Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models

Jin Chen, Sylvie Lalonde, Petr Obrdlik, Azam Noorani Vatani, Saman A. Parsa, Cristina Vilarino, Jose Luis Revuelta, Wolf B. Frommer, Seung Y. Rhee

Research output: Contribution to journalArticlepeer-review

36 Scopus citations

Abstract

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.

Original languageEnglish
Article number124
JournalFrontiers in Plant Science
Volume3
Issue numberJUN
DOIs
StatePublished - Jun 21 2012

Keywords

  • Arabidopsis
  • Classification
  • Membrane
  • Protein-protein interaction
  • Split ubiquitin system
  • Transporter

ASJC Scopus subject areas

  • Plant Science

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