Effect of biotin starvation on gene expression in industrially significant yeast Komagataella phaffii

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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