I. Systems Biology of acclimation responses
Rationale
All organisms have to cope with changes in environmental conditions and do this at many different levels. These include fast changes by regulating enzyme activities allosterically or by post-translational modifications, and more slow changes by regulating the abundance of various proteins. In the past few years, new technologies based on nanotechnology, mass spectrometry and imaging have revolutionized life sciences and have enabled top-down Systems Biology approaches. With these, responses of biological systems to changing environmental conditions may be acquired at an unprecedented width and depth: alterations in the metabolome, lipidome, transcriptome, and (phospho)proteome can be monitored and correlated to reveal patterns in acclimation responses hidden to the more targeted approaches taken until now.
Aim
To monitor cellular responses to perturbations like changing environmental conditions or disruption of gene functions by Systems Biology approaches.
Current state and Focus
We are taking advantage of top-down Systems Biology approaches to monitor changes at the various system levels using mainly Chlamydomonas reinhardtii as a model system. We are specializing on the (phospho)proteome and lipidome levels and for this have established the experimental setup (mass spectrometry on the Triple-TOF 5600+ and 4000 QTRAP instruments) and a data processing platform (IOMIQS – Integration Of Mass spectrometry Identification and Quantification Software). IOMIQS is a cloud-based soft- and hardware solution particularly suited for the processing of very large data sets based on 15N isotope labeling. IOMIQS combines four search engines to increase peptide identification rates and two quantification algorithms. Furthermore, IOMIQS features the storage and sharing of raw and processed data in a relational database and its visualization, ranging from individual annotated fragment spectra to whole chromatograms. IOMIQS also allows the integration of data across experiments and their export for further statistical analyses. We are currently applying this setup to monitor changes in the Chlamydomonas proteome arising from acclimation responses to changing environmental conditions (heat stress, light intensity, etc.) and upon the inducible downregulation of target genes (HSP70B, VIPP1, etc.).
