Ogataea polymorpha is a thermotolerant, methylotrophic yeast with significant industrial applications. While previously mainly used for protein synthesis, it also holds promise for producing platform chemicals. O. polymorpha holds the distinct advantage of using methanol as a substrate, which could be potentially derived from carbon capture and utilization streams. Full development of the organism into a production strain and estimation of the metabolic capabilities require additional strain design, guided by metabolic modeling with a genome-scale metabolic model. However, to date, no genome-scale metabolic model is available for O. polymorpha.
To overcome this limitation, we used a published reconstruction of the closely related yeast Komagataella phaffii as a reference and corrected reactions based on KEGG and MGOB annotation. Additionally, we conducted phenotype microarray experiments to test the suitability of 190 substrates as carbon sources. Over three-quarter of the substrate use was correctly reproduced by the model and 27 new substrates were added, that were not present in the K. phaffii reference model.
The developed genome-scale metabolic model of O. polymorpha will support the engineering of synthetic metabolic capabilities and enable the optimization of production processes, thereby supporting a sustainable future methanol economy.
Liebal, UW., Fabry, BA., Ravikrishnan A., Schedel, CVL., Schmitz, S., Blank, LM., Ebert, BE. (2020). Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha. under revision
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Ogataea polymorpha has the potential to produce useful chemicals from methanol, a C1 carbon molecule that can be sourced sustainably from CO2 and green hydrogen. Our focus was on generating acetone, malate, and isoprene as examples of industrially relevant products with different carbon atom counts. We successfully modified O. polymorpha to produce these compounds using methanol as a carbon source. Notably, we found that O. polymorpha is well-suited for malate production, and introducing an efficient malate transporter is crucial for this process. Through optimizing cultivation conditions, we achieved high yields of malate (13 g/L) and demonstrated the production of acetone and isoprene as well. These results suggest O. polymorpha could be a versatile tool for producing various biochemicals from methanol, contributing to our understanding of using methylotrophic yeasts for sustainable chemical production. This study can guide future efforts in metabolic engineering and process optimization for producing platform chemicals from renewable C1 carbon sources.
The simulations for this work have bee done with the Jupyter Notebook code/Model-Analysis.ipynb and the GSMM used is the latest development of the O. polymorpha model model/iOpol23.xml.
Wefelmeier, K., Schmitz, S., Kösters, BJ., Liebal, UW., Blank, LM. Methanol bioconversion into C3, C4, and C5 platform chemicals by the yeast Ogataea polymorpha. submitted and under revision
Biotechnology; Genome-Scale metabolic model; Metabolic reconstruction; Metabolic engineering; COBRA; Methylotrophy
Utilisation: experimental data reconstruction; in silico strain design; model template Field: metabolic reactions only Type of model: comparative; curated Model source: iMT1026v3 Omic source: genomics Taxonomy: Eurkaryota, Fungi, Dikarya, Ascomycota, Saccharomycotina, Saccharomycetes, Saccharomycetales, Pichiaceae, Ogataea, Ogataea polymorpha
Metabolic system: general metabolism, methylotrophy Tissue: NA
Bioreactor: Batch, Chemostat Cell type: NA
Cell line: NA
Strain: NCYC495 Condition: aerobic; glucose-limited; methanol-limited, defined media
Clone the repository and examine the Jupyter Notebooks in the code folder to run simulations.