Abstract
Free full text
![Logo of compfungen](/http/europepmc.org/corehtml/pmc/pmcgifs/logo-compfungen.gif)
The Evolution of Protein Interaction Networks in Regulatory Proteins
Abstract
Interactions between proteins are essential for intracellular communication. They form complex networks which have become an important source for functional analysis of proteins. Combining phylogenies with network analysis, we investigate the evolutionary history of interaction networks from the bHLH, NR and bZIP transcription-factor families. The bHLH and NR networks show a hub-like structure with varying γ values. Mutation and gene duplication play an important role in adding and removing interactions. We conclude that in several of the protein families that we have studied, networks have primarily arisen by the development of heterodimerizing transcription factors, from an ancestral gene which interacts with any of the newly emerging proteins but also homodimerizes.
Full Text
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Angel P, Karin M. The role of Jun, Fos and the AP-1 complex in cell-proliferation and transformation. Biochim Biophys Acta. 1991 Dec 10;1072(2-3):129–157. [Abstract] [Google Scholar]
- Apic G, Gough J, Teichmann SA. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol. 2001 Jul 6;310(2):311–325. [Abstract] [Google Scholar]
- Atchley WR, Fitch WM. A natural classification of the basic helix-loop-helix class of transcription factors. Proc Natl Acad Sci U S A. 1997 May 13;94(10):5172–5176. [Europe PMC free article] [Abstract] [Google Scholar]
- Bornberg-Bauer E, Rivals E, Vingron M. Computational approaches to identify leucine zippers. Nucleic Acids Res. 1998 Jun 1;26(11):2740–2746. [Europe PMC free article] [Abstract] [Google Scholar]
- Brannetti B, Via A, Cestra G, Cesareni G, Helmer-Citterich M. SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family. J Mol Biol. 2000 Apr 28;298(2):313–328. [Abstract] [Google Scholar]
- Bu Dongbo, Zhao Yi, Cai Lun, Xue Hong, Zhu Xiaopeng, Lu Hongchao, Zhang Jingfen, Sun Shiwei, Ling Lunjiang, Zhang Nan, et al. Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res. 2003 May 1;31(9):2443–2450. [Europe PMC free article] [Abstract] [Google Scholar]
- Escriva H, Safi R, Hänni C, Langlois MC, Saumitou-Laprade P, Stehelin D, Capron A, Pierce R, Laudet V. Ligand binding was acquired during evolution of nuclear receptors. Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6803–6808. [Europe PMC free article] [Abstract] [Google Scholar]
- Ito Takashi, Ota Kazuhisa, Kubota Hiroyuki, Yamaguchi Yoshihiro, Chiba Tomoko, Sakuraba Kazumi, Yoshida Mikio. Roles for the two-hybrid system in exploration of the yeast protein interactome. Mol Cell Proteomics. 2002 Aug;1(8):561–566. [Abstract] [Google Scholar]
- Jeong H, Mason SP, Barabási AL, Oltvai ZN. Lethality and centrality in protein networks. Nature. 2001 May 3;411(6833):41–42. [Abstract] [Google Scholar]
- Laudet V. Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor. J Mol Endocrinol. 1997 Dec;19(3):207–226. [Abstract] [Google Scholar]
- Ledent V, Vervoort M. The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis. Genome Res. 2001 May;11(5):754–770. [Europe PMC free article] [Abstract] [Google Scholar]
- Newman John R S, Keating Amy E. Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science. 2003 Jun 27;300(5628):2097–2101. [Abstract] [Google Scholar]
- O'Shea EK, Rutkowski R, Kim PS. Mechanism of specificity in the Fos-Jun oncoprotein heterodimer. Cell. 1992 Feb 21;68(4):699–708. [Abstract] [Google Scholar]
- Pastor-Satorras Romualdo, Smith Eric, Solé Ricard V. Evolving protein interaction networks through gene duplication. J Theor Biol. 2003 May 21;222(2):199–210. [Abstract] [Google Scholar]
- Rzhetsky A, Gomez SM. Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics. 2001 Oct;17(10):988–996. [Abstract] [Google Scholar]
- Salwinski Lukasz, Eisenberg David. Computational methods of analysis of protein-protein interactions. Curr Opin Struct Biol. 2003 Jun;13(3):377–382. [Abstract] [Google Scholar]
