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1.	Ahmad, Khadija Mohamed, et al. (författare) Genome structure and dynamics of the yeast pathogen Candida glabrata 2014 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 14:4, s. 529-535 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.
2.	Dashko, Sofia, et al. (författare) Why, when and how did yeast evolve alcoholic fermentation? 2014 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 14:6, s. 826-832 Forskningsöversikt (refereegranskat)abstract The origin of modern fruits brought to microbial communities an abundant source of rich food based on simple sugars. Yeasts, especially Saccharomyces cerevisiae, usually become the predominant group in these niches. One of the most prominent and unique features and likely a winning trait of these yeasts is their ability to rapidly convert sugars to ethanol at both anaerobic and aerobic conditions. Why, when and how did yeast remodel their carbon metabolism to be able to accumulate ethanol under aerobic conditions and at the expense of decreasing biomass production? We hereby review the recent data on the carbon metabolism in Saccharomycetaceae species, and attempt to reconstruct the ancient environment, which could promote the evolution of alcoholic fermentation. We speculate that the first step towards the so-called alcoholic fermentation lifestyle was the exploration of anaerobic niches resulting in an increased metabolic capacity to degrade sugar to ethanol. The strengthened glycolytic flow had in parallel a beneficial effect on the microbial competition outcome, and later evolved as a "new" tool promoting the yeast competition ability under aerobic conditions. The basic aerobic alcoholic fermentation ability was subsequently "upgraded" in several lineages by evolving additional regulatory steps, like glucose repression in the S. cerevisiae clade, to achieve a more precise metabolic control. This article is protected by copyright. All rights reserved.
3.	David, Florian, 1981, et al. (författare) Advances in yeast genome engineering 2015 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 15:1 Tidskriftsartikel (refereegranskat)abstract Genome engineering based on homologous recombination has been applied to yeast for many years. However, the growing importance of yeast as a cell factory in metabolic engineering and chassis in synthetic biology demands methods for fast and efficient introduction of multiple targeted changes such as gene knockouts and introduction of multistep metabolic pathways. In this review, we summarize recent improvements of existing genome engineering methods, the development of novel techniques, for example for advanced genome redesign and evolution, and the importance of endonucleases as genome engineering tools.
4.	Guo, Zhongpeng, 1983, et al. (författare) Physiological response of Saccharomyces cerevisiae to weak acids present in lignocellulosic hydrolysate 2014 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 14:8, s. 1234-1248 Tidskriftsartikel (refereegranskat)abstract Weak acids are present in lignocellulosic hydrolysate as potential inhibitors that can hamper the use of this renewable resource for fuel and chemical production. To study the effects of weak acids on yeast growth, physiological investigations were carried out in batch cultures using glucose as carbon source in the presence of acetic, formic, levulinic, and vanillic acid at three different concentrations at pH 5.0. The results showed that acids at moderate concentrations can stimulate the glycolytic flux, while higher levels of acid slow down the glycolytic flux for both aerobically and anaerobically grown yeast cells. In particular, the flux distribution between respiratory and fermentative growth was adjusted to achieve an optimal ATP generation to allow a maintained energy level as high as it is in nonstressed cells grown exponentially on glucose under aerobic conditions. In addition, yeast cells exposed to acids suffered from severe reactive oxygen species stress and depletion of reduced glutathione commensurate with exhaustion of the total glutathione pool. Furthermore, a higher cellular trehalose content was observed as compared to control cultivations, and this trehalose probably acts to enhance a number of stress tolerances of the yeast.
5.	Hou, Jin, 1982, et al. (författare) Management of the endoplasmic reticulum stress by activation of the heat shock response in yeast 2014 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 14:3, s. 481-494 Tidskriftsartikel (refereegranskat)abstract In yeast Saccharomyces cerevisiae, accumulation of misfolded proteins in the endoplasmic reticulum (ER) causes ER stress and activates the unfolded protein response (UPR), which is mediated by Hac1p. The heat shock response (HSR) mediated by Hsf1p, mainly regulates cytosolic processes and protects the cell from stresses. Here, we find that a constitutive activation of the HSR could increase ER stress resistance in both wild-type and UPR-deficient cells. Activation of HSR decreased UPR activation in the WT (as shown by the decreased HAC1 mRNA splicing). We analyzed the genome-wide transcriptional response in order to propose regulatory mechanisms that govern the interplay between UPR and HSR and followed up for the hypotheses by experiments in vivo and in vitro. Interestingly, we found that the regulation of ER stress response via HSR is (1) only partially dependent on over-expression of Kar2p (ER resident chaperone induced by ER stress); (2) does not involve the increase in protein turnover via the proteasome activity; (3) is related to the oxidative stress response. From the transcription data, we also propose that HSR enhances ER stress resistance mainly through facilitation of protein folding and secretion. We also find that HSR coordinates multiple stress-response pathways, including the repression of the overall transcription and translation.
6.	Jensen, N. B., et al. (författare) EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae 2014 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 14:2, s. 238-248 Tidskriftsartikel (refereegranskat)abstract Development of strains for efficient production of chemicals and pharmaceuticals requires multiple rounds of genetic engineering. In this study, we describe construction and characterization of EasyClone vector set for baker's yeast Saccharomyces cerevisiae, which enables simultaneous expression of multiple genes with an option of recycling selection markers. The vectors combine the advantage of efficient uracil excision reaction-based cloning and Cre-LoxP-mediated marker recycling system. The episomal and integrative vector sets were tested by inserting genes encoding cyan, yellow, and red fluorescent proteins into separate vectors and analyzing for co-expression of proteins by flow cytometry. Cells expressing genes encoding for the three fluorescent proteins from three integrations exhibited a much higher level of simultaneous expression than cells producing fluorescent proteins encoded on episomal plasmids, where correspondingly 95% and 6% of the cells were within a fluorescence interval of Log(10) mean +/- 15% for all three colors. We demonstrate that selective markers can be simultaneously removed using Cre-mediated recombination and all the integrated heterologous genes remain in the chromosome and show unchanged expression levels. Hence, this system is suitable for metabolic engineering in yeast where multiple rounds of gene introduction and marker recycling can be carried out.
