FEMS yeast research最新文献

The transporters of the ATP-Binding Cassette (ABC) Superfamily involved in the Multidrug Resistance (MDR) phenomena are also known as ABC-Pleiotropic Drug Resistance (PDR) proteins. The homologs of the Saccharomyces cerevisiae SNQ2 and PDR18 genes were identified in 171 yeast genomes, representing 68 different hemiascomycetous species. All early-divergent yeast species analyzed in this work lack Snq2/Pdr18 homologs, suggesting that the origin of these ABC-PDR genes in hemiascomycete yeasts resulted from a horizontal transfer event. The evolutionary pathway of the Snq2/Pdr18 protein subfamily in pathogenic Candida species was also reconstructed, revealing a main gene lineage leading to the Candida albicans SNQ2 gene. The results indicate that, after the gene duplication event at the origin of the SNQ2/PDR18 paralogs, the PDR18 ortholog has been under strong diversifying selection and suggest that a small portion of the sequence of the SNQ2 ancestral ortholog might have been under mild positive selection. The results also showed that strong positive selection was exerted over one of the two paralogs generated by the Whole Genome Duplication (WGD) event, corresponding to the duplicate at the origin of a "short-lived" WGD sublineage.

Yeast biodiversity has been extensively investigated by wealthy countries of the Northern Hemisphere. In contrast, despite the widespread use of fermentation practices in the Southern Hemisphere, yeast diversity in this region remains largely underexplored. However, this trend is beginning to shift as several reports have started to document yeast populations both in the natural environment and in association with the fermentation of various substrates, including grape and apple juice, cocoa and coffee beans, grains, fruits, or tree sap. Numerous yeast species from the Southern Hemisphere have now been described and characterized, with whole-genome sequencing providing essential insights into the evolutionary history of wild yeast isolates from this region. This review highlights the emerging research on yeast biodiversity in the Southern Hemisphere and explores the application of diverse yeast species in the food and beverage industries.

Riboflavin (RF, vitamin B2) serves as a precursor for the flavin coenzymes FAD and FMN, which are involved in numerous redox reactions in cells. RF is produced on an industrial scale. The yeast Candida famata overproduces RF under iron-starvation conditions, and mutants have been isolated that accumulate large amounts of RF. Overexpression of Sef1, the transcription factor of the zinc cluster family, increases RF production in C. famata; however, the specific mechanism remains unknown. Here, we report that SEF1 expression is upregulated under iron deficiency. We developed a yeast one-hybrid system based on the yeast Saccharomyces cerevisiae to study the role of Sef1 in regulation of RF biosynthesis. We found that Sef1 activates the promoters of the RIB1, RIB3, RIB5, RIB6, and RIB7 genes. Additionally, SEF1 was shown to undergo autoregulation. For the RIB1 promoter, a Sef1-binding sequence has been identified. The ability of Sef1 to activate RIB genes expression was further validated in the native C. famata system.

Pulcherriminic acid is an iron chelator produced by some Kluyveromyces and Metschnikowia yeasts. Its biosynthesis is encoded by the four-gene PUL cluster, where PUL1 and PUL2 are the biosynthetic enzymes, PUL3 mediates the uptake of iron-bound pulcherrimin, and PUL4 is a putative regulator. Pulcherriminic acid holds antifungal potential, as the growth of organisms unable to uptake pulcherrimin is inhibited by deficit of essential iron. Thus, a heterologous production system to further characterize and optimize its biosynthesis would be valuable. Using our in-house yeast collection and genomes available in databases, we cloned PUL1 and PUL2 genes from Kluyveromyces lactis and one of our wild Metschnikowia isolates and built an effective production system in Saccharomyces cerevisiae able to inhibit pathogenic growth. In this context, the K. lactis genes yielded faster pulcherriminic acid production than those from the Metschnikowia isolate and a combinatorial approach showed PUL1 to be the production bottleneck. We further showed that Pul3 is an importer of pulcherrimin, but also mediates the export of pulcherriminic acid and that the growth of pathogens such as Candidozyma auris and organisms encoding PUL3 in their genome, previously called "cheaters," is inhibited by pulcherriminic acid, highlighting its potential as an antimicrobial agent.

Yeasts have emerged as well-suited microbial cell factory for the sustainable production of biofuels, organic acids, terpenoids, and specialty chemicals. This ability is bolstered by advances in genetic engineering tools, including CRISPR-Cas systems and modular cloning in both conventional (Saccharomyces cerevisiae) and non-conventional (Yarrowia lipolytica, Rhodotorula toruloides, Candida krusei) yeasts. Additionally, genome-scale metabolic models and machine learning approaches have accelerated efforts to create a broad range of compounds that help reduce dependency on fossil fuels, mitigate climate change, and offer sustainable alternatives to petrochemical-derived counterparts. In this review, we highlight the cutting-edge genetic tools driving yeast metabolic engineering and then explore the diverse applications of yeast-based platforms for producing value-added products. Collectively, this review underscores the pivotal role of yeast biotechnology in efforts to build a sustainable bioeconomy.

