FEMS yeast research最新文献

Our laboratory previously established variants of the Saccharomyces cerevisiae strain CEN.PK113-1A able to grow in synthetic glycerol medium. One approach focused on improving the endogenous l-glycerol-3-phosphate (G3P) pathway, while a second approach aimed to replace the endogenous pathway with the dihydroxyacetone (DHA) pathway. The latter approach led to a significantly higher maximum specific growth rate (µmax) of 0.26 h-1 compared to 0.14 h-1. The current study focused on combining all genetic modifications in one strain. Apart from the so-called "TWO pathway strain" (CEN TWOPW), two isogenic control strains, CEN G3PPW and CEN DHAPW, were constructed. The µmax of CEN TWOPW (∼0.24 h-1) was virtually identical to that of CEN DHAPW. Remarkable characteristics of the strain CEN TWOPW compared to CEN DHAPW include a higher specific glycerol consumption rate, the capacity to deplete glycerol completely, and a much higher ethanol and lower biomass formation during oxygen-limited shake flask cultivations. The results obtained with different alleles of the GUT1 gene, encoding for glycerol kinase, suggest that the phenotype of the strain CEN TWOPW is at least partly attributed to the particular point mutation in the GUT1 allele used from the strain JL1, which was previously generated through adaptive laboratory evolution.

Yeasts play a crucial role in the maturation of fermented foods, with Saccharomyces cerevisiae standing out as the most prominent among them. However, in recent years, there has been a growing interest in the roles and applications of non-Saccharomyces yeasts in fermented products. Their contribution to shape the characteristics of fermented foods like wine, beer, sourdough bread, cheese, and kombucha is undeniable, yet our understanding of the specific effects of each species remains incomplete in certain cases. In this mini-review, we collected and summarized studies that aimed to gain deeper understanding of the microbial dynamics and roles of non-Saccharomyces yeasts during the fermentation and development of alcoholic and non-alcoholic fermentations, as well as highlight that non-Saccharomyces yeasts are recently also recognized for benefiting the human microbiome as probiotics, further expanding their potential contributions to human health and supplementation.

This review highlights the potential of Yarrowia lipolytica and other yeasts as sustainable producers of bio-based succinic acid (SA), a key platform chemical with applications in bioplastics, solvents, and pharmaceuticals. Recent advances in metabolic engineering have substantially improved SA titers, yields, and productivities in yeasts. These improvements were achieved by reconstructing biosynthetic pathways, disrupting gene involved in side-metabolism and/or expressing heterologous genes involved in critical metabolic functions. The use of renewable feedstocks, including crude glycerol, agricultural residues, food waste hydrolysates, and industrial by-products, has shown promise in reducing both production costs and environmental impacts. Innovative downstream separation techniques, such as in situ extraction, membrane filtration, and crystallization, further contribute to process sustainability. Integrating yeast-based SA production into circular biorefineries and adopting continuous production systems are promising strategies for enhancing economic feasibility and minimizing ecological footprints. Although challenges related to scale-up and process integration persist, ongoing advancements in genetic engineering and bioprocessing technologies position yeast-based processes as a viable route for sustainable, large-scale bio-based SA production within a circular bioeconomy framework.

Awareness is rising that antifungal resistance poses a threat to agriculture, food safety, biodiversity, and human health. There is a limited number of antifungals available and resistance to all of them has been reported. The development of novel antifungals is complex, as eukaryotic organisms have very few selective drug targets that distinguish them from the infected plant, human, or animal host. Yeasts produce different compounds with antifungal activity, ranging from small molecules such as iron chelators, biosurfactants, and volatile organic compounds, to proteins like myocins and hydrolytic enzymes. Those could be further developed into new antifungals; however, there is a scarcity of fundamental knowledge on their chemical structure, their mode of action, their biosynthesis, and its regulation. Given the opportunities that yeasts display as industrial hosts and the synthetic biology tools available, a deeper understanding of these molecular aspects could enable a wider range of yet underexplored applications for the producer yeast and their molecules, from biocontrol to food preservation and human health. To facilitate this exploration, we here consolidate current molecular knowledge on these compounds, suggest readily available methodologies to screen for different molecule classes in natural yeast isolates and discuss how they could be further studied and engineered towards their eventual application.

Yeast biodiversity and machine learning (ML) are transforming the landscape of metabolic engineering. While Saccharomyces cerevisiae remains foundational to industrial biotechnology due to its genetic tractability and robust growth, it struggles to synthesize complex metabolites, utilize alternative feedstocks, and withstand industrial stresses. Non-conventional yeasts such as Yarrowia lipolytica and Ogataea polymorpha possess traits such as thermotolerance, acid resistance, and lipid accumulation, making them promising alternatives. However, broader adoption remains limited by insufficient genetic tools and low predictability of engineered components across species. Recent ML advances are addressing these gaps by enabling accurate prediction of genetic part function, optimizing gene expression, and discovering novel biosynthetic components in diverse yeasts. These tools support rational selection of genetic elements and pathway configurations tailored to non-model hosts, streamlining the design-build-test-learn cycle. Leveraging biodiversity expands the available yeast chassis and toolkits, improving strain robustness under industrial conditions. This mini-review discusses how yeast biodiversity is being harnessed to broaden engineering strategies and highlights recent ML advances driving data-guided strain and pathway design. Special attention is given to ML-guided identification and optimization of genetic elements. Together, evolutionary diversity and intelligent computation promise more modular, predictive, and scalable yeast platforms for next-generation metabolic engineering.

