The GoFORSYS Systems Biology project - Quantitative shotgun proteomics as a tool for monitoring proteome dynamics in Chlamydomonas
Michael Schroda, Dorothea Hemme, Timo Mühlhaus, Julia Weiss, and Frederik Sommer
Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
GoFORSYS is a Systems Biology project to analyze photosynthesis and its regulation in response to defined environmental conditions using Chlamydomonas reinhardtii as major model organism ( The project is a collaborative effort of the University of Potsdam and the Max Planck Institutes of Molecular Plant Physiology and Colloids and Interfaces. Chlamydomonas reinhardtii was chosen as model system because of its unicellularity, which precludes influences by tissue heterogeneity and development, and because it can be cultivated under controlled conditions in bioreactors. In our Core Experiments, selected environmental conditions are changed and cellular responses are monitored over time at various system levels. For each system level analyzed, high-throughput platforms were adapted or newly devised. For example, we developed a shotgun proteomics approach using metabolic labelling to measure changes in soluble and membrane proteins. Combined with our newly developed IOMIQS framework (Integration Of Mass spectrometry Identification and Quantification Software), we are able to quantify in time courses the dynamics of hundreds of proteins with very high accuracy. In first Core Experiments, photoautotrophically grown cells were shifted from low to saturating light intensities and activities of photosystems, b6f complex and ATP synthase, NPQ, the expression of 736 nuclear and 137 organellar genes, polysome loading, the composition of 121 lipids and 128 metabolites, and dynamics of 467 proteins were monitored. An overview to GoFORSYS and a more detailed description of our proteomics platform will be presented.
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