Multi-omics approaches to unravel regulatory dynamics in yeast bioreactor cultivations
Doctoral thesis, 2024

Climate change is a multifaceted problem that requires multiple scientific discoveries and engineering innovations. Among the innovations that have emerged in recent years are microbial cell factories, engineered microorganisms that produce desired molecules through their metabolism.

A promising microbial cell factory is Yarrowia lipolytica, an oleaginous yeast that has gained significant traction since it proved a versatile host to produce lipids as well as both bulk and fine chemicals. However, further research is needed to better understand this host and to design better bioprocesses.

To improve the current understanding of Y. lipolytica as a microbial cell factory, I combined chemostat cultivations with transcriptomic analysis. I studied the underlying biology of a platform strain with disrupted lipid synthesis, revealing that abolishing storage lipids induces protein misfolding and stress responses. I then explored the use of urea as an alternative and more sustainable nitrogen source, demonstrating that it does not alter the cell transcriptome and can reduce media acidification. I combined this information to improve a fed-batch cultivation to produce high titres of itaconic acid.

Meanwhile, I laid the foundations for single-cell transcriptomics to explore cell heterogeneity in bioreactor cultivations. I performed a proof-of-concept analysis in the well‑characterized yeast Saccharomyces cerevisiae to understand the potential challenges in translating single‑cell transcriptomics to Y. lipolytica. I found that cell cycle genes are a major source of variability that needs to be minimized.

The work performed combines bioreactor cultivation with omics analyses to inform and guide future strain improvement. Overall, this thesis explores and expands knowledge in relevant areas to develop Y. lipolytica as a microbial cell factory for the sustainable production of non‑lipid chemicals.

fed batch

bioreactor

chemostat

itaconic acid

Transcriptomics

RNA sequencing

single-cell RNA sequencing

Chemistry building, room 10:an
Opponent: Tristan Rossignol

Author

Simone Zaghen

Chalmers, Life Sciences, Systems and Synthetic Biology

Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica

Journal of Industrial Microbiology and Biotechnology,;Vol. 50(2023)

Journal article

Quantification of stochastic gene expression in S. cerevisiae using single cell RNA-sequencing

The human population is constantly growing, leading to an increasing demand for food and goods. This significantly impacts our planet. Climate change is a major challenge we need to address through scientific discoveries and engineering innovations.

One such innovation is the development of microbial cell factories - designed (engineered) microorganisms that can transform a variety of sustainable biomasses into useful products such as foods or goods.

Yarrowia lipolytica, a promising cell factory, has gained attention for its ability to produce a wide range of valuable molecules used in the food, biofuel, and pharmaceutical industries. However, to fully leverage Y. lipolytica’s potential, more research is needed.

In this thesis I investigated the underlying biology of a Y. lipolytica strain whose lipid synthesis is disrupted. This strain can be used for production of non-lipid molecules. However, disrupting lipid synthesis induced stress responses, suggesting that a downregulation of these processes might be a better strategy. I then explored the use of urea as an alternative and more sustainable nitrogen source, showing that it does not alter cell physiology and can also reduce issues related to media acidification. I leveraged this information to improve a fed-batch cultivation to produce high titres of itaconic acid, a chemical that finds applications in the food, textile, and pharmaceutical industries. Additionally, I laid the foundations for single-cell transcriptomics to explore cell heterogeneity in bioreactor cultivations and developed a computational framework to minimise the variability of cell cycle genes.

Overall, this thesis explores and expands knowledge in relevant areas to develop Y. lipolytica as a microbial cell factory for the sustainable production of non-lipid chemicals.

Awakening of cryptic biosynthetic gene clusters using obese red yeast

Swedish Research Council (VR) (2019-04624), 2019-12-01 -- 2023-11-30.

Optimera mikrobiell tillverkning av itakonat för hållbar plast och tvättmedel

Formas (2018-00597), 2019-01-01 -- 2021-12-31.

Driving Forces

Sustainable development

Subject Categories

Biochemistry and Molecular Biology

Microbiology

Bioinformatics and Systems Biology

Control Engineering

Infrastructure

Chalmers Infrastructure for Mass spectrometry

C3SE (Chalmers Centre for Computational Science and Engineering)

Areas of Advance

Energy

ISBN

978-91-8103-070-9

Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie: 5528

Publisher

Chalmers

Chemistry building, room 10:an

Opponent: Tristan Rossignol

More information

Latest update

8/29/2024