7.	Johansson, Nina, 1983, et al. (författare) Ethylene production in relation to nitrogen metabolism in Saccharomyces cerevisiae 2014 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 14:7, s. 1110-1118 Tidskriftsartikel (refereegranskat)abstract We have previously shown that ethylene production in Saccharomyces cerevisiae expressing the ethylene-forming enzyme (EFE) from Pseudomonas syringae is strongly influenced by variations in the mode of cultivation as well as the choice of nitrogen source. Here, we have studied the influence of nitrogen metabolism on the production of ethylene further. Using ammonium, glutamate, glutamate/arginine, and arginine as nitrogen sources, it was found that glutamate (with or without arginine) correlates with a high ethylene production, most likely linked to an observed increase in 2-oxoglutarate levels. Arginine as a sole nitrogen source caused a reduced ethylene production. A reduction of arginine levels, accomplished using an arginine auxotrophic ARG4-deletion strain in the presence of limiting amounts of arginine or through CAR1 overexpression, did however not correlate with an increased ethylene production. As expected, arginine was necessary for ethylene production as ethylene production in the ARG4-deletion strain ceased at the time when arginine was depleted. In conclusion, our data suggest that high levels of 2-oxoglutarate and a limited amount of arginine are required for successful ethylene production in yeast.
8.	Martinez Ruiz, Jose Luis, 1981, et al. (författare) Gcn4p and the Crabtree effect of yeast: drawing the causal model of the Crabtree effect in Saccharomyces cerevisiae and explaining evolutionary trade-offs of adaptation to galactose through systems biology 2014 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 14:4, s. 654-662 Tidskriftsartikel (refereegranskat)abstract By performing an integrated comparative analysis on the physiology and transcriptome of four different S.cerevisiae strains growing on galactose and glucose, it was inferred that the transcription factors Bas1p, Pho2p, and Gcn4p play a central role in the regulatory events causing the Crabtree effect in S.cerevisiae. The analysis also revealed that a point mutation in the RAS2 observed in a galactose-adapted strain causes a lower Crabtree effect and growth rate on glucose by decreasing the activity of Gcn4p while at the same time is at the origin of higher growth rate on galactose due to a lower activity of the transcriptional repressor Sok2p. The role of Gcn4p on the trade-off effect observed on glucose was confirmed experimentally. This was done by showing that the point mutation in RAS2 does not result in a lower growth rate on glucose if it is introduced in a GCN4-negative background.
9.	Michan, C., et al. (författare) Salt and oxidative stress tolerance in Debaryomyces hansenii and Debaryomyces fabryi 2013 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 13:2, s. 180-188 Tidskriftsartikel (refereegranskat)abstract We report the characterization of five strains belonging to the halotolerant highly related Debaryomyces hansenii/fabryi species. The analysis performed consisted in studying tolerance properties, membrane characteristics, and cation incell amounts. We have specifically investigated (1) tolerance to different chemicals, (2) tolerance to osmotic and salt stress, (3) tolerance and response to oxidative stress, (4) reactive oxygen species (ROS) content, (5) relative membrane potential, (6) cell volume, (7) K+ and Na+ ion content, and (8) membrane fluidity. Unexpectedly, no direct relationship was found between one particular strain, Na+ content and its tolerance to NaCl or between its ROS content and its tolerance to H2O2. Results show that, although in general, human origin D.fabryi strains were more resistant to oxidative stress and presented shorter doubling times and smaller cell volume than food isolated D.hansenii ones, strains belonging to the same species can be significantly different. Debaryomyces fabryi CBS1793 strain highlighted for its extremely tolerant behavior when exposed to the diverse stress factors studied.
10.	Mirisola, M. G., et al. (författare) Approaches to study yeast cell aging and death 2014 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 14:1, s. 109-118 Tidskriftsartikel (refereegranskat)abstract For millennia, yeast has been exploited to obtain fermentation products, such as foods and beverages. For c. 50years, yeast has been an established model organism for basic and applied research, and more specifically, for c. 15years, this unicellular organism has been applied to dissect molecular mechanisms of cell aging and programmed cell death. In this review, we present an overview of approaches to study cell aging and death in yeast, including lifespan assessments, calorie restriction, cell viability, survival, and death markers.
11.	Nielsen, Jens B, 1962 (författare) Maintaining a strong yeast research community 2014 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 14:4, s. 527-528 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
12.	Petranovic Nielsen, Dina, 1975, et al. (författare) Yeast cell aging and death 2014 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 14:1, s. 1-1 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
13.	Beck, Halfdan, et al. (författare) Saccharomyces kluyveri as a model organism to study pyrimidine degradation. 2008 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 8:8, s. 1209-1213 Tidskriftsartikel (refereegranskat)abstract Abstract The yeast Saccharomyces kluyveri (Lachancea kluyveri), a far relative of Saccharomyces cerevisiae, is not a widely studied organism in the laboratory. However, significant contributions to the understanding of nucleic acid precursors degradation in eukaryotes have been made using this model organism. Here we review eukaryotic pyrimidine degradation with emphasis on the contributions made with S. kluyveri and how this increases our understanding of human disease. Additionally, we discuss the possibilities and limitations of this nonconventional yeast as a laboratory organism.
14.	Chen, Yun, 1978, et al. (författare) Enhancing the copy number of episomal plasmids in Saccharomyces cerevisiae for improved protein production 2012 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 12:5, s. 598-607 Tidskriftsartikel (refereegranskat)abstract 2 mu m-based episomal expression vectors are widely used in Saccharomyces cerevisiae for recombinant protein production and synthetic pathway optimization. In this study, we report a new approach to increase the plasmid copy number (PCN) and thus improve the expression of plasmid-encoded proteins. This was achieved by combining destabilization of the marker protein with decreasing the marker gene transcription level. Destabilization of the marker protein alone by fusing a ubiquitin/N-degron tag (ubi-tag) to the N-terminus of the Ura3 marker protein could increase the PCN and activity of LacZ expressed from the same vector. When arginine was exposed at the N-terminus of the marker protein after cleavage of ubiquitin, the PCN and LacZ activity were increased by 7080%. Replacement of the native URA3 promoter with the HXT1, KEX2 or URA3-d promoter resulted in an increase in the PCN and LacZ activity by about 30100%. Combining the ubi-tag and promoter modification of the marker gene, increased the PCN and LacZ activity by threefold. We also demonstrated that this new expression vectors can be used to increase enzyme activity by improving patchoulol production by threefold.
