| 1. |
- Sibirny, Andriy, et al.
(författare)
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Development of the thermotolerant methylotrophic yeast hansenula polymorpha as efficient ethanol producer
- 2017
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Ingår i: Yeast Diversity in Human Welfare. - Singapore : Springer Singapore. - 9789811026201 - 9789811026218 ; , s. 257-282
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Bokkapitel (refereegranskat)abstract
- Until recently, the methylotrophic yeasts, including Hansenula polymorpha, have not been considered as a potential producer of biofuels, particularly, ethanol from lignocellulosics. However it is already known that the thermotolerant methylotrophic yeast H. polymorpha is capable to ferment xylose, glucose and cellobiose, the main sugars of lignocellulosic hydrolysates, under elevated temperature. These observations allow considering H. polymorpha as a promising organism for high temperature alcoholic fermentation in industrial applications. Although the amount of ethanol produced from xylose by the wild-type strains of H. polymorpha is extremely low, the successful approaches of metabolic engineering and classical selection had been developed during last decade, which permitted to increase ethanol accumulation from xylose 30-fold. The available strains accumulate 12.5 g of ethanol per liter from xylose at 45 °C. In this article, we present published and new approaches and main achievements on metabolic engineering and selection of H. polymorpha for improved producers of ethanol from xylose, starch, xylan, and glycerol, as well as that of strains with increased tolerance to high temperatures and ethanol.
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| 2. |
- Ahmad, Khadija Mohamed, et al.
(författare)
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Genome structure and dynamics of the yeast pathogen Candida glabrata
- 2014
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Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 14:4, s. 529-535
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Forskningsöversikt (refereegranskat)abstract
- The yeast pathogen Candida glabrata is the second most frequent cause of Candida infections. However, from the phylogenetic point of view, C. glabrata is much closer to Saccharomyces cerevisiae than to Candida albicans. Apparently, this yeast has relatively recently changed its life style and become a successful opportunistic pathogen. Recently, several C. glabrata sister-species, among them clinical and environmental isolates, have had their genomes characterized. Also, hundreds of C. glabrata clinical isolates have been characterized for their genomes. These isolates display enormous genomic plasticity. The number and size of chromosomes vary drastically, as well as intra- and inter-chromosomal segmental duplications occur frequently. The observed genome alterations could affect phenotypic properties and thus help to adapt to the highly variable and harsh habitats this yeast finds in different human patients and their tissues. Further genome sequencing of pathogenic isolates will provide a valuable tool to understand the mechanisms behind genome dynamics and help to elucidate the genes contributing to the virulence potential.
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| 3. |
- Ahmad, Khadija Mohamed, et al.
(författare)
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Small chromosomes among Danish Candida glabrata isolates originated through different mechanisms.
- 2013
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Ingår i: Antonie van Leeuwenhoek. - : Springer Science and Business Media LLC. - 1572-9699 .- 0003-6072. ; 104:1, s. 111-122
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Tidskriftsartikel (refereegranskat)abstract
- We analyzed 192 strains of the pathogenic yeast Candida glabrata from patients, mainly suffering from systemic infection, at Danish hospitals during 1985-1999. Our analysis showed that these strains were closely related but exhibited large karyotype polymorphism. Nine strains contained small chromosomes, which were smaller than 0.5 Mb. Regarding the year, patient and hospital, these C. glabrata strains had independent origin and the analyzed small chromosomes were structurally not related to each other (i.e. they contained different sets of genes). We suggest that at least two mechanisms could participate in their origin: (i) through a segmental duplication which covered the centromeric region, or (ii) by a translocation event moving a larger chromosome arm to another chromosome that leaves the centromere part with the shorter arm. The first type of small chromosomes carrying duplicated genes exhibited mitotic instability, while the second type, which contained the corresponding genes in only one copy in the genome, was mitotically stable. Apparently, in patients C. glabrata chromosomes are frequently reshuffled resulting in new genetic configurations, including appearance of small chromosomes, and some of these resulting "mutant" strains can have increased fitness in a certain patient "environment".
