Sequencing of a dairy isolate unlocks Kluyveromyces marxianus as a host for lactose valorization

Thornbury, M.; Knoops, A.; Summerby-Murray, I.; Dhaliwal, J.; Johnson, S.; Utomo, J.; Joshi, J.; Narcross, L.; Remondetto, G.; Pouliot, M.; Whiteway, M.; Martin, V. J. J.

doi:10.1101/2025.02.03.636257

bioRxiv · 10.1101/2025.02.03.636257

Sequencing of a dairy isolate unlocks Kluyveromyces marxianus as a host for lactose valorization

Thornbury, M.·Knoops, A.·Summerby-Murray, I.·Dhaliwal, J.·Johnson, S.·Utomo, J.·Joshi, J.·Narcross, L.·Remondetto, G.·Pouliot, M.·Whiteway, M.·Martin, V. J. J.

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Abstract

The use of genetically modified non-conventional yeast provides significant potential for the bioeconomy by diversifying the tools available for the development of sustainable and novel products. In this study, we sequenced and annotated the genome of Kluyveromyces marxianus Y-1190 to establish it as a platform for lactose valorization. The strain was chosen for rapid growth on lactose-rich dairy permeate, high transformation efficiency, and ease of culturing in bioreactors. Genomic sequencing revealed that K. marxianus Y-1190 possesses single nucleotide polymorphisms associated with efficient lactose metabolism. The strain is diploid with notable genomic heterogeneity, which appears to be critical for its robust growth and acid tolerance. To further exploit this platform strain, we developed protocols for gene and chromosome manipulation using CRISPR editing, constructed and validated a series of promoters compatible with MoClo vectors, and designed synthetically inducible promoters for K. marxianus. These tools enable precise control over gene expression, allowing for the tailored optimization of metabolic pathways and production processes. The synthetic promoters provide flexibility for dynamic expression tuning, while the CRISPR-based editing protocols facilitate targeted genetic modifications with high efficiency. Together, these advancements significantly enhance the genetic toolbox for K. marxianus, positioning it as a versatile platform for industrial biotechnology. These tools open new opportunities for the sustainable production of bio-based chemicals, fuels, and high-value products, leveraging lactose-rich feedstocks to contribute to a circular economy.

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Thornbury, M., Knoops, A., Summerby-Murray, I., Dhaliwal, J., Johnson, S., Utomo, J., Joshi, J., Narcross, L., Remondetto, G., Pouliot, M., Whiteway, M., Martin, V. J. J.. 2025-02-03. Sequencing of a dairy isolate unlocks Kluyveromyces marxianus as a host for lactose valorization. https://doi.org/10.1101/2025.02.03.636257

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