Engineering Saccharomyces cerevisiae for ethanol production from glycerol, xylose, acetic acid, and glucose

Global bioethanol production exceeds 110 billion liters annually, yet its expansion remains constrained by the limited range of carbon sources fermentable by Saccharomyces cerevisiae. Glycerol—a major byproduct of biodiesel production—has recently gained attention as both a biomass pretreatment solvent and a fermentable substrate in emerging integrated biorefineries. However, native S. cerevisiae cannot efficiently ferment glycerol, xylose, or acetic acid, and no single engineered strain has previously demonstrated co-fermentation of all these substrates with glucose. In this study, we expanded the metabolic capacity of the previously engineered strain SK-FGG4 (capable of fermenting glycerol and glucose) to enable co-utilization of xylose and acetic acid, generating strain SK2-5. Using CRISPR-based genome editing, we replaced the native ALD6 with a Pichia stipitis xylose assimilation pathway (PsXR, PsXDH), co-expressed with xylulose kinase. Mitochondrial NDE1 and NDE2 were replaced with Salmonella enterica acetylating acetaldehyde dehydrogenase (SeEutE). Overexpression of JEN1 and a mutated ACS1 (L707P) further enhanced acetic acid assimilation, while an additional PsXDH copy improved xylose fermentation efficiency. Under microaerobic conditions, strain SK2-5 achieved over 95% theoretical ethanol conversion efficiency from a mixed substrate of glycerol, xylose, acetic acid, and glucose. To our knowledge, this is the first demonstration of a single S. cerevisiae strain capable of efficiently co-fermenting all four carbon sources. These results establish a flexible metabolic framework for future strain development in glycerol-integrated biorefineries and support coupling with acid-catalyzed glycerolysis and biodiesel–ethanol co-production.