15.	Costenoble, R., et al. (författare) Engineering of the metabolism of Saccharomyces cerevisiae for anaerobic production of mannitol 2003 Ingår i: Fems Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 3:1, s. 17-25 Tidskriftsartikel (refereegranskat)abstract Under anaerobic conditions, Saccharomyces cerevisiae uses NADH-dependent glycerol-3-phosphate dehydrogenase (Gpd1p and Gpd2p) to re-oxidize excess NADH, yielding substantial amounts of glycerol. In a Deltagpd1 Deltagpd2 double-null mutant, the necessary NAD(+) regeneration through glycerol production is no longer possible, and this mutant does not grow under anaerobic conditions. The excess NADH formed can potentially be used to drive other NADH-dependent reactions or pathways. To investigate this possibility, a double-null mutant was transformed with a heterologous gene (mt1D) from Escherichia coli, coding for NADH-dependent mannitol-I-phosphate dehydrogenase. Expression of this gene in S. cerevisiae should result in NADH oxidation by the NADH-requiring formation of mannitol-1-phosphate from fructose-6-phosphate. The strain was characterized using step-change experiments, in which, during the exponential growth phase, the inlet gas was changed from air to nitrogen. It was found that the mutant produced mannitol only under anaerobic conditions. However, anaerobic growth was not regained, which was probably due to the excessive accumulation of mannitol in the cells. (C) 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
16.	Fekete, Veronika, et al. (författare) Transition of the ability to generate petites in the Saccharomyces/Kluyveromyces complex 2007 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 7:8, s. 1237-1247 Tidskriftsartikel (refereegranskat)abstract Petite-positivity - the ability to tolerate the loss of mtDNA - was examined after the treatment with ethidium bromide (EB) in over hundred isolates from the Saccharomyces/Kluyveromyces complex. The identity of petite mutants was confirmed by the loss of specific mtDNA DAPI staining patterns. Besides unequivocal petite-positive and petite-negative phenotypes, a few species exhibited temperature sensitive petite positive phenotype and petiteness of a few other species could be observed only at the elevated EB concentrations. Several yeast species displayed a mixed 'moot' phenotype, where a major part of the population did not tolerate the loss of mtDNA but several cells did. The genera from postwhole-genome duplication lineages (Saccharomyces, Kazachstania, Naumovia, Nakaseomyces) were invariably petite-positive. However, petite-positive traits could also be observed among the prewhole-genome duplication species.
17.	Fonseca, Alvaro, et al. (författare) Professor Isabel Spencer-Martins 1951-2008 OBITUARY 2008 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 8:7, s. 1208-1208 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
18.	Hong, Kuk-ki, 1976, et al. (författare) Dynamic (13) C-labelling experiments prove important differences in protein turnover rate between two Saccharomyces cerevisiae strains 2012 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 12:7, s. 741-747 Tidskriftsartikel (refereegranskat)abstract We developed a method for quantification of protein turnover using (13) C-labelled substrates combined with analysis of the labeling pattern of proteinogenic amino acids. Using this method the specific amino acid turnover rates between proteins and the pool of free amino acids were determined for eight different amino acids (alanine, valine, proline, aspartic acid, glycine, leucine, isoleucine and threonine) in two Saccharomyces cerevisiae strains (CEN.PK 113-7D and YSBN2). Furthermore, proteasome activities were compared for both strains. Both results confirmed the hypothesis of a higher protein turnover rates in CEN.PK 113-7D, which was generated in a previous comparative systems biology study of these two yeast strains. The ATP costs associated with the observed differences in protein turnover were quantified and could explain accurately the differences in biomass yield between both strains that are observed in chemostat cultures. The percent of maintenance ATP associated to protein polymerization (polymerization for growth and re-polymerization due to turnover) and degradation was estimated to be 72% for YSBN2 and 79% for CEN.PK 113-7D, which makes these processes the dominant non-biosynthetic drain of ATP in living cells, and hence it represents an energetic parameter of great relevance.
19.	Hou, Jin, 1982, et al. (författare) Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae 2012 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 12:5, s. 491-510 Tidskriftsartikel (refereegranskat)abstract The yeast Saccharomyces cerevisiae is a widely used cell factory for the production of fuels and chemicals, and it is also provides a platform for the production of many heterologous proteins of medical or industrial interest. Therefore, many studies have focused on metabolic engineering S similar to cerevisiae to improve the recombinant protein production, and with the development of systems biology, it is interesting to see how this approach can be applied both to gain further insight into protein production and secretion and to further engineer the cell for improved production of valuable proteins. In this review, the protein post-translational modification such as folding, trafficking, and secretion, steps that are traditionally studied in isolation will here be described in the context of the whole system of protein secretion. Furthermore, examples of engineering secretion pathways, high-throughput screening and systems biology applications of studying protein production and secretion are also given to show how the protein production can be improved by different approaches. The objective of the review is to describe individual biological processes in the context of the larger, complex protein synthesis network.
20.	Johansson, Björn, et al. (författare) The non-oxidative pentose phosphate pathway controls the fermentation rate of xylulose but not of xylose in Saccharomyces cerevisiae TMB3001 2002 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 2:3, s. 277-282 Tidskriftsartikel (refereegranskat)abstract Saccharomyces cerevisiae is able to ferment xylose, when engineered with the enzymes xylose reductase (XYL1) and xylitol dehydrogenase (XYL2). However, xylose fermentation is one to two orders of magnitude slower than glucose fermentation. S. cerevisiae has been proposed to have an insufficient capacity of the non-oxidative pentose phosphate pathway (PPP) for rapid xylose fermentation. Strains overproducing the non-oxidative PPP enzymes ribulose 5-phosphate epimerase (EC 5.1.3.1), ribose 5-phosphate ketol isomerase (EC 5.3.1.6), transaldolase (EC 2.2.1.2) and transketolase (EC 2.2.1.1), as well as all four enzymes simultaneously, were compared with respect to xylose and xylulose fermentation with their xylose-fermenting predecessor S. cerevisiae TMB3001, expressing XYL1, XYL2 and only overexpressing XKS1 (xylulokinase). The level of overproduction in S. cerevisiae TMB3026, overproducing all four non-oxidative PPP enzymes, ranged between 4 and 23 times the level in TMB001. Overproduction of the non-oxidative PPP enzymes did not influence the xylose fermentation rate in either batch cultures of 50 g l(-1) xylose or chemostat cultures of 20 g l(-1) glucose and 20 g l(-1) xylose. The low specific growth rate on xylose was also unaffected. The results suggest that neither of the non-oxidative PPP enzymes has any significant control of the xylose fermentation rate in S. cerevisiae TM133001. However, the specific growth rate on xylulose increased from 0.02-0.03 for TMB3001 to 0.12 for the strain overproducing only transaldolase (TAL1) and to 0.23 for TMB3026, suggesting that overproducing all four enzymes has a synergistic effect. TMB3026 consumed xylulose about two times faster than TMB30001 in batch culture of 50 g l(-1) xylulose. The results indicate that growth on xylulose and the xylulose fermentation rate are partly controlled by the non-oxidative PPP, whereas control of the xylose fermentation rate is situated upstream of xylulokinase, in xylose transport, in xylose reductase, and/or in the xylitol dehydrogenase. (C) 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
21.	Kim, Il-Kwon, 1969, et al. (författare) A systems-level approach for metabolic engineering of yeast cell factories 2012 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 12:2, s. 228-248 Forskningsöversikt (refereegranskat)abstract The generation of novel yeast cell factories for production of high-value industrial biotechnological products relies on three metabolic engineering principles: design, construction, and analysis. In the last two decades, strong efforts have been put on developing faster and more efficient strategies and/or technologies for each one of these principles. For design and construction, three major strategies are described in this review: (1) rational metabolic engineering; (2) inverse metabolic engineering; and (3) evolutionary strategies. Independent of the selected strategy, the process of designing yeast strains involves five decision points: (1) choice of product, (2) choice of chassis, (3) identification of target genes, (4) regulating the expression level of target genes, and (5) network balancing of the target genes. At the construction level, several molecular biology tools have been developed through the concept of synthetic biology and applied for the generation of novel, engineered yeast strains. For comprehensive and quantitative analysis of constructed strains, systems biology tools are commonly used and using a multi-omics approach. Key information about the biological system can be revealed, for example, identification of genetic regulatory mechanisms and competitive pathways, thereby assisting the in silico design of metabolic engineering strategies for improving strain performance. Examples on how systems and synthetic biology brought yeast metabolic engineering closer to industrial biotechnology are described in this review, and these examples should demonstrate the potential of a systems-level approach for fast and efficient generation of yeast cell factories.