Plant-based milk contains high nutritional value with enriched vitamins, minerals, and essential amino acids. This study aimed to enhance the biochemical and biological properties of rice milk through yeast fermentation, using the novel fermenting strain Saccharomyces cerevisiae RSO4, which has superb fermenting ability for an innovative functional beverage. An integrated omics approach identified specific genes that exhibited genetic variants related to various cellular processes, including flavor and aroma production (ARO10, ADH1-5, and SFA1), whereas the proteomic profiles of RSO4 identified key enzymes whose expression was upregulated during fermentation of cooked rice, including the enzymes in glycogen branching (Glc3), glycolysis (Eno1, Pgk1, and Tdh1/2), stress response (Hsp26 and Hsp70), amino acid metabolism, and cell wall integrity. Biochemical and metabolomic analyses of the fermented rice milk by the RSO4 strain using the two rice varieties, Homali (Jasmine) white rice or Riceberry colored rice, detected differentially increased levels of bioactive compounds, such as β-glucan, vitamins, di- and tripeptides, as well as pleasant flavors and aromas. The results of this study highlight the importance of selecting an appropriate fermenting yeast strain and rice variety to improve property of plant-based products as innovative functional foods.

Optogenetics is an empowering technology that uses light-responsive proteins to control biological processes. Because of its genetic tractability, abundance of genetic tools, and robust culturing conditions, Saccharomyces cerevisiae has served for many years as an ideal platform in which to study, develop, and apply a wide range of optogenetic systems. In many instances, yeast has been used as a steppingstone in which to characterize and optimize optogenetic tools to later be deployed in higher eukaryotes. More recently, however, optogenetic tools have been developed and deployed in yeast specifically for biotechnological applications, including in nonconventional yeasts. In this review, we summarize various optogenetic systems responding to different wavelengths of light that have been demonstrated in diverse yeast species. We then describe various applications of these optogenetic tools in yeast, particularly in metabolic engineering and recombinant protein production. Finally, we discuss emerging applications in yeast cybergenetics-the interfacing of yeast and computers for closed-loop controls of yeast bioprocesses-and the potential impact of optogenetics in other future biotechnological applications.

Yeast is a widely utilized chassis for heterologous protein production, with Komagataella phaffii well-established as a prominent nonconventional yeast in this field. Despite its widespread recognition, there remains considerable potential to further optimize these cell factories to meet high production demands in a cost-effective and sustainable manner. Understanding the cellular response to the challenges of heterologous protein production can equip genetic engineers with crucial knowledge to develop enhanced strategies for constructing more efficient cell factories. In this study, we explore the molecular response of various K. phaffii strains that produce either the human insulin precursor or Mambalgin-1, examining changes in transcription and changes in intra- and extracellular protein levels. Our findings provide valuable insights into the molecular mechanisms that regulate the behaviour of K. phaffii production strains under the stress of producing different heterologous proteins. We believe that these results will serve as a foundation for identifying new genetic targets to improve strain robustness and productivity. In conclusion, we present new cellular and molecular insights into the response of K. phaffii cell factories to the challenges of burdensome heterologous protein production and our findings point to different engineering strategies for improved cell factory performance.

The human fungal pathogen Candida glabrata is closely related to the budding yeast Saccharomyces cerevisiae. The sexual cycle in S. cerevisiae has been extensively characterized. Haploid cells 'a' and alpha secrete pheromones involved in mating of the opposite cell type leading to the formation of a diploid cell. Under harsh conditions, diploid cells undergo meiosis for the formation of four haploid spores. In C. glabrata, cells are also found as 'a' and alpha and this organism possesses most S. cerevisiae homologous genes involved in meiosis and mating. However, mating has never been observed in C. glabrata. In S. cerevisiae, the non-essential UME6 gene is involved in controlling the expression of meiotic genes. We have previously shown that Zcf11, a putative homolog of Ume6, is encoded by an essential gene but its function is unknown. Here, we show that the expression of UME6 in C. glabrata can partially complement a Zcf11 knock-down and that these factors recognize the same DNA sequence. Importantly, expression profiling using a Zcf11 knock-down strain revealed that this factor is a negative regulator of meiotic genes expression as well as some genes involved in mating. Thus, regulation of the expression of meiotic genes is functional in this organism reinforcing the view that C. glabrata may have a sexual cycle under specific conditions.

Polyethylene terephthalate (PET) is one of the most used polymers in the packaging industry; enzymatic recycling is emerging as a sustainable strategy to deal with waste PET, producing the virgin monomers terephthalic acid and ethylene glycol (EG). These monomers can be feedstocks for further microbial transformations. While EG metabolism has been uncovered in bacteria, in yeast the pathway for the oxidation to glycolic acid (GA) has only been proposed, but never experimentally elucidated. In this work, we investigated in Saccharomyces cerevisiae the potential contribution to this metabolism of two endogenous genes, YLL056C (a putative alcohol dehydrogenase) and GOR1 (glyoxylate reductase). Secondly, the possible role of alcohol dehydrogenases (ADHs) was considered, too. Finally, two heterologous genes (gox0313 from Gluconobacter oxydans and AOX1 from Komagataella phaffii) were expressed with the intent to push EG oxidation toward GA. Our main findings revealed that (i) Gor1, Yll056c, and ADHs are not involved in EG oxidation and (ii) the bottleneck of the catabolism is the first step in the pathway, due to the endogenous mechanisms for aldehyde detoxification. Multiomics studies are required to completely elucidate the pathway for EG catabolism, while further engineering directed toward relieving the bottleneck is needed to fully unleash the potential of yeasts for the upcycling of EG to GA.