteins that associate with Dsh/Dvl and their significance to Wnt signal transduction. Development. Biol. 2003, 253: 1-17.
39. Kurland, C.G., Collins, L.J. and Penny, D. Genomics and the irreducible nature of eukaryote cells. Science 2006, 312: 1011-1014.
40. Miller, W., Makova, K.D., Nekrutenko, A. and Hardison, R.C. Comparative genomics. Annu. Rev. Genomics Hum. Genet. 2004, 5:15-56.
41. Rosenberg, M.S. and Kumar, S. Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Mol. Biol. Evol. 2003, 20: 610-621.
42. Vingron, M. and Waterman, M.S. Sequence alignment and penalty choice. Review of concepts, case studies and implications. J. Mol. Biol. 1994, 235: 1-12.
43. Felsenstein, J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 1981, 17: 368-376.
44. Guindon, S.p. and Gascuel, O. A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Syst. Biol. 2003, 52: 696-704.
45. Swofford, D. PAUP* 4.0. Sinauer Associates 2001.
46. Huelsenbeck, J.P. and Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17: 754-755.
47. Lunter, G., Miklos, I., Drummond, A., Jensen, J. and Hein, J. Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics 2005, 6: 83.
48. Kumar, S. and Filipski, A. Multiple sequence alignment: In pursuit of homologous DNA positions. Genome Res. 2007, 17: 127-135.
49. Apic, G., Gough, J. and Teichmann, S.A. An insight into domain combinations. Bioinformatics 2001, 17: S83-89.
50. Han, J., Batey, S., Nickson, A.A., Teichmann, S.A. and Clarke, J. The folding and evolution of multidomain proteins. Nat. Rev. Mol. Cell Biol. 2007, 8: 319-330.
51. Wolf, Y.I., Grishin, N.V. and Koonin, E.V. Estimating the number of protein folds and families from complete genome data. J. Mol. Biol. 2000, 299: 897-904.
52. Wilson, D., Madera, M., Vogel, C., Chothia, C. and Gough, J. The SUPERFAMILY database in 2007: families and functions. Nucl. Acids Res. 2007, 35: D308-313.
53. Chothia, C. and Lesk, A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986, 5: 823-826.
54. Orengo, C.A. and Thornton, J.M. Protein families and their evolution: a structural perspective. Ann. Rev. Biochem. 2005, 74: 847-900.
55. Benner, S.A., Cohen, M.A. and Gonnet, G.H. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J. Mol. Biol. 1993, 30, 1065-1082.
56. Pascarella, S. and Argos, P. Analysis of insertions/deletions in protein structures. J. Mol. Biol. 1992, 224: 461-471.
57. Panchenko, A.and Madej, T. Structural similarity of loops in protein families: toward the understanding of protein evolution, BMC Evol. Biol. 2005, 5: 10.
58. Tavares, G.A., Panepucci, E.H. and Brunger, A.T. Structural characterization of the intramolecular interaction between the SHA3 and guanylate kinase domains of PSD-95. Mol. Cell. 2001, 8: 1313-1325.
59. McGee, A.W. and Bredt, D.S. Identification of an Intramolecular Interaction between the SH3 and Guranylate Kinase Domains of PSD-95. J. Biol. Chem. 1999 274: 1743-17436.
60. te Velthuis, A., Admiraal, J. and Bagowski, C. Molecular evolution of the MAGUK family in metazoan genomes. BMC Evol. Biol. 2007, 7: 129.
61. Olsen, O. and Bredt, D.S. Functional Analysis of the Nucleotide Binding Domain of Membrane-associated Guanylate Kinases. J. Biol. Chem. 2003, 278: 6873-6878.
62. Stuart, J.M., Segal, E., Koller, D. and Kim, S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302: 294-255.
63. Bergmann, S., Ihmels, J. and Barkai, N. Similarities and Differences in Genome-Wide Expression Data of Six Organisms. PLoS Biol. 2004, 2: e9.
64. Tirosh, I., Bilu, Y. and Barkai, N. Comparative biology: beyond sequence analysis. Curr. Opin. Biotechnol. 2007, 18: 371-377.
