Public defence, Biotechnology, MSc (Tech.) Laura Niemelä

Title of the thesis: Shaping the endoplasmic reticulum membrane of Saccharomyces cerevisiae to enhance its capability as a cell factory

Thesis defender: Laura Niemelä
Opponent: Prof. Diethard Mattanovich, BOKU, Austria
Custos: Prof. Alexander Frey, Aalto University School of Chemical Engineering

The yeast Saccharomyces cerevisiae is a widely used organism in biotechnology, serving as a model organism and production organism for pharmaceuticals, enzymes, and other high-value biomolecules. This research demonstrated that engineering the architecture of the endoplasmic reticulum (ER) membrane can remarkably improve the ability of yeast to produce antibodies and modify lipid droplet (LD) formation.

The study focused on the ER, a phospholipid membrane bilayer enclosed organelle that plays a central role in protein and lipid synthesis. The structure of the ER is closely linked to its function. This research investigated how altering ER membrane morphology affects yeast physiology and its capability as a microbial cell factory.

Genes controlling the shape of the ER membrane were targeted to either increase membrane curvature or to reduce it and expand the ER membrane. These changes had broad effects on the cells, including altered cell and ER size, altered fatty acid composition, and LD formation, demonstrating that ER architecture is a key regulator of cellular physiology.

A major finding was that expanding the ER and increasing the proportion of sheet-like membrane structures substantially enhanced the secretion of full-length IgG antibodies, which are structurally complex proteins. In contrast, production of smaller and structurally simpler nanobody-based antibodies benefited less from ER expansion. Instead, their secretion was significantly improved by optimizing the cultivation medium and process and by using a yeast strain engineered to reduce proteolytic degradation. Together, these approaches markedly increased the production of several antibody variants compared with the control strain.

The study also revealed that ER morphology influences the unfolded protein response (UPR), the cell’s response to maintain homeostasis under stressful situations. Increased membrane curvature intensified this stress response, whereas ER expansion attenuated it, providing new insight into how the physical organization of the ER membranes effects the UPR intensity.

Overall, the findings demonstrate that targeted engineering of ER membrane morphology can modulate cellular physiology and significantly enhance the capacity of S. cerevisiae as a cell factory for biotechnological applications.

Keywords: Yeast, endoplasmic reticulum, morphology, membrane curvature inducing protein, reticulon, lipid droplet, antibody, unfolded protein response, genetic engineering 

Contact information: laura.niemela@aalto.fi 

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