Protein interaction networks in plants
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Protein–protein interactions are fundamental to virtually every aspect of cellular functions. With the development of high-throughput technologies of both the yeast two-hybrid system and tandem mass spectrometry, genome-wide protein-linkage mapping has become a major objective in post-genomic research. While at least partial “interactome” networks of several model organisms are already available, in the plant field, progress in this respect is slow. However, even with comprehensive protein interaction data still missing, substantial recent advance in the graph-theoretical functional interpretation of complex network architectures might pave the way for novel approaches in plant research. This article reviews current progress and discussions in network biology. Emphasis is put on the question of what can be learned about protein functions and cellular processes by studying the topology of complex protein interaction networks and the evolutionary mechanisms underlying their development. Particularly the intermediate and local levels of network organization—the modules, motifs and cliques—are increasingly recognized as the operational units of biological functions. As demonstrated by some recent results from systematic analyses of plant protein families, protein interaction networks promise to be a valuable tool for a molecular understanding of functional specificities and for identifying novel regulatory components and pathways.
KeywordsNetwork topology Functional modules Functional specificity Gene duplication Interactome
I would like to thank Francesco Salamini, Peter Schreier and Martin Hülskamp for constant support and helpful discussions and Klaus Richter for help with the bioinformatic network analysis. I apologize to those colleagues whose work was not cited because of space limitations. The work was supported by the Arabidopsis Functional Genomics Network (DFG) and the Max Planck Society.
- Arita M (2005) Scale-freeness and biological networks. J Biochem (Tokyo) 138:1–4Google Scholar
- Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433:531–537CrossRefPubMedGoogle Scholar
- Goehler H, Lalowski M, Stelzl U, Waelter S, Stroedicke M, Worm U, Droege A, Lindenberg KS, Knoblich M, Haenig C, Herbst M, Suopanki J, Scherzinger E, Abraham C, Bauer B, Hasenbank R, Fritzsche A, Ludewig AH, Bussow K, Coleman SH, Gutekunst CA, Landwehrmeyer BG, Lehrach H, Wanker EE (2004) A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington’s disease. Mol Cell 15:853–865CrossRefPubMedGoogle Scholar
- Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han JD, Hao T, Berriz GF, Bertin N, Huang J, Chuang LS, Li N, Mani R, Hyman AA, Sonnichsen B, Echeverri CJ, Roth FP, Vidal M, Piano F (2005) Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 436:861–865CrossRefPubMedGoogle Scholar
- Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y (2000) Toward a protein–protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci USA 97:1143–1147CrossRefPubMedGoogle Scholar
- Mizoguchi T, Ichimura K, Irie K, Morris P, Giraudat J, Matsumoto K, Shinozaki K (1998) Identification of a possible MAP kinase cascade in Arabidopsis thaliana based on pairwise yeast two-hybrid analysis and functional complementation tests of yeast mutants. FEBS Lett 437:56–60CrossRefPubMedGoogle Scholar
- Parenicova L, de Folter S, Kieffer M, Horner DS, Favalli C, Busscher J, Cook HE, Ingram RM, Kater MM, Davies B, Angenent GC, Colombo L (2003) Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell 15:1538–1551PubMedGoogle Scholar
- Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksoz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE (2005) A human protein–protein interaction network: a resource for annotating the proteome. Cell 122:957–968CrossRefPubMedGoogle Scholar
- Tewari M, Hu PJ, Ahn JS, Ayivi-Guedehoussou N, Vidalain PO, Li S, Milstein S, Armstrong CM, Boxem M, Butler MD, Busiguina S, Rual JF, Ibarrola N, Chaklos ST, Bertin N, Vaglio P, Edgley ML, King KV, Albert PS, Vandenhaute J, Pandey A, Riddle DL, Ruvkun G, Vidal M (2004) Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol Cell 13:469–482CrossRefPubMedGoogle Scholar
- Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM (2000) A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403:623–627CrossRefPubMedGoogle Scholar