How do engineered Yarrowia lipolytica strains secrete free fatty acids: hints from comparative transcriptomics

Comparative transcriptomics between an engineered fatty acid secreting Yarrowia lipolytica yeast and the wild-type helps to identify proteins linked to the cell wall and involved in fatty acid export. Yarrowia lipolytica has been considered one of the most promising platforms for the microbial production of fatty acids and derived products. The deletion of the faa1 gene coding for an acyl-CoA synthetase leads to the accumulation and secretion of free fatty acids (FFAs) into the extracellular space. The secretion of products is beneficial for the development of microbial cell factories to avoid intracellular inhibitory effects and reduce downstream processing costs. However, the mechanism behind the secretion of fatty acids is not well known. As a starting point, we compared the transcriptome of this mutant showing FFA secretion to a wildtype-like strain not showing this phenotype. The 12 most upregulated genes were evaluated for involvement in FFA secretion by the creation of deletion and overexpression mutants, among them MCH2, YMOH, three cell wall proteins CWP3, CWP4, and CWP11, M12B, and three proteins with unknown functions YUP1, YUP2, and YUP3. None of these proteins take a clear or isolated role in FFA export. As the transcriptomic data revealed an overrepresentation of cell wall-related proteins, some of them were further examined on a theoretical and experimental way. Surprisingly, overexpression of Ygpi led to the production of FFAs in the wildtype-like genetic background. Finally, some of the evaluated genes showed involvement in resistance to FFA toxicity.

Automated summary

Comparative transcriptomics was conducted to identify proteins involved in fatty acid export through the cell wall in an engineered fatty acid secreting Yarrowia lipolytica yeast. The study revealed that the deletion of the faa1 gene led to the accumulation and secretion of free fatty acids (FFAs). By comparing the transcriptome of the mutant with a wildtype-like strain, several upregulated genes were identified, including cell wall proteins and proteins with unknown functions. However, none of these proteins had a clear role in FFA export.