65. Hooper, S.D., Boue, S., Krause, R., Jensen, L.J., Mason, C.E., Ghanim, M., White, K.P., Furlong, E.E.M. and Bork, P. Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Mol. Syst. Biol. 2007, 3.
66. McCarroll, S.A., Murphy, C.T., Zou, S., Pletcher, S.D., Chin, C.-S., Jan, Y.N., Kenyon, C., Bargmann, C.I. and Li, H. Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat. Genet. 2004, 36: 197-204.
67. Jeon, J., Park, S., Chi, M., Choi, J., Park, J., Rho, H., Kim, S., Goh, J., You, S., Choi, J., Park, J., Yi, M., Yang, S., Kwon, M., Han, S., Kim, B.R., Khang, C.H., Park, B., Lim, S., Jung, K., Kong, F., Karunakaran, M., Oh, H., Kim, H., Kim, S., Park, J., Kang, S., Choi, W., Kang, S. and Lee, Y. Genome-wide functional analysis of pathogenicity genes in the rice blast fungus. Nat. Genet. 2007, 39: 561-565.
68. Torarinsson, E., Yao, Z., Wiklund, E.D., Bramsen, J.B., Hansen, C., Kjems, J., Tommerup, N., Ruzzo, W.L. and Gorodkin, J. Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Res. 2008, 18: 242-251.
69. Rifkin, S.A., Houle, D., Kim, J. and White, K.P. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature 2005, 438: 220-223.
70. Rifkin, S.A., Kim, J. and White, K.P. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet. 2003, 33: 138-144.
71. Ranz, J.M., Castillo-Davis, C.I., Meiklejohn, C.D. and Hartl, D.L. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 2003, 300: 1742-1745.
72. White, K.P., Rifkin, S.A., Hurban, P. and Hogness, D.S. Microarray analysis of Drosophila development during metamorphosis. Science 1999, 286: 2179-2184.
73. Tirosh, I., Weinberger, A., Carmi, M. and Barkai, N. A genetic signature of interspecies variations in gene expression. Nat. Genet. 2006, 38: 830-834.
74. Landry, C.R., Oh, J., Hartl, D.L. and Cavalieri, D. Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. Gene 2006, 366: 343-351.
75. Jordan, I.K., Marino-Ramirez, L., Wolf, Y.I. and Koonin, E.V. Conservation and Coevolution in the Scale-Free Human Gene Co-expression Network. Mol. Biol. Evol. 2004, 21: 2058-2070.
76. Oldham, M.C., Horvath, S. and Geschwind, D.H. Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc. Natl. Acad. Sci. USA 2006, 103: 17973-17978.
77. Sharan, R., Ulitsky, I. and Shamir, R. Network-based prediction of protein function. Mol. Syst. Biol. 2007, 3.
78. Linding, R., Jensen, L.J., Ostheimer, G.J., van Vugt, M.A., Jørgensen, C., Miron, I.M., Diella, F., Colwill, K., Taylor, L., Elder, K., Metalnikov, P., Nguyen, V., Pasculescu, A., Jin, J., Park, J.G., Samson, L.D., Woodgett, J.R., Russell, R.B., Bork, P., Yaffe, M.B. and T., P. Systematic discovery of in vivo phosphorylation networks. Cell 2007, 129: 1415-1426.
79. Kuhn, M., von Mering, C., Campillos, M., Jensen, L.J. and Bork, P. STITCH: interaction networks of chemicals and proteins. Nucl. Acids Res. 2008, 36: D684-688.
80. Frazer, K.A., Elnitski, L., Church, D.M., Dubchak, I. and Hardison, R.C. Cross-Species Sequence Comparisons: A Review of Methods and Available Resources. Genome Res. 2003, 13: 1-12.
81. Blouin, C., Butt, D. and Roger, A.J. Impact of Taxon Sampling on the Estimation of Rates of Evolution at Sites. Mol. Biol. Evol. 2005, 22: 784-791.
82. Jensen, L.J., Jensen, T.S., de Lichtenberg, U., Brunak, S. and Bork, P. Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature 2006, 443: 594-597.
83. Guex, N. and Peitsch, M.C. SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling. Electrophoresis 1997, 18: 2714-2723.