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https://www.readbyqxmd.com/read/29457628/a-coupled-in-vitro-in-vivo-approach-for-engineering-a-heterologous-type-iii-pks-to-enhance-polyketide-biosynthesis-in-saccharomyces-cerevisiae
#1
Christopher R Vickery, Javier Cardenas, Marianne Bowman, Michael D Burkart, Nancy A Da Silva, Joseph P Noel
Polyketides are attractive compounds for uses ranging from biorenewable chemical precursors to high-value therapeutics. In many cases, synthesis in a heterologous host is required to produce these compounds in industrially relevant quantities. The type III polyketide synthase 2-pyrone synthase (2-PS) from Gerbera hybrida was used for the production of triacetic acid lactone (TAL) in Saccharomyces cerevisiae. Initial in vitro characterization of 2-PS led to the identification of active site variants with improved kinetic properties relative to wildtype...
February 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29457321/wine-aromatic-compound-production-and-fermentative-behavior-within-different-non-saccharomyces-species-and-clones
#2
Rocío Escribano, Lucía González-Arenzana, Javier Portu, Patrocinio Garijo, Isabel López-Alfaro, Rosa López, Pilar Santamaría, Ana Rosa Gutiérrez
AIMS: 25 enological yeasts belonging to 9 different species (Candida zeylanoides, Cryptococcus uzbekistanensis, Debaryomyces hansenii, Lachancea thermotolerans, Metschnikowia pulcherrima, Torulaspora delbrueckii, Williopsis pratensis, Zygosaccharomyces bailii and Saccharomyces cerevisiae) were screened for aroma formation and fermentative behavior as part of a non-Saccharomyces yeasts selection program. METHODS AND RESULTS: Pure cultures were inoculated in pasteurized grape juice in order to perform alcoholic fermentations...
February 19, 2018: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29456549/global-dna-methylation-in-the-chestnut-blight-fungus-cryphonectria-parasitica-and-genome-wide-changes-in-dna-methylation-accompanied-with-sectorization
#3
Kum-Kang So, Yo-Han Ko, Jeesun Chun, Jyotiranjan Bal, Junhyun Jeon, Jung-Mi Kim, Jaeyoung Choi, Yong-Hwan Lee, Jin Hoe Huh, Dae-Hyuk Kim
Mutation in CpBck1 , an ortholog of the cell wall integrity mitogen-activated protein kinase kinase kinase (MAPKKK) of Saccharomyces cerevisiae , in the chestnut blight fungus Cryphonectria parasitica resulted in a sporadic sectorization as culture proceeded. The progeny from the sectored area maintained the characteristics of the sector, showing a massive morphogenetic change, including robust mycelial growth without differentiation. Epigenetic changes were investigated as the genetic mechanism underlying this sectorization...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29456524/-saccharomyces-cerevisiae-and-s-kudriavzevii-synthetic-wine-fermentation-performance-dissected-by-predictive-modeling
#4
David Henriques, Javier Alonso-Del-Real, Amparo Querol, Eva Balsa-Canto
Wineries face unprecedented challenges due to new market demands and climate change effects on wine quality. New yeast starters including non-conventional Saccharomyces species, such as S. kudriavzevii , may contribute to deal with some of these challenges. The design of new fermentations using non-conventional yeasts requires an improved understanding of the physiology and metabolism of these cells. Dynamic modeling brings the potential of exploring the most relevant mechanisms and designing optimal processes more systematically...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29455333/stress-response-factors-drive-regrowth-of-quiescent-cells
#5
REVIEW
Zheng Kuang, Hongkai Ji, Jef D Boeke
Quiescent cells exploit an array of transcription factors to activate stress response machinery and maintain survival under nutrient-limited conditions. Our recent findings reveal that these transcription factors also play an important role in the exit of quiescence and regrowth. By studying Saccharomyces cerevisiae under a continuous, nutrient-limited condition, we found that Msn2 and Msn4 function as master regulators of glycolytic genes in the quiescent-like phase. They control the timing of transition from quiescence to growth by regulating the accumulation rate of acetyl-CoA, a key metabolite that is downstream of glycolysis and drives growth...
