Batch reactor operation (BR) is the most common industrial fermentation process due to its simplicity, but it also carries significant downtime linked to lag phase, clean up and sterilization between batches. In self-cycling fermentation (SCF), an advanced semi-continuous mode of operation, metabolic activity is monitored and once the limiting nutrient is depleted, cycling is performed by draining half the working volume of the fermenter and replenishing it with fresh medium; this approach excludes lag and stationary phases between cycles and reduces the overall downtime during operation. Consequently, the productivity in SCF operation is often greatly improved compared to BR. In the present study, the performance of cultures of Saccharomyces cerevisiae engineered to overproduce shikimic acid grown under BR and SCF operation is compared. Both productivity and yield of shikimic acid are 4-fold greater in SCF operation. Transcriptomic analyses, assisted by RNA-Seq and qPCR, were used to uncover the potential transcriptional mechanisms leading to these improvements. Significant up-regulation of most genes associated with the TCA cycle and oxidative phosphorylation early and late into the SCF cycles suggests higher production of shikimic acid precursors and energy in those stages. ARO4fbr, a gene added to promote shikimic acid production, was overexpressed early in the cycles, facilitating the conversion of the precursors accumulated at the start of the cycle and the end of the previous cycle. Moreover, for the first time, synchrony, one of the characteristic features of SCF operation, was confirmed through transcriptomic evidence. These results help demonstrate how SCF operation can lead to greater productivity and yield in microbial bioproduction.

Understanding the improved productivity of self-cycling fermentation – an automated semi-continuous fermentation process – at the transcriptomic level

ACS Spring Meeting 2021

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