Modified Yeast Strains Research Articles

QM/MM Study of the Reaction Mechanism of L-Tyrosine Hydroxylation Catalyzed by the Enzyme CYP76AD1.

We have studied the hydroxylation mechanism of l-Tyr by the heme-dependent enzyme CYP76AD1 from the sugar beet (Beta vulgaris). This enzyme has a promising biotechnological application in modified yeast strains to produce medicinal alkaloids, an alternative to the traditional opium poppy harvest. A generative machine learning software based on AlphaFold was used to build the structure of CYP76AD1 since there are no structural data for this specific enzyme. After model validation, l-Tyr was docked in the active site of CYP76AD1 to assemble the reactive complex, whose catalytic distances remained stable throughout the 100 ns of MD simulation. Subsequent QM/MM calculations elucidated that l-Tyr hydroxylation occurs in two steps: hydrogen abstraction from l-Tyr by CpdI, forming an l-Tyr radical, and subsequent radical rebound, corresponding to a rate-limiting step of 16.0 kcal·mol-1. Our calculations suggest that the hydrogen abstraction step should occur in the doublet state, while the radical rebound should happen in the quartet state. The clarification of the reaction mechanism of CYP76AD1 provides insights into the rational optimization of the biosynthesis of alkaloids to eliminate the use of opium poppy.

The Production of Bioactive Hydroxytyrosol in Fermented Beverages: The Role of Must Composition and a Genetically Modified Yeast Strain

Hydroxytyrosol (HT) is a well-known compound for its bioactive properties. It is naturally present in olives, olive oil, and wine. Its presence in wines is partly due to its production during alcoholic fermentation by yeast through a hydroxylation of tyrosol formed through the Ehrlich pathway. This work aims to explore the influence of yeast assimilable nitrogen (YAN) and glucose content as precursors of HT formation during alcoholic fermentation. Commercial Saccharomyces cerevisiae QA23 and its metabolically engineered strain were used to ferment synthetic must. Each strain was tested at two different YAN concentrations (210 and 300 mg L−1) and two glucose concentrations (100 and 240 g L−1). This work confirms that the less YAN and the more glucose, the higher the HT content, with fermentations carried out with the metabolically engineered strain being the ones with the highest HT content (0.6 mg L−1).

Biolistic Transformation of Cryptococcus neoformans.

Biolistic transformation of Cryptococcus neoformans is used as a molecular tool to genetically alter or delete targeted genes. The DNA is introduced into the yeast on DNA-coated gold beads by a helium shock wave produced using a biolistic particle system. The procedure often involves insertion of a dominant selectable marker into the desired site by homologous recombination. To increase the likelihood of homologous recombination, large fragments of overlapping DNA are used. The two most used dominant selectable markers are nourseothricin and Geneticin. With the need to generate multiple gene deletions in the same strain, there are recyclable marker systems, such as the bacteriophage P1 Cre-loxP system or CRISPR that provide additional useful molecular tools. While newer strategies exist to generate deletions and introduce markers and other gene modifications, biolistic transformation has remained a viable tool to facilitate the construction of genetically modified yeast strains. This chapter provides a working protocol on how to delete and restore a gene in C. neoformans.

Bio-Dealcoholization of Wines: Can Yeast Make Lighter Wines?

The relationship between climate change and viticulture has become increasingly apparent in recent years. Rising temperatures have been a critical factor in early grape ripening. This, in turn, has led to wines with imbalanced acidity and, more importantly, higher alcohol content and pH values. Today, consumers demand high-quality and healthy products, and this trend has extended to wine consumption. Consumers prefer wines with reduced alcohol content due to the health risks associated with alcohol consumption. To meet this demand, researchers have developed modified yeast strains that reduce wine alcohol content during fermentation. These strains ferment less sugar or redirect carbon metabolism. However, their use may pose challenges, such as producing undesired secondary metabolites that can affect wine characteristics. Additionally, consumers are still divided on using genetically modified organisms (GMOs) in food and beverages. This review examines the impact of climate change on wine quality and consumer perception, taking into account new technologies used to reduce wine alcohol content or produce low-alcohol-content wines, such as low-cost techniques like bio-dealcoholization performed by non-GMO wine yeast, Saccharomyces, and non-Saccharomyces.

