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https://www.readbyqxmd.com/read/29345746/history-of-genome-editing-in-yeast
#1
Marcin G Fraczek, Samina Naseeb, Daniela Delneri
For thousands of years humans have used the budding yeast Saccharomyces cerevisiae for production of bread and alcohol, however only for the last 30-40 years our understanding of the yeast biology has dramatically increased enabling us to modify its genome. Although S. cerevisiae has been the main focus of many research groups, other non-conventional yeasts have also been studied and exploited for biotechnological purposes. Our experiments and knowledge have evolved from recombination, to high-throughput PCR based transformations, to highly accurate CRISPR methods, in order to alter yeast traits for either research of industrial purposes...
January 18, 2018: Yeast
https://www.readbyqxmd.com/read/29322598/erythritol-production-by-yeasts-a-snapshot-of-current-knowledge
#2
REVIEW
Frédéric Carly, Patrick Fickers
Erythritol is a four-carbon sugar alcohol produced by microorganisms as an osmoprotectant. It could be used as a natural sweetener in the pharmaceutical and food industries. Here, a snapshot on current knowledge on erythritol metabolism and synthesis, optimization of its production, more precisely process and producer strain improvement is presented.
January 11, 2018: Yeast
https://www.readbyqxmd.com/read/29322557/veni-vidi-vici-the-success-of-wtf-meiotic-drivers-in-fission-yeast
#3
José Fabricio López Hernández, Sarah E Zanders
Meiotic drivers are selfish DNA loci that can bias their own transmission into gametes. Due to their transmission advantages, meiotic drivers can spread in populations even if the drivers or linked variants decrease organismal fitness. Meiotic drive was first formally described in the 1950s and is thought to be a powerful force shaping eukaryotic genomes. Classic genetic analyses have detected the action of meiotic drivers in plants, filamentous fungi, insects, and vertebrates. Several of these drive systems have limited experimental tractability and relatively little is known about the molecular mechanisms of meiotic drive...
January 11, 2018: Yeast
https://www.readbyqxmd.com/read/29322552/gene-gene-and-gene-environment-interactions-in-complex-traits-in-yeast
#4
Anupama Yadav, Himanshu Sinha
One of the fundamental question in biology is how the genotype regulates the phenotype. An increasing number of studies indicate that in most cases, the effect of a genetic locus on the phenotype is context-dependent, i.e. it is influenced by the genetic background and the environment in which the phenotype is measured. Still, the majority of the studies, in both model organisms and humans, that map the genetic regulation of phenotypic variation in complex traits primarily identify additive loci with independent effects...
January 10, 2018: Yeast
https://www.readbyqxmd.com/read/29320804/misidentification-of-genome-assemblies-in-public-databases-the-case-of-naumovozyma-dairenensis-and-proposal-of-a-protocol-to-correct-misidentifications
#5
Aimilia A Stavrou, Verónica Mixão, Teun Boekhout, Toni Gabaldón
Online sequence databases such as NCBI GenBank serve as a tremendously useful platform for researchers to share and reuse published data. However, submission systems lack control for errors such as organism misidentification, which once entered in the database can be propagated and mislead downstream analyses. Here we present an illustrating case of misidentification of Candida albicans from a clinical sample as Naumovozyma dairenensis based on whole-genome shotgun data. Analyses of phylogenetic markers, read mapping and single nucleotide polymorphisms (SNP) served to correct the identification...
January 10, 2018: Yeast
https://www.readbyqxmd.com/read/29277924/identification-and-characterization-of-novel-promoters-for-recombinant-protein-production-in-yeast-pichia-pastoris
#6
Ning Xu, Jinxiang Zhu, Qiaoyun Zhu, Yanzi Xing, Menghao Cai, Tianyi Jiang, Mian Zhou, Yuanxing Zhang
Pichia pastoris expression system has been widely used in recombinant protein production. So far the majority of heterologous proteins are expressed by methanol inducible promoter PAOX1 and constitutive promoter PGAP . The use of other promoters is rather limited. Here we selected 16 potentially efficient and regulatory promoter candidates based on the RNA-seq and RNA folding free energy ΔG data. GFP and recombinant amylase were inserted after these promoters to reveal their strength and efficiency under different carbon sources and culture scales...
December 26, 2017: Yeast
https://www.readbyqxmd.com/read/29277922/glutathione-levels-influence-chronological-life-span-of-saccharomyces-cerevisiae-in-a-glucose-dependent-manner
#7
Mayra Fabiola Tello-Padilla, Alejandra Yudid Perez-Gonzalez, Melina Canizal-García, Juan Carlos González-Hernández, Christian Cortes-Rojo, Ivanna Karina Olivares-Marin, Luis Alberto Madrigal-Perez
Diet plays a key role in determining the longevity of the organisms since it has been demonstrated that glucose restriction increases lifespan whereas a high-glucose diet decreases it. However, the molecular basis of how diet leads to the aging process is currently unknown. We propose that the quantity of glucose that fuels respiration influences ROS generation and glutathione levels, and both chemical species impact in the aging process. Herein, we provide evidence that mutation of the gene GSH1 in S. cerevisiae diminishes glutathione levels...
