Browse > Article

Biological Network Evolution Hypothesis Applied to Protein Structural Interactome  

Bolser, Dan M. (MRC-DUNN Human Nutrition Unit, Hills Road, Cambridge, CB2 2XY, England)
Park, Jong Hwa (MRC-DUNN Human Nutrition Unit, Hills Road, Cambridge, CB2 2XY, England, Object Interaction Technologies Inc. (OITEK))
Abstract
The latest measure of the relative evolutionary age of protein structure families was applied (based on taxonomic diversity) using the protein structural interactome map (PSIMAP). It confirms that, in general, protein domains, which are hubs in this interaction network, are older than protein domains with fewer interaction partners. We apply a hypothesis of 'biological network evolution' to explain the positive correlation between interaction and age. It agrees to the previous suggestions that proteins have acquired an increasing number of interaction partners over time via the stepwise addition of new interactions. This hypothesis is shown to be consistent with the scale-free interaction network topologies proposed by other groups. Closely co-evolved structural interaction and the dynamics of network evolution are used to explain the highly conserved core of protein interaction pathways, which exist across all divisions of life.
Keywords
Network Evolution; Structure family Evolution; Protein Interaction; Protein Structural Interactome; PSIMAP; Interactomics.;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Benton, BK., Tinkelenberg, Gonzalez, I. and Cross, FR. (1997). Cla4p, a Saccharomyces- Cerevisiae Cdc42p-activated kinase involved in cytokinesis is activated at mitosis. Mol. Cell. Bioi. 17, 5067-5076   DOI
2 Henrick, K & Thornton, J. M. (1998). PQS: a protein quaternary structure file server. Trends Biochem. Sci.23(9), 358-361   DOI   PUBMED   ScienceOn
3 Jeong, H., Mason, S., Barabasi, A. & Oltvai, Z. (2001). Lethality and centrality in protein networks. Nature, 411 , 41-42   DOI   ScienceOn
4 Ju, BH, Park, B, Park, JH, and Han, K, (2003) Visualization and analysis of protein interactions. Bioinformatics 2003, 19, 317-318   DOI   ScienceOn
5 Kauffman, SA. (1993). The Origins of Order, New York, Oxford, Oxford University Press, pp. 39-67
6 Park, J., Teichmann, S. A., Hubbard, T., and Chothia, C., (1997) Intermediate sequences increase the detection of distant sequence homologies. J. Mol.Biol. 273, 349-354   DOI   ScienceOn
7 Puniyani, A. R. & Lukose, R. M. (2001). Growing random networks under constraints. http://xxx.lanl.gov/abs/condmat/0107391
8 Shindyalov I. N. & Bourne P. E. (1998). Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering, 11(9) 739-747   DOI   PUBMED
9 Tsai, C., Lin, S. L., Wolfson, H. J. & Nussinov, R. (1996). A Dataset of Protein-Protein Interfaces Generated with a Sequence-order-independent Comparison Technique. J. Mol. Biol., 260, 604-620   DOI   ScienceOn
10 Wagner, A. & Fell, D. A. (2001). The small world inside large metabolic networks. Proc. R. Soc. Lond. 268, 1803-1810   DOI   ScienceOn
11 Wheeler, D. L., Chappey, C., Lash, A. E., Leipe, D. D., Madden, T. L., Schuler, G. D., Tatusova, T. A., & Rapp, B. A. (2000). Database resources of the National Center for Biotechnology Information. Nucl. Acids Res. 28, 10-14. (http://www.ncbi.nlm.nih.gov/ Taxonomy/taxonomy home.html/index.cgi)   DOI   ScienceOn
12 Teichmann, SA, Chothia, C., Church, GM., and Park, J. (2000) Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Bioinformatics, 16, 117-124   DOI   ScienceOn
13 Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. & Barabasi, A. L. (2000). The large-scale organization of metabolic networks. Nature, 407, 651-654   DOI   ScienceOn
14 Wang, Z. X. (1996). How many fold types of protein are there in nature? Proteins. 26. 186-191   DOI   ScienceOn
15 Bairoch A. & Apweiler R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45-48   DOI   ScienceOn
16 Doolittle, R. F.(1999). Do you dig my groove? Nat Genet, 23, 6-8
17 Dorogovtsev, S. N. & Mendes, J. F. F. (2000). Evolution of reference networks with ageing. http://xxx.lanl.gov/abs/condmat/0001419
18 Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T and Chothia, C (1998). Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. BioI., 284, 1201-1210   DOI   ScienceOn
19 Ponting, C. P., Aravind, L., Schultz, J., Bork, P. & Koonin, E. V. (1999). Eukaryotic signaling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J. Mol. BioI. 289, 729-745   DOI   ScienceOn
20 Morowitz, H. J. (1999). A theory of biochemical organization, metabolic pathways and evolution. Complexity, 4, 39
21 Apic, G., Gough, J. & Teichmann, S. A. (2001a). An Insight into Domain Combinations. Bioinformatics. 17, 83S-89S   DOI   ScienceOn
22 Bennett, M. J., Choe, S. & Eisenberg. D. (1994). Domain swapping: Entangling alliances between proteins. Proc. Natl. Acad. Sci. U.S.A. 91, 3127-3131   DOI   ScienceOn
23 Apic, G., Gough, J. & Teichmann, S. A. (2001b). Domain Combinations in Archaeal, Eubacterial and Eukaryotic Proteomes. J. Mol. Biol. 310, 311-325   DOI   ScienceOn
