Engineering yeast for tailored fatty acid profiles

Applied Microbiology and Biotechnology (2025) 109:101 https://doi.org/10.1007/s00253-025-13487-1 MINI-REVIEW Engineering yeast for tailored fatty acid profiles Simon Kobalter1 · Tamara Wriessnegger1 · Harald Pichler1,2 Received: 24 January 2025 / Revised: 7 April 2025 / Accepted: 8 April 2025 © The Author(s) 2025 Abstract The demand for sustainable and eco-friendly alternatives to fossil and plant oil-derived chemicals has spurred interest in microbial production of lipids, particularly triacylglycerols, fatty acids, and their derivatives. Yeasts are promising platforms for synthesizing these compounds due to their high lipid accumulation capabilities, robust growth, and generally recognized as safe (GRAS) status. There is vast interest in fatty acid and triacylglycerol products with tailored fatty acid chain lengths and compositions, such as polyunsaturated fatty acids and substitutes for cocoa butter and palm oil. However, microbes naturally produce a limited set of mostly long-chain fatty acids, necessitating the development of microbial cell factories with customized fatty acid profiles. This review explores the capabilities of key enzymes involved in fatty acid and triacylglycerol synthesis, including fatty acid synthases, desaturases, elongases, and acyltransferases. It discusses factors influencing fatty acid composition and presents engineering strategies to enhance fatty acid synthesis. Specifically, we highlight successful engineering approaches to modify fatty acid profiles in triacylglycerols and produce tailored fatty acids, and we offer recommendations for host selection to streamline engineering efforts. Key points • Detailed overview on all basic aspects of fatty acid metabolism in yeast • Comprehensive description of fatty acid profile tailoring in yeast • Extensive summary of applying tailored fatty acid profiles in production processes Keywords Yeast · Lipid · Fatty acid · Metabolic engineering · Cell factory · Renewable resources Abbreviations FA Fatty acid FFA Free fatty acid TAG Triacylglycerol MCFA Medium-chain fatty acid LCFA Long-chain fatty acid VLCFA Very long-chain fatty acid VPUFA Very long-chain polyunsaturated fatty acid DHA Docosahexaenoic acid EPA Eicosapentaenoic acid ARA Arachidonic acid PA Phosphatidic acid PL Phospholipid * Harald Pichler 1 Austrian Centre of Industrial Biotechnology (acib) GmbH, Petersgasse 14, 8010 Graz, Austria 2 Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Petersgasse 14, 8010 Graz, Austria SE Sterol ester DAG Diacylglycerol FAEE Fatty acid ethyl ester FAME Fatty acid methyl ester Introduction The continued reliance on fossil oils has raised significant environmental and sustainability concerns, yet the demand for oleochemicals continues to grow. Triacylglycerols (TAGs), fatty acids (FAs), and their derivatives can serve as sustainable substitutes for fossil oils, enabling the production of oleochemical-derived products such as fuels, surfactants, lubricants, cosmetics, and pharmaceuticals. Moreover, TAGs are extensively used in the food industry, and high-value FAs find applications as nutritional supplements. Currently, the production of TAGs and FAs primarily relies on extraction from oil-rich plants, with a smaller contribution from animal fat and fish oil. However, the use of plants for oleochemical production processes presents various drawbacks, e.g., Vol.:(0123456789) 101 Page 2 of 31 competing for farmland with food crops, fluctuating yields due to environmental variations, limiting productivity due to extended lifecycles, and deforestation for new farmland (Meijaard et al. 2020). Notably, extracting oils from fish and animal fats raises sustainability concerns, as extensive animal and fish farming contributes to pollution and increased greenhouse gas emissions. Microbial production processes, on the other hand, offer a greener, more sustainable, and efficient alternative for synthesizing oleochemical products as reviewed (Liu et al. 2021). Conventional and oleaginous yeast species represent versatile platforms for producing a wide range of bio-based products, including recombinant proteins, peptides, terpenoids, TAGs, FAs, and FA derivatives (Arhar et al. 2021; Cao et al. 2018; Wriessnegger et al. 2014; Xue et al. 2013; Zhou et al. 2016; Zhu et al. 2018). These microorganisms naturally exhibit high lipid accumulation capabilities and robust growth to high cell densities and, in most cases, are classified as generally recognized as safe (GRAS) and qualified presumption of safety (QPS) by regulatory agencies, enhancing their industrial appeal. Furthermore, the genomes of many yeast species have been sequenced, lipid synthesis metabolic pathways are well understood, and efficient genome editing tools, including CRISPR/Cas9, along with efficient transformation protocols and strategies for fine-tuned expression of complex metabolic pathways, have been established (Abeln and Chuck 2021; Schindler 2020). Particularly, Saccharomyces cerevisiae and Yarrowia lipolytica are well-studied regarding lipid storage and have been extensively engineered to increase TAG and FA titers, yields, and productivity (Arhar et al. 2021; Qiao et al. 2017). Consequently, these yeasts serve as hosts and model organisms for studying lipid metabolism. There is a growing interest in FAs with specific chain lengths and in TAGs with customized FA compositions. FAs with industrial importance include short-chain fatty acids (SCFAs), medium-chain fatty acids (MCFAs), longchain fatty acids (LCFAs), and very long-chain fatty acids (VLCFAs) with varying degrees of saturation. S/MCFAs (C6–C12) and their derivatives are used as herbicides, antimicrobials, lubricants, plastic monomers, and jet fuel replacements (Sarria et al. 2017). LCFAs (C14–C20) and derivatives find applications in biodiesel, cosmetics, nutritional supplements, and coating materials (Runguphan and Keasling 2014). VLCFAs (C20–C26), especially polyunsaturated types like docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), offer various health benefits and have been shown to prevent cancer, diabetes, and cardiovascular diseases (Deckelbaum and Torrejon 2012). Additionally, these FAs function as crucial precursors to signaling compounds in the human body (Funk 2001). The need for customized fats stems from the increasing interest in developing substitutes for cocoa butter and palm oil (Bergenholm et al. Applied Microbiology and Biotechnology (2025) 109:101 2018; Karamerou et al. 2021). The major fatty acid species found in yeasts typically have lengths of 16 or 18 carbon atoms with up to three double bonds and smaller fractions of C12, C14, and C20–C26 species (Kaneko et al. 1976). Given the restricted set of FA species produced by wildtype yeasts and the ongoing demand in FAs and TAGs with tailored chain lengths and compositions, there is a significant interest in engineering yeasts for o (...truncated)