Single carbon (C1) molecules are considered as valuable substrates for biotechnology, as they serve as intermediates of carbon dioxide recycling, and enable bio-based production of a plethora of substances of our daily use without relying on agricultural plant production. Yeasts are valuable chassis organisms for biotech production, and they are able to use C1 substrates either natively or as synthetic engineered strains. This minireview highlights native yeast pathways for methanol and formate assimilation, their engineering, and the realization of heterologous C1 pathways including CO2, in different yeast species. Key features determining the choice among C1 substrates are discussed, including their chemical nature and specifics of their assimilation, their availability, purity, and concentration as raw materials, as well as features of the products to be made from them.

A complete iron deficiency in iron-sensitive oleaginous yeast showed insufficient biomass, resulting in a lower lipid amount, although lipid accumulation was greater compared to deficiency in other ions. In this study, the effect of functional iron deficiency on lipid production on Rhodotorula toruloides NBRC 0559 was examined. Two supplements, an iron-added (growth) supplement and an iron-free (lipid-producing) supplement were tested for detecting functional iron deficiency. The addition of iron-added supplement increased the biomass by 1.5-fold. Furthermore, the addition of iron-free supplement stimulated the growth of R. toruloides NBRC 0559 without loss of biomass (indeed, the biomass increased 1.2-fold) while also resulting in a deficiency of the iron needed for improved growth. Through iron-free supplement, the functional iron starvation effect resulted in improved lipid yield (1.7-fold) and an improved ratio of oleic acid (1.2-fold), which is considered an appropriate material for biodiesel, compared to the non-supplement-treated medium. Moreover, functional iron deficiency led to a 3.4-fold increase in the oleic acid rate compared to when all iron was completely removed from the medium. This study presents the effects and importance of iron in improving biomass and lipid production through the functional iron deficiency.

Pectinolytic enzymes secreted by yeasts have an untapped potential in industry, particularly in wine-making. This study addresses the limitations of the current screening methods in reliably predicting the capacity of pectinolytic yeast strains to secrete polygalacturonase (PGase) under industrial conditions, suggesting a novel screening approach. Using the context of wine-making as an example, a diverse collection of 512 yeast strains from 17 species was analysed for PGase secretion, a key enzyme in pectinolysis. The traditional halo assay on solid yeast-pepton-dextrose (YPD) medium revealed 118 strains from nine genera being PGase positive. Screening these strains by incubating them at 20°C on a solid synthetic grape juice medium containing polygalacturonic acid (PG) significantly reduced the number of promising strains to 35. They belong to five genera: Kluyveromyces sp., Cryptococcus, Pichia, Torulaspora, and Rhodotorula. Afterward, a newly developed pectin-iodine assay was used to precisely quantify the PGase activity of the best-performing strains in a liquid medium. Strains from Kluyveromyces and Cryptococcus sp. stood out regarding high pectinolytic activity. Our methodological advancements tailored to identify highly promising pectinolytic yeasts for industrial use open new avenues for wine-making and other industrial processes encompassing media rich in pectin and sugars.

The global transition to renewable energy sources requires efficient microbial platforms capable of fermenting carbon sources present in lignocellulosic biomass. Conventional yeasts like Saccharomyces cerevisiae face critical limitations, particularly in pentose sugar utilization and inhibitor resistance. This review focuses on two emerging nonconventional yeasts, Candida famata and Ogataea polymorpha, which exhibit native or engineered capacities to overcome these bottlenecks. We present a comparative analysis of their stress tolerance, metabolic versatility, and recent advances in genetic engineering, adaptive laboratory evolution, and heterologous expression systems. Their ability to grow on a wide range of sugars, tolerate fermentation inhibitors, and operate under industrial conditions underscores their potential as microbial platforms for sustainable bioprocessing. Key challenges and future directions are discussed to guide further development.

Ribosomes, once considered uniform protein biosynthesis machines, are now recognized as heterogeneous and dynamic entities with specialized functions. In Saccharomyces cerevisiae, ribosomal heterogeneity arises from variability in ribosomal protein (RP) composition, rRNA sequence polymorphisms, post-transcriptional modifications, and associations with ribosome-associated factors and noncoding RNAs. RP gene (RPG) paralogs and their differential expression influence growth, stress resistance, and drug responses. Introns and untranslated regions in RPGs regulate expression under stress, while ribosome composition adjusts to environmental cues via altered RP stoichiometry and post-translational modifications, such as phosphorylation and ubiquitination. Additionally, ribosome-associated factors contribute to selective translation of specific mRNA subsets. Ribosomal RNA heterogeneity, though less studied in yeast, is evident through polymorphisms in rDNA arrays and post-transcriptional modifications like pseudouridylation and 2'-O-ribose methylation. Furthermore, transient associations with small noncoding RNAs (e.g. tRNA-, snoRNA-, and mRNA-derived fragments) modulate translation in a stress-dependent manner, supporting the concept of specialized ribosomes. Despite growing evidence, functional significance of ribosome specialization remains under debate. Future research aims to uncover the extent, regulation, and biological roles of ribosome heterogeneity across organisms and conditions. Emerging tools such as ribosome sequencing, single-molecule fluorescence resonance energy transfer, and single-molecule fluorescence resonance energy transfer offer promising avenues to resolve these questions and reveal how specialized ribosomes contribute to adaptive gene expression.