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https://www.readbyqxmd.com/read/28096519/the-nuclear-poly-a-binding-protein-of-mammals-but-not-of-fission-yeast-participates-in-mrna-polyadenylation
#1
Uwe Kühn, Juliane Buschmann, Elmar Wahle
The nuclear poly(A) binding protein (PABPN1) has been suggested, on the basis of biochemical evidence, to play a role in mRNA polyadenylation by strongly increasing the processivity of poly(A) polymerase. While experiments in metazoans have tended to support such a role, the results were not unequivocal, and genetic data show that the S. pombe orthologue of PABPN1, Pab2, is not involved in mRNA polyadenylation. The specific model that PABPN1 increases the rate of poly(A) tail elongation has never been examined in vivo...
January 17, 2017: RNA
https://www.readbyqxmd.com/read/28054638/functional-constraints-on-adaptive-evolution-of-protein-ubiquitination-sites
#2
Liang Lu, Yang Li, Zhongyang Liu, Fengji Liang, Feifei Guo, Shuai Yang, Dan Wang, Yangzhige He, Jianghui Xiong, Dong Li, Fuchu He
It is still unclear whether there exist functional constraints on the evolution of protein ubiquitination sites, because most previous studies regarded all protein ubiquitination sites as a whole or only focused on limited structural properties. We tried to clarify the relation between functional constraints and ubiquitination sites evolution. We investigated the evolutionary conservation of human ubiquitination sites in a broad evolutionary scale from G. gorilla to S. pombe, and we found that in organisms originated after the divergence of vertebrate, ubiquitination sites are more conserved than their flanking regions, while the opposite tendency is observed before this divergence time...
January 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28003514/s-cerevisiae-trm140-has-two-recognition-modes-for-3-methylcytidine-modification-of-the-anticodon-loop-of-trna-substrates
#3
Lu Han, Erin Marcus, Sonia D'Silva, Eric M Phizicky
The 3-methylcytidine (m3C) modification is ubiquitous in eukaryotic tRNA, widely found at C32 in the anticodon loop of tRNAThr, tRNASer, and some tRNAArg species, as well as in the variable loop (V-loop) of certain tRNASer species. In the yeast Saccharomyces cerevisiae, formation of m3C32 requires Trm140 for six tRNA substrates, including three tRNAThr species and three tRNASer species, whereas in Schizosacchomyces pombe, two Trm140 homologs are employed, one for tRNAThr and one for tRNASer. The occurrence of a single Trm140 homolog is conserved broadly among Ascomycota, whereas multiple Trm140-related homologs are found in metazoans and other fungi...
December 21, 2016: RNA
https://www.readbyqxmd.com/read/27999345/combined-use-of-s-pombe-and-l-thermotolerans-in-winemaking-beneficial-effects-determined-through-the-study-of-wines-analytical-characteristics
#4
Ángel Benito, Fernando Calderón, Santiago Benito
The most common way to produce red wine is through the use of Saccharomyces cerevisiae strains for alcoholic fermentation and lactic acid bacteria for malolactic fermentation. This traditional winemaking methodology produces microbiologically stable red wines. However, under specific conditions off-flavours can occur, wine quality can suffer and human health problems are possible, especially after the second fermentation by the lactic acid bacteria. In warm countries, problems during the malolactic fermentation arise because of the high pH of the must, which makes it very difficult to properly control the process...
December 18, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27988464/synthesis-and-biological-screening-of-novel-2-morpholinoquinoline-nucleus-clubbed-with-1-2-4-oxadiazole-motifs
#5
Sharad C Karad, Vishal B Purohit, Rahul P Thummar, Beena K Vaghasiya, Ronak D Kamani, Parth Thakor, Vasudev R Thakkar, Sampark S Thakkar, Arabinda Ray, Dipak K Raval
Novel series of 2-morpholinoquinoline scaffolds (6a-n), containing the 1,2,4-oxadiazole and moiety, was designed and synthesized in good yield (76-86%). The synthesized compounds were screened for their preliminary in vitro antimicrobial activity against a panel of pathogenic strains of bacteria and fungi. Molecular docking and pharmacokinetic study were carried out for the prepared compounds. The cytotoxicity of the synthesized compounds was tested at different concentrations using bioassay of S. pombe cells at the cellular level...
