Abstract Despite their distinct biological functions, structural maintenance of chromosomes (SMC) complexes, including cohesin, condensin, and SMC5/6, preferentially accumulate at transcriptionally active loci, with recent studies revealing that SMC5/6 also shares the loop extrusion mechanism previously considered a hallmark of cohesin and condensin. Using yeast as a model system, this review discusses how RNA polymerases I, II, and III, together with their associated transcriptional machinery, contribute to the recruitment of SMC complexes to specific genomic sites. We examined the reciprocal interplay between transcription and SMC complexes, highlighting how transcription activity and SMC-driven chromatin organization influence each other. We further explore how SMC complexes recognize and respond to transcription-induced topological changes, such as positive supercoiling and R-loops. We propose that SMC complexes and transcription machineries form a dynamic regulatory network that coordinates the three-dimensional genome architecture with gene expression. Defining how each SMC complex is distinctly coordinated with RNA polymerase machineries and their associated factors, and how these complexes sense and resolve transcription-associated DNA topologies, represents an important frontier for future research.
Abstract Lager beer, made by fermentation of barley malt using the hybrid yeast Saccharomyces pastorianus, is extremely popular worldwide. The low genetic variation of S. pastorianus strains limits the scope of development for novel lager beer types. The wild ancestor Saccharomyces eubayanus has potential for lager brewing, but its application is constrained by formation of phenolic off-flavours (POF+ phenotype) and limited uptake of the wort α-oligoglucosides maltose and maltotriose. Here, we addressed both limitations, using screening and evolutionary engineering of the Himalayan S. eubayanus strain ABFM5L.1, one of the closest known relatives of S. eubayanus sub-genome of modern hybrid lager yeasts. Prior to improving α-oligoglucoside utilisation, 4-vinyl guaiacol formation was abolished by mutagenesis and screening for POF⁻ mutants. Subsequently, evolution for improved sugar utilisation and reverse engineering identified SeMALR1 (the S. eubayanus ortholog of S. cerevisiae MAL63) as a key regulatory control point. Single-nucleotide substitutions in this maltose regulon activator gene enabled rapid maltose uptake and partial maltotriose utilisation in a previously maltose-negative background. The evolved non-genetically modified POF⁻ strains showed near-complete maltose consumption (>90–95%) and partial maltotriose consumption (approximately 25–32%) in industrial wort. These results reveal substantial regulatory flexibility in Holarctic S. eubayanus and support its further development as a novel lager brewing yeast.
Abstract There is increasing demand for sustainable alternatives to chemical fungicides and preservatives due to the negative impact that they have on the environment, human and animal health. This has led to intensified interest in microbial biocontrol and bioprotection strategies. Oxidative and weakly fermentative yeasts represent an underexplored group of microorganisms with considerable potential for managing undesirable microorganisms. These yeasts produce limited amounts of ethanol and carbon dioxide while exhibiting diverse mechanisms of antagonism against spoilage and pathogenic microorganisms. Their biocontrol and bioprotection activity is mediated through nutrient and space competition, antimicrobial metabolites and hydrolytic enzymes production, biofilm formation, induction of host resistance, and modulation of microbial communities. These characteristics make such yeasts particularly attractive for applications in fresh produce, fermented beverages, and agricultural systems where minimal alteration of the final product is desirable. Furthermore, their reduced fermentative activity lowers the risk of undesirable sensory changes while maintaining effective suppression of fruit and beverage spoilage microorganisms. Despite these advantages, their commercial application remains limited. This review examines current knowledge of oxidative and weakly fermentative yeasts as biological control agents, highlights their applications in fruits and beverages, factors affecting their efficacy, and challenges for their integration into sustainable biocontrol and bioprotection strategies.
Abstract Episomal plasmids are widely used in yeast metabolic engineering for their flexibility and high transformation efficiency. However, their application in Yarrowia lipolytica is often limited by low copy number and insufficient genetic stability. In this study, a robust episomal plasmid that balanced genetic stability and protein expression capacity was developed in Y. lipolytica. The autonomously replicating sequence (ARS) elements were selected, and ARS1 was identified as a favorable element that balanced genetic stability and gene expression capacity. To improve plasmid copy number, different ubiquitin degrons were used to tune selection marker abundance, and Ubi-R-Δk-mediated marker resulted in an approximately fourfold increase in plasmid copy number (from ∼1 to ∼5 copies per cell). The copy number of the engineered plasmid was one of the highest–copy episomal systems in Y. lipolytica. To further evaluate the engineered plasmid, we applied it to β–carotene biosynthesis. The results showed that the β–carotene titer was 3.43–fold higher than that of the non–optimized plasmid. Collectively, this work expands the episomal plasmid toolbox for Y. lipolytica and establishes a generalizable framework for robust protein expression plasmid engineering in non-conventional yeasts.
Abstract High- and very-high-gravity (HG/VHG) fermentation increases substrate loading and product titers, thereby improving fermenter utilisation and potentially reducing water use and downstream processing requirements. Initially developed for brewing and fuel ethanol production, these approaches are now applied more broadly in food, beverage, and bioproduct manufacturing. This MiniReview summarises operational definitions and industrial drivers of HG/VHG fermentation and examines the associated constraints in rheology, mass and heat transfer, osmotic and ethanol stress, nutrient availability, and oxidative damage. Yeast improvement strategies are reviewed, including adaptive laboratory evolution, mutagenesis, genome shuffling, multiplex genome editing, non-conventional yeasts, and multi-omics-guided selection. Process developments such as no-cook simultaneous liquefaction, saccharification and fermentation (SLSF), enzyme formulation, nutrient management, and in situ product recovery are considered together with applications in alcoholic beverages, organic acids, microbial lipids, and other value-added products. The review also discusses coproduct valorisation and the need to integrate strain development with process design. Current evidence supports HG/VHG fermentation as a useful process-intensification platform, although performance and sustainability depend strongly on feedstock, operating conditions, product requirements, and the basis used to report fermentation outcomes.
