Quantitative proteomics of Saccharomyces cerevisiae vacuoles and stress responses in Lactococcus lactis

PhD ceremony: Ms. E. Wiederhold, 16.15 uur, Academiegebouw, Broerstraat 5, Groningen

Thesis: Quantitative proteomics of Saccharomyces cerevisiae vacuoles and stress responses in Lactococcus lactis

Promotor(s): Prof. D.J. Slotboom, Prof. B. Poolman

Faculty: Mathematics and Natural Sciences

Each living organism is built up of diverse types of molecules, the complete collections of which are described as '-omes', e.g. gen-ome (DNA), transcript-ome (RNA) and prote-ome (proteins). The study of proteomes extents beyond the question of expression (presence, absence, quantity of each protein) but also addresses cellular localization, interactions, activity, modifications and different isoforms. Often the proteomic studies have been qualitative, aiming at determining which proteins are present in the sample, providing a snap-shot overview of the proteome. However, proteomes - in contrast to genomes - are dynamic and change in time, space and in response to stimuli. Quantitative proteomics can provide insights into the dynamic changes of proteomes and aims at determining how much of each protein is present in the sample at a particular time, and how the abundances change over time. The present thesis describes two large-scale quantitative proteomics studies using isotope labeling of peptides (with the molecule iTRAQ), which were subsequently analyzed by mass spectrometry. This technique allowed detecting novel proteins in the vacuolar membrane, and determining physiological responses of the bacterium Lactocussus lactis to overexpression of the human CFTR protein which is – if mutated – is responsible for the cystic fibrosis disease. In addition sample, preparation, data analysis, and validation of the outcome of the proteomics studies are discussed.