24 Benner, S. A., Ellington, A. D. & Tauer, A. (1989). Modern metabolism as a palimpsest of the RNA world. Proc. Natl Acad. Sci. USA, 86, 7054-7058   DOI   ScienceOn
25 Overbeek, R., Fonstien, M., D'Souza, M., Pusch, G. & Maltsev, N. (1999). The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. U.S.A. 96, 2896- 2901   DOI   ScienceOn
26 Watts, D. J. & Strogatz, S. H. (1998). Collective dynamics of 'small-world' networks. Nature, 393, 440-442   DOI   PUBMED   ScienceOn
27 Enright, A. J., Iliopoulos, I., Kyrpides, N. C. & Ouzounis, C. A. (1999). Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90   DOI   ScienceOn
28 Jones, S., Marin, A. & Thornton, J. M. (2000). Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Eng. 13, 77-82   DOI   PUBMED
29 Miller, S. (1989). The structure of interfaces between subunits of dimeric and tetrameric proteins. Protein Eng 3, 77-83   DOI   PUBMED
30 Park, J and Bolser, D, (2001). Conservation of protein interaction network in evolution. Genome Informatics, 12, 135-140
31 Chothia, C. (1992). One thousand families for the molecular biologist. Nature, 357, 543-544   DOI   PUBMED   ScienceOn
32 Gough, J., Karplus, K., Hughey, R. & Chothia, C. (2001). Assignment of homology to genomes sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. BioI., 313, 903-919   DOI   ScienceOn
33 Long, M and Langley, CH. (1993). Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science, 260, 91-95   DOI   PUBMED
34 Marcotte, E.M., Pellegrini, M., Ng, H., Rice, D. W., Yeates, T. O. & Eisenberg, D. (1999). Detecting Protein Function and Protein-Protein Interactions from Genome Sequences. Science, 285, 751-753   DOI   PUBMED   ScienceOn
35 Orengo, C. A., Jones, D. T., & Thornton, J. M. (1994). Protein superfamilies and domain superfolds. Nature, 372, 631-634   DOI   ScienceOn
36 Zhang, C. T. (1997). Relations of the numbers of protein sequences, families and folds. Protein Engineering, 10, 757-761   DOI   PUBMED
37 Bairoch A. (2000). The ENZYME database in 2000. Nucleic Acids Res. 28, 304-305   DOI   PUBMED   ScienceOn
38 Dandekar, T., Snel, B., Huynen, M. & Bork, P. (1998). Conservation of gene order: a finger-print of proteins that physically interact. Trends Biochem. Sci. 23, 324-328   DOI   PUBMED   ScienceOn
39 Huynen, M. A., Dandekar, T. & Bork, P. (1999). Variation and evolution of the citric acid cycle: a genomic perspective. Trends Microbiol. 7, 281-291   DOI   ScienceOn
40 Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. BioI. 247, 536-540
41 Alexandrov, N. N. & Go, N. (1995). Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins. Protein Sci. 3, 866-875   DOI   ScienceOn
42 Fraser, H. B., Hirsh, A. E., Steinmetz, L. M., Scharfe, C. & Feldman, M. W. (2002). Evolutionary Rate in the Protein Interaction Network. Science, 296, 750-752   DOI   PUBMED   ScienceOn
43 Tsaur SC, Ting CT, and Wu CI. (1998) Positive selection driving the evolution of a gene of male reproduction, Acp26Aa, of Drosophila: II. Divergence versus polymorphism. Mol. BioI. Evol. 15, 1040-1046   DOI   ScienceOn
44 Snel B., Bork P. & Huynen, M.A. Genomes in flux: The evolution of archaeal and proteobacterial genecontent. (2002). Genome Res. 12, 17-25   DOI   ScienceOn
45 Anantharaman, V., Koonin, E. V. & Aravind, L. (2001). Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J. Mol. Biol., 307, 1271-1292   DOI   ScienceOn
46 Cirera, S, and Aguade M. (1998) Molecular evolution of a duplication: the sex-peptide (Acp70A) gene region of Drosophila subobscura and Drosophila madeirensis. Mol. BioI. Evol. 15, 988-996   DOI   ScienceOn
47 Morowitz, H. J. (1992). Beginnings of cellular life: metabolism recapitulates biogenesis, New Haven, Yale University Press
48 Berman, H. M.,Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P.E. (2000). The Protein Data Bank. Nucl. Acids Res., 28, 235-241   DOI   ScienceOn
49 Dorogovtsev, S. N. & Mendes, J. F. F. (2001). Evolution of networks. http://xxx.lanl.gov/abs/cond-mat/0106144
50 Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, QureshiEmili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, and Rothberg JM. (2000), A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627   DOI   ScienceOn
51 Altschul, S. F., Madden, T. L., Schaffer, A .A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J., (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402   DOI   ScienceOn
52 Enright, A. J. & Ouzounis, C.A. (2001). Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusion. Genome Biology, 2(9), research0034.1-7
53 Barabasi, A. & Albert, R. (1999). Emergence of Scaling in Random Networks. Science, 286, 509-512   DOI   PUBMED   ScienceOn
54 Huynen, M., Snel, B., Lathe, W. & Bork P. (2000). Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences. Genome Res. 10, 1204-1210   DOI   ScienceOn
55 Park, J., Lappe, M. & Teichmann, S. A. (2001). Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction Repertoires in the PDB and Yeast. J. Mol. Biol.307, 929-938   DOI   ScienceOn
56 Wagner, A. (2001). The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 18, 1283-1292   DOI   PUBMED   ScienceOn