Research highlight: Shedding light on protein interaction networks

Researchers succeeded for the first time in mapping protein-protein interactions in living developing plant roots. The findings of the international team of the department of Plant Developmental Biology at Wageningen University and Research, the section of Molecular Cytology at the University of Amsterdam and the University of Düsseldorf were published in Nature . The study, entitled “In vivo FRET-FLIM reveals cell type-specific protein interactions in Arabidopsis roots”, was coordinated by Ikram Blilou at Wageningen

This work is considered as a breakthrough in the field of cell and developmental biology because it is now possible to visualize interactions between proteins under physiological conditions within intact living tissue in a non-invasive manner. This approach will allow better understanding of protein-binding events, which are essential for cellular function as well as their dysfunction in diseases.

Understanding root growth
At the tip of a developing and growing root a population of “stem cells” reside. These cells divide and differentiate into different cell types generating different tissues in the plant root. The fate of each cell, hence what kind of root tissue it will become, is determined by special proteins, among which transcription factors play a crucial role. In order to better understand how these proteins regulate root growth the team of Ikram Blilou, together with Yuchen Long, set out to determine the interactions between a set of key transcription factors. In particular they focused on how these interactions change during growth and subsequent impact on cell fate and root development

Technical challenge
It is technically very challenging to elucidate protein interactions in living organisms at the cellular level because the expression level of these proteins is low, making it difficult to pick up these interactions in living tissue. In this study the researchers used state-of-the-art functional imaging and molecular biology techniques to visualize specific interactions using FRET-FLIM (Förster Resonance Energy Transfer –fluorescence lifetime imaging) technique in combination with genetics and gene expression analysis. Proteins interact by direct binding, this means they come very close to each other and in particular FRET techniques can be used to detect these interactions by tagging the proteins of interest with genetically encoded fluorescent proteins.

Combined expertise
This study is the result of a successful collaboration between three international teams, together with Plant Developmental Biology at Wageningen University, also involving Prof. Theodorus Gadella from the Van Leeuwenhoek Centre for Advanced Microscopy in Amsterdam and Prof. Rudiger Simon from Düsseldorf University. The team of Prof. Gadella, including Dr. Joachim Goedhart and Dr. Marten Postma, has a long standing expertise in optimization of fluorescent proteins, quantitative microscopy and advanced FRET-FLIM analysis.

Publication details
Yuchen Long, Yvonne Stahl, Stefanie Weidtkamp-Peters, Marten Postma, Wenkun Zhou, Joachim Goedhart, María-Isabel Sánchez-Pérez, Theodorus W. J. Gadella, Rüdiger Simon, Ben Scheres & Ikram Blilou  ‘In vivo FRET–FLIM reveals cell-type-specific protein interactions in Arabidopsis roots’, in Nature (26 July 2017). 10.1038/nature23317