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| 4. |
- Chen, Xin, 1980, et al.
(författare)
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Dataset for suppressors of amyloid-beta toxicity and their functions in recombinant protein production in yeast
- 2022
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Ingår i: Data in Brief. - : Elsevier BV. - 2352-3409. ; 42
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Tidskriftsartikel (refereegranskat)abstract
- The production of recombinant proteins at high levels often induces stress-related phenotypes by protein misfolding or aggregation. These are similar to those of the yeast Alzheimer's disease (AD) model in which amyloid-beta peptides (A beta 42) were accumulated [1,2] . We have previously identified suppressors of A beta 42 cytotoxicity via the genome-wide synthetic genetic array (SGA) [3] and here we use them as metabolic engineering targets to evaluate their potentiality on recombinant protein production in yeast Saccharomyces cerevisiae. In order to investigate the mechanisms linking the genetic modifications to the improved recombinant protein production, we perform systems biology approaches (transcriptomics and proteomics) on the resulting strain and intermediate strains. The RNAseq data are preprocessed by the nf-core/RNAseq pipeline and analyzed using the Platform for Integrative Analysis of Omics (PIANO) package [4] . The quantitative proteome is analyzed on an Orbitrap Fusion Lumos mass spectrometer interfaced with an Easy-nLC1200 liquid chromatography (LC) system. LC-MS data files are processed by Proteome Discoverer version 2.4 with Mascot 2.5.1 as a database search engine. The original data presented in this work can be found in the research paper titled "Suppressors of Amyloid-beta Toxicity Improve Recombinant Protein Produc-tion in yeast by Reducing Oxidative Stress and Tuning Cellu-lar Metabolism", by Chen et al. [5] . (C) 2022 The Author(s). Published by Elsevier Inc.
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| 5. |
- Chen, Xin, 1980, et al.
(författare)
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Suppressors of amyloid-β toxicity improve recombinant protein production in yeast by reducing oxidative stress and tuning cellular metabolism
- 2022
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Ingår i: Metabolic Engineering. - : Elsevier BV. - 1096-7176 .- 1096-7184. ; 72, s. 311-324
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Tidskriftsartikel (refereegranskat)abstract
- High-level production of recombinant proteins in industrial microorganisms is often limited by the formation of misfolded proteins or protein aggregates, which consequently induce cellular stress responses. We hypothesized that in a yeast Alzheimer's disease (AD) model overexpression of amyloid-β peptides (Aβ42), one of the main peptides relevant for AD pathologies, induces similar phenotypes of cellular stress. Using this humanized AD model, we previously identified suppressors of Aβ42 cytotoxicity. Here we hypothesize that these suppressors could be used as metabolic engineering targets to alleviate cellular stress and improve recombinant protein production in the yeast Saccharomyces cerevisiae. Forty-six candidate genes were individually deleted and twenty were individually overexpressed. The positive targets that increased recombinant α-amylase production were further combined leading to an 18.7-fold increased recombinant protein production. These target genes are involved in multiple cellular networks including RNA processing, transcription, ER-mitochondrial complex, and protein unfolding. By using transcriptomics and proteomics analyses, combined with reverse metabolic engineering, we showed that reduced oxidative stress, increased membrane lipid biosynthesis and repressed arginine and sulfur amino acid biosynthesis are significant pathways for increased recombinant protein production. Our findings provide new insights towards developing synthetic yeast cell factories for biosynthesis of valuable proteins.
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| 6. |
- Guo, Xiaoxian, et al.
