Yeast Metabolic Engineering

Food colors made by yeast fermentation
We are developing yeast-based fermentation processes for making various betalain-type food colors. The methhod is more cost-effective and sustainable than extracting colors from plants, where color content is very low. 

Selected publications: 

• Thomsen PT, Nielsen SR, Borodina I (2024). “Recent advances in engineering microorganisms for the production of natural food colorants”.  Curr Opin Chem Biol, 81:102477.
• Thomsen P, Meramo S, Ninivaggi L, Pasutto E, Babaei M, Avila-Neto P, Pastor M, Sabri P, Rago D, Parekh T, Hunding S, Christiansen L, Sukumara S, Borodina I (2023). “Beet red food colorant can be more sustainably produced with engineered Yarrowia lipolytica”. Nat Microbiol, 8: 2290–2303.
• Babaei M, Thomsen PT, Dyekjær JD, Glitz CU, Pastor MC, Gockel P, Körner JD, Rago D, Borodina I (2023). “Combinatorial engineering of betalain biosynthesis pathway in yeast Saccharomyces cerevisiae”. Biotechnol Biofuels Bioprod, 16:128.
• Popular article and video: https://sciencenews.dk/en/beet-red-reimagined-how-engineered-yeast-is-revolutionising-natural-colourings

Characterizing and engineering the transport of small molecules
We are developing methods for transporter function characterization based on Xenopus expression with LC-MS and Solid-Supported Membrane Electrophysiology. We also engineer the transport of small metabolites in order to improve the performance of the cell factories.

Selected publications:

• Dong F, Lojko P, Bazzone A, Bernhard F, Borodina I (2024). “Transporter function characterization via continuous-exchange cell-free synthesis and solid supported membrane-based electrophysiology”. Bioelectrochemistry, 159: 108732.
• Stanchev LD, Møller-Hansen I, Lojko P, Rocha C, Borodina I (2023). ”Screening of Saccharomyces cerevisiae metabolite transporters by 13C isotope substrate labeling." Front Microbiol, 14:1286597.
• Darbani B, Stovicek V, van der Hoek SA, Borodina I (2019). ”Engineering energetically efficient transport of dicarboxylic acids in yeast Saccharomyces cerevisiae.” Proc Natl Acad Sci U S A, 116(39):19415-19420.

High-throughput metabolic engineering methodologies
We develop genome editing toolboxes and methods that allow parallel creation and screening of multiple strain designs for accelerating strain development programs. 
Our toolkits are available via AddGene or by personal contact: https://www.addgene.org/Irina_Borodina/ 

Selected publications:

• Jiang W, Wang S, Avila P, Jørgensen TS, Yang Z, Borodina I (2024) “Combinatorial iterative method for metabolic engineering of Yarrowia lipolytica: application for betanin biosynthesis”. Metab Eng, S1096-7176(24)00110-1.  
• Babaei M, Thomsen PT, Pastor MC, Jensen MK, Borodina I (2024). “Coupling High-Throughput and Targeted Screening for Identification of Nonobvious Metabolic Engineering Targets”. ACS Synth Biol, 13(1): 168–182.  
• Wang G, Møller-Hansen I, Babaei M, D'Ambrosio V, Christensen HB, Darbani B, Jensen MK, Borodina I (2021). ”Transportome-wide engineering of Saccharomyces cerevisiae.” Metab Eng, 64:52-63.

The Yeast Metabolic Engineering group is headed by Professor Irina Borodina and is located at Lyngby Campus, Building 220. Don't hesitate to contact us if you are interested in collaboration, exchange, student projects, etc.