December 9, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27974503/traffic-through-the-trans-golgi-network-and-the-endosomal-system-requires-collaboration-between-exomer-and-clathrin-adaptors-in-fission-yeast
#6
Marta Hoya, Francisco Yanguas, Sandra Moro, Cristina Prescianotto-Baschong, Cristina Doncel, Nagore de León, M-Ángeles Curto, Anne Spang, M-Henar Valdivieso
Despite its biological and medical relevance, traffic from the Golgi to the plasma membrane is one of the least understood steps of secretion. Exomer is a protein complex that mediates the trafficking of certain cargoes from the trans-Golgi network/early endosomes to the plasma membrane in budding yeast. Here we show that in Schizosaccharomyces pombe the Cfr1 and Bch1 proteins constitute the simplest form of an exomer. Cfr1 co-immunoprecipitates with AP-1, AP-2 and GGA subunits, and cfr1(+) interacts genetically with AP-1 and GGA genes...
December 14, 2016: Genetics
https://www.readbyqxmd.com/read/27935167/ck2-phospho-independent-assembly-of-the-tel2-associated-stress-signaling-complexes-in-schizosaccharomyces-pombe
#7
Haruna Inoue, Shizuka Sugimoto, Yumiko Takeshita, Miho Takeuchi, Mitsuko Hatanaka, Koji Nagao, Takeshi Hayashi, Aya Kokubu, Mitsuhiro Yanagida, Junko Kanoh
An evolutionarily conserved protein Tel2 regulates a variety of stress signals. In mammals, TEL2 associates with TTI1 and TTI2 to form the Triple T (TTT: TEL2-TTI1-TTI2) complex as well as with all the phosphatidylinositol 3-kinase-like kinases (PIKKs) and the R2TP (Ruvbl1-Ruvbl2-Tah1-Pih1 in budding yeast)/prefoldin-like complex that associates with HSP90. The phosphorylation of TEL2 by casein kinase 2 (CK2) enables direct binding of PIHD1 (mammalian Pih1) to TEL2 and is important for the stability and the functions of PIKKs...
December 9, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/27934694/metabolomic-analysis-of-schizosaccharomyces-pombe-sample-preparation-detection-and-data-interpretation
#8
Tomáš Pluskal, Mitsuhiro Yanagida
Metabolomics is a modern field of chemical biology that strives to simultaneously quantify hundreds of cellular metabolites. Techniques for metabolomic analysis in Schizosaccharomyces pombe have only recently been developed. Here we introduce methods that provide a complete workflow for metabolomic analysis in S. pombe Based on available literature, we estimate the yeast metabolome to comprise on the order of several thousand different metabolites. We discuss the feasibility of extraction and detection of such a large number of metabolites, and the influences of various parameters on the results...
December 1, 2016: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/27916534/critical-role-of-the-proton-dependent-oligopeptide-transporter-pot-in-the-cellular-uptake-of-the-peptidyl-nucleoside-antibiotic-blasticidin-s
#9
Kenji Kitamura, Eldaa Zefany Banami Kinsui, Fumiyoshi Abe
Blasticidin S (BlaS) interferes in the cell growth of both eukaryotes and prokaryotes. Its mode of action as a protein synthesis inhibitor has been investigated extensively. However, the mechanism of BlaS transport into the target cells is not understood well. Here, we show that Ptr2, a member of the proton-dependent oligopeptide transporter (POT) family, is responsible for the uptake of BlaS in yeasts Schizosaccharomyces pombe and Saccharomyces cerevisiae. Notably, some mutants of Ptr2 that are dysfunctional in dipeptide uptake were still competent to transport BlaS...
February 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27906621/isolation-of-a-novel-protein-p12-from-adult-drosophila-melanogaster-that-inhibits-deoxyribonucleoside-and-protein-kinase-activities-and-activates-3-5-exonuclease-activity
#10
Louise Slot Christiansen, Gabriella van Zanten, Dvora Berenstein, Marianne Lauridsen, Søren Kjærulff, Leif Søndergaard, Birgitte Munch-Petersen
We have previously found that Drosophila melanogaster only has one deoxyribonucleoside kinase, Dm-dNK, however, capable to phosphorylate all four natural deoxyribonucleosides. Dm-dNK was originally isolated from an embryonic cell line. We wanted to study the expression of Dm-dNK during development from embryonic cells to adult flies and found declining Dm-dNK activity during development and no activity in adult flies. Surprisingly, the extract from adult flies exhibited a strong inhibitory effect on deoxyribonucloside kinase activity...
