Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs

Gene

Volumn 347, Issue 2 SPEC. ISS., 2005, Pages 247-253

  Amoutzias, Gregory D ^a   Weiner, January ^b   Bornberg Bauer, Erich ^b  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Eukaryotic transcription factors; Gene duplication; Homo hetero dimerisation; Phylogenetic profiling; Protein protein interaction networks; Small world networks

Indexed keywords

CELL NUCLEUS RECEPTOR; TRANSCRIPTION FACTOR;

ARTICLE; EUKARYOTE; EVOLUTION; GENE DUPLICATION; GENE REARRANGEMENT; GENOMICS; PHYLOGENY; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEOMICS; THEORETICAL MODEL;

EID: 15544385734     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2004.12.031     Document Type: Article

References (49)

1. P. Aloy, and R. Russell Taking the mystery out of biological networks EMBO Rep. 5 2004 349 350
2. G. Amoutzias, D. Robertson, and E. Bornberg-Bauer The evolution of protein interaction networks in regulatory proteins Compar. Funct. Genom. 5 2004 79 84
3. G. Amoutzias, D. Robertson, S. Oliver, and E. Bornberg-Bauer Convergent networks by single-gene duplications in higher eukaryotes EMBO Rep. 5 2004 274 279
4. Amoutzias, G., Weiner, J., Robertson, D., Oliver, S., Bornberg-Bauer, E., 2004c. Unpublished results.
5. P. Angel, and M. Karin The role of jun, fos and the ap-1 complex in cell-proliferation and transfor-mation Biochim. Biophys. Acta 1072 1991 129 157
6. W.R. Atchley, and W.M. Fitch A natural classification of the basic helix-loop-helix class of transcription factors Proc. Natl. Acad. Sci. 94 1997 5172 5176
7. A. Barabasi, and Z. Oltvai Network biology: understanding the cell's functional organization Nat. Rev., Genet. 5 2004 101 113
8. E. Bornberg-Bauer Chain growth algorithms for HP type lattice proteins RECOMB Proceedings 1997 ACM Press New York 47 55
9. E. Bornberg-Bauer, E. Rivals, and M. Vingron Computational approaches to identify leucine zippers Nucleic Acids Res. 26 1998 2740 2746
10. D.B. Bu Topological structure analysis of the protein-protein interaction network in budding yeast Nucleic Acids Res. 31 2003 2443 2450
11. C. Conant, and A. Wagner Convergent evolution of gene circuits Nat. Genet. 34 2003 264 266
12. T. Dandekar, S. Schuster, B. Snel, M. Huynen, and P. Bork Pathway alignment: application to the comparative analysis of glycolytic enzymes Biochem. J. 343 Pt 1 1999 115 124
13. Z. Dezso, Z. Oltvai, and A. Barabasi Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae Genome Res. 13 2003 2450 2454
14. H. Escriva Ligand binding was acquired during evolution of nuclear receptors Proc. Natl. Acad. Sci. U. S. A. 94 1997 6803 6808
15. C. Forst, and K. Schulten Phylogenetic analysis of metabolic pathways J. Mol. Evol. 52 2001 471 489
16. H. Fraser, A. Hirsh, L. Steinmetz, C. Scharfe, and M. Feldman Evolutionary rate in the protein interaction network Science 296 2002 750 752
17. N. Guelzim, S. Bottani, P. Bourgine, and F. Kepes Topological and causal structure of the yeast transcriptional regulatory network Nat. Genet. 31 2002 60 63
18. N.H. Horowitz On the evolution of biochemical synthesis Proc. Natl. Acad. Sci. U. S. A. 31 1945 152 157
19. H. Hurst bZIP proteins Protein Profile 2 1994 105 106
20. R. Jensen Enzyme recruitement in evolution of new function Annu. Rev. Microbiol. 30 1967 409 425
21. H. Jeong, S.P. Mason, A. Barabasi, and Z. Oltvai Lethality and centrality in protein networks Nature 411 2001 41 42
22. H. Kacser, and R. Beeby Evolution of catalytic proteins or on the origin of enzyme species by means of natural selection J. Mol. Evol. 20 1984 38 51
