Integrating proteomics, transcriptomics, and metabolic flux analysis in non-canonical yeast species

Abstract

The exploitation of microbes as factories for bioproduct synthesis is a process commonly used in household settings such as baking and brewing, as well as in many research and development fields including biomedical engineering, nutrition, and biofuels. This work seeks to integrate fundamental biological processes—namely transcriptomics, proteomics, and metabolic flux—to examine non-canonical yeast species as potential targets for bioengineering. Unlike much previous work that has focused on the model yeast S. cerevisiae (baker’s yeast), this research additionally integrates the yeasts I. orientalis and R. toruloides, which both have unique biosynthetic capabilities. For all three yeasts, absolute proteomics data was measured using spike-in proteins of known concentration. Comparison between S. cerevisiae and I. orientalis revealed higher correlation of absolute protein expression than absolute mRNA expression. Additionally, relative proteomics for each of the three yeasts in four nutrient-limited growth conditions revealed similar protein expression in the same conditions in different yeasts, despite over 250mya of evolutionary distance. Further methods were also developed to measure relative protein expression across yeasts directly. Integration of metabolic flux data from the Rabinowitz lab revealed high correlation between protein abundance and flux in several central metabolic pathways. These results support increased annotation of the non-canonical yeast species I. orientalis and R. toruloides in addition to developing proteomic methods for comparison across yeast species. This utilization of non-model yeast species provides a platform for future engineering of microbial factories, providing new and improved avenues for production of desirable biomolecules.