Transcriptome Analysis Unveils the Effects of Proline on Gene Expression in the Yeast Komagataella phaffii

Komagataella phaffii yeast is one of the most important biocompounds producing microorganisms in modern biotechnology. Optimization of media recipes and cultivation strategies is key to successful synthesis of recombinant proteins. The complex effects of proline on gene expression in the yeast K. phaffii was analyzed on the transcriptome level in this work. Our analysis revealed drastic changes in gene expression when K. phaffii was grown in proline-containing media in comparison to ammonium sulphate-containing media. Around 18.9% of all protein-encoding genes were differentially expressed in the experimental conditions. Proline is catabolized by K. phaffii even in the presence of other nitrogen, carbon and energy sources. This results in the repression of genes involved in the utilization of other element sources, namely methanol. We also found that the repression of AOX1 gene promoter with proline can be partially reversed by the deletion of the KpPUT4.2 gene.

Automated summary

This study analyzed the complex effects of proline on gene expression in Komagataella phaffii yeast, revealing differential expression of around 18.9% of protein-encoding genes in proline-containing media. The presence of proline does not inhibit the catabolism of proline by K. phaffii, and it represses genes involved in the utilization of other element sources. The repression of the AOX1 gene promoter with proline can be partially reversed by the deletion of the KpPUT4.2 gene.