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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION OF FUNCTIONAL SEQUENCE IN PLANT GENOMES THROUGH BIOINFORMATIC, GENOMIC, AND GENETIC APPROACHES

Location: Plant, Soil and Nutrition Research

Title: Evidence for network evolution in an arabidopsis interactome map

Authors
item Matija, Dreze -
item Ruxandra Carvunis, Anne -
item Charloteaux, Benoit -
item Galli, Mary -
item Pevzner, Samuel -
item Tasan, Murat -
item Stein, Joshua -
item Spooner, William -
item WARE, DOREEN
item Braun, Pascal -
item Ecker, Joseph -
item Hill, David -
item Roth, Frederick -
item Vidal, Marc -

Submitted to: Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 15, 2011
Publication Date: July 29, 2011
Citation: Matija, D., Ruxandra Carvunis, A., Charloteaux, B., Galli, M., Pevzner, S.J., Tasan, M., Stein, J., Spooner, W., Ware, D., Braun, P., Ecker, J.R., Hill, D.E., Roth, F.P., Vidal, M. 2011. Evidence for network evolution in an arabidopsis interactome map. Science. 333(6042):601-607.

Interpretive Summary: In order to understand how proteins work together to bring about cellular functions, ~2,700 proteins of Arabidopsis thaliana were tested for the ability to interact with one-another using a yeast two-hybrid assay. From thousands of observed interactions many signaling networks were deduced. The evolution of protein-protein interaction networks was examined by comparing how many interactions are shared between proteins derived from duplicated genes (paralogs). The paralogs were dated using a phylogenetic approach. It was observed that gene duplication results in rapid divergence in function and rewiring of protein-protein interaction networks. Over time this process stabilizes as the rate of functional divergences slows down. This study dramatically increases the number of proteins for which interactions are known and provides a valuable resource for understanding gene function.

Technical Abstract: Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins. A global organization of plant biological processes emerges from community analyses of the resulting network, together with large numbers of novel hypothetical functional links between proteins and pathways. We observe a dynamic rewiring of interactions following gene duplication events, providing evidence for a model of evolution acting upon interactome networks. This and future plant interactome maps should facilitate systems approaches to better understand plant biology and improve crops.

Last Modified: 9/10/2014