Comparison of the metabolic response to over-production of p-coumaric acid in two yeast strains

The development of robust and efficient cell factories requires understanding of the metabolic changes triggered by the production of the targeted compound. Here we aimed to study how production of p-coumaric acid, a precursor of multiple secondary aromatic metabolites, influences the cellular metabolism of Saccharomyces cerevisiae. We evaluated the growth and p-coumaric acid production in batch and chemostat cultivations and analyzed the transcriptome and intracellular metabolome during steady state in low- and high-producers of p-coumaric acid in two strain backgrounds, S288c or CEN.PK. We found that the same genetic modifications resulted in higher production of p-coumaric acid in the CEN.PK background than in the S288c background. Moreover, the CEN.PK strain was less affected by the genetic engineering as was evident from fewer changes in the transcription profile and intracellular metabolites concentrations. Surprisingly, for both strains we found the largest transcriptional changes in genes involved in transport of amino acids and sugars, which were downregulated. Additionally, in S288c amino acid and protein biosynthesis processes were also affected. We systematically overexpressed or deleted genes with significant transcriptional changes in CEN.PK low and high-producing strains. The knockout of some of the downregulated transporters triggered a 20-50% improvement in the synthesis of p-CA in the CEN.PK high-producing strain. This study demonstrates the importance of transporters in the engineering of cell factories for production of small molecules.