Original Research ARTICLE
Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models
- 1 Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- 2 MSU-DOE Plant Research Laboratory, Computer Science and Engineering Department, Michigan State University, East Lansing, MI, USA
- 3 IonGate Biosciences GmbH, Frankfurt, Germany
- 4 Departamento de Microbiología y Genética, Instituto de Biología Funcional y Genomica, Universidad de Salamanca-Consejo Superior de Investigaciones Científicas, Salamanca, Spain
High-throughput data are a double-edged sword; for the benefit of large amount of data, there is an associated cost of noise. To increase reliability and scalability of high-throughput protein interaction data generation, we tested the efficacy of classification to enrich potential protein–protein interactions. We applied this method to identify interactions among Arabidopsis membrane proteins enriched in transporters. We validated our method with multiple retests. Classification improved the quality of the ensuing interaction network and was effective in reducing the search space and increasing true positive rate. The final network of 541 interactions among 239 proteins (of which 179 are transporters) is the first protein interaction network enriched in membrane transporters reported for any organism. This network has similar topological attributes to other published protein interaction networks. It also extends and fills gaps in currently available biological networks in plants and allows building a number of hypotheses about processes and mechanisms involving signal-transduction and transport systems.
Keywords: Arabidopsis, protein–protein interaction, membrane, transporter, split ubiquitin system, classification
Citation: Chen J, Lalonde S, Obrdlik P, Noorani Vatani A, Parsa SA, Vilarino C, Revuelta JL, Frommer WB and Rhee SY (2012) Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models. Front. Plant Sci. 3:124. doi: 10.3389/fpls.2012.00124
Received: 22 February 2012; Paper pending published: 29 March 2012;
Accepted: 24 May 2012; Published online: 21 June 2012.
Edited by:Burkhard Schulz, Purdue University, USA
Copyright: © 2012 Chen, Lalonde, Obrdlik, Noorani Vatani, Parsa, Vilarino, Revuelta, Frommer and Rhee. This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.
*Correspondence: Jin Chen, MSU-DOE Plant Research Laboratory, Computer Science and Engineering Department, Michigan State University, 612 Wilson Road, East Lansing, MI 40024, USA. e-mail: email@example.com;; Seung Y. Rhee, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA. e-mail: firstname.lastname@example.org