December 26, 2017: Yeast
https://www.readbyqxmd.com/read/29247562/a-history-of-genome-editing-in-saccharomyces-cerevisiae
#8
William G Alexander
Genome editing is a form of highly precise genetic engineering which produces alterations to an organism's genome as small as a single base pair with no incidental or auxiliary modifications; this technique is crucial to the field of synthetic biology, which requires such precision in the installation of novel genetic circuits into host genomes. While a new methodology for most organisms, genome editing capabilities have been used in the budding yeast Saccharomyces cerevisiae for decades. In this review, I will present a brief history of genome editing in S...
December 16, 2017: Yeast
https://www.readbyqxmd.com/read/29159981/understanding-the-metabolic-burden-of-recombinant-antibody-production-in-saccharomyces-cerevisiae-using-a-quantitative-metabolomics-approach
#9
Jorg C de Ruijter, Essi V Koskela, Jatin Nandania, Alexander D Frey, Vidya Velagapudi
The cellular changes induced by heterologous protein expression in the yeast Saccharomyces cerevisiae have been analyzed on many levels and found to be significant. However, even though high-level protein production poses a metabolic burden, evaluation of the expression host at the level of the metabolome has often been neglected. We present a comparison of metabolite profiles of a wild-type strain with those of three strains producing recombinant antibody variants of increasing size and complexity: a scFv fragment, a scFv-Fc fusion protein, and a full-length IgG molecule...
November 20, 2017: Yeast
https://www.readbyqxmd.com/read/29143358/melatonin-improves-survival-and-respiratory-activity-of-yeast-cells-challenged-by-alpha-synuclein-and-menadione
#10
Mariana A Zampol, Mario H Barros
One of the hallmarks of Parkinson disease is α-synuclein aggregate deposition that leads to ER stress, Golgi fragmentation, and impaired energy metabolism with consequent redox imbalance. In the last decade, many studies have used Saccharomyces cerevisiae as a model in order to explore the intracellular consequences of α-synuclein overexpression. In this study we propose to evaluate the respiratory outcome of yeast cells expressing α-synuclein. Cell viability, or growth on selective media for respiratory activity was mainly affected in the α-synuclein expressing cells if they were also treated with menadione, which stimulates ROS production...
November 16, 2017: Yeast
https://www.readbyqxmd.com/read/29143357/influence-of-phosphatidylserine-and-phosphatidylethanolamine-on-farnesol-tolerance-in-candida-albicans
#11
Sahar Hasim, Elyse N Vaughn, Dallas Donohoe, Donna M Gordon, Susan Pfiffner, Todd B Reynolds
Candida albicans is the most common human fungal pathogen. The ability to undergo the morphological transition from yeast to hyphal growth is critical for its pathogenesis. Farnesol, a precursor in the isoprenoid/sterol pathway, is a quorum-sensing molecule produced by C. albicans that inhibits hyphal growth in this polymorphic fungus. Interestingly, C. albicans can tolerate farnesol concentrations that are toxic to other fungi. We hypothesized that changes in phospholipid composition are one of the factors contributing to farnesol tolerance in C...
November 16, 2017: Yeast
https://www.readbyqxmd.com/read/29131448/saccharomyces-cerevisiae-x-saccharomyces-uvarum-hybrids-generated-under-different-conditions-share-similar-winemaking-features
#12
Origone Andrea Cecilia, Rodríguez María Eugenia, Oteiza Juan Martín, Querol Amparo, Lopes Christian Ariel
Interspecific hybrids among species in the Saccharomyces genus are frequently detected in anthropic habitats and can also be obtained easily in the laboratory. This occurs because the most important genetic barriers among Saccharomyces species are post-zygotic. Depending on several factors, including the involved strains, the hybridisation mechanism and stabilisation conditions, the hybrids that bear differential genomic constitutions, and hence phenotypic variability, can be obtained. In the present study, Saccharomyces cerevisiae x Saccharomyces uvarum hybrids were constructed using genetically and physiologically different S...
November 13, 2017: Yeast
https://www.readbyqxmd.com/read/29131388/saccharomyces-interspecies-hybrids-as-model-organisms-for-studying-yeast-adaptation-to-stressful-environments
#13
Ksenija Lopandic
The strong development of molecular biology techniques and next-generation sequencing technologies in the last two decades has significantly improved our understanding of the evolutionary history of Saccharomyces yeasts. It has been shown that many strains isolated from man-made environments are not pure genetic lines, but contain genetic materials from different species that substantially increase their genome complexity. A number of strains have been described as interspecies hybrids, implying different yeast species that under specific circumstances exchange and recombine their genomes...
