LC-MS/MS shotgun proteome analysis of Saccharomyces cerevisiae lysates

N-terminal acetylation is a highly abundant protein modification in eukaryotes which impacts a wide range of cellular processes and protein properties. This modification was proven to be essential for development and viability of multiple eukaryotes. Still the molecular mechanisms at play and the protein-specific consequences of N-terminal acetylation have only been elucidated for a limited number of substrates. In this label-free shotgun proteomics study we aimed to look at the changes in overall protein abundance linked to N-terminal acetylation levels. BY4742 yeast cell pellets were obtained at 6 different metabolic conditions: yeast cultures grown for 6 h, 3 days, 8 days, 9 days + 0% glucose, 9 days + 2% glucose, and 9 days + 10% of glucose. Cells were lysed with urea buffer, extracted proteins were digested with trypsin and the resulting peptides were analyzed by LC-MS/MS. Proteins were identified and quantified with the MaxQuant software leading to identification of 2,707 proteins and quantification of 1,918 proteins. A two-way ANOVA test was performed to reveal 401 proteins which were significantly regulated between the different metabolic conditions. Gene ontology analysis revealed a strong enrichment for genes involved in oxidation-reduction processes and translation. Yeast cells redirect their cellular metabolism from fermentation to respiration when glucose becomes exhausted from the growth medium. This reprogramming is accompanied by reduced gene expression and protein translation. Thus, these findings are in agreement with known proteome changes in response to prolonged growth.