High titer (>100 g/L) ethanol production from pretreated corn stover hydrolysate by modified yeast strains

Developing a reliable lignocellulose pretreatment method to extract mixed sugars and engineering efficient strains capable of utilizing xylose are crucial for advancing cellulosic ethanol production. In this study, chemical and characterization analyses revealed that alkali cooking can significantly remove lignin from lignocellulose crops. The highest amount of mixed sugar was obtained from corn stover hydrolysates with a 15 % solid loading. Our genetically engineered yeast strain ΔsnR4, derived from a well-staged WXY70, demonstrated excellent performance in low 10 % solids loading corn stover hydrolysate, producing a high ethanol yield of 0.485 g/g total sugars. When a combined NaOH-ball milling pretreatment strategy was applied at high solids loading, ΔsnR4 exhibited the maximum ethanol titer of 110.9 g/L within 36 h, achieving an ethanol yield of 92.9 % theoretical maximum. Therefore, ΔsnR4 is highly compatible with high solid loading NaOH-ball milling pretreatment, making it a potential candidate for industrial cellulosic ethanol.

Evaluation of Three ISO Estrogen Receptor Transactivation Assays Applied to 52 Domestic Effluent Samples.

Estrogens are released to the aquatic environment by wastewater treatment plant (WWTP) effluents and can affect wildlife. In the last three decades, many in vitro assay platforms have been developed to detect and quantify estrogenicity in water. In 2018, the International Organization for Standardization (ISO) standardized protocols became available for three types of in vitro estrogen receptor transactivation assays (ERTAs) detecting estrogenicity in 96-well plates (ISO19040 1-3). Two ERTAs-lyticase Yeast Estrogen Screen (L-YES) and Arxula YES (A-YES)-use genetically modified yeast strains, whereas the third utilizes stably transfected human cells. One human cell based assay is ERα-CALUX, which is based on a genetically modified human bone osteosarcoma cell line. In the present study, we characterized the performance, comparability, and effectiveness of these three ERTAs, including an evaluation involving proposed water quality thresholds (effect-based trigger values [EBTs]). For a robust evaluation, we collected 52 effluent samples over three sampling campaigns at 15 different WWTPs in Switzerland. Estrogen receptor transactivation assay results were correlated and compared with results from chemical analysis targeting known estrogens. The three ERTAs showed comparable data over all campaigns. However, the selection of EBTs plays a significant role in the interpretation and comparison of bioassay resultsto distinguish between acceptable and unacceptable water quality. Applying a fixed cross-assay EBT for effluent of 4 ng L-1 resulted in varying numbers of threshold exceedances ranging between zero and four samples depending on the ERTA used. Using assay-specific EBTs showed exceedances in eight samples (ERα-CALUX) and in one sample (A-YES), respectively. Thus, proposed EBTs do not produce similar risk profiles across samples and further refinement of assay-specific EBTs is needed to account for assay-specific differences and to enable the application of ERTAs as effect-based methods in environmental monitoring. Environ Toxicol Chem 2022;41:2512-2526. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Insertion orientation within the cassette affects gene-targeting success during ends-out recombination in the yeast Saccharomyces cerevisiae.

Gene-targeting is one of the most important molecular tools for genomic manipulations for research and industrial purposes. However, many factors influence targeting fidelity undermining the efforts for accurate, fast, and reliable construction of genetically modified yeast strains. Therefore, it is of great academic interest that we uncover as many as possible parameters affecting the recombination mechanisms that enable targeting. Since usually, researchers choose the orientation of the insertion (marker) within the module at random, it seemed interesting to see whether the same module will achieve essentially the same targeting efficiency when the same marker was oriented alternatively concerning the same target gene. Thus, two loci (URA3 and LEU2) and one allele (ura3-52) in a haploid yeast genetic background were targeted by artificial modules bearing homologous insertions in alternative orientations being flanked by long asymmetrical targeting homology to either replace or disrupt a genomic target. Results showed that insertion orientation within the targeting module strongly influences targeting in yeast, regardless of the targeting approach.

Functional variability in adhesion and flocculation of yeast megasatellite genes.

