Harnessing natural diversity of Saccharomyces cerevisiae for enhanced resistance to weak acids

Abstract

Abstract The production of second-generation bioethanol from lignocellulosic biomass is a promising solution for sustainable energy, yet it faces significant challenges also due to the inhibitory effects of weak acids released during biomass pretreatment, particularly acetic, formic and levulinic acids. This review describes the ability of Saccharomyces cerevisiae, with a focus on natural isolates, in overcoming these challenging compounds. Indeed, natural isolates exhibit greater genetic and phenotypic diversity than laboratory and industrial strains, offering unique traits such as enhanced stress tolerance, metabolic efficiency, and adaptive responses to weak acids. This investigation explores the transcriptional and genomic mechanisms underlying yeast adaptive responses, emphasizing key regulatory networks and resistance pathways, including drug H+ antiporters, Reactive Oxygen Species (ROS) mitigation strategies, and membrane composition adjustments. Strategies for strains improvement, involving adaptive laboratory evolution (ALE), genome shuffling, and hybridization, are also discussed as complementary approaches to develop robust yeast capable of thriving under stressful industrial fermentation conditions. The integration of these techniques, along with genomic and transcriptomic insights, provides a comprehensive framework for engineering high-performance yeast strains. Ultimately, this review underscores the potential of leveraging natural diversity and innovative biotechnological strategies to advance the scalability and efficiency of lignocellulosic bioethanol production through S. cerevisiae fermentation. Graphical abstractMulti-panel diagram illustrating Saccharomyces cerevisiae isolates, genomic exploration, and metabolic engineering techniques.The figure features three connected panels detailing research on Saccharomyces cerevisiae. The first panel illustrates yeast cell icons with phenotypic traits: "High fermentative," "Weak acid resistant," "High secretory pathway," "Thermotolerant," and "Osmotic tolerant," with a glucose structure below. The second showcases a circular diagram of a "Mosaic genome," "Copy Number Variations," and single nucleotide polymorphisms (SNPs), with a heatmap for transcriptomics. The third illustrates metabolic engineering techniques, including CRISPR/Cas9, genome editing, Delta-integration, and transformation within yeast cells. STATEMENT OF SIGNIFICANCE Weak acids represent major inhibitory compounds in lignocellulosic fermentations, affecting the industrial viability of second-generation bioethanol. While most research has focused on laboratory or engineered strains, natural isolates of Saccharomyces cerevisiae can be still considered a resource of unexplored tolerance traits. This review highlights how omics-based insights into natural strains’ adaptive responses provide novel opportunities for metabolic engineering, particularly in weak acid resistance. By integrating genetic variability, ploidy diversity, and systems biology perspectives, a yeast strain capable of overcoming industrial-relevant stresses such as weak acids can be designed, advancing sustainable bioethanol production and expanding the scope of microbial biotechnology.