Public defence, Biotechnology, MSc (Tech) Natalia Kakko von Koch

Title of the thesis: Novel methods for diverting microbial cells’ resources from growth to production and assessing the robustness of engineered production

Thesis defender: Natalia Kakko von Koch
Opponent: Prof. Paola Branduardi, University of Milano-Bicocca, Italy
Custos: Prof. Paula Jouhten, Aalto University School of Chemical Engineering

Microbial cell factories can produce many compounds from fuels to pharmaceuticals. Cells have evolved to prioritise survival and growth over production though. Therefore, the economic feasibility of microbial chemical production requires optimisation of cells’ resource distribution. However, when cells’ resources are diverted to production, cell growth and viability are often compromised. This thesis aimed at developing solutions for these challenges of competition between cell growth and production.  

The first solution aimed at time-separating growth and production to improve the yield of desired compounds. To achieve a switch from growth to production, an inducible synthetic regulation system was developed in baker’s yeast. After biomass accumulation, a growth essential enzyme was degraded with the synthetic regulation system, diverting resources to production instead. The yields of industrially relevant heterologous compounds muconic acid and glycolic acid were improved using this method.

The second method aimed at modifying the metabolic pathways and the chemical environment of cells to render production necessary for growth. Genome-scale metabolic model simulations were used to identify suitable genetic modifications and chemical environments that would couple production to growth. Then, improving growth by adaptive laboratory evolution would enable simultaneously selecting for enhanced producers. With this method, glycolic acid production was improved in baker’s yeast.

Finally, the evolutionary robustness of resource consuming heterologous production was assessed in baker’s yeast. Production was assessed over similar generation numbers as in biotechnological processes. Blue indigoidine pigmentation declined rapidly in a favoured chemical environment. In contrast, red bikaverin production remained robust in an unusual chemical environment, where fitness gains resulted from improved nutrient utilisation. Thus, the robustness of engineered traits appeared dependent on challenges in the environment, and the availability and fitness benefits of adaptive solutions.

Chemical production from renewable raw material using microbial cells is increasingly attractive. Unfortunately, the industrial feasibility of biotechnological chemical production is still limited by strain development. The outcomes of this doctoral thesis provide methods and knowledge for optimising strains for the biotechnological production of relevant and potentially lucrative compounds.

Keywords: Synthetic biology, adaptive laboratory evolution, genome-scale metabolic modelling 

Thesis available for public display 7 days prior to the defence at Aalto University's public display page.