System-wide Analysis of Protein Dynamics in Arabidopsis thaliana
Genome-wide proteomic and transcriptomic analyses have shown significant variance between transcript and protein dynamics. This phenomenon was observed many pro- and eukaryotic organisms including Arabidopsis thaliana, indicating that the predominant view on the regulation of protein dynamics is an over-simplification. In order to unveil the deeper regulatory principles on a system-wide scale, we aim to expand this analysis by obtaining four quantitative, genome-wide datasets: 1) total mRNA using RNA-Seq, 2) actively transcribed mRNAs using polysome fractionation followed by RNA-Seq, 3) total protein quantification using mass spectrometry and SILAC and 4) protein degradation rates with mass spectrometry and dynamic SILAC. These different datasets cover the regulatory processes that determine protein dynamics and thus contain all information on governing regulatory principles. To extract these systematics, we will integrate all four datasets into a count-based, statistical and mathematical model.
We will establish this methodology on A. thaliana suspension cell cultures, which can easily be grown under various conditions. We will primarily investigate the influence of biotic (light deprivation) and abiotic stresses (triggering of the immune system) on the plant regulatory machinery.
In summary, this IPhD project is aimed to obtain a system-wide understanding of the regulation of protein and mRNA dynamics.
Keywords: mRNA and Protein Dynamics, Dynamic SILAC, Mass Spectrometry, Arabidopsis thaliana, Polysome Profiling, RNA-Seq, Statistical and Mathematical Modellingback