Megasatellites are large tandem repeats found in all fungal genomes but especially abundant in the opportunistic pathogen Candida glabrata. They are encoded in genes involved in cell-cell interactions, either between yeasts or between yeast and human cells. In the present work, we have been using an iterative genetic system to delete several Candida glabrata megasatellite-containing genes and found that 2 of them were positively involved in adhesion to epithelial cells, whereas 3 genes negatively controlled adhesion. Two of the latter, CAGL0B05061g or CAGL0A04851g, were also negative regulators of yeast-to-yeast adhesion, making them central players in controlling Candida glabrata adherence properties. Using a series of synthetic Saccharomyces cerevisiae strains in which the FLO1 megasatellite was replaced by other tandem repeats of similar length but different sequences, we showed that the capacity of a strain to flocculate in liquid culture was unrelated to its capacity to adhere to epithelial cells or to invade agar. Finally, to understand how megasatellites were initially created and subsequently expanded, an experimental evolution system was set up, in which modified yeast strains containing different megasatellite seeds were grown in bioreactors for more than 200 generations and selected for their ability to sediment at the bottom of the culture tube. Several flocculation-positive mutants were isolated. Functionally relevant mutations included general transcription factors as well as a 230-kbp segmental duplication.

Determination of the lipid composition of the GPI anchor.

In eukaryotic cells, a subset of cell surface proteins is attached by the glycolipid glycosylphosphatidylinositol (GPI) to the external leaflet of the plasma membrane where they play important roles as enzymes, receptors, or adhesion molecules. Here we present a protocol for purification and mass spectrometry analysis of the lipid moiety of individual GPI-anchored proteins (GPI-APs) in yeast. The method involves the expression of a specific GPI-AP tagged with GFP, solubilization, immunoprecipitation, separation by electrophoresis, blotting onto PVDF, release and extraction of the GPI-lipid moiety and analysis by mass spectrometry. By using this protocol, we could determine the precise GPI-lipid structure of the GPI-AP Gas1-GFP in a modified yeast strain. This protocol can be used to identify the lipid composition of the GPI anchor of distinct GPI-APs from yeast to mammals and can be adapted to determine other types of protein lipidation.

Production of Recombinant Human Ceruloplasmin: Improvements and Perspectives.

The ferroxidase ceruloplasmin (CP) plays a crucial role in iron homeostasis in vertebrates together with the iron exporter ferroportin. Mutations in the CP gene give rise to aceruloplasminemia, a rare neurodegenerative disease for which no cure is available. Many aspects of the (patho)physiology of CP are still unclear and would benefit from the availability of recombinant protein for structural and functional studies. Furthermore, recombinant CP could be evaluated for enzyme replacement therapy for the treatment of aceruloplasminemia. We report the production and preliminary characterization of high-quality recombinant human CP in glycoengineered Pichia pastoris SuperMan5. A modified yeast strain lacking the endogenous ferroxidase has been generated and employed as host for heterologous expression of the secreted isoform of human CP. Highly pure biologically active protein has been obtained by an improved two-step purification procedure. Glycan analysis indicates that predominant glycoforms HexNAc2Hex8 and HexNAc2Hex11 are found at Asn119, Asn378, and Asn743, three of the canonical four N-glycosylation sites of human CP. The availability of high-quality recombinant human CP represents a significant advancement in the field of CP biology. However, productivity needs to be increased and further careful glycoengineering of the SM5 strain is mandatory in order to evaluate the possible therapeutic use of the recombinant protein for enzyme replacement therapy of aceruloplasminemia patients.

Promoters are key organizers of the duplication of vertebrate genomes.

In vertebrates, single cell analyses of replication timing patterns brought to light a very well controlled program suggesting a tight regulation on initiation sites. Mapping of replication origins with different methods has revealed discrete preferential sites, enriched in promoters and potential G-quadruplex motifs, which can aggregate into initiation zones spanning several tens of kilobases (kb). Another characteristic of replication origins is a nucleosome-free region (NFR). A modified yeast strain containing a humanized origin recognition complex (ORC) fires new origins at NFRs revealing their regulatory role. In cooperation with NFRs, the histone variant H2A.Z facilitates ORC loading through di-methylation of lysine 20 of histone H4. Recent studies using genome editing methods show that efficient initiation sites associated with transcriptional activity can synergize over several tens of kb by establishing physical contacts and lead to the formation of early domains of DNA replication demonstrating a co-regulation between replication initiation and transcription.