February 17, 2018: Current Genetics
https://www.readbyqxmd.com/read/29453625/effects-of-feedstock-and-co-culture-of-lactobacillus-fermentum-and-wild-saccharomyces-cerevisiae-strain-during-fuel-ethanol-fermentation-by-the-industrial-yeast-strain-pe-2
#6
Vanda R Reis, Ana Paula G Bassi, Bianca C Cerri, Amanda R Almeida, Isis G B Carvalho, Reinaldo G Bastos, Sandra R Ceccato-Antonini
Even though contamination by bacteria and wild yeasts are frequently observed during fuel ethanol fermentation, our knowledge regarding the effects of both contaminants together is very limited, especially considering that the must composition can vary from exclusively sugarcane juice to a mixture of molasses and juice, affecting the microbial development. Here we studied the effects of the feedstock (sugarcane juice and molasses) and the co-culture of Lactobacillus fermentum and a wild Saccharomyces cerevisiae strain (rough colony and pseudohyphae) in single and multiple-batch fermentation trials with an industrial strain of S...
February 16, 2018: AMB Express
https://www.readbyqxmd.com/read/29452922/structural-biology-of-the-separase-securin-complex-with-crucial-roles-in-chromosome-segregation
#7
REVIEW
Shukun Luo, Liang Tong
The cysteine protease separase opens the cohesin ring by cleaving its kleisin subunit and is a pivotal cell cycle factor for the transition from metaphase to anaphase. It is inhibited by forming a complex with the chaperone securin, and in vertebrates, also by the Cdk1-cyclin B1 complex. Separase is activated upon the destruction of securin or cyclin B1 by the proteasome, after ubiquitination by the anaphase-promoting complex/cyclosome (APC/C). Here we review recent structures of the active protease segment of Chaetomium thermophilum separase in complex with a substrate-mimic inhibitor and full-length Saccharomyces cerevisiae and Caenorhabditis elegans separase in complex with securin...
February 13, 2018: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29452364/4-phenylbutyrate-suppresses-the-unfolded-protein-response-without-restoring-protein-folding-in-saccharomyces-cerevisiae
#8
Chi Thanh Mai, Quynh Giang Le, Yuki Ishiwata-Kimata, Hiroshi Takagi, Kenji Kohno, Yukio Kimata
Accumulation of unfolded secretory proteins in the endoplasmic reticulum (ER), namely ER stress, is hazardous to eukaryotic cells and promotes the unfolded protein response (UPR). Ire1 is an ER-located transmembrane protein that senses ER stress and triggers the UPR. According to previous in vitro experiments, 4-phenylbutyrate (4-PBA) works as a chemical molecular chaperone. Since 4-PBA attenuates the UPR in mammalian tissue cultures, this chemical may have clinical potential for restoring ER-stressing conditions...
February 14, 2018: FEMS Yeast Research
https://www.readbyqxmd.com/read/29452354/alpha-synuclein-inhibits-snx3-retromer-mediated-retrograde-recycling-of-iron-transporters-in-s-cerevisiae-and-c-elegans-models-of-parkinson-s-disease
#9
Dhaval Patel, Chuan Xu, Sureshbabu Nagarajan, Zhengchang Liu, Wayne O Hemphill, Runhua Shi, Vladimir N Uversky, Guy A Caldwell, Kim A Caldwell, Stephan N Witt
We probed the role of alpha-synuclein (α-syn) in modulating sorting nexin 3 (Snx3)-retromer-mediated recycling of iron transporters in Saccharomyces cerevisiae and Caenorhabditis elegans. In yeast, the membrane-bound heterodimer Fet3/Ftr1 is the high affinity iron importer. Fet3 is a membrane-bound multicopper ferroxidase, whose ferroxidase domain is orthologous to human ceruloplasmin (Cp), that oxidizes external Fe+2 to Fe+3; the Fe+3 ions then channel through the Ftr1 permease into the cell. When the concentration of external iron is low (< 1 µM), Fet3/Ftr1 is maintained on the plasma membrane by retrograde endocytic-recycling; whereas, when the concentration of external iron is high (> 10 µM), Fet3/Ftr1 is endocytosed and shunted to the vacuole for degradation...
