Proteomic characterization of yeast secretion mutants

Saccharomyces cerevisiae is a popular yeast expression system for recombinant protein production for its utility and profitability to grow. However, it can be plagued with low functional yields compared to other higher complexity eukaryotic host systems and often requires further optimization. A less explored strategy is to modify the organization of subcellular organelles, with the endoplasmic reticulum (ER) being a good target for investigation due to its critical role in protein secretion. This study aims to assess changes in relative secretion capacity and then further characterize the proteomic profile of five yeast mutant cell lines that have unique ER morphologies. A label-free DIA-MS quantitative proteomics approach led to a maximum identification of 3195 proteins from 30677 precursors obtained. Two mutants performed over 50% better than the control strain in relative secretion capacity through an O-nitrophenyl-beta-D-galactopyranoside assay. Differential protein abundance analysis showed there were seven common significant proteins across mutants relating to metabolic pathways of energy production and membrane stress. These results led to the conclusion that a balance between increased demand for protein translation must be met with adjustments to supply energy for an ER mutant strain to successfully achieve both a stable ER morphology and up-regulated protein secretion.