From baker's yeast to genetically modified budding yeasts: the scientific evolution of bioethanol industry from sugarcane.

The peculiarities of Brazilian fuel ethanol fermentation allow the entry of native yeasts that may dominate over the starter strains of Saccharomyces cerevisiae and persist throughout the sugarcane harvest. The switch from the use of baker's yeast as starter to selected budding yeasts obtained by a selective pressure strategy was followed by a wealth of genomic information that enabled the understanding of the superiority of selected yeast strains. This review describes how the process of yeast selection evolved in the sugarcane-based bioethanol industry, the selection criteria and recent advances in genomics that could advance the fermentation process. The prospective use of genetically modified yeast strains, specially designed for increased robustness and product yield, with special emphasis on those obtained by the CRISPR (clustered regularly interspaced palindromic repeats)-Cas9 (CRISPR-associated protein 9) genome-editing approach, is discussed as a possible solution to confer higher performance and stability to the fermentation process for fuel ethanol production.

Improvement of D‐lactic acid production at low pH through expressing acid‐resistant gene IoGAS1 in engineered Saccharomyces cerevisiae

AbstractBACKGROUNDBlending d‐lactic acid (d‐LA) with l‐lactic acid can significantly improve the thermostability of polylactic (PLA). Although microbial production of d‐LA under acidic conditions is beneficial for the reduction of production costs, the yield is low due to the acidic toxicity of the source strains. Herein, an Issatchenkia orientalis glycosylphosphatidylinositol‐anchored protein IoGas1, which is required for resistance to low pH and salt stress, was expressed in the YIP‐J‐C‐D‐A1 yeast strain. This strain was integrated with Escherichia coli d‐lactate dehydrogenase gene and several attenuated key pathway genes, including pyruvate decarboxylases (PDC1, PDC6), JEN1 (a monocarboxylate transporter), d‐lactate dehydrogenase1 (DLD1), l‐lactate cytochrome‐c oxidoreductase (CYB2) and alcohol dehydrogenase 1(ADH1).RESULTSThe results revealed that the production of d‐LA by the modified strain YIP‐I‐J‐C‐D‐A1 was remarkably improved and reached 85.3 g L–1 d‐LA, with a yield of 0.71 g g–1 and a productivity of 1.20 g L h–1 in batch‐fed fermentation. The d‐LA production of the YIP‐I‐J‐C‐D‐A1 strain (CGMCC2.5785) was further improved by attenuating the ethanol and glycerol pathways. The resulting strain YIP‐A15G12 (CGMCC2.5803) produced 92.0 g L–1 d‐LA with a yield of 0.70 g g–1 and a productivity of 1.21 g L h–1 in batch‐fed fermentation at a final pH of 3.58.CONCLUSIONTaken together, the expression of the acid‐resistant gene IoGAS1 in a modified yeast strain can significantly improve the efficiency of producing d‐LA at low pH, which may prove beneficial for the industrial production of the biodegradable material, PLA.

Rpn4 and proteasome-mediated yeast resistance to ethanol includes regulation of autophagy.

Distilled spirits production using Saccharomyces cerevisiae requires understanding of the mechanisms of yeast cell response to alcohol stress. Reportedly, specific mutations in genes of the ubiquitin-proteasome system, e.g., RPN4, may result in strains exhibiting hyper-resistance to different alcohols. To study the Rpn4-dependent yeast response to short-term ethanol exposure, we performed a comparative analysis of the wild-type (WT) strain, strain with RPN4 gene deletion (rpn4-Δ), and a mutant strain with decreased proteasome activity and consequent Rpn4 accumulation due to PRE1 deregulation (YPL). The stress resistance tests demonstrated an increased sensitivity of mutant strains to ethanol compared with WT. Comparative proteomics analysis revealed significant differences in molecular responses to ethanol between these strains. GO analysis of proteins upregulated in WT showed enrichments represented by oxidative and heat responses, protein folding/unfolding, and protein degradation. Enrichment of at least one of these responses was not observed in the mutant strains. Moreover, activity of autophagy was not increased in the RPN4 deletion strain upon ethanol stress which agrees with changes in mRNA levels of ATG7 and PRB1 genes of the autophagy system. Activity of the autophagic system was clearly induced and accompanied with PRB1 overexpression in the YPL strain upon ethanol stress. We demonstrated that Rpn4 stabilization contributes to the PRB1 upregulation. CRISPR-Cas9-mediated repression of PACE-core Rpn4 binding sites in the PRB1 promoter inhibits PRB1 induction in the YPL strain upon ethanol treatment and results in YPL hypersensitivity to ethanol. Our data suggest that Rpn4 affects the autophagic system activity upon ethanol stress through the PRB1 regulation. These findings can be a basis for creating genetically modified yeast strains resistant to high levels of alcohol, being further used for fermentation in ethanol production.