February 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29449883/production-of-2r-3r-2-3-butanediol-using-engineered-pichia-pastoris-strain-construction-characterization-and-fermentation
#10
Zhiliang Yang, Zisheng Zhang
Background: 2,3-butanediol (2,3-BD) is a bulk platform chemical with various potential applications such as aviation fuel. 2,3-BD has three optical isomers: (2R, 3R)-, (2S, 3S)- and meso-2,3-BD. Optically pure 2,3-BD is a crucial precursor for the chiral synthesis and it can also be used as anti-freeze agent due to its low freezing point. 2,3-BD has been produced in both native and non-native hosts. Several pathogenic bacteria were reported to produce 2,3-BD in mixture of its optical isomers including Klebsiella pneumoniae and Klebsiella oxytoca ...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29449612/ixr1-regulates-ribosomal-gene-transcription-and-yeast-response-to-cisplatin
#11
Ángel Vizoso-Vázquez, Mónica Lamas-Maceiras, M Isabel González-Siso, M Esperanza Cerdán
Ixr1 is a Saccharomyces cerevisiae HMGB protein that regulates the hypoxic regulon and also controls the expression of other genes involved in the oxidative stress response or re-adaptation of catabolic and anabolic fluxes when oxygen is limiting. Ixr1 also binds with high affinity to cisplatin-DNA adducts and modulates DNA repair. The influence of Ixr1 on transcription in the absence or presence of cisplatin has been analyzed in this work. Ixr1 regulates other transcriptional factors that respond to nutrient availability or extracellular and intracellular stress stimuli, some controlled by the TOR pathway and PKA signaling...
February 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29449198/a-rare-colonization-in-the-peritonitis-following-blunt-abdominal-trauma
#12
Oana Bulat, Cristian Bulat, Mihaela Blaj, Ioana Lupusoru, Viorel Scripcariu
BACKGROUND: Schewanella spp. is Gram-negative bacteria, saprophytes and rarely pathogenic. Initially isolated in 193, these belong to the marine environment; Schewanella (Pseudomonas) putrefaciens was found in water, soil and animal sources and produces hydrogen sulphide. Saccharomyces cerevisiae is the well-known yeast used for fermentation in industry and in molecular biology for research. In humans, it is a very rare pathogen which colonises the digestive tract and its utility has been linked to the treatment and prevention of diarrhoea associated with Clostridium difficile...
February 15, 2018: Balkan Medical Journal
https://www.readbyqxmd.com/read/29448386/theoretical-analysis-of-the-distribution-of-isolated-particles-in-totally-asymmetric-exclusion-processes-application-to-mrna-translation-rate-estimation
#13
Khanh Dao Duc, Zain H Saleem, Yun S Song
The Totally Asymmetric Exclusion Process (TASEP) is a classical stochastic model for describing the transport of interacting particles, such as ribosomes moving along the messenger ribonucleic acid (mRNA) during translation. Although this model has been widely studied in the past, the extent of collision between particles and the average distance between a particle to its nearest neighbor have not been quantified explicitly. We provide here a theoretical analysis of such quantities via the distribution of isolated particles...
January 2018: Physical Review. E
https://www.readbyqxmd.com/read/29448154/a-serine-carboxypeptidase-like-acyltransferase-catalyzes-synthesis-of-indole-3-acetic-iaa-ester-conjugate-in-rice-oryza-sativa
#14
Anna Ciarkowska, Maciej Ostrowski, Anna Jakubowska
Indole-3-acetic acid (IAA) conjugation is one of mechanisms responsible for regulation of free auxin levels in plants. A new member of the serine carboxypeptidase-like (SCPL) acyltransferases family from Oryza sativa has been cloned and characterized. 1-O-indole-3-acetyl-β-D-glucose (1-O-IAGlc): myo-inositol acyltransferase (IAInos synthase) is an enzyme of IAA ester conjugates biosynthesis pathway that catalyzes transfer of IAA moiety from 1-O-IAGlc to myo-inositol forming IA-myo-inositol (IAInos). The OsIAA-At cDNA has been cloned and expressed using yeast and bacterial expression systems...
February 9, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29447073/the-benefits-and-risks-of-expressing-the-pot-and-fot-family-of-oligopeptide-transporters-in-saccharomyces-cerevisiae
#15
Kenji Kitamura, Eldaa Zefany Banami Kinsui
In the yeast Saccharomyces cerevisiae, all strains possess a gene for the evolutionarily conserved POT family peptide transporter, Ptr2; however, the genes for a novel FOT family transporter were found only in some wine brewing strains. The substrate specificity of the POT and FOT family of transporters was compared. Among the naturally occurring oligopeptides that were tested, Lys-Leu and Arg-Phe were Ptr2-specific substrates. Artificial dipeptide aspartame was imported specifically through the FOT transporter, but the structurally similar Asp-Phe was a substrate of both FOT and Ptr2 transporters...
