Systems-based Saccharomyces cerevisiae strain design for improved squalene synthesis

• Published in: Biochemical engineering journal 2019-08, Vol.148, p.37-45
• Main Authors: Paramasivan, Kalaivani, Kumar HN, Punil, Mutturi, Sarma
• Format: Article
• Language: English
• Subjects: Fed-batch; Genome-scale model; LYS1; S. cerevisiae; Squalene
• ISSN: 1369-703X; 1873-295X
• DOI: 10.1016/j.bej.2019.04.025

[Display omitted] •Composition of in-silico medium affects identification of gene knock-outs.•LYS1 and ADK1 were identified as deletion targets for improved squalene flux.•LYS1Δ, ADK1Δ and POS5 (with mitochondrial signal) overexpression improves squalene.•Fed-batch cultivation under low aerobic cultivation increased squalene to 1.9 g/L. Constraint-based flux balance analysis of S. cerevisiae has led to the identification of a novel gene deletion targets, LYS1 and ADK1, for enhancement of squalene flux. LYS1 deletion resulted in 2-fold improvement in squalene when compared to reference strain BY4741 with a maximum yield of 33.1 mg/g DCW. A double mutant of ADK1 and LYS1 genes has increased the squalene yield to 38 mg/g DW which is 2.38-fold higher over the control strain. Furthermore, single copies of tHMG1 and POS5 (with mitochondrial signal sequence) genes have been integrated into this double mutant in order to enhance the precursor pool and the cofactor regeneration capacity, respectively, for enhanced squalene synthesis. The improved strain, SK22 has resulted in squalene yield of 65 mg/g DW which is 4-folds higher than the control strain. Finally, the engineered strain was cultivated in a bioreactor using fed-batch strategy to improve the titer and productivity of squalene. Exponential feeding (open-loop strategy) using high residual glucose (˜40–60 g/L) has increased the squalene titer to a maximum of 1.9 g/L with a yield of 0.15 g/g DCW, which is several folds higher than the shake-flask results. Redirecting the lysine synthesis by external supplementation could potentially improve squalene flux in S. cerevisiae.