22.	Logg, Katarina, 1979, et al. (författare) Investigations on light-induced stress in fluorescence microscopy using nuclear localization of the transcription factor Msn2p as a reporter 2009 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 9:6, s. 875-884 Tidskriftsartikel (refereegranskat)abstract We utilized the nuclear localization of a stress-sensitive transcription factor, Msn2p, to study light-induced stress caused by time-lapse fluorescence imaging of green fluorescent protein (GFP) in budding yeast Saccharomyces cerevisiae. A range of exposure times, light intensities and intervals between exposures were tested in order to provide guidelines for noninvasive imaging. We found that the cellular response, revealed as an enhanced nuclear shuttling of Msn2p-GFP, is induced at significantly lower light exposures than those causing observable changes in cell morphology or cell growth. However, no stress induction was observed if the accumulated photon energy per area unit used to obtain an image was maintained at 0.16 J cm−2 or below. Above this 'safe' level, the stress response is determined by both the intensity and the exposure time. In particular, for a given accumulated photon energy per area unit, a high intensity applied during a short exposure causes more stress than vice versa. Interestingly, no correlation was found between the degree of stress and the absolute fluorescence signal, indicating that light-induced cellular stress in the studied system is not specifically related to GFP excitation.
23.	Martinez Ruiz, Jose Luis, 1981, et al. (författare) Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii 2012 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 12:6, s. 651-661 Tidskriftsartikel (refereegranskat)abstract In this work, we performed for the first time a proteomic approach to the processes induced by long-term potassium starvation in the halotolerant yeast Debaryomyces hansenii. The proteomic profile under this ionic stress conditions shows that important changes in gene expression take place as an adaptive response. We found a significant protein expression repression as well as metabolic changes such as the inhibition of the upper part of the glycolysis, the amino acid synthesis, and the Krebs cycle. On the other hand, genes related to stress responses, protein degradation, and sterols synthesis were upregulated in response to potassium deprivation. The findings in this study provide important information about how this particular yeast copes with ionic stress at molecular levels, which might further enrich the global understanding of salt tolerance processes in eukaryal systems and moreover highlighting the importance of the omics approaches as a complement to the classical physiological studies.
24.	Merico, Annamaria, et al. (författare) The oxygen level determines the fermentation pattern in Kluyveromyces lactis 2009 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 9:5, s. 749-756 Tidskriftsartikel (refereegranskat)abstract Yeasts belonging to the lineage that underwent whole-genome duplication (WGD) possess a good fermentative potential and can proliferate in the absence of oxygen. In this study, we analyzed the pre-WGD yeast Kluyveromyces lactis and its ability to grow under oxygen-limited conditions. Under these conditions, K. lactis starts to increase the glucose metabolism and accumulates ethanol and glycerol. However, under more limited conditions, the fermentative metabolism decreases, causing a slow growth rate. In contrast, Saccharomyces cerevisiae and Saccharomyces kluyveri in anaerobiosis exhibit almost the same growth rate as in aerobiosis. In this work, we showed that in K. lactis, under oxygen-limited conditions, a decreased expression of RAG1 occurred. The activity of glucose-6-phosphate dehydrogenase also decreased, likely causing a reduced flux in the pentose phosphate pathway. Comparison of related and characterized yeasts suggests that the behavior observed in K. lactis could reflect the lack of an efficient mechanism to maintain a high glycolytic flux and to balance the redox homeostasis under hypoxic conditions. This could be a consequence of a recent specialization of K. lactis toward living in a niche where the ethanol accumulation at high oxygen concentrations and the ability to survive at a low oxygen concentration do not represent an advantage.
25.	Muñoz Arellano, Ana Joyce, 1983, et al. (författare) Systems biology of yeast cell death 2012 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 12:2, s. 249-265 Forskningsöversikt (refereegranskat)abstract Programmed cell death (PCD) (including apoptosis) is an essential process, and many human diseases of high prevalence such as neurodegenerative diseases and cancer are associated with deregulations in the cell death pathways. Yeast Saccharomyces cerevisiae, a unicellular eukaryotic organism, shares with multicellular organisms (including humans) key components and regulators of the PCD machinery. In this article, we review the current state of knowledge about cell death networks, including the modeling approaches and experimental strategies commonly used to study yeast cell death. We argue that the systems biology approach will bring valuable contributions to our understanding of regulations and mechanisms of the complex cell death pathways.
26.	Nielsen, Jens B, 1962, et al. (författare) Metabolic engineering, synthetic biology and systems biology 2012 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 12:2, s. 103-103 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
27.	Petranovic Nielsen, Dina, 1975, et al. (författare) Prospects of yeast systems biology for human health: integrating lipid, protein and energy metabolism 2010 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 10:8, s. 1046-1059 Tidskriftsartikel (refereegranskat)abstract The yeast Saccharomyces cerevisiae is a widely used model organism for studying cell biology, metabolism, cell cycle and signal transduction. Many regulatory pathways are conserved between this yeast and humans, and it is therefore possible to study pathways that are involved in disease development in a model organism that is easy to manipulate and that allows for detailed molecular studies. Here, we briefly review pathways involved in lipid metabolism and its regulation, the regulatory network of general metabolic regulator Snf1 (and its human homologue AMPK) and the proteostasis network with its link to stress and cell death. All the mentioned pathways can be used as model systems for the study of homologous pathways in human cells and a failure in these pathways is directly linked to several human diseases such as the metabolic syndrome and neurodegeneration. We demonstrate how different yeast pathways are conserved in humans, and we discuss the possibilities of using the systems biology approach to study and compare the pathways of relevance with the objective to generate hypotheses and gain new insights.
