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InterATOME: the IPS2 protein-protein interaction platform

Protein-protein interactions are critical elements of biological systems and their analysis can provide valuable hints about functions of proteins. To date, the yeast 2 hybrid (Y2H) system is the only method to probe protein-protein interactions routinely in vivo and with a high-throughput. The Organelle Gene Expression-OGE team at IPS2 has been involved in an international project of Arabidopsis Interactome Mapping coordinated by Pr Joseph Ecker (Salk Institute, San Diego) and Pr Marc Vidal (DFCI, Boston). This plant protein interactome network map was generated using the improved Y2H assay developed at DFCI for C. elegans, human and yeast proteins. The first data set from this project was published in 2011 (AIM, Science 2011) where a proteome-wide binary protein-protein interaction map containing about 6200 high quality interactions between about 2700 proteins was described.

In 2014, the team was funded by the Saclay Plant Sciences–SPS Labex and by INRA (Plant Breeding Division) in order to set up a Y2H pilot project. By improving the protocol which was previously used for the AIM-project, they have developed and validated an Y2H high-throughput liquid pipeline. In 2016, the InterATOME plateform was settled up and opened!

Using 384-well plates, successive culture replication in liquid media and robots, the InterATOME Platform is able to screen a pool of 50 hybrid proteins against the Arabidopsis library (about 12000 proteins). Mapping screenings are done using instruments which were partially funded by the SPS LabEx: the Genetix Qpix2XT colony picker robot, the ThermoFisher-Scientific MULTIDROP 384 plate filler and the Orbitor RS Microplate Mover robotized arm (currently being installed).

In addition to providing collaborators with new protein interaction data, the InterATOME platform combines Y2H interacting results with the AIM network in order to continue building up the Arabidopsis interactome network. This data will facilitate future system approaches to better understand plant biology and improve crops.