A systematic phosphoproteome screen to identify targets of the Target of Rapamycin (TOR) kinase in Arabidopsis thaliana

ABSTRACT: The target of rapamycin (TOR) kinase is a central regulatory hub that translates environmental and nutritional information into permissive or restrictive growth decisions. Although the TOR pathway is conserved among eukaryotes, plants developed unique adaptations to this pathway to cope with their autotrophic and sessile nature. Here, we captured for the first time a proteome-wide view of the plant TOR phosphorylation and interaction landscape. After sampling four biological repeats, proteins were extracted, digested and phosphopeptides were enriched. In total, 8302 phosphopeptides on 2558 proteins were identified from all samples. After label free quantitative analysis, a filtered dataset of 5500 phosphopeptides on 2056 proteins was retained. To identify TOR-dependent sites, the control-, AZD8055- and rapamycin-treated samples were statistically analyzed using a linear mixed model to evaluate the effect of the treatment, time and the interaction between both. For T10, T20 and T40, the sucrose control samples were compared to the AZD8055 or rapamycin samples. In addition, the AZD8055 samples were compared to the rapamycin samples, and the sucrose control samples (T10, T20, T40) were compared to T0. Overall, the strongest effect occurred with AZD8055. Therefore, an additional filter was applied retrieving only phosphopeptides that changed at least two-fold upon AZD8055 treatment. In total, 96 unambiguous TOR-dependent phosphosites were detected on 66 proteins, linking TOR to a plethora of biological processes.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Cell Culture

SUBMITTER: Jelle Van Leene  

LAB HEAD: Geert De Jaeger

PROVIDER: PXD008355 | Pride | 2019-07-17

REPOSITORIES: Pride