23. B. Kelley, B. Yuan, F. Lewitter, R. Sharan, B. Stockwell, and T. Ideker PathBLAST: a tool for alignment of protein interaction networks Nucleic Acids Res. 32 2004 W83 W88
24. W.H. Landschulz, P.F. Johnson, and S.L. McKnight The leucine zipper: a hypothetical structure common to a new clas of DNA binding proteins Science 240 1988 1759 1764
25. V. Laudet Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor J. Mol. Endicronol. 19 1997 207 226
26. V. Ledent, and M. Vervoot The basic helix-loop-helix protein family: comparative genomics and phylogenetics analysis Genome Res. 11 2001 754 770
27. T. Littlewood, and G.I. Evan Transcription factors 2: helix-loop-helix Protein Profile 2 1995 621 702
28. C. Muhle-Goll, M. Nilges, and A. Pastore The leucine zippers of the HLH-LZ proteins max and c-myc preferentially form heterodimers Biochemistry 34 1995 13554 13564
29. J.R. Newman, and A.E. Keating Comprehensive identification of human bzip interactions with coiled-coil arrays Science 300 2003 2001 2097
30. A. Ogura, K. Ikeo, and T. Gojobori Comparative analysis of gene expression for convergent evolution of camera eye between octopus and human Genome Res. 14 2004 1555 1561
31. E.K. O'Shea, R. Rutkowski, and P.S. Kim Mechanism of specificity in the fos-jun oncoprotein heterodimer Cell 68 1992 699 708
32. P. Pagel, H. Mewes, and D. Frishman Conservation of protein-protein interactions-lessons from ascomycota Trends Genet. 20 2004 72 76
33. R. Pastor-Satorras, E. Smith, and R.V. Sole Evolving protein interaction networks through gene duplication J. Theor. Biol. 222 2002 199 210
34. D. Reiss, and B. Schwikowski Predicting protein-peptide interactions via a network-based motif sampler Bioinformatics 20 Suppl. 1 2004 I274 I282
35. M. Remm, C. Storm, and E. Sonnhammer Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J. Mol. Biol. 314 2001 1041 1052
36. A. Rives, and T. Galitski Modular organization of cellular networks Proc. Natl. Acad. Sci. U. S. A. 100 2003 1128 1133
37. R. Russell A structural perspective on protein-protein interactions Curr. Opin. Struct. Biol. 14 2004 313 324
38. A. Rzhetsky, and S.M. Gomez Birth of scale-free, molecular networks and the number of distinct dna and protein domains per genome Bioinformatics 17 2001 988 996
39. J. Schwabe, and S. Teichmann Nuclear receptors: the evolution of diversity Sci. STKE 2004 pe4
40. B. Schwikowski, P. Uetz, and S. Fields A network of protein-protein interactions in yeast Nat. Biotechnol. 18 2000 1257 1261
41. M. Sirava BioMiner-modeling, analyzing, and visualizing biochemical pathways and networks Bioinformatics 18 Suppl. 2 2002 S219 S230
42. E. Sprinzak, S. Sattath, and H. Margalit How reliable are experimental protein-protein interaction data? J. Mol. Biol. 327 2003 919 923
43. A. Valencia, and F. Pazos Prediction of protein-protein interactions from evolutionary information Methods Biochem. Anal. 44 2003 411 426
44. V. van Noort, B. Snel, and M. Huynen The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model EMBO Rep. 5 2004 280 284
45. A. Vazquez, A. Flammini, A. Maritan, and A. Vespignani Global protein function prediction from protein-protein interaction networks Nat. Biotechnol. 21 2003 697 700
46. A. Vazquez, A. Flammini, A. Maritan, and A. Vespignani Modeling of protein interaction networks Complexus 1 2003 38 44
47. A. Wagner How the global structure of protein interaction networks evolves Proc. R. Soc. Lond., B 270 2003 457 466
48. M. Wiens, R. Batel, M. Korzhev, and W. Muller Retinoid X receptor and retinoic acid response in the marine sponge suberites domuncula J. Exp. Biol. 206 2003 2171 3261
49. S. Wuchty Evolution and topology in the yeast protein interaction network Genome Res. 14 2004 1310 1314