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Saccharomyces cerevisiae

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https://www.readbyqxmd.com/read/28549188/eif5a-facilitates-translation-termination-globally-and-promotes-the-elongation-of-many-non-polyproline-specific-tripeptide-sequences
#1
Vicent Pelechano, Paula Alepuz
eIF5A is an essential protein involved in protein synthesis, cell proliferation and animal development. High eIF5A expression is observed in many tumor types and has been linked to cancer metastasis. Recent studies have shown that eIF5A facilitates the translation elongation of stretches of consecutive prolines. Activated eIF5A binds to the empty E-site of stalled ribosomes, where it is thought to interact with the peptidyl-tRNA situated at the P-site. Here, we report a genome-wide analysis of ribosome stalling in Saccharomyces cerevisiae eIF5A depleted cells using 5Pseq...
May 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28549155/evidence-for-double-strand-break-mediated-mitochondrial-dna-replication-in-saccharomyces-cerevisiae
#2
Kanchanjunga Prasai, Lucy C Robinson, Rona S Scott, Kelly Tatchell, Lynn Harrison
The mechanism of mitochondrial DNA (mtDNA) replication in Saccharomyces cerevisiae is controversial. Evidence exists for double-strand break (DSB) mediated recombination-dependent replication at mitochondrial replication origin ori5 in hypersuppressive ρ- cells. However, it is not clear if this replication mode operates in ρ+ cells. To understand this, we targeted bacterial Ku (bKu), a DSB binding protein, to the mitochondria of ρ+ cells with the hypothesis that bKu would bind persistently to mtDNA DSBs, thereby preventing mtDNA replication or repair...
May 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28548095/metabolic-engineering-of-saccharomyces-cerevisiae-for-production-of-very-long-chain-fatty-acid-derived-chemicals
#3
Tao Yu, Yongjin J Zhou, Leonie Wenning, Quanli Liu, Anastasia Krivoruchko, Verena Siewers, Jens Nielsen, Florian David
Production of chemicals and biofuels through microbial fermentation is an economical and sustainable alternative for traditional chemical synthesis. Here we present the construction of a Saccharomyces cerevisiae platform strain for high-level production of very-long-chain fatty acid (VLCFA)-derived chemicals. Through rewiring the native fatty acid elongation system and implementing a heterologous Mycobacteria FAS I system, we establish an increased biosynthesis of VLCFAs in S. cerevisiae. VLCFAs can be selectively modified towards the fatty alcohol docosanol (C22H46O) by expressing a specific fatty acid reductase...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28547648/clinical-and-phenotypic-differences-in-inflammatory-bowel-disease-among-arab-and-jewish-children-in-israel
#4
Firas Rinawi, Amit Assa, Husam Bashir, Sarit Peleg, Raanan Shamir
BACKGROUND: Data on inflammatory bowel disease (IBD) phenotypes among the Arab population in Israel or in the neighboring Arab countries is scarce. AIM: We aimed to assess differences in disease phenotype among Arab and Jewish children living in Israel. METHODS: We performed a retrospective chart review of pediatric IBD cases, which were diagnosed at the Schneider Children's Medical Center and Ha'Emek Medical Center in Israel between 2000 and 2014...
May 25, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28547322/metabolic-engineering-of-saccharomyces-cerevisiae-for-production-of-germacrene-a-a-precursor-of-beta-elemene
#5
Yating Hu, Yongjin J Zhou, Jichen Bao, Luqi Huang, Jens Nielsen, Anastasia Krivoruchko
Beta-elemene, a sesquiterpene and the major component of the medicinal herb Curcuma wenyujin, has antitumor activity against various types of cancer and could potentially serve as a potent antineoplastic drug. However, its current mode of production through extraction from plants has been inefficient and suffers from limited natural resources. Here, we engineered a yeast cell factory for the sustainable production of germacrene A, which can be transformed to beta-elemene by a one-step chemical reaction in vitro...
May 25, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28542452/the-role-of-aspartyl-aminopeptidase-ape4-in-cryptococcus-neoformans-virulence-and-authophagy
#6
Fabiano de Assis Gontijo, Amanda Teixeira de Melo, Renata C Pascon, Larissa Fernandes, Hugo Costa Paes, J Andrew Alspaugh, Marcelo A Vallim
In order to survive and cause disease, microbial pathogens must be able to proliferate at the temperature of their infected host. We identified novel microbial features associated with thermotolerance in the opportunistic fungal pathogen Cryptococcus neoformans using a random insertional mutagenesis strategy, screening for mutants with defective growth at 37°C. Among several thermosensitive mutants, we identified one bearing a disruption in a gene predicted to encode the Ape4 aspartyl aminopeptidase protein...