(författare)
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Understand the genomic diversity and evolution of fungal pathogen Candida glabrata by genome-wide analysis of genetic variations
- 2020
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Ingår i: Methods. - : Elsevier BV. - 1095-9130 .- 1046-2023. ; 176, s. 82-90
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Tidskriftsartikel (refereegranskat)abstract
- The yeast Candida glabrata, an opportunistic human fungal pathogen, is the second most prevalent cause of candidiasis worldwide, with an infection incidence that has been increasing in the past decades. The completion of the C. glabrata reference genome made fundamental contributions to the understanding of the molecular basis of its pathogenic phenotypes. However, knowledge of genome-wide genetic variations among C. glabrata strains is limited. In this study, we present a population genomic study of C. glabrata based on whole genome re-sequencing of 47 clinical strains to an average coverage of ∼63×. Abundant genetic variations were identified in these strains, including single nucleotide polymorphisms (SNPs), small insertion/deletions (indels) and copy number variations (CNVs). The observed patterns of variations revealed clear population structure of these strains. Using population genetic tests, we detected fast evolution of several genes involved in C. glabrata adherence ability, such as EPA9 and EPA10. We also located genome structural variations, including aneuploidies and large fragment CNVs, in regions that are functionally related to virulence. Subtelometric regions were hotspots of CNVs, which may contribute to variation in expression of adhesin genes that are important for virulence. We further conducted a genome-wide association study that identified two SNPs in the 5′UTR region of CST6 that were associated with fluconazole susceptibility. These observations provide convincing evidence for the highly dynamic nature of the C. glabrata genome with potential adaptive evolution to clinical environments, and offer valuable resources for investigating the mechanisms underlying drug resistance and virulence in this fungal pathogen. (249 words)
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| 7. |
- Ishchuk, Olena, 1980, et al.
(författare)
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Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:30
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Tidskriftsartikel (refereegranskat)abstract
- Heme is an oxygen carrier and a cofactor of both industrial enzymes and food additives. The intracellular level of free heme is low, which limits the synthesis of heme proteins. Therefore, increasing heme synthesis allows an increased production of heme proteins. Using the genome-scale metabolic model (GEM) Yeast8 for the yeast Saccharomyces cerevisiae, we identified fluxes potentially important to heme synthesis. With this model, in silico simulations highlighted 84 gene targets for balancing biomass and increasing heme production. Of those identified, 76 genes were individually deleted or overexpressed in experiments. Empirically, 40 genes individually increased heme production (up to threefold). Heme was increased by modifying target genes, which not only included the genes involved in heme biosynthesis, but also those involved in glycolysis, pyruvate, Fe-S clusters, glycine, and succinyl-coenzyme A (CoA) metabolism. Next, we developed an algorithmic method for predicting an optimal combination of these genes by using the enzyme-constrained extension of the Yeast8 model, ecYeast8. The computationally identified combination for enhanced heme production was evaluated using the heme ligand-binding biosensor (Heme-LBB). The positive targets were combined using CRISPR-Cas9 in the yeast strain (IMX581-HEM15-HEM14-HEM3- δshm1-HEM2-δhmx1-FET4-δgcv2-HEM1-δgcv1-HEM13), which produces 70-foldhigher levels of intracellular heme.
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| 8. |
- Ishchuk, Olena, 1980, et al.
(författare)
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Improved production of human hemoglobin in yeast by engineering hemoglobin degradation
- 2021
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Ingår i: Metabolic Engineering. - : Elsevier BV. - 1096-7176 .- 1096-7184. ; 66, s. 259-267
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Tidskriftsartikel (refereegranskat)abstract
- With the increasing demand for blood transfusions, the production of human hemoglobin (Hb) from sustainable sources is increasingly studied. Microbial production is an attractive option, as it may provide a cheap, safe, and reliable source of this protein. To increase the production of human hemoglobin by the yeast Saccharomyces cerevisiae, the degradation of Hb was reduced through several approaches. The deletion of the genes HMX1 (encoding heme oxygenase), VPS10 (encoding receptor for vacuolar proteases), PEP4 (encoding vacuolar proteinase A), ROX1 (encoding heme-dependent repressor of hypoxic genes) and the overexpression of the HEM3 (encoding porphobilinogen deaminase) and the AHSP (encoding human alpha-hemoglobin-stabilizing protein) genes — these changes reduced heme and Hb degradation and improved heme and Hb production. The reduced hemoglobin degradation was validated by a bilirubin biosensor. During glucose fermentation, the engineered strains produced 18% of intracellular Hb relative to the total yeast protein, which is the highest production of human hemoglobin reported in yeast. This increased hemoglobin production was accompanied with an increased oxygen consumption rate and an increased glycerol yield, which (we speculate) is the yeast's response to rebalance its NADH levels under conditions of oxygen limitation and increased protein-production.