28.	Prochazka, Emanuel, et al. (författare) Mitochondrial genome from the facultative anaerobe and petite-positive yeast Dekkera bruxellensis contains the NADH dehydrogenase subunit genes 2010 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 10:5, s. 545-557 Tidskriftsartikel (refereegranskat)abstract The progenitor of the Dekkera/Brettanomyces clade separated from the Saccharomyces/Kluyveromyces clade over 200 million years ago. However, within both clades, several lineages developed similar physiological traits. Both Saccharomyces cerevisiae and Dekkera bruxellensis are facultative anaerobes; in the presence of excess oxygen and sugars, they accumulate ethanol (Crabtree effect) and they both spontaneously generate respiratory-deficient mutants (petites). In order to understand the role of respiratory metabolism, the mitochondrial DNA (mtDNA) molecules of two Dekkera/Brettanomyces species were analysed. Dekkera bruxellensis mtDNA shares several properties with S. cerevisiae, such as the large genome size (76 453 bp), and the organization of the intergenic sequences consisting of spacious AT-rich regions containing a number of hairpin GC-rich cluster-like elements. In addition to a basic set of the mitochondrial genes coding for the components of cytochrome oxidase, cytochrome b, subunits of ATPase, two rRNA subunits and 25 tRNAs, D. bruxellensis also carries genes for the NADH dehydrogenase complex. Apparently, in yeast, the loss of this complex is not a precondition to develop a petite-positive, Crabtree-positive and anaerobic nature. On the other hand, mtDNA from a petite-negative Brettanomyces custersianus is much smaller (30 058 bp); it contains a similar gene set and has only short intergenic sequences.
29.	Rhodin, Jenny, et al. (författare) Highly sequence-specific binding is retained within the DNA-binding domain of the Saccharomyces castellii Cdc13 telomere-binding protein 2008 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 8:8, s. 1289-1302 Tidskriftsartikel (refereegranskat)abstract The essential protein Cdc13p binds the single-stranded telomeric 3' overhangs in Saccharomyces cerevisiae and takes part in the regulation of telomere length. The DNA-binding domain (DBD) of Cdc13p is structurally established by an oligonucleotide/oligosaccharide-binding (OB)-fold domain. The sequence homolog in Saccharomyces castellii (scasCDC13) was characterized previously, and the full-length protein was found to bind telomeric DNA specifically. Here, the DBD of scasCdc13p was defined to the central part (402-658) of the protein. The region necessary for forming the scasCdc13p-DBD is larger than the minimal DBD of S. cerevisiae Cdc13p. Deletion of this extended DBD region from the full-length protein completely abolished the DNA binding, indicating the importance of the extended region for the correct formation of a binding-competent DBD. The scasCdc13p-DBD bound the same 8-mer minimal binding site as the full-length protein, but an extension of the target site in the 3' end increased the stability of the DNA-protein complex. Significantly, scasCdc13p-DBD showed a retained high sequence specific binding, where the four nucleotides of most importance for the sequence specificity are highly conserved in eukaryotic telomeric repeats. Thus, the unique single-stranded DNA-binding properties of the full-length protein are entirely retained within the isolated scasCdc13p-DBD.
30.	Rozpedowska, Elzbieta, et al. (författare) Candida albicans- a pre-whole genome duplication yeast is predominantly aerobic and a poor ethanol producer. 2011 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 11:3, s. 285-291 Tidskriftsartikel (refereegranskat)abstract Yeast species belonging to the lineage that underwent the whole genome duplication (WGD), and including Saccharomyces cerevisiae, can grow under anaerobiosis and accumulate ethanol in the presence of glucose and oxygen. The pre-WGD yeasts, which branched from the S. cerevisiae lineage just prior to the WGD event, including Kluyveromyces lactis, are more dependent on oxygen and do not accumulate large amounts of ethanol in the presence of excess oxygen. Yeasts that belong to the so-called 'lower branches' of the yeast phylogenetic tree and diverged from S. cerevisiae more than 200 million years ago, have so far not been thoroughly investigated for their physiology and carbon metabolism. We have hereby studied several isolates of Candida albicans and Debaryomyces hansenii for their dependence on oxygen. C. albicans grew very poorly at oxygen concentration below 1 p.p.m. and D. hansenii could not grow at all. In aerobic batch cultivations C. albicans exhibited a predominately aerobic metabolism, accumulating only small amounts of ethanol (0.01-0.09 g g(-1) glucose). Apparently, C. albicans and several other pre-WGD yeasts still exhibit the original traits of the yeast progenitor: poor accumulation of ethanol under aerobic conditions and strong dependence on the presence of oxygen.
31.	Scalcinati, Gionata, 1981, et al. (författare) Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption 2012 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 12:5, s. 582-597 Tidskriftsartikel (refereegranskat)abstract Industrial biotechnology aims to develop robust microbial cell factories, such as Saccharomyces cerevisiae, to produce an array of added value chemicals presently dominated by petrochemical processes. Xylose is the second most abundant monosaccharide after glucose and the most prevalent pentose sugar found in lignocelluloses. Significant research efforts have focused on the metabolic engineering of S similar to cerevisiae for fast and efficient xylose utilization. This study aims to metabolically engineer S similar to cerevisiae, such that it can consume xylose as the exclusive substrate while maximizing carbon flux to biomass production. Such a platform may then be enhanced with complementary metabolic engineering strategies that couple biomass production with high value-added chemical. Saccharomyces cerevisiae, expressing xylose reductase, xylitol dehydrogenase and xylulose kinase, from the native xylose-metabolizing yeast Pichia stipitis, was constructed, followed by a directed evolution strategy to improve xylose utilization rates. The resulting S similar to cerevisiae strain was capable of rapid growth and fast xylose consumption producing only biomass and negligible amount of byproducts. Transcriptional profiling of this strain was employed to further elucidate the observed physiology confirms a strongly up-regulated glyoxylate pathway enabling respiratory metabolism. The resulting strain is a desirable platform for the industrial production of biomass-related products using xylose as a sole carbon source.