Development of a Biosensor for Detection of Benzoic Acid Derivatives in Saccharomyces cerevisiae.

4-hydroxybenzoic acid (pHBA) is an important industrial precursor of muconic acid and liquid crystal polymers whose production is based on the petrochemical industry. In order to decrease our dependency on fossil fuels and improve sustainability, microbial engineering is a particularly appealing approach for replacing traditional chemical techniques. The optimization of microbial strains, however, is still highly constrained by the screening stage. Biosensors have helped to alleviate this problem by decreasing the screening time as well as enabling higher throughput. In this paper, we constructed a synthetic biosensor, named sBAD, consisting of a fusion of the pHBA-binding domain of HbaR from R. palustris, the LexA DNA binding domain at the N-terminus and the transactivation domain B112 at the C-terminus. The response of sBAD was tested in the presence of different benzoic acid derivatives, with cell fluorescence output measured by flow cytometry. The biosensor was found to be activated by the external addition of pHBA in the culture medium, in addition to other carboxylic acids including p-aminobenzoic acid (pABA), salicylic acid, anthranilic acid, aspirin, and benzoic acid. Furthermore, we were able to show that this biosensor could detect the in vivo production of pHBA in a genetically modified yeast strain. A good linearity was observed between the biosensor fluorescence and pHBA concentration. Thus, this biosensor would be well-suited as a high throughput screening tool to produce, via metabolic engineering, benzoic acid derivatives.

A Future Place for Saccharomyces Mixtures and Hybrids in Wine Making

Each year, winemakers can face sluggish or stuck fermentations during wine making, especially when a spontaneous fermentation is performed, even if strains of the classical wine yeast Saccharomyces cerevisiae are applied. Problems are inevitable when low ammonium concentrations (<160 mg L−1 grape must) or an excess of fructose compared to glucose are observed during grape must fermentation. S. cerevisiae strains cannot use all kinds of amino acids as the sole nitrogen source but usually need free ammonium (optimal concentration: 600 mg L−1 grape must). It preferably consumes glucose, leading often to an excess of fructose in the fermenting must, which contains glucose and fructose in an equal ratio at the beginning of fermentation. Yeast hybrids have been isolated from wines several times and different strains are already commercially available. The united properties of the parent strains can provide advantages under sophisticated fermentation conditions. However, the involvement of a hybrid yeast for the rectification of fermentation disorders in spontaneous fermentations has only been described recently in the literature. Recent investigations have provided convincing evidence that fermentation problems can be overcome when must fermentations are successively performed with Saccharomyces bayanus strain HL 77 and the triple hybrid S. cerevisiae × Saccharomyces kudriavzevii × S. bayanus strain HL 78. The triple hybrid strain HL 78 uses amino acids as a nitrogen source in the absence of ammonium and it also exhibits a fructophilic character with an enhanced uptake of fructose in comparison to glucose. The application of genetically modified yeast strains is not allowed for starter cultures in wine making, but the usage of yeast mixtures and hybrid strains could be a promising tool for winemakers to solve fermentation problems during spontaneous fermentation or for the creation of novel wine types with desired sensory characteristics under more challenging conditions, especially when the composition of the must components is not optimal because of, e.g., critical climatic or soil conditions.

Additive Manufacturing of Catalytically Active Living Materials.