February 15, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29446764/antibodies-against-glycoprotein-2-display-diagnostic-advantages-over-asca-in-distinguishing-cd-from-intestinal-tuberculosis-and-intestinal-beh%C3%A3-et-s-disease
#16
Shulan Zhang, Jing Luo, Ziyan Wu, Dirk Roggenbuck, Peter Schierack, Dirk Reinhold, Ji Li, Xiaofeng Zeng, Fengchun Zhang, Jiaming Qian, Yongzhe Li
OBJECTIVES: There is an increasing need to identify reliable biomarkers for distinguishing Crohn's disease (CD) from other gastrointestinal disorders sharing similar clinical and pathological features. This study aimed at evaluating the diagnostic potential of antibodies to zymogen granule glycoprotein GP2 (aGP2) in a large, well-defined Chinese cohort with a special focus on their role in discriminating CD from intestinal Behçet's disease (BD) and intestinal tubercolosis (ITB). METHODS: A total of 577 subjects were prospectively enrolled, including 171 patients with CD, 208 patients with ulcerative colitis (UC), 71 with BD, 57 with ITB and 70 healthy controls (HC)...
February 15, 2018: Clinical and Translational Gastroenterology
https://www.readbyqxmd.com/read/29444801/widespread-and-precise-reprogramming-of-yeast-protein-genome-interactions-in-response-to-heat-shock
#17
Vinesh Vinayachandran, Rohit Reja, Matthew J Rossi, Bongsoo Park, Lila Rieber, Chitvan Mittal, Shaun Mahony, B Franklin Pugh
Gene expression is controlled by a variety of proteins that interact with the genome. Their precise organization and mechanism of action at every promoter remains to be worked out. To better understand the physical interplay among genome-interacting proteins, we examined the temporal binding of a functionally diverse subset of these proteins: nucleosomes (H3), H2AZ (Htz1), SWR (Swr1), RSC (Rsc1, Rsc3, Rsc58, Rsc6, Rsc9, Sth1), SAGA (Spt3, Spt7, Ubp8, Sgf11), Hsf1, TFIID (Spt15/TBP and Taf1), TFIIB (Sua7), TFIIH (Ssl2), FACT (Spt16), Pol II (Rpb3), and Pol II carboxyl-terminal domain (CTD) phosphorylation at serines 2, 5, and 7...
February 14, 2018: Genome Research
https://www.readbyqxmd.com/read/29444384/osmoadaptation-of-wine-yeast-saccharomyces-cerevisiae-during-icewine-fermentation-leads-to-high-levels-of-acetic-acid
#18
C Heit, S J Martin, F Yang, D L Inglis
AIMS: Volatile acidity production along with gene expression patterns, encoding enzymes involved in both acetic acid production and utilization, were investigated to relate gene expression patterns to the production of undesired volatile acidity during Icewine fermentation. METHODS AND RESULTS: Icewine juice and diluted Icewine juice were fermented using the Saccharomyces cerevisiae wine yeast K1-V1116. Acetic acid production increased 6-fold during the Icewine fermentation versus the diluted juice condition, while ethyl acetate production increased 2...
February 14, 2018: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29443970/structural-and-evolutionary-insights-into-ribosomal-rna-methylation
#19
REVIEW
Petr V Sergiev, Nikolay A Aleksashin, Anastasia A Chugunova, Yury S Polikanov, Olga A Dontsova
Methylation of nucleotides in ribosomal RNAs (rRNAs) is a ubiquitous feature that occurs in all living organisms. Identification of all enzymes responsible for rRNA methylation, as well as mapping of all modified rRNA residues, is now complete for a number of model species, such as Escherichia coli and Saccharomyces cerevisiae. Recent high-resolution structures of bacterial ribosomes provided the first direct visualization of methylated nucleotides. The structures of ribosomes from various organisms and organelles have also lately become available, enabling comparative structure-based analysis of rRNA methylation sites in various taxonomic groups...
February 14, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29443015/isolation-and-cultivation-of-neural-progenitors-followed-by-chromatin-immunoprecipitation-of-histone-3-lysine-79-dimethylation-mark
#20
Patrick Bovio, Deborah Roidl, Stefanie Heidrich, Tanja Vogel, Henriette Franz
Brain development is a complex process, which is controlled in a temporo-spatial manner by gradients of morphogens and different transcriptional programs. Additionally, epigenetic chromatin modifications, like histone methylation, have an important role for establishing and maintaining specific cell fates within this process. The vast majority of histone methylation occurs on the flexible histone tail, which is accessible to histone modifiers, erasers, and histone reader proteins. In contrast, H3K79 methylation is located in the globular domain of histone 3 and is implicated in different developmental functions...
January 26, 2018: Journal of Visualized Experiments: JoVE
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