32.	Kerkhoven, Eduard, 1985, et al. (författare) Applications of computational modeling in metabolic engineering of yeast 2015 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 15:1 Tidskriftsartikel (refereegranskat)abstract Generally, a microorganism's phenotype can be described by its pattern of metabolic fluxes. Although fluxes cannot be measured directly, inference of fluxes is well established. In biotechnology the aim is often to increase the capacity of specific fluxes. For this, metabolic engineering methods have been developed and applied extensively. Many of these rely on balancing of intracellular metabolites, redox, and energy fluxes, using genome-scale models (GEMs) that in combination with appropriate objective functions and constraints can be used to predict potential gene targets for obtaining a preferred flux distribution. These methods point to strategies for altering gene expression; however, fluxes are often controlled by post-transcriptional events. Moreover, GEMs are usually not taking into account metabolic regulation, thermodynamics and enzyme kinetics. To facilitate metabolic engineering, tools from synthetic biology have emerged, enabling integration and assembly of naturally nonexistent, but well-characterized components into a living organism. To describe these systems kinetic models are often used and to integrate these systems with the standard metabolic engineering approach, it is necessary to expand the modeling of metabolism to consider kinetics of individual processes. This review will give an overview about models available for metabolic engineering of yeast and discusses their applications.
33.	Marek, Magdalena, et al. (författare) Serum albumin promotes ATP-binding cassette transporter-dependent sterol uptake in yeast 2014 Ingår i: FEMS yeast research (Print). - : Oxford Academic. - 1567-1356 .- 1567-1364. ; 14:8, s. 1223-1233 Tidskriftsartikel (refereegranskat)abstract Sterol uptake in fungi is a multistep process that involves interaction between external sterols and the cell wall, incorporation of sterol molecules into the plasma membrane, and subsequent integration into intracellular membranes for turnover. ATP-binding cassette (ABC) transporters have been implicated in sterol uptake, but key features of their activity remain to be elucidated. Here, we apply fluorescent cholesterol (NBD-cholesterol) to monitor sterol uptake under anaerobic and aerobic conditions in two fungal species, Candida glabrata (Cg) and Saccharomyces cerevisiae (Sc). We found that in both fungal species, ABC transporter-dependent uptake of cholesterol under anaerobic conditions and in mutants lacking HEM1 gene is promoted in the presence of the serum protein albumin that is able to bind the sterol molecule. Furthermore, the C. glabrataABC transporter CgAus1p expressed in S. cerevisiae requires the presence of serum or albumin for efficient cholesterol uptake. These results suggest that albumin can serve as sterol donor in ABC transporter-dependent sterol uptake, a process potentially important for growth of C. glabrata inside infected humans.Serum albumin can serve as sterol donor in ATP-binding cassette-transporter-dependent sterol uptake, a process potentially important for growth of Candida glabrata inside infected humans.Serum albumin can serve as sterol donor in ATP-binding cassette-transporter-dependent sterol uptake, a process potentially important for growth of Candida glabrata inside infected humans.
34.	Nielsen, Jens B, 1962 (författare) From the Chief Editor 2013 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 13:1, s. 1-1 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
35.	Druvefors, U., et al. (författare) Efficacy of the biocontrol yeast Pichia anomala during long-term storage of moist feed grain under different oxygen and carbon dioxide regimens 2002 Ingår i: FEMS yeast research (Print). - 1567-1356 .- 1567-1364. ; 2:3, s. 389-394 Tidskriftsartikel (refereegranskat)abstract The yeast Pichia anomala inhibits the spoilage mold Penicillium roqueforti in laboratory experiments with high-moisture wheat in malfunctioning airtight storage. The ability of P. anomala to prevent mold growth during 14 months of grain storage was evaluated in outdoor silos with different air permeabilities. Freshly harvested wheat in 160-kg portions was inoculated with 102 colony-forming units (cfu) g-1 P. roqueforti, alone or together with 104 cfu g-1 P. anomala. During the first month P. anomala increased to about 106 cfu g-1 in the treated silos to reach 107 cfu g-1 after 9 months. Naturally occurring P. anomala in the untreated silos increased from 102 to about 103 cfu g-1 during the first month and reached the same level as the treated silos after 9 months. Oxygen levels were reduced below the detection limit within 1 day, while carbon dioxide levels increased to 80-90% during the first month. P. roqueforti did not grow in wheat treated with P. anomala, regardless of silo permeability, but had increased to 105 cfu g-1 in the untreated silos after 14 months of storage. © 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
36.	Druvefors, Ulrika, et al. (författare) Efficacy of the biocontrol yeast Pichia anomala during long-term storage of moist feed grain under different oxygen and carbon dioxide regimens 2002 Ingår i: FEMS yeast research (Print). - : Elsevier. - 1567-1356 .- 1567-1364. ; 2:3, s. 389-394 Tidskriftsartikel (refereegranskat)abstract The yeast Pichia anomala inhibits the spoilage mold Penicillium roqueforti in laboratory experiments with high-moisture wheat in malfunctioning airtight storage. The ability of P. anomala to prevent mold growth during 14 months of grain storage was evaluated in outdoor silos with different air permeabilities. Freshly harvested wheat in 160-kg portions was inoculated with 10(2) colony-forming units (cfu) g(-1) P. roqueforti, alone or together with 10(4) cfu, g(-1) P. anomala. During the first month P. anomala increased to about 10(6) cfu g(-1) in the treated silos to reach 10(7) cfu g(-1) after 9 months. Naturally occurring P. anomala in the untreated silos increased from 10(2) to about 10(3) cfu g(-1) during the first month and reached the same level as the treated silos after 9 months. Oxygen levels were reduced below the detection limit within 1 day, while carbon dioxide levels increased to 80-90% during the first month. P. roqueforti did not grow in wheat treated with P. anomala, regardless of silo permeability, but had increased to 10(5) cfu g(-1) in the untreated silos after 14 months of storage.
37.	Fredlund, Elisabeth, et al. (författare) Physiological characteristics of the biocontrol yeast Pichia anomala J121 2002 Ingår i: FEMS yeast research (Print). - : Elsevier. - 1567-1356 .- 1567-1364. ; 2:3, s. 395-402 Tidskriftsartikel (refereegranskat)abstract The yeast Pichia anomala J121 prevents mold spoilage and enhances preservation of moist grain in malfunctioning storage systems. Development of P. anomala J121 as a biocontrol agent requires in-depth knowledge about its physiology. P. anomala J121 grew under strictly anaerobic conditions, at temperatures between 3degreesC and 37degreesC, at pH values between 2.0 and 12.4, and at a water activity of 0.92 (NaCl) and 0.85 (glycerol). It could assimilate a wide range of C- and N-sources and produce killer toxin. A selective medium containing starch, nitrate, acetic acid, and chloramphenicol was developed for P. anomala. P. anomala was equally sensitive as Candida albicans to common antifungal compounds. Growth ability at a range of environmental conditions contributes to the competitive ability of the biocontrol yeast P. anomala J121.