Living materials, which are composites of living cells residing in a polymeric matrix, are designed to utilize the innate functionalities of the cells to address a broad range of applications such as fermentation and biosensing. Herein, we demonstrate the additive manufacturing of catalytically active living materials (AMCALM) for continuous fermentation. A multi-stimuli-responsive yeast-laden hydrogel ink, based on F127-dimethacrylate, was developed and printed using a direct-write 3D printer. The reversible stimuli-responsive behaviors of the polymer hydrogel inks to temperature and pressure are critical, as they enabled the facile incorporation of yeast cells and subsequent fabrication of 3D lattice constructs. Subsequent photo-cross-linking of the printed polymer hydrogel afforded a robust elastic material. These yeast-laden living materials were metabolically active in the fermentation of glucose into ethanol for 2 weeks in a continuous batch process without significant reduction in efficiency (∼90% yield of ethanol). This cell immobilization platform may potentially be applicable toward other genetically modified yeast strains to produce other high-value chemicals in a continuous biofermentation process.

Rps10 Protein Contribution to Ribosomal mRNA Selectivity

Previous work from the Karbstein Lab on ribosomal biogenesis has shown that interactions between the ribosomal protein Rps26 and the mRNA promotes mRNA selectivity, thereby shaping protein homeostasis. Importantly, cells lacking sufficient amounts of Rps26 follow a distinct translational program, which might explain in part the pathogenesis of Diamond‐Blackfan Anemia (DBA), a disease caused by lack of ribosomal proteins, including both Rps26 and Rps10. Both Rps26 and Rps10 are located near the translated mRNA within the entry channel and can be used to predict contact with mRNA downstream of the start and stop codon during translation initiation and termination, respectively. Initial tests were conducted to observe the effects from mutation of the putative Rps10‐contact region on translation. Five mutated plasmids were studied for their affect on Rps10 binding. Results from dual luciferase assays have shown a significant decrease in protein production as a result of mutations in the mRNA plasmid. This decrease appears be dependent on Rps10 levels when compared to the traditional Kozak sequence. To test this hypothesis three different yeast strains were used, WT, TEF and Dox yeast strains. Wild type yeast cells contain their own endogenous copies of the Rps10 genes. TEF and Dox are both genetically modified yeast strains in which the endogenous copies of Rps10 were removed from the genome and replaced by a newly introduced copy in a plasmid under control of either a TEF or Dox promoter. These promoters allow for controlled Rps10 production levels. Doxycycline can be added to cells to further repress their Rps10 production. Using western analysis, we observed that yeast cells with the Dox promoter and treated with doxycycline had significantly reduced levels of Rps10 in their ribosomes. Cells that were successfully depleted of Rps10 had significantly lower protein production then their Rps10 replete counterparts. This translational difference is believed to be a result of a decreased ability of the ribosome to bind mRNA as a result of diminished Rps10 levels.Support or Funding InformationK. Karbstein is an HHMI Faculty ScholarThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Yeast as a Versatile System for Heterologous Protein Expression; Genetically Modified Yeast Strain to Express Human Drug Metabolism Enzymes

Yeast as a versatile system for heterologous protein expression genetically modified yeast strain to express human drug metabolism enzymes

In Saccharomyces cerevisiae gene targeting fidelity depends on a transformation method and proportion of the overall length of the transforming and targeted DNA.

Gene replacement is one of the most essential approaches in construction of the genetically modified yeast strains. However, the fidelity of gene targeting and the effort needed for construction of a particular strain can vary significantly. We investigated the influence of two important factors-the choice of the transformation method and the design of the transforming DNA fragment, which can vary in overall length (including flanking regions and selectable marker) compared to the length of the targeted region in the genome. Gene replacement fidelity was determined in several assays using electroporation and spheroplast transformation, and compared with our previous results obtained by lithium acetate. We have demonstrated clearly that gene targeting fidelity depends on the transformation protocol, being highest for lithium acetate method. In contrast, lower fidelity was observed with electroporation and spheroplast transformation. Additionally, the fidelity also depends on a design of the transformation assay, since a higher overall length ratio of the transforming DNA and targeted region results in higher fidelity. Moreover, the karyotype analysis of the aberrant transformants by qPCR demonstrates that gene targeting can result in diploidisation of haploid strains, most likely via targeted chromosome duplication followed by subsequent duplication of other chromosomes.