December 2016: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/27902423/characterization-of-cis-elements-in-the-promoter-of-trz2-encoding-schizosaccharomyces-pombe-mitochondrial-trna-3-end-processing-enzyme
#11
Jinyu Liu, Linting Huang, Yirong Wang, Ying Huang
The endonuclease tRNase Z is responsible for the 3'-end processing of tRNA precursors, which is one of the essential steps in tRNA maturation. The fission yeast Schizosaccharomyces pombe contains two essential tRNase ZL genes (trz1 and trz2) involved in nuclear and mitochondrial tRNA 3'-end processing, respectively. Our previous studies suggest that trz2 is expressed at a very low level. Here we report characterization of the trz2 promoter. Using lacZ as a reporter, we show that the trz2 promoter contains a HomolD box and a very weak diverged TATA element...
November 22, 2016: Microbiology
https://www.readbyqxmd.com/read/27896529/acetaldehyde-kinetics-of-enological-yeast-during-alcoholic-fermentation-in-grape-must
#12
Erhu Li, Ramón Mira de Orduña
Acetaldehyde strongly binds to the wine preservative SO2 and, on average, causes 50-70 mg l(-1) of bound SO2 in red and white wines, respectively. Therefore, a reduction of bound and total SO2 concentrations necessitates knowledge of the factors that affect final acetaldehyde concentrations in wines. This study provides a comprehensive analysis of the acetaldehyde production and degradation kinetics of 26 yeast strains of oenological relevance during alcoholic fermentation in must under controlled anaerobic conditions...
November 28, 2016: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27890612/in%C3%A2-vitro-reconstitution-and-biochemical-analyses-of-the-schizosaccharomyces-pombe-nucleosome
#13
Masako Koyama, Wataru Nagakura, Hiroki Tanaka, Tomoya Kujirai, Yuji Chikashige, Tokuko Haraguchi, Yasushi Hiraoka, Hitoshi Kurumizaka
Schizosaccharomyces pombe, which has a small genome but shares many physiological functions with higher eukaryotes, is a useful single-cell, model eukaryotic organism. In particular, many features concerning chromatin structure and dynamics, including heterochromatin, centromeres, telomeres, and DNA replication origins, are well conserved between S. pombe and higher eukaryotes. However, the S. pombe nucleosome, the fundamental structural unit of chromatin, has not been reconstituted in vitro. In the present study, we established the method to purify S...
January 22, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27886462/loss-of-ppr3-ppr4-ppr6-or-ppr10-perturbs-iron-homeostasis-and-leads-to-apoptotic-cell-death-in-schizosaccharomyces-pombe
#14
Yang Su, Yanmei Yang, Ying Huang
: Pentatricopeptide repeat (PPR) proteins characterized by tandem arrays of a degenerate 35-amino-acid repeat belong to a large family of RNA-binding proteins that are involved in post-transcriptional control of organelle gene expression. PPR proteins are ubiquitous in eukaryotes, and particularly prevalent in higher plants. Schizosaccharomyces pombe has 10 PPR proteins. Among them, ppr3, ppr4, ppr6, and ppr10 participate in mitochondrial post-transcriptional processes and are required for mitochondrial electron transport chain (ETC) function...
November 25, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27884105/structural-features-of-dna-that-determine-rna-polymerase-ii-core-promoter
#15
Irina A Il'icheva, Mingian V Khodikov, Maria S Poptsova, Dmitry Yu Nechipurenko, Yury D Nechipurenko, Sergei L Grokhovsky
BACKGROUND: The general structure and action of all eukaryotic and archaeal RNA polymerases machinery have an astonishing similarity despite the diversity of core promoter sequences in different species. The goal of our work is to find common characteristics of DNA region that define it as a promoter for the RNA polymerase II (Pol II). RESULTS: The profiles of a large number of physical and structural characteristics, averaged over representative sets of the Pol II minimal core promoters of the evolutionary divergent species from animals, plants and unicellular fungi were analysed...
