The cellular factories that churn out recombinant proteins may adopt their own version of lean manufacturing: intensify everything that adds value and curtail everything else. To date, yeast and other tiny protein factories have resisted such a systemic, rational approach. Living cells involve so many interconnected processes that obviously productive activities are often entangled with seemingly unproductive activities—but not always.

According to a new study from a team of European researchers, a handful of genetic sacrifices doubled protein production in the yeast Saccharomyces cerevisiae. The researchers, acting like latter-day Frederick Winslow Taylors, carried out cell-scale time-and-motion studies. Essentially, they optimized yeast strains through a combination of RNA interference and high-throughput microfluidic single-cell screening.

The researchers—who were affiliated with the Novo Nordisk Foundation Center for Biosustainability at Technical University of Denmark (DTU), Chalmers University of Technology, and KTH Royal Institute of Technology—published their findings in the Proceedings of the National Academy of Sciences, in an article titled, “RNAi expression tuning, microfluidic screening, and genome recombineering for improved protein production in Saccharomyces cerevisiae.”

“We found that genes with functions in cellular metabolism (YDC1, AAD4, ADE8, and SDH1), protein modification and degradation (VPS73, KTR2, CNL1, and SSA1), and cell cycle (CDC39), can all impact recombinant protein production when expressed at differentially down-regulated levels,” the article’s authors wrote. “By establishing a workflow that incorporates Cas9-mediated recombineering, we demonstrated how we could tune the expression of the identified gene targets for further improved protein production for specific proteins.”

The researchers analyzed approximately 243,000 silencing effectors in yeast by looking at the enhanced secretion of α-amylase as an indicator of improved recombinant protein production. Using extensive screening of tiny droplets containing single cells secreting the enzyme, the researchers managed to pick out nine genes, which upon silencing improved protein secretion. These genes are involved in cellular metabolism, cell cycle, as well as protein modification and degradation.

“All these genes can impact recombinant protein production when expressed at differentially downregulated levels,” said the article’s first author Guokun Wang, PhD, a postdoc at the Novo Nordisk Foundation Center for Biosustainability at DTU. “This knowledge is really important when trying to build optimized yeast cell factories for the production of industrial enzymes or biopharmaceutical proteins.”

The scientists first screened beneficial RNAi targets. Afterward, they looked at combinations of silencing, leading to a so-called semirational approach.

“The concept can be extended to other yeast protein producers, even some filamentous fungi and mammalian cell factories,” Wang added. “Any organization that works with superior protein producers can use these findings.”

“Our findings offer a high-throughput and semirational platform design,” the authors concluded, “which will improve not only the production of a desired protein but even more importantly, shed additional light on connections between protein production and other cellular processes.”

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