2017: PloS One
https://www.readbyqxmd.com/read/28541389/cell-cycle-dependent-control-of-homologous-recombination
#7
Xin Zhao, Chengwen Wei, Jingjing Li, Poyuan Xing, Jingyao Li, Sihao Zheng, Xuefeng Chen
DNA double-strand breaks (DSBs) are among the most deleterious type of DNA lesions threatening genome integrity. Homologous recombination (HR) and non-homologous end joining (NHEJ) are two major pathways to repair DSBs. HR requires a homologous template to direct DNA repair, and is generally recognized as a high-fidelity pathway. In contrast, NHEJ directly seals broken ends, but the repair product is often accompanied by sequence alterations. The choice of repair pathways is strictly controlled by the cell cycle...
May 25, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/28541304/digital-logic-circuits-in-yeast-with-crispr-dcas9-nor-gates
#8
Miles W Gander, Justin D Vrana, William E Voje, James M Carothers, Eric Klavins
Natural genetic circuits enable cells to make sophisticated digital decisions. Building equally complex synthetic circuits in eukaryotes remains difficult, however, because commonly used components leak transcriptionally, do not arbitrarily interconnect or do not have digital responses. Here, we designed dCas9-Mxi1-based NOR gates in Saccharomyces cerevisiae that allow arbitrary connectivity and large genetic circuits. Because we used the chromatin remodeller Mxi1, our gates showed minimal leak and digital responses...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28541284/a-scalable-double-barcode-sequencing-platform-for-characterization-of-dynamic-protein-protein-interactions
#9
Ulrich Schlecht, Zhimin Liu, Jamie R Blundell, Robert P St Onge, Sasha F Levy
Several large-scale efforts have systematically catalogued protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies, which assay one PPI at a time, are too low throughput to make it practical to study protein interactome dynamics. Here, we develop a highly parallel protein-protein interaction sequencing (PPiSeq) platform that uses a novel double barcoding system in conjunction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28540744/production-of-single-cell-protein-scp-from-food-and-agricultural-waste-by-using-saccharomyces-cerevisiae
#10
Teresa Gervasi, Vito Pellizzeri, Giorgio Calabrese, Giuseppa Di Bella, Nicola Cicero, Giacomo Dugo
Food waste is the single-largest component of the waste stream, in order to protect and safeguard the public health, useful and innovative recycling methods are investigated. The conversion of food wastes in value-added products is becoming a more economically viable and interesting practice. Food waste, collected in the distribution sector and citrus industries, was characterised for its potential as a raw material to use in fermentation processes. In this study, the production of single-cell protein (SCP) using food waste as a substrate was investigated...
May 25, 2017: Natural Product Research
https://www.readbyqxmd.com/read/28540704/colony-pcr
#11
Flávio Azevedo, Humberto Pereira, Björn Johansson
Escherichia coli and Saccharomyces cerevisiae are currently the two most important organisms in synthetic biology. E.coli is almost always used for fundamental DNA manipulation while yeast is the simplest host system for studying eukaryotic gene expression and performing large scale DNA assembly. Yeast expression studies may also require altering of the chromosomal DNA by homologous recombination. All these studies require the verification of the expected DNA sequence and the fastest method of screening is colony PCR, which is direct PCR of DNA in cells without prior DNA purification...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540421/yeast-env9-encodes-a-conserved-lipid-droplet-ld-short-chain-dehydrogenase-involved-in-ld-morphology
#12
Ikha M Siddiqah, Surya P Manandhar, Stephanie M Cocca, Teli Hsueh, Vanessa Cervantes, Editte Gharakhanian
Lipid droplets (LDs) have emerged as dynamic and interactive organelles with important roles in lipid metabolism and membrane biogenesis. Here, we report that Saccharomyces cerevisiae Env9 is a novel conserved oxidoreductase involved in LD morphology. Microscopic and biochemical studies confirm localization of tagged Env9 to LDs and implicate its C-terminal hydrophobic domain (aa241-265) in its membrane association and stability. Confocal studies reveal a role for Env9 in LD morphology. Env9 positively affects both formation of large LDs upon overexpression and LD proliferation under poor carbon source...
May 24, 2017: Current Genetics
https://www.readbyqxmd.com/read/28539411/substrate-binding-by-the-yeast-hsp110-nucleotide-exchange-factor-and-molecular-chaperone-sse1-is-not-obligate-for-its-biological-activities
#13
Veronica M Garcia, Nadinath B Nillegoda, Bernd Bukau, Kevin A Morano
The highly conserved heat-shock protein 70 (Hsp70) is a ubiquitous molecular chaperone essential for maintaining cellular protein homeostasis. The related protein Hsp110 (Sse1/Sse2 in Saccharomyces cerevisiae) functions as a nucleotide exchange factor (NEF) to regulate the protein folding activity of Hsp70. Hsp110/Sse1 can additionally prevent protein aggregation in vitro via its substrate binding domain (SBD), but the cellular roles of this "holdase" activity remain poorly defined. We generated and characterized an Sse1 mutant that separates, for the first time, its nucleotide exchange and substrate binding functions...