November 25, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27875300/the-fission-yeast-pre-mrna-processing-factor-18-prp18-has-intron-specific-splicing-functions-with-links-to-g1-s-cell-cycle-progression
#16
Nagampalli Vijaykrishna, Geetha Melangath, Rakesh Kumar, Piyush Khandelia, Pushpinder Bawa, Raghavan Varadarajan, Usha Vijayraghavan
The fission yeast genome, which contains numerous short introns, is an apt model for studies on fungal splicing mechanisms and splicing by intron definition. Here we perform a domain analysis of the evolutionarily conserved Schizosaccharomyces pombe pre-mRNA-processing factor, SpPrp18. Our mutational and biophysical analyses of the C-terminal α-helical bundle reveal critical roles for the conserved region as well as helix five. We generate a novel conditional missense mutant, spprp18-5 To assess the role of SpPrp18, we performed global splicing analyses on cells depleted of prp18(+) and the conditional spprp18-5 mutant, which show widespread but intron-specific defects...
December 30, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27844442/quantifying-force-and-viscoelasticity-inside-living-cells-using-an-active-passive-calibrated-optical-trap
#17
Christine M Ritter, Josep Mas, Lene Oddershede, Kirstine Berg-Sørensen
As described in the previous chapters, optical tweezers have become a tool of precision for in vitro single-molecule investigations, where the single molecule of interest most often is studied in purified form in an experimental assay with a well-controlled fluidic environment. A well-controlled fluidic environment implies that the physical properties of the liquid, most notably the viscosity, are known and the fluidic environment can, for calibrational purposes, be treated as a simple liquid.In vivo, however, optical tweezers have primarily been used as a tool of manipulation and not so often for precise quantitative force measurements, due to the unknown value of the spring constant of the optical trap formed within the cell's viscoelastic cytoplasm...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27837315/cloning-and-characterization-of-decaprenyl-diphosphate-synthase-from-three-different-fungi
#18
Daisuke Moriyama, Tomohiro Kaino, Kazuyoshi Yajima, Ryota Yanai, Yasuhiro Ikenaka, Junzo Hasegawa, Motohisa Washida, Hirokazu Nanba, Makoto Kawamukai
Coenzyme Q (CoQ) is composed of a benzoquinone moiety and an isoprenoid side chain of varying lengths. The length of the side chain is controlled by polyprenyl diphosphate synthase. In this study, dps1 genes encoding decaprenyl diphosphate synthase were cloned from three fungi: Bulleromyces albus, Saitoella complicata, and Rhodotorula minuta. The predicted Dps1 proteins contained seven conserved domains found in typical polyprenyl diphosphate synthases and were 528, 440, and 537 amino acids in length in B. albus, S...
November 11, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27825301/analysis-of-the-association-between-codon-optimality-and-mrna-stability-in-schizosaccharomyces-pombe
#19
Yuriko Harigaya, Roy Parker
BACKGROUND: Recent experiments have shown that codon optimality is a major determinant of mRNA stability in Saccharomyces cerevisiae and that this phenomenon may be conserved in Escherichia coli and some metazoans, although work in Neurospora crassa is not consistent with this model. RESULTS: We examined the association between codon optimality and mRNA stability in the fission yeast Schizosaccharomyces pombe. Our analysis revealed the following points. First, we observe a genome-wide association between codon optimality and mRNA stability also in S...
November 8, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27803257/chromatin-immunoprecipitation-chip-in-schizosaccharomyces-pombe
#20
Hugh P Cam, Simon Whitehall
Chromatin immunoprecipitation (ChIP), the cross-linking of chromatin followed by immunoprecipitation with antibodies against a chromatin target, is a key method for measuring association of proteins with a specific genomic region(s). As a negative control, a mock ChIP experiment in which no antibody is added to the immunoprecipitation reaction is included. Enriched DNA fragments from a ChIP experiment can be analyzed in a variety of ways. For semiquantitative analysis, a region of interest can be amplified using standard polymerase chain reaction (PCR) techniques...
November 1, 2016: Cold Spring Harbor Protocols
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