The target of rapamycin (TOR) kinase is a conserved regulatory hub that translates environmental and nutritional information into permissive or restrictive growth decisions. Despite the increased appreciation of the essential role of the TOR complex in plants, no large-scale phosphoproteomics or interactomics studies have been performed to map TOR signalling events in plants. To fill this gap, we combined a systematic phosphoproteomics screen with a targeted protein complex analysis in the model plant Arabidopsis thaliana. Integration of the phosphoproteome and protein complex data on the one hand shows that both methods reveal complementary subspaces of the plant TOR signalling network, enabling proteome-wide discovery of both upstream and downstream network components. On the other hand, the overlap between both data sets reveals a set of candidate direct TOR substrates. The integrated network embeds both evolutionarily-conserved and plant-specific TOR signalling components, uncovering an intriguing complex interplay with protein synthesis. Overall, the network provides a rich data set to start addressing fundamental questions about how TOR controls key processes in plants, such as autophagy, auxin signalling, chloroplast development, lipid metabolism, nucleotide biosynthesis, protein translation or senescence.
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The custom code used for the phosphosite conservation analysis is available on request from the corresponding author.
The data that support the findings of this study are available from the corresponding author on reasonable request. The protein interactions from this publication have also been deposited to the IMEx consortium (http://www.imexconsortium.org) through IntAct and assigned the identifier IM-26172. The MS phosphoproteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the data set identifier PXD008355. The Cytoscape file covering the integrated TOR kinase signalling network as well as all discussed subnetworks is available as Supplementary Dataset.
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We thank A. Bleys for help in preparing the manuscript, K.-i. Hayashi (Okayama University of Science, Japan) for providing PEO-IAA, M. Vuylsteke for help with statistical analyses and D. Inzé, S. Vanneste, N. Besbrugge and M. Bontinck for the fruitful discussions. C.H. was funded by a Belspo Grant.
The authors declare no competing interests.
Journal peer review information: Nature Plants thanks Leslie Hicks and Christian Meyer and other anonymous reviewer(s) for their contribution to the peer review of this work.
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Supplementary Figures 1–8, Supplementary Table Legends, Supplementary Dataset Legends, Supplementary Notes, Supplementary Methods and Supplementary References.
Supplementary Tables 1a–e.
Supplementary Tables 2a–e.
Supplementary Tables 3a and b.
Supplementary Tables 4a–d.
Supplementary Tables 5a and b.
List of oligos used for cloning.
Cytoscape file corresponding to the integrated TOR kinase signalling network.
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Cell Reports (2019)
Journal of Experimental Botany (2019)
Current Opinion in Plant Biology (2019)
Frontiers in Plant Science (2019)