38.	Gombault, Aurélie, et al. (författare) A phenotypic study of TFS1 mutants differentially altered in the inhibition of Ira2p or CPY. 2009 Ingår i: FEMS yeast research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 9:6, s. 867-74 Tidskriftsartikel (refereegranskat)abstract The Saccharomyces cerevisiae protein Tfs1p is known as a dual protein. On the one hand, it inhibits the carboxypeptidase Y protease, and on the other, it inhibits Ira2p, a GTPase-activating protein of Ras. We managed to dissect precise areas of Tfs1p specifically involved in only one of those functions. Based on these data, specific Tfs1p point mutants affected in only one of these two functions were constructed. In order to obtain insights on the physiological role of these functions, systematic phenotypic tests were performed on strains expressing these specific Tfs1p mutants. The results obtained demonstrate that the inhibition of Ira2p by Tfs1p is the predominant function under the conditions tested.
39.	Mapelli, Valeria, 1978, et al. (författare) The interplay between sulphur and selenium metabolism in yeast influences the intracellular redox balance 2012 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 12:1, s. 20-32 Tidskriftsartikel (refereegranskat)abstract Selenium is an essential element for most eukaryotic organisms, including humans. The balance between Se toxicity and its beneficial effects is very delicate. It has been demonstrated that a diet enriched of Se has cancer prevention potential in humans. The most popular commercial Se supplementation is selenized yeast, which is produced in a fermentation process using an inorganic source of Se. Here we show that uptake of Se, Se toxic effects and intracellular Se-metabolite profile are largely influenced by the level of sulphur source supplied during the fermentation. A Yap1-dependent oxidative stress response is active when yeast actively metabolizes Se and this response is linked to the generation of an intracellular redox imbalance. The redox imbalance derives from a disproportionate ratio between the reduced and oxidized form of glutathione and also from the influence of Se metabolism on the central carbon metabolism. The observed increase of glycerol production rate concomitant with the inhibition of ethanol formation in the presence of Se can be ascribed to the occurrence of redox imbalance that triggers glycerol biosynthesis to replenish the pool of NAD+.
40.	Olstorpe, Matilda, et al. (författare) Screening of yeast strains for phytase activity 2009 Ingår i: FEMS yeast research (Print). - Oxford, United Kingdom : Oxford University Press. - 1567-1356 .- 1567-1364. ; 9:3, s. 478-488 Tidskriftsartikel (refereegranskat)abstract A screening method was developed to elucidate the ability of different yeast strains to utilize phytic acid as sole phosphorus source. The growth test in liquid culture in a microtiter plate with phytic acid as sole phosphorus source was shown to be a reliable, fast and easy-to-use screening method. We tested 122 strains from 61 species with our method and observed growth differences among species and strains that were not detectable on solid medium. Specific phytase activities were measured for 10 yeasts strains, selected due to their strong growth in the liquid medium. Strains of Arxula adeninivorans and Pichia anomala reached the highest volumetric phytase activities. Arxula adeninivorans also displayed the highest intra- and extracellular specific activities. There were large differences in both extra- and intracellular phytase activities among species. Strain-specific extracellular phytase activities were detected in P. anomala. The presence of free phosphate in the media completely suppressed the extracellular phytase activity and also reduced intracellular phytase activity for all tested yeast strains.
41.	Passoth, V., et al. (författare) Biotechnology, physiology and genetics of the yeast Pichia anomala 2006 Ingår i: FEMS yeast research (Print). - Oxon, United Kingdom : Blackwell Publishing. - 1567-1356 .- 1567-1364. ; 6:1, s. 3-13 Forskningsöversikt (refereegranskat)abstract The ascomycetous yeast Pichia anomala is frequently associated with food and feed products, either as a production organism or as a spoilage yeast. It belongs to the nonSaccharomyces wine yeasts and contributes to the wine aroma by the production of volatile compounds. The ability to grow in preserved food and feed environments is due to its capacity to grow under low pH, high osmotic pressure and low oxygen tension. A new application of P. anomala is its use as a biocontrol agent, which is based on the potential to inhibit a variety of moulds in different environments. Although classified as a biosafety class-1 organism, cases of P. anomala infections have been reported in immunocompromised patients. On the other hand, P. anomala killer toxins have a potential as antimicrobial agents. The yeast can use a broad range of nitrogen and phosphor sources, which makes it a potential agent to decrease environmental pollution by organic residues from agriculture. However, present knowledge of the physiological basis of its performance is limited. Recently, the first studies have been published dealing with the global regulation of the metabolism of P. anomala under different conditions of oxygenation.
42.	Passoth, Volkmar (författare) Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities 2012 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 12, s. 382-386 Tidskriftsartikel (refereegranskat)abstract The ascomycetous yeast Wickerhamomyces anomalus (formerly Pichia anomala and Hansenula anomala) exhibits antimicrobial activities and flavoring features that are responsible for its frequent association with food, beverage and feed products. However, limited information on the genetic background of this yeast and its multiple capabilities are currently available. Here, we present the draft genome sequence of the neotype strain W. anomalus DSM 6766. On the basis of pyrosequencing, a de novo assembly of this strain resulted in a draft genome sequence with a total size of 25.47 Mbp. An automatic annotation using RAPYD generated 11 512 protein-coding sequences. This annotation provided the basis to analyse metabolic capabilities, phylogenetic relationships, as well as biotechnologically important features and yielded novel candidate genes of W. anomalus DSM 6766 coding for proteins participating in antimicrobial activities.