November 13, 2017: Yeast
https://www.readbyqxmd.com/read/29084380/a-combinatorial-approach-to-synthetic-transcription-factor-promoter-combinations-for-yeast-strain-engineering
#14
Zain Y Dossani, Amanda Reider Apel, Heather S Middleton, Nathan J Hillson, Samuel Deutch, Jay D Keasling, Aindrila Mukhopadhyay
Despite the need for inducible promoters in strain development efforts, the majority of engineering in Saccharomyces cerevisiae continues to rely on a few constitutively active or inducible promoters. Building on advances that use the modular nature of both transcription factors and promoter regions, we have built a library of hybrid promoters that are regulated by a synthetic transcription factor. The hybrid promoters consist of native S. cerevisiae promoters, in which the operator regions have been replaced with sequences that are recognized by the bacterial LexA DNA binding protein...
October 30, 2017: Yeast
https://www.readbyqxmd.com/read/29084364/the-natural-diversity-and-ecology-of-fission-yeast
#15
Daniel C Jeffares
While the fission yeast is a powerful model of eukaryote biology, there have been few studies of quantitative genetics, phenotypic or genetic diversity. Here I survey the small collection of fission yeast diversity research. I discuss what we can infer about the ecology and origins of Schizosaccharomyces pombe from microbiology field studies and the few strains that have been collected.
October 30, 2017: Yeast
https://www.readbyqxmd.com/read/29077225/an-efficient-method-for-isolating-mating-competent-cells-from-bottom-fermenting-yeast-using-mating-pheromone-supersensitive-mutants
#16
Taku Ota, Keiko Kanai, Hisami Nishimura, Satoshi Yoshida, Hiroyuki Yoshimoto, Osamu Kobayashi
Crossbreeding is an effective approach to construct novel yeast strains with preferred characteristics; however, it is difficult to crossbreed strains of brewer's yeast, especially the bottom-fermenting yeast Saccharomyces pastorianus, because of the relative inefficiency of the available methods to obtain mating-competent cells (MCCs). Here, we describe a productive method for the isolation of MCCs without artificial genetic modification. We focused on the characteristics of two mating pheromone-supersensitive (PS) mutants, Δbar1 and Δsst2, that show a growth defect in presence of the mating pheromone...
October 27, 2017: Yeast
https://www.readbyqxmd.com/read/29336080/special-issues-for-a-special-community
#17
EDITORIAL
Gilles Fischer, Gianni Liti
No abstract text is available yet for this article.
January 2018: Yeast
https://www.readbyqxmd.com/read/28752642/genome-wide-map-of-apn1-binding-sites-under-oxidative-stress-in-saccharomyces-cerevisiae
#18
Lydia P Morris, Andrew B Conley, Natalya Degtyareva, I King Jordan, Paul W Doetsch
The DNA is cells is continuously exposed to reactive oxygen species resulting in toxic and mutagenic DNA damage. Although the repair of oxidative DNA damage occurs primarily through the base excision repair (BER) pathway, the nucleotide excision repair (NER) pathway processes some of the same lesions. In addition, damage tolerance mechanisms, such as recombination and translesion synthesis, enable cells to tolerate oxidative DNA damage, especially when BER and NER capacities are exceeded. Thus, disruption of BER alone or disruption of BER and NER in Saccharomyces cerevisiae leads to increased mutations as well as large-scale genomic rearrangements...
November 2017: Yeast
https://www.readbyqxmd.com/read/29065217/the-fission-yeast-mapk-spc1-senses-perturbations-in-cdc25-and-wee1-activities-and-targets-rad24-to-restore-this-balance
#19
Madhurima Paul, Agamani Ghosal, Sushobhana Bandyopadhyay, G Prakadeeswari, Upasna Selvam, Neeraj Rai, Geetanjali Sundaram
Mitogen Activated Protein Kinases (MAPKs) play vital roles in multiple cellular processes and represent prominently pursued targets for development of therapeutic regimes. The MAPK Spc1 (p38 homolog) is known to be very important for both mitotic promotion and delay in Schizosaccharomyces pombe. However, the mechanism responsible for mitotic inhibition has remained elusive. Cdc25 (Cdc2 activator) and Wee1 (Cdc2 inhibtor) are important determinants of mitotic timing in all eukaryotes. Our results show that Spc1 can sense the perturbations in the balance of Cdc25 and Wee1 activities in S...
October 24, 2017: Yeast
https://www.readbyqxmd.com/read/29065215/on-the-catabolism-of-amino-acids-in-the-yeast-dekkera-bruxellensis-and-the-implications-to-industrial-fermentation-processes
#20
Denise Castro Parente, Danielli Batista Bezerra Cajueiro, Irina Charlot Peña Moreno, Fernanda Cristina Bezerra Leite, Will de Barros Pita, Marcos Antonio de Morais
In the last years several reports have reported the capacity of the yeast Dekkera (Brettanomyces) bruxellensis to survive and adapt to the industrial process of alcoholic fermentation. Much of this feature seems to relate to the ability to assimilate limiting sources of nutrients, or somehow some that are inaccessible to Saccharomyces cerevisiae, in particular the sources of nitrogen. Among them, amino acids (AA) are relevant in terms of beverage musts, and could also be important for bioethanol. In view of the limited knowledge on the control of AA, the present work combines physiological and genetic studies to understand how it operates in D...
October 24, 2017: Yeast
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