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Effect of biotin starvation on gene expression in industrially significant yeast Komagataella phaffii
- Authors: Makeeva A.S.1, Sidorin A.V.1, Ishtuganova V.V.1, Padkina M.V.1, Rumyantsev A.M.1
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Affiliations:
- Saint Petersburg State University
- Issue: Vol 21 (2023): Спецвыпуск
- Pages: 14-15
- Section: Genetically modified organism. The Нistory, Achivements, Social and Environmental Riscs
- URL: https://journals.eco-vector.com/ecolgenet/article/view/568379
- DOI: https://doi.org/10.17816/ecogen568379
- ID: 568379
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Abstract
Komagataella phaffii (Pichia pastoris) is known to be an excellent producer of recombinant proteins for industrial and research purposes. Protein synthesis improvement in this yeast includes selection of optimal cultivation parameters [1, 2]. Therefore, much attention is paid to the influence of media components on physiology of this yeast [3–5].
One of the essential media components is biotin. In yeast cells it plays a crucial role as a cofactor of enzymes, providing carboxylation reactions in lipo-, gluconeogenesis, and nitrogen metabolism. K. phaffii is biotin auxotrophic organism unable to synthesize this vitamin de novo. Thus, it necessarily requires adding of biotin in the media.
In this study, we analyzed the effect of biotin starvation on gene expression in K. phaffii cells during its growth on methanol- and glycerin-containing media. These carbon sources are the most commonly used in standard protocols for recombinant protein biosynthesis in K. phaffii.
It was shown, that biotin starvation cell response significantly depends on carbon source. In glycerol-containing media biotin deficiency enhanced transcription of genes involved in biotin and thiamine metabolism, glyoxylate cycle, synthesis of acetyl-CoA in cytoplasm and its carnitine-mediated transport into mitochondria. Genes involved in biosynthesis of lipids and glucose were repressed in media with glycerol. In methanol-containing media the biotin deficiency effect was more pronounced and led to repression of numerous genes involved in protein and amino acids synthesis and activation of cell response to oxidative stress.
The obtained results are thought to be important for optimizing the culture conditions in the K. phaffii expression systems.
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Komagataella phaffii (Pichia pastoris) is known to be an excellent producer of recombinant proteins for industrial and research purposes. Protein synthesis improvement in this yeast includes selection of optimal cultivation parameters [1, 2]. Therefore, much attention is paid to the influence of media components on physiology of this yeast [3–5].
One of the essential media components is biotin. In yeast cells it plays a crucial role as a cofactor of enzymes, providing carboxylation reactions in lipo-, gluconeogenesis, and nitrogen metabolism. K. phaffii is biotin auxotrophic organism unable to synthesize this vitamin de novo. Thus, it necessarily requires adding of biotin in the media.
In this study, we analyzed the effect of biotin starvation on gene expression in K. phaffii cells during its growth on methanol- and glycerin-containing media. These carbon sources are the most commonly used in standard protocols for recombinant protein biosynthesis in K. phaffii.
It was shown, that biotin starvation cell response significantly depends on carbon source. In glycerol-containing media biotin deficiency enhanced transcription of genes involved in biotin and thiamine metabolism, glyoxylate cycle, synthesis of acetyl-CoA in cytoplasm and its carnitine-mediated transport into mitochondria. Genes involved in biosynthesis of lipids and glucose were repressed in media with glycerol. In methanol-containing media the biotin deficiency effect was more pronounced and led to repression of numerous genes involved in protein and amino acids synthesis and activation of cell response to oxidative stress.
The obtained results are thought to be important for optimizing the culture conditions in the K. phaffii expression systems.
About the authors
Anastasia S. Makeeva
Saint Petersburg State University
Email: anastasimakeeva@mail.ru
ORCID iD: 0000-0002-7181-0495
research engineer, department of genetics and biotechnology
Russian Federation, Saint PetersburgAnton V. Sidorin
Saint Petersburg State University
Email: spacerocketpilot@gmail.com
master of science, phd student, department of genetics and biotechnology
Russian Federation, Saint PetersburgValeriia V. Ishtuganova
Saint Petersburg State University
Email: st086860@student.spbu.ru
student, department of genetics and biotechnology
Russian Federation, Saint PetersburgMarina V. Padkina
Saint Petersburg State University
Email: mpadkina@mail.ru
ORCID iD: 0000-0002-4051-4837
dr. sci (biol.), professor of the department of genetics and biotechnology
Russian Federation, Saint PetersburgAndrei M. Rumyantsev
Saint Petersburg State University
Author for correspondence.
Email: rumyantsev-am@mail.ru
ORCID iD: 0000-0002-1744-3890
cand. sci. (biol.), senior researcher of the department of genetics and biotechnology
Russian Federation, Saint PetersburgReferences
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- Ergün BG, Berrios J, Binay B, Fickers P. Recombinant protein production in Pichia pastoris: from transcriptionally redesigned strains to bioprocess optimization and metabolic modelling. FEMS Yeast Res. 2021;21(7):foab057. doi: 10.1093/femsyr/foab057
- Ianshina T, Sidorin A, Petrova K, et al. Effect of methionine on gene expression in Komagataella phaffii cells. Microorganisms. 2023;11(4):877. doi: 10.3390/microorganisms11040877
- Rumiantsev AM, Padkina MV, Sambuk EV. Effect of nitrogen source on gene expression of first steps of methanol utilization pathway in Pichia pastoris. Genetika. 2013;49(4):454–460. (In Russ.) doi: 10.7868/S0016675813040115
- Rumjantsev AM, Bondareva OV, Padkina MV, and Sambuk EV. Effect of nitrogen source and inorganic phosphate concentration on methanol utilization and PEX genes expression in Pichia pastoris. Scientific World Journal. 2014;2014:743615. doi: 10.1155/2014/743615
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