43.	Wilson, D, et al. (författare) Identifying infection-associated genes of Candida albicans in the postgenomic era 2009 Ingår i: FEMS yeast research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 9:5, s. 688-700 Tidskriftsartikel (refereegranskat)
44.	Zvyagilskaya, Renata A., et al. (författare) Characterization of the Pho89 phosphate transporter by functional hyperexpression in Saccharomyces cerevisiae 2008 Ingår i: FEMS yeast research (Print). - : Oxford University Press. - 1567-1356 .- 1567-1364. ; 8:5, s. 685-696 Tidskriftsartikel (refereegranskat)abstract The Na(+)-coupled, high-affinity Pho89 plasma membrane phosphate transporter in Saccharomyces cerevisiae has so far been difficult to study because of its low activity and special properties. In this study, we have used a pho84Deltapho87Deltapho90Deltapho91Delta quadruple deletion strain of S. cerevisiae devoid of all transporter genes specific for inorganic phosphate, except for PHO89, to functionally characterize Pho89 under conditions where its expression is hyperstimulated. Under these conditions, the Pho89 protein is strongly upregulated and is the sole high-capacity phosphate transporter sustaining cellular acquisition of inorganic phosphate. Even if Pho89 is synthesized in cells grown at pH 4.5-8.0, the transporter is functionally active under alkaline conditions only, with a K(m) value reflecting high-affinity properties of the transporter and with a transport rate about 100-fold higher than that of the protein in a wild-type strain. Even under these hyperexpressive conditions, Pho89 is unable to sense and signal extracellular phosphate levels. In cells grown at pH 8.0, Pho89-mediated phosphate uptake at alkaline pH is cation-dependent with a strong activation by Na(+) ions and sensitivity to carbonyl cyanide m-chlorophenylhydrazone. The contribution of H(+)- and Na(+)-coupled phosphate transport systems in wild-type cells grown at different pH values was quantified. The contribution of the Na(+)-coupled transport system to the total cellular phosphate uptake activity increases progressively with increasing pH.
45.	Alper, H. S., et al. (författare) Editorial: Yeast synthetic biology: new tools to unlock cellular function 2015 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 15:1 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
46.	Baumann, Leonie, et al. (författare) Transcriptomic response of Saccharomyces cerevisiae to octanoic acid production 2021 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 21:2 Tidskriftsartikel (refereegranskat)abstract The medium-chain fatty acid octanoic acid is an important platform compound widely used in industry. The microbial production from sugars in Saccharomyces cerevisiae is a promising alternative to current non-sustainable production methods, however, titers need to be further increased. To achieve this, it is essential to have in-depth knowledge about the cell physiology during octanoic acid production. To this end, we collected the first RNA-Seq data of an octanoic acid producer strain at three time points during fermentation. The strain produced higher levels of octanoic acid and increased levels of fatty acids of other chain lengths (C6-C18) but showed decreased growth compared to the reference. Furthermore, we show that the here analyzed transcriptomic response to internally produced octanoic acid is notably distinct from a wild type's response to externally supplied octanoic acid as reported in previous publications. By comparing the transcriptomic response of different sampling times, we identified several genes that we subsequently overexpressed and knocked out, respectively. Hereby we identified RPL40B, to date unknown to play a role in fatty acid biosynthesis or medium-chain fatty acid tolerance. Overexpression of RPL40B led to an increase in octanoic acid titers by 40%.
47.	Bergman, Alexandra Linda, 1985, et al. (författare) Effects of overexpression of STB5 in Saccharomyces cerevisiae on fatty acid biosynthesis, physiology and transcriptome 2019 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 19:3 Tidskriftsartikel (refereegranskat)abstract Microbial conversion of biomass to fatty acids (FA) and products derived thereof is an attractive alternative to the traditional oleochemical production route from animal and plant lipids. This study examined if NADPH-costly FA biosynthesis could be enhanced by overexpressing the transcription factor Stb5 in Saccharomyces cerevisiae. Stb5 activates expression of multiple genes encoding enzymes within the pentose phosphate pathway (PPP) and other NADPH-producing reactions. Overexpression of STB5 led to a decreased growth rate and an increased free fatty acid (FFA) production during growth on glucose. The improved FFA synthetic ability in the glucose phase was shown to be independent of flux through the oxidative PPP. RNAseq analysis revealed that STB5 overexpression had wide-ranging effects on the transcriptome in the batch phase, and appeared to cause a counterintuitive phenotype with reduced flux through the oxidative PPP. During glucose limitation, when an increased NADPH supply is likely less harmful, an overall induction of the proposed target genes of Stb5 (eg. GND1/2, TAL1, ALD6, YEF1) was observed. Taken together, the strategy of utilizing STB5 overexpression to increase NADPH supply for reductive biosynthesis is suggested to have potential in strains engineered to have strong ability to consume excess NADPH, alleviating a potential redox imbalance.
48.	Blomberg, Anders, 1956 (författare) Yeast osmoregulation - glycerol still in pole position 2022 Ingår i: Fems Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 22:1 Tidskriftsartikel (refereegranskat)abstract In response to osmotic dehydration cells sense, signal, alter gene expression, and metabolically counterbalance osmotic differences. The main compatible solute/osmolyte that accumulates in yeast cells is glycerol, which is produced from the glycolytic intermediate dihydroxyacetone phosphate. This review covers recent advancements in understanding mechanisms involved in sensing, signaling, cell-cycle delays, transcriptional responses as well as post-translational modifications on key proteins in osmoregulation. The protein kinase Hog1 is a key-player in many of these events, however, there is also a growing body of evidence for important Hog1-independent mechanisms playing vital roles. Several missing links in our understanding of osmoregulation will be discussed and future avenues for research proposed. The review highlights that this rather simple experimental system-salt/sorbitol and yeast-has developed into an enormously potent model system unravelling important fundamental aspects in biology. Yeast osmoregulation is a multifaceted response that integrates sensing, signaling, cell cycle delay, transcriptional changes, and metabolic adjustments.
49.	Blomqvist, Johanna, et al. (författare) Dekkera bruxellensis-spoilage yeast with biotechnological potential, and a model for yeast evolution, physiology and competitiveness 2015 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 15, s. 9- Forskningsöversikt (refereegranskat)abstract Dekkera bruxellensis is a non-conventional yeast normally considered a spoilage organism in wine (off-flavours) and in the bioethanol industry. But it also has potential as production yeast. The species diverged from Saccharomyces cerevisiae 200 mya, before the whole genome duplication. However, it displays similar characteristics such as being Crabtree-and petite positive, and the ability to grow anaerobically. Partial increases in ploidy and promoter rewiring may have enabled evolution of the fermentative lifestyle in D. bruxellensis. On the other hand, it has genes typical for respiratory yeasts, such as for complex I or the alternative oxidase AOX1. Dekkera bruxellensis grows more slowly than S. cerevisiae, but produces similar or greater amounts of ethanol, and very low amounts of glycerol. Glycerol production represents a loss of energy but also functions as a redox sink for NADH formed during synthesis of amino acids and other compounds. Accordingly, anaerobic growth required addition of certain amino acids. In spite of its slow growth, D. bruxellensis outcompeted S. cerevisiae in glucose-limited cultures, indicating a more efficient energy metabolism and/or higher affinity for glucose. This review tries to summarize the latest discoveries about evolution, physiology and metabolism, and biotechnological potential of D. bruxellensis.
50.	Bon, Elba, et al. (författare) Yeasts in green chemistry 2004 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1364 .- 1567-1356. ; 5:3, s. 299-300 Tidskriftsartikel (refereegranskat)

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