Potential of a constitutive-UPR and histone deacetylase A-deficient Saccharomyces cerevisiae strain for biomolecule production

The endoplasmic reticulum (ER) is an organelle responsible for the production of secretory proteins and lipid molecules. In many ascomycetous yeasts, including Saccharomyces cerevisiae , HAC1 mRNA undergoes splicing to yield HAC1 i mRNA (“i” denotes induced), which is translated into the nuclear transcription factor Hac1 upon ER dysfunction. The extensive transcriptome change triggered by Hac1 is called the unfolded protein response (UPR), which leads to ER enforcement. As an unregulated UPR continuously elevates ER activity and size, S. cerevisiae cells exhibit increased production of secretory proteins and lipid molecules when Hac1 is constitutively and artificially expressed. While this technique holds promise for industrial bioproduction, it has a notable drawback, as cells strongly expressing Hac1 exhibit slow growth, making it difficult to handle and store them. To address this issue, in this study, we searched for fast-growing mutants of HAC1 i cells carrying the HAC1 i sequence at the HAC1 locus to express Hac1 constitutively. We found that histone deacetylase A (HDA)-deficient mutations, including Δhda3 , accelerated the growth of Hac1-expressing cells. Despite their increased growth rate, Δhda3HAC1 i cells showed stronger expression of prominent UPR target genes related to ER function than HAC1 i cells. Moreover, Δhda3HAC1 i cells carried a structurally complex and expanded ER and exhibited high-yield production of triglycerides and of different heterologous model biomolecules, β-carotene and Taka amylase A. In conclusion, we propose that combining artificial Hac1 expression with mutations that affect the chromosomal status holds promise for optimizing yeast-based bioproduction systems. IMPORTANCE The production of commercially valuable biomolecules using genetically modified Saccharomyces cerevisiae is an important biotechnological process that has been partly industrialized. Because secretory proteins and many lipid molecules are produced in and/or from the endoplasmic reticulum (ER), their production is expected to be improved by artificial enhancement of ER functions. This can be accomplished by artificial and constitutive expression of the nuclear transcription factor Hac1. In wild-type cells, Hac1 is induced upon ER dysfunction and upregulates its functions. A major drawback of cells artificially overexpressing Hac1 is their slow-growing phenotype. Here, we showed that the growth of artificially Hac1-expressing cells is fastened by histone deacetylase A-deficient mutations, leading to efficient biomolecule production. Our study provides an intriguing example of how the properties of a genetically modified yeast strain can be improved by a mutation that alters its chromosomal status.