Comparative transcriptomics analysis of fatty acid-secreting Yarrowia lipolytica reveals importance of cell wall proteins

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. In this research, we compared the transcriptome of this mutant showing FFA secretion to a wildtype-like strain not showing this phenotype. Both toxicity and growth assays, as well as deletion and overexpression mutants of candidate genes were used to assess the effects of candidate genes on the export of FFAs. Although no clear transporter of fatty acids was identified, the analysis of the transcriptomic data revealed an overrepresentation of cell wall-related proteins. Based on this results, a literature search allowed to retrieve proteins related to the cell wall previously associated to lipid. Experiments performed on these candidates proved their involvement in resistance to FFAs toxicity, with one of them being a potential acyl-CoA export protein. Overall design: Quintuplates were analysed, comparing a wild-type strain with a mutant (faa1 knockout) able to secrete fatty acids when growing in high C/N ratio