A workflow to explore elongase diversity and extend the repertoire of fatty acids produced by Yarrowia lipolytica

Fatty acids display highly diverse structures that confer these molecules unique chemical properties and distinct physiological functions. Identifying the substrate specificity of enzymes active on fatty acids is crucial, both for understanding their function in natural organisms and for developing efficient cell factories to produce original fatty acids. However, these enzymes are often membrane-bound and/or act on esterified substrates and studying them in vitro is thus challenging. This is why in vivo characterization of these enzymes’ specificity is an interesting approach. Herein, we harness the industrially relevant oleaginous Yarrowia lipolytica as a chassis for characterizing heterologous enzymes active on fatty acids, which can be used to diversify its fatty acid composition. As a case study, we investigated fatty acid elongases (ELO) responsible for the synthesis of very long-chain fatty acids (> 20 carbons), which are specific of given chain lengths and/or unsaturation patterns. Despite their interest, investigation and utilization of these membrane enzymes remain largely underexplored. We developed a workflow for characterizing heterologous elongases in Y. lipolytica, addressing several limitations to increase throughput. First, we set up a strain engineering strategy to easily integrate the ELO cassettes into targeted loci using CRISPR-Cas9, where screening of homologous recombination events is facilitated by fluorescence. We demonstrated that the native elongase YlELO2, responsible for the elongation of saturated and monounsaturated fatty acids up to 26 carbons, has to be inactivated to avoid functional redundancy and finely characterize heterologous elongase specificity. As it is an essential gene, we designed an optimized strategy for YlELO2 Knock-Out by a Knock-In of the elongase cassette. We then miniaturized cultures and fatty acid extraction in 96-well plates format. Using this workflow, we characterized seven human elongases on endogenous fatty acids and on five exogenous polyunsaturated fatty acids in a single series of experiments. We have developed tools and methods to characterize elongase specificity, from strain design to fatty acid production and analysis. Applicable to any fatty acid–modifying enzymes, these methodological developments will be useful to expand the repertoire of enzymes usable in Y. lipolytica and pave the way to produce new original fatty acids in this chassis.