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| 9. |
- Ishchuk, Olena, 1980, et al.
(författare)
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Improving the Production of Cofactor-Containing Proteins: Production of Human Hemoglobin in Yeast
- 2019
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Ingår i: Methods in Molecular Biology. - New York, NY : Springer New York. - 1940-6029 .- 1064-3745. ; 1923, s. 243-264
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Human hemoglobin is an essential protein, whose main function as an oxygen carrier is indispensable for life. Hemoglobin is a cofactor-containing protein with heme as prosthetic group. Same as in humans, heme is synthesized in many organisms in a complex pathway involving two cellular compartments (mitochondria and cytosol), which is tightly regulated. Red blood cells (erythrocytes) are specialized and adapted for production and transport of the hemoglobin molecules. In addition to oxygen binding, hemoglobin can participate in a variety of chemical reactions by its iron and heme and may become toxic when released from erythrocytes. Hemoglobin is a major target for the development of blood substitutes/oxygen carriers, and therefore its microbial production is attractive, as it may provide a cheap and reliable source of human hemoglobin. Significant efforts have been dedicated to this task for the last three decades. Moreover since the first generation of cell-free blood substitutes based on unmodified hemoglobin failed human trials, mutant forms became of great interest.In this chapter we summarize the existing knowledge about human hemoglobin, challenges of its microbial production, and its improvement, with a particular focus upon yeast as production host.
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| 10. |
- Ishchuk, Olena P., et al.
(författare)
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Novel centromeric loci of the wine and beer yeast dekkera bruxellensis CEN1 and CEN2
- 2016
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:8
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Tidskriftsartikel (refereegranskat)abstract
- The wine and beer yeast Dekkera bruxellensis thrives in environments that are harsh and limiting, especially in concentrations with low oxygen and high ethanol. Its different strains' chromosomes greatly vary in number (karyotype). This study isolates two novel centromeric loci (CEN1 and CEN2), which support both the yeast's autonomous replication and the stable maintenance of plasmids. In the sequenced genome of the D. bruxellensis strain CBS 2499, CEN1 and CEN2 are each present in one copy. They differ from the known "point" CEN elements, and their biological activity is retained within ~900-1300 bp DNA segments. CEN1 and CEN2 have features of both "point" and "regional" centromeres: They contain conserved DNA elements, ARSs, short repeats, one tRNA gene, and transposon-like elements within less than 1 kb. Our discovery of a miniature inverted-repeat transposable element (MITE) next to CEN2 is the first report of such transposons in yeast. The transformants carrying circular plasmids with cloned CEN1 and CEN2 undergo a phenotypic switch: They form fluffy colonies and produce three times more biofilm. The introduction of extra copies of CEN1 and CEN2 promotes both genome rearrangements and ploidy shifts, with these effects mediated by homologous recombination (between circular plasmid and genome centromere copy) or by chromosome breakage when integrated. Also, the proximity of the MITE-like transposon to CEN2 could translocate CEN2 within the genome or cause chromosomal breaks, so promoting genome dynamics. With extra copies of CEN1 and CEN2, the yeast's enhanced capacities to rearrange its genome and to change its gene expression could increase its abilities for exploiting new and demanding niches.
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