- Schächter Vincent. Bioinformatics of large-scale protein interaction networks. Biotechniques. 2002 Mar;Suppl:16–27. [Abstract] [Google Scholar]
- Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol. 2000 Dec;18(12):1257–1261. [Abstract] [Google Scholar]
- Vazquez Alexei, Flammini Alessandro, Maritan Amos, Vespignani Alessandro. Global protein function prediction from protein-protein interaction networks. Nat Biotechnol. 2003 Jun;21(6):697–700. [Abstract] [Google Scholar]
- Villanueva Josep, Fernández-Ballester Gregorio, Querol Enrique, Aviles Francesc X, Serrano Luis. Ligand screening by exoproteolysis and mass spectrometry in combination with computer modelling. J Mol Biol. 2003 Jul 25;330(5):1039–1048. [Abstract] [Google Scholar]
- Vinson Charles, Myakishev Max, Acharya Asha, Mir Alain A, Moll Jonathan R, Bonovich Maria. Classification of human B-ZIP proteins based on dimerization properties. Mol Cell Biol. 2002 Sep;22(18):6321–6335. [Europe PMC free article] [Abstract] [Google Scholar]
- Wagner Andreas. How the global structure of protein interaction networks evolves. Proc Biol Sci. 2003 Mar 7;270(1514):457–466. [Europe PMC free article] [Abstract] [Google Scholar]
- Wiens Matthias, Batel Renato, Korzhev Michael, Müller Werner E G. Retinoid X receptor and retinoic acid response in the marine sponge Suberites domuncula. J Exp Biol. 2003 Sep;206(Pt 18):3261–3271. [Abstract] [Google Scholar]
- Wolf Yuri I, Karev Georgy, Koonin Eugene V. Scale-free networks in biology: new insights into the fundamentals of evolution? Bioessays. 2002 Feb;24(2):105–109. [Abstract] [Google Scholar]
- Wuchty S. Scale-free behavior in protein domain networks. Mol Biol Evol. 2001 Sep;18(9):1694–1702. [Abstract] [Google Scholar]
Articles from Comparative and Functional Genomics are provided here courtesy of Wiley
Full text links
Read article at publisher's site: https://doi.org/10.1002/cfg.365
Read article for free, from open access legal sources, via Unpaywall:
https://downloads.hindawi.com/journals/ijg/2004/395105.pdf
Open access at hindawi.com
http://www.hindawi.com/GetPDF.aspx?doi=10.1002/cfg.365
Citations & impact
Impact metrics
Citations of article over time
Article citations
Domain Architecture Based Methods for Comparative Functional Genomics Toward Therapeutic Drug Target Discovery.
J Mol Evol, 91(5):598-615, 25 Aug 2023
Cited by: 0 articles | PMID: 37626222
Review
Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction.
Curr Genomics, 21(6):454-463, 01 Sep 2020
Cited by: 16 articles | PMID: 33093807 | PMCID: PMC7536797
Review Free full text in Europe PMC
Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.).
PeerJ, 8:e9319, 03 Jul 2020
Cited by: 4 articles | PMID: 32704439 | PMCID: PMC7341539
Construction, comparison and evolution of networks in life sciences and other disciplines.
J R Soc Interface, 17(166):20190610, 06 May 2020
Cited by: 5 articles | PMID: 32370689 | PMCID: PMC7276545
Review Free full text in Europe PMC
Genome-Wide Identification and Characterization of the Potato bHLH Transcription Factor Family.
Genes (Basel), 9(1):E54, 22 Jan 2018
Cited by: 47 articles | PMID: 29361801 | PMCID: PMC5793205
Go to all (15) article citations
Similar Articles
To arrive at the top five similar articles we use a word-weighted algorithm to compare words from the Title and Abstract of each citation.
Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs.
Gene, 347(2):247-253, 24 Feb 2005
Cited by: 5 articles | PMID: 15777629
Reconstruction of ancestral protein interaction networks for the bZIP transcription factors.
Proc Natl Acad Sci U S A, 104(51):20449-20453, 12 Dec 2007
Cited by: 26 articles | PMID: 18077348 | PMCID: PMC2154451
Gene regulatory network growth by duplication.
Nat Genet, 36(5):492-496, 11 Apr 2004
Cited by: 296 articles | PMID: 15107850
Evolutionary and comparative analysis of MYB and bHLH plant transcription factors.
Plant J, 66(1):94-116, 01 Apr 2011
Cited by: 573 articles | PMID: 21443626
Review
Structure and evolution of transcriptional regulatory networks.
Curr Opin Struct Biol, 14(3):283-291, 01 Jun 2004
Cited by: 379 articles | PMID: 15193307
Review
Funding
Funders who supported this work.