Systems Biology of Yeast Lipid Metabolism

Doctoral thesis, 2012

Lipid metabolism plays an important role in the development of many different life-style related diseases, such as type 2 diabetes and atherosclerosis, and understanding the molecular mechanisms behind regulation of lipid biosynthesis and degradation may lead to development of new therapies. In this project we undertook a global study of lipid metabolism in the eukaryotic model organism Saccharomyces cerevisiae. The objective of this project is to quantify how the fluxes in lipid metabolism of eukaryotic cells are controlled by different component of the regulatory network. Using systems biology approaches there was established a global regulatory model for lipid metabolism, and it was quantified how the fluxes toward different lipid components are regulated. Using different mutants that carry deletion in genes encoding key transcriptional factors and protein kinases involved in lipid regulation, the fluxes towards the different lipid components was perturbed. The wild-type yeast strain CEN.PK113-7D and the yeast mutants opi1∆, snf1∆, tor1∆, ino2∆, ino4∆, and ino2∆ino4∆ were grown in chemostat cultures at carbon or nitrogen-limited conditions and also high or low inositol-choline (IC) condition at a dilution rate of 0.1 h-1. At steady state conditions samples were withdrawn for analysis of the transcriptome, the metabolome and the lipidome. There was also developed 3 high-throughput methods for lipid quantification, i) for storage lipid monitoring at single-cell level using CARS microscopy, ii) for lipid classes analysis based on microwave-assisted extraction, HPLC-CAD, and iii) for fatty acids species analysis based on microwave-assisted derivatization. Through combined measurements of the transcriptome, the metabolome, the lipidome and the fluxome it was possible to obtain a large dataset that could be used to identify correlations between the different components such as the co-influences of Snf1-IC effects, INO-level, and Snf1-TORC1 effects on yeast lipid metabolism.