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Effect of Biotin Starvation on Gene Expression in Komagataella phaffii Cells

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Abstract

Methylotrophic yeast Komagataella phaffii is widely used in biotechnology for recombinant protein production. Due to the practical significance of these yeasts, it is extremely important to properly select cultivation conditions and optimize the media composition. In this study the effect of biotin starvation on gene expression in K. phaffii at transcriptome level was investigated. It was demonstrated, that the response of K. phaffii cell to biotin deficiency strongly depends on the carbon source in the medium. In the media containing glycerol, biotin deficiency led to activation of the genes involved in biotin metabolism, glyoxylate cycle, and synthesis of acetyl-CoA in cytoplasm, as well as repression of the genes, involved in lipo- and gluconeogenesis. In the methanol-containing media, biotin deficiency primarily led to repression of the genes, involved in protein synthesis, and activation of cell response to oxidative stress.

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Abbreviations

AltOx:

alternative oxidase

GAP:

glyceraldehyde 3-phosphate

OxAc:

oxaloacetate

PEP:

phosphoenolpyruvate

PEPCK:

phosphoenolpyruvate carboxykinase

ROS:

reactive oxygen species

TCA:

tricarboxylic acid cycle

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Funding

This work was supported by the Ministry of Science and Higher Education of the Russian Federation in accordance with agreement no. 075-15-2022-322, April 22, 2022 on providing a grant in the form of subsidies from the Federal budget of the Russian Federation. The grant was provided for State support for creation and development of a world-class Scientific Center “Agrotechnologies for the Future”.

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Authors and Affiliations

  1. Department of Genetics and Biotechnology, Saint Petersburg State University, 199034, Saint Petersburg, Russia

    Anastasiya S. Makeeva, Anton V. Sidorin, Valeria V. Ishtuganova, Marina V. Padkina & Andrey M. Rumyantsev

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  1. Anastasiya S. Makeeva
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  2. Anton V. Sidorin
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  3. Valeria V. Ishtuganova
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  4. Marina V. Padkina
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  5. Andrey M. Rumyantsev
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Contributions

A.M.R., M.V.P. – conceived and supervised the study; A.S.M., V.V.I. – carried out experiments; A.V.S. – performed a bioinformatic analysis; A.S.M., A.M.R. – discussed the results of experiments with input from all authors; A.S.M., A.M.R. – wrote the manuscript; A.M.R. and M.V.P. – edited the manuscript.

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Correspondence to Andrey M. Rumyantsev.

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The authors declare no conflicts of interest in financial or any other sphere. This article does not contain any studies involving human participants or animals performed by any of the authors.

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Makeeva, .S., Sidorin, A.V., Ishtuganova, V.V. et al. Effect of Biotin Starvation on Gene Expression in Komagataella phaffii Cells. Biochemistry Moscow 88, 1368–1377 (2023). https://doi.org/10.1134/S000629792309016X

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