A Predicted Interactome for Arabidopsis

Abstract

The complex cellular functions of an organism frequently rely on physical interactions between proteins. A map of all proteinprotein interactions, an interactome, is thus an invaluable tool. We present an interactome for Arabidopsis (Arabidopsis thaliana) predicted from interacting orthologs in yeast (Saccharomyces cerevisiae), nematode worm (Caenorhabditis elegans), fruitfly (Drosophila melanogaster), and human (Homo sapiens). As an internal quality control, a confidence value was generated based on the amount of supporting evidence for each interaction. A total of 1,159 high confidence, 5,913 medium confidence, and 12,907 low confidence interactions were identified for 3,617 conserved Arabidopsis proteins. There was significant coexpression of genes whose proteins were predicted to interact, even among low confidence interactions. Interacting proteins were also significantly more likely to be found within the same subcellular location, and significantly less likely to be found in conflicting localizations than randomly paired proteins. A notable exception was that proteins located in the Golgi were more likely to interact with Golgi, vacuolar, or endoplasmic reticulum sorted proteins, indicating possible docking or trafficking interactions. These predictions can aid researchers by extending known complexes and pathways with candidate proteins. In addition we have predicted interactions for many previously unknown proteins in known pathways and complexes. We present this interactome, and an online Web interface the Arabidopsis Interactions Viewer, as a first step toward understanding global signaling in Arabidopsis, and to whet the appetite for those who are awaiting results from high-throughput experimental approaches.

iTRAQ Protein Profile Analysis of Arabidopsis Roots Reveals New Aspects Critical for Iron Homeostasis

“…openfoundry.org/) based on the Interactome 2.0 (Geisler- Lee et al, 2007) downloaded from The Arabidopsis Information Resource database (ftp://ftp. arabidopsis.org/home/tair/Proteins/Interactome2.0/).…”

Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources

“…Although there have been several PPI studies in Arabidopsis, their main focus lay in building the interactome rather than on breaking down the network to the module level (Fujikawa and Kato, 2007;Geisler-Lee et al, 2007;Van Leene et al, 2007;Arabidopsis Interactome Mapping Consortium, 2011;Li et al, 2011). Studies that did explore the network module contexts found modules recapitulating known biological functions and also suggesting new biological hypotheses for several plant-specific genes, often through the integration with expression data (De Bodt et al, 2009Boruc et al, 2010;Arabidopsis Interactome Mapping Consortium, 2011).…”

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“…Furthermore, PIN is an effective tool for understanding the complex world of biological processes inside the cell and solving various biological problems in signal transduction, gene regulation, and metabolism. [9] Given the significant importance of PINs, proteome-wide interaction networks have been studied in many organisms from prokaryote [10] to eukaryote [11], from unicellular [12] to human [13]. The technique of collecting protein interaction datasets for reconstructing a PIN is improving and the applications of PINs have spread into more to be more closely determined by their interactions than by the characteristics of their individual components.…”