We are currently working with various yeasts, including:

• S. cerevisiae
• R. toruloides
• Y. lipolytica
• K. marxianus

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The transition towards a clean economy requires novel processes for chemical, material, and liquid fuel production that use sustainable substrates, have improved life cycle, and hence a reduced carbon footprint. Cell factories provide the ultimate platform for this purpose to drive the world economy and mitigate risks emanating from climate change.

In this project, we use computational metabolic modeling to design novel cell factories and metabolic engineering to construct them. We aim to design cell factories which use various organic waste as a substrate to valorize it into food and feed components, but also into bio-materials and chemicals

Related publications:

• Senatore VG, Reķēna A, Mapelli V, Lahtvee P-J, Branduardi P. (2025). Ethylene glycol metabolism in the oleaginous yeast Rhodotorula toruloides. Appl Microbiol Biotechnol, 109, 114, DOI: 10.1007/s00253-025-13504-3
• Reķēna A, Pals K, Gavrilović S, Lahtvee P-J. (2025). The role of ATP citrate lyase, phosphoketolase, and malic enzyme in oleaginous Rhodotorula toruloides. Appl Microbiol Biotechnol, 109, 77, DOI: 10.1007/s00253-025-13454-w
• Sjöberg G, Reķēna A, Fornstad M, Lahtvee P-J, van Maris AJA (2024). Evaluation of enzyme-constrained genome-scale model through metabolic engineering of anaerobic co-production of 2,3-butanediol and glycerol by Saccharomyces cerevisiae. Metab. Eng., DOI: https://doi.org/10.1016/j.ymben.2024.01.007.
• Reķēna A, Pinheiro M.J, Bonturi N, Belouah I, Tammekivi E, Herodes K, Kerkhoven E.J, Lahtvee P.J (2023). Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides. PLoS Comput. Biol., DOI: https://doi.org/10.1371/journal.pcbi.1011009
• Pinheiro MJ, Bonturi N, Belouah I, Miranda EA, Lahtvee PJ (2020). Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery. Front. Bioeng. Biotechnol, DOI: 10.3389/fbioe.2020.01008
• Lopes H.J.S., Bonturi N., Kerkhoven E.J., Miranda E.A., Lahtvee P.J. (2020). C/N ratio and carbon source-dependent lipid production profiling in Rhodotorula toruloides. Appl Microbiol Biotechnol, DOI: 10.1007/s00253-020-10386-5

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Our competence is complete with state-of-the-art equipment, which enables automated high-throughput for strain or media screening combined with AI-based data analysis. The automated laboratory comprises a liquid handling robot, a colony picker and a growth profiler.

Tallinn´s branch of the biofoundry is focused on:

• Enzyme design
• Strain engineering
• Bioinformatics

The project has received 15 million € from the European Commission and 15 million € from the Estonian government.

The duration of the project is September 2023 – August 2029.

See more from the project website https://digibio.ut.ee/

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The 3D printing of living materials allows immobilization of biological catalysts and has numerous advantages, e.g.:

(i) printing of co-cultures without the risk of strains out-competing each other; 

(ii) significantly extended cell retention and material stability;

(iii) possibility to functionalize the material; 

(iv) decoupling of biomass production from product formation, which increases substrate-to-product yield.

Related publications:

• Sapulveda Del Rio Hamacek, H., Tingajeva, O., Ostertag, K. S., Reķēna, A.,  Illarionov, A. Jõul, P. Oliveira, P. M., Martín-Hernández, G. de La C. Müller, B., Bonturi, N.  Passoth, V.  Lahtvee, P- J., Kumar. R. (2025). Acidification by nitrogen metabolism triggers extracellular biopolymer production in an oleaginous yeast. DOI: https://doi.org/10.1101/2025.05.04.652101
• Johnston TG, Fillman JP, Priks H, Butelmann T, Tamm T, Kumar R, Lahtvee PJ, Nelsson A (2020). Cell‐Laden Hydrogels for Multikingdom 3D Printing. Macromolecular Bioscience, 2000121, DOI: 10.1002/mabi.202000121
• Priks H, Butelmann T, Illarionov A, Johnston TG, Fellin C, Tamm T, Nelsson A, Kumar R, Lahtvee PJ (2020). Physical confinement impacts cellular phenotype within living materials. ACS Applied Bio Materials, DOI: 10.1021/acsabm.0c00335

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SAFE – Sustainable Aquaculture Feed Based on Novel Biomass from Wood By-products

The SAFE project, funded by NordForsk, aims to utilize the potential of oleaginous yeast and thraustochytrids and develop high-value oil-enriched biomass containing carotenoids, astaxanthin and beta-glucans for salmon feed from wood-based materials.

The project started in May 2021 and ended in 2024.

See more from pthe roject website: SAFE | NMBU

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The  PERFECOAT project, funded by Bio Based Industries Joint Undertaking under the EU Horizon 2020 programme (ID: 101022370) developed and validated a new generation of wood and decorative coatings with more than 25 % bio-based components.

The project duration was May 2021 – November 2024.

Find out more https://perfecoat-project.eu/

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This Action brings together an innovative group of researchers with the combination of skills and experience to unravel how non-conventional yeast can be successfully implemented in a biotechnology industry. Besides, the Action gathers European top scientists in the field and thus become an important pillar worldwide.

Find more info on the project webpage or from the project Linkedin and Twitter profiles.

www.yeast4bio.eu

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• Bioconversion of residual carbon sources into mono-terpenes using R. toruloides. Development of new tools for metabolic engineering. Establishment of rapid screening of terpene-producing strains using (FTIR) platform.
• Enzyme design towards more efficient production of mono-terpenes used in SAFs. Development of bioinformatics tools for enzyme design. Automatization of metabolic engineering and enzyme design and engineering
• Development of new tools to accelerate the production of sustainable aviation fuels (SAF) in Y. lipolytica by: 1) Development of a multiplexed CRISPR-based toolbox, which makes strain improvement 2-5 times faster. 2) Use genome-scale models to predict targets for the multiplexed technology to redirect metabolic fluxes toward SAF precursors. 3) Use the toolbox to accumulate either terpenes or fatty acids.

The project, funded by the European Commission under Horizon Europe Marie Skłodowska-Curie program, runs from 1.12.2023 – 30.11.2027

More information can be found on the project website.

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The project ran from 1.11.2023 – 31.10.2024

Find more and read the Baltic Biotech Action Plan on the project website BIOCONNECT – Towards an integrated Baltic-Nordic biotech cluster (bioconnectproject.eu)

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