Increasing the expression of a secreted protein in Pichia pastoris


Our customer’s commercialization goals required g/L quantities of a protein which was only reported to be produced at the mg/L scale in the literature.

Ginkgo’s cell-engineering platform was able to deliver 1,000-fold improvement in titers and provide data-driven guidance during strain engineering to help them achieve commercialization.

The challenge

A nutrition and wellness startup identified a valuable protein used in supplements, which is traditionally sourced from animals. Aware of the high costs and environmental impact associated with animal-based production, they explored an alternative: producing this protein through precision fermentation. However, the academic literature showed that production levels of their protein using the yeast Pichia pastoris (Komagataella phaffii) were extremely low. In order to compete with the market for the animal-derived protein, they needed to boost production by more than 1000x.

Eager to understand whether their strategy for the market was feasible without investing in costly lab facilities and equipment, the startup turned to Ginkgo, leveraging our end-to-end Protein Expression Services. This move gave them access to Ginkgo’s advanced cell-engineering technology and vast knowledge-base, equipping the startup with the data and insights necessary to refine their commercial strategy and potentially transform the production process.

Our work

Ginkgo Bioworks’ Protein Expression Services consists of four discrete R&D offerings:

  • Host evaluation: used to evaluate and compare different host strains
  • Strain optimization: metabolic engineering of strains with genome modifications for better titer or functionality
  • Classical strain improvement: unbiased strain engineering for better titer or functionality
  • Scale & fermentation: in-house pilot and commercial scale fermentation to increase yield

Our partner initiated their evaluation with Host Selection Services: 

  • Ginkgo’s engineering team expressed our partner’s protein—while maintaining its amino acid sequence—across various Pichia host backgrounds to identify host backgrounds that could enhance protein titers. 
  • The insights gained from this Host Selection process suggested that there was significant room for improvement in protein titers–beyond what had been reported in the academic literature.

Strain Optimization Services steadily improved the target protein’s titer while providing our partners with valuable information about what improvements could be expected. 

  • Ginkgo’s engineers employed rational engineering approaches to boost protein production. Through three progressive stages of strain refinement, the team achieved a remarkable improvement in protein yield, boosting titers more than 1000x the starting strain and what was reported in the literature. 
  • This progress was achieved by methodically incorporating secretion tags, promoters, and genomic modifications to enhance yield incrementally.
  • Although it was available, the data from these three rounds of engineering suggested that our partner didn’t need to engage with the Classical Strain improvement offering at this time.

Protein Expression Service’s Scaling & Fermentation Offering gave our partner further improvements and information about their precision-fermentation-derived protein compared to the existing animal-derived protein market.

  • Utilizing Ginkgo’s Ambr 250 systems, the team conducted numerous parallel experiments to perform comprehensive Design of Experiment (DoE) analyses. This allowed for the identification of key parameters to further improve yield.
  • Scaling-up the resulting fermentation protocol ensured that the improvements found in the  Ambr 250 systems were functional under industry-relevant conditions.
  • Upstream and downstream protocols were developed on material from the fermentation;  successful purification allowed Ginkgo’s engineers to validate that the fermentation-derived material had the same functionality as the animal-derived product already in the market.

The structured approach of Ginkgo’s Protein Expression Services suite of offerings informed our partner’s strategic decisions: iterative, data-driven progress through projects allowed our partner to make informed decisions about their project and their entry to market.


Titer Improvement
Ginkgo’s Protein Services to achieve >1,000x improvement in protein titers over what was reported in the literature for our partner–this improvement allowed our partner to proceed to commercialization.

Functionality Testing
Throughout strain development and optimization we were able to test protein functionality in custom-built assays. We found that our fermentation-derived product functioned as well as the animal-sourced products already on the market.

Gated Program Progress
Ginkgo provided our customer with discrete work packages and data read-outs after completion. This approach empowered our partner to make data-driven decisions about whether to continue development or to shift focus to a different product.

Data-informed decisions
In addition to informing go/no-go decision points during the project, our partner was able to gain insight into the potential specifications (eg, likely titer, functionality, fermentation COGS) of their final product. These data provided our partner with valuable insights on how to move forward with commercialization.

Work with us

Ginkgo’s Protein Service offerings leverage our advanced cell engineering platform to transform your product idea into commercial reality. Our comprehensive services span the entire project lifecycle, offering solutions that harness the power of our knowledge-base and expertise at any stage of the R&D process. Ginkgo’s Foundry acts as an extension of your capabilities, allowing you to focus on strategic decisions and market development while our structured, data-driven process provides a clear, gated pathway for your project’s development.  Navigate your path from concept to product with Ginkgo’s Protein Service offerings.