May 24, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28539364/integrative-proteomics-and-biochemical-analyses-define-ptc6p-as-the-saccharomyces-cerevisiae-pyruvate-dehydrogenase-phosphatase
#14
Xiao Guo, Natalie M Niemi, Joshua J Coon, Dave J Pagliarini
The pyruvate dehydrogenase complex (PDC) is the primary metabolic checkpoint connecting glycolysis and mitochondrial oxidative phosphorylation, and is important for maintaining cellular and organismal glucose homeostasis. Phosphorylation of the PDC E1 subunit was identified as a key inhibitory modification in bovine tissue approximately 50 years ago, and this regulatory process is now known to be conserved throughout evolution. Although Saccharomyces cerevisiae is a pervasive model organism for investigating cellular metabolism and its regulation by signaling processes, the phosphatase(s) responsible for activating the PDC in S...
May 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28539363/identification-of-karyopherins-involved-in-the-nuclear-import-of-rna-exosome-subunit-rrp6-in-saccharomyces-cerevisiae
#15
Fernando A Gonzales-Zubiate, Ellen K Okuda, Julia Pc Da Cunha, Carla Columbano Oliveira
The exosome is a conserved multiprotein complex essential for RNA processing and degradation. The nuclear exosome is a key factor for pre-rRNA processing through the activity of its catalytic subunits, Rrp6 and Rrp44. In Saccharomyces cerevisiae, Rrp6 is exclusively nuclear and has been shown to interact with exosome cofactors. With the aim of analyzing proteins associated with the nuclear exosome, in this work, we purified the complex with Rrp6-TAP, identified the co-purified proteins by mass spectrometry, and found karyopherins to be one of the major groups of proteins enriched in the samples...
May 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28539187/heterologous-expression-of-bacterial-phosphoenol-pyruvate-carboxylase-and-entner-doudoroff-pathway-in-saccharomyces-cerevisiae-for-improvement-of-isobutanol-production
#16
Keisuke Morita, Yuta Nomura, Jun Ishii, Fumio Matsuda, Akihiko Kondo, Hiroshi Shimizu
Bacterial phosphoenol pyruvate carboxylase (PPC) and enzymes in the Entner-Doudoroff (ED) pathway were heterologously expressed in Saccharomyces cerevisiae to improve the NADPH supply required for the bio-production of chemicals such as isobutanol. The heterologous expression of PPC from Synechocystis sp. PCC6803 increased in the isobutabol titer 1.45-fold (93.2±1.6 mg/L) in metabolically engineered S. cerevisiae strains producing isobutanol. This result suggested that the pyruvate and NADPH supply for isobutanol biosynthesis was activated by PPC overexpression...
May 20, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28538144/probing-the-potential-role-of-non-b-dna-structures-at-yeast-meiosis-specific-dna-double-strand-breaks
#17
Rucha Kshirsagar, Krishnendu Khan, Mamata V Joshi, Ramakrishna V Hosur, K Muniyappa
A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28537556/the-dynamic-three-dimensional-organization-of-the-diploid-yeast-genome
#18
Seungsoo Kim, Ivan Liachko, Donna G Brickner, Kate Cook, William S Noble, Jason H Brickner, Jay Shendure, Maitreya J Dunham
The budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes. However, even in this well-studied model, it is unclear how homolog pairing in diploids or environmental conditions influence overall genome organization. Here, we performed high-throughput chromosome conformation capture on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid yeasts. After controlling for the Rabl-like orientation using a polymer model, we observe significant homolog proximity that increases in saturated culture conditions...
May 24, 2017: ELife
https://www.readbyqxmd.com/read/28537551/rna-dependent-chromatin-association-of-transcription-elongation-factors-and-pol-ii-ctd-kinases
#19
Sofia Battaglia, Michael Lidschreiber, Carlo Baejen, Phillipp Torkler, Seychelle M Vos, Patrick Cramer
For transcription through chromatin, RNA polymerase (Pol) II associates with elongation factors (EFs). Here we show that many EFs crosslink to RNA emerging from transcribing Pol II in the yeast Saccharomyces cerevisiae. Most EFs crosslink preferentially to mRNAs, rather than unstable non-coding RNAs. RNA contributes to chromatin association of many EFs, including the Pol II serine 2 kinases Ctk1 and Bur1 and the histone H3 methyltransferases Set1 and Set2. The Ctk1 kinase complex binds RNA in vitro, consistent with direct EF-RNA interaction...
May 24, 2017: ELife
https://www.readbyqxmd.com/read/28537243/-rnq1-protein-protects-psi-prion-from-effect-of-the-pnm-mutation
#20
S A Bondarev, D V Likholetova, M V Belousov, G A Zhouravleva
The interaction of [PSI^(+)] and [PIN^(+)] factors in yeast Saccharomyces cerevisiae is known as the first evidence of prions networks. In [PIN^(+)] cells, Rnq1p prion aggregates work as a template for Sup35p aggregation, which is essential for [PSI^(+)] induction. No additional factors are required for subsequent Sup35p aggregation. Nevertheless, several recent reports provide data that indicate a more complex interplay between these prions. Our results show that the presence of Rnq1p in the cell significantly decreases the loss of [PSI^(+)] prion, which is caused by a double mutation in SUP35 (Q61K, Q62K substitutions in the Sup35 protein)...
March 2017: Molekuliarnaia Biologiia
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