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Saccharomyces cerevisiae

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https://www.readbyqxmd.com/read/28646149/crucial-role-of-4-deoxy-l-erythro-5-hexoseulose-uronate-reductase-for-alginate-utilization-revealed-by-adaptive-evolution-in-engineered-saccharomyces-cerevisiae
#1
Fumiya Matsuoka, Makoto Hirayama, Takayuki Kashihara, Hideki Tanaka, Wataru Hashimoto, Kousaku Murata, Shigeyuki Kawai
In brown macroalgae, alginate and D-mannitol are promising carbohydrates for biorefinery. Saccharomyces cerevisiae is widely used as a microbial cell factory, but this budding yeast is unable to utilize either alginate or D-mannitol. Alginate can be depolymerized by both endo-type and exo-type alginate lyases, yielding a monouronate, 4-deoxy-L-erythro-5-hexoseulose uronate (DEH), a key intermediate in the metabolism of alginate. Here, we constructed engineered two S. cerevisiae strains that are able to utilize both DEH and D-mannitol on two different strain backgrounds, and we also improved their aerobic growth in a DEH liquid medium through adaptive evolution...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646139/genome-wide-identification-of-major-intrinsic-proteins-in-glycine-soja-and-characterization-of-gmtip2-1-function-under-salt-and-water-stress
#2
Da-Yong Zhang, Manoj Kumar, Ling Xu, Qun Wan, Yi-Hong Huang, Zhao-Long Xu, Xiao-Lan He, Jin-Biao Ma, Girdhar K Pandey, Hong-Bo Shao
In different plant species, aquaporins (AQPs) facilitate water movement by regulating root hydraulic conductivity under diverse stress conditions such as salt and water stresses. To improve survival and yield of crop plants, a detailed understanding of stress responses is imperative and required. We used Glycine soja genome as a tool to study AQPs, considering it shows abundant genetic diversity and higher salt environment tolerance features and identified 62 Gs AQP genes. Additionally, this study identifies major aquaporins responsive to salt and drought stresses in soybean and elucidates their mode of action through yeast two-hybrid assay and BiFC...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646136/recurrent-background-mutations-in-whi2-impair-proteostasis-and-degradation-of-misfolded-cytosolic-proteins-in-saccharomyces-cerevisiae
#3
Sophie A Comyn, Stéphane Flibotte, Thibault Mayor
Proteostasis promotes viability at both the cellular and organism levels by maintaining a functional proteome. This requires an intricate protein quality control (PQC) network that mediates protein folding by molecular chaperones and removes terminally misfolded proteins via the ubiquitin proteasome system and autophagy. How changes within the PQC network can perturb proteostasis and shift the balance between protein folding and proteolysis remain poorly understood. However, given that proteostasis is altered in a number of conditions such as cancer and ageing, it is critical that we identify the factors that mediate PQC and understand the interplay between members of the proteostatic network...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28645374/reconstituted-system-for-the-examination-of-repair-dna-synthesis-in-homologous-recombination
#4
Youngho Kwon, James M Daley, Patrick Sung
In homologous recombination (HR), DNA polymerase δ-mediated DNA synthesis occurs within the displacement loop (D-loop) that is made by the recombinase Rad51 in conjunction with accessory factors. We describe in this chapter the reconstitution of the D-loop and repair DNA synthesis reactions using purified Saccharomyces cerevisiae HR (Rad51, RPA, and Rad54) and DNA replication (PCNA, RFC, and DNA polymerase δ) proteins and document the role of the Pif1 helicase in DNA synthesis via a migrating DNA bubble intermediate...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28643238/characterization-of-the-complex-involved-in-regulating-v-atpase-activity-of-the-vacuolar-and-endosomal-membrane
#5
REVIEW
Zhenyu Zhang, Xiaojiao Wang, Tangjie Gao, Chunyin Gu, Fubao Sun, Lin Yu, Jinguang Hu
Regulator of the H(+)-ATPase of the vacuolar and endosomal membranes (RAVE) is essential for the reversible assembly of H(+)-ATPase. RAVE primarily consists of three subunits: Rav1p, Rav2p and Skp1p. To characterize these subunits, in this study, four strains derived from Saccharomyces cerevisiae BY4742 were constructed with a FLAG tag on the Rav1p and Rav2p subunits. Then, the corresponding RAVE containing complex was isolated by affinity purification. Western blot and MALDI-TOF mass spectrometry analyses showed that the RAVE complex contains not only the known V1-ATPase subunits (Vma1p and Vma2p) but also a newly found Leu1p that interacts with the RAVE subunit...
June 22, 2017: Journal of Bioenergetics and Biomembranes
https://www.readbyqxmd.com/read/28642757/the-fungal-pathogen-candida-glabrata-does-not-depend-on-surface-ferric-reductases-for-iron-acquisition
#6
Franziska Gerwien, Abu Safyan, Stephanie Wisgott, Sascha Brunke, Lydia Kasper, Bernhard Hube
Iron acquisition is a crucial virulence determinant for many bacteria and fungi, including the opportunistic fungal pathogens Candida albicans and C. glabrata. While the diverse strategies used by C. albicans for obtaining iron from the host are well-described, much less is known about the acquisition of this micronutrient from host sources by C. glabrata - a distant relative of C. albicans with closer evolutionary ties to Saccharomyces cerevisiae, which nonetheless causes severe clinical symptoms in humans...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28642742/microbial-resources-and-enological-significance-opportunities-and-benefits
#7
REVIEW
Leonardo Petruzzi, Vittorio Capozzi, Carmen Berbegal, Maria R Corbo, Antonio Bevilacqua, Giuseppe Spano, Milena Sinigaglia
Among the innovative trends in the wine sector, the continuous exploration of enological properties associated with wine microbial resources represents a cornerstone driver of quality improvement. Since the advent of starter cultures technology, the attention has been focused on intraspecific biodiversity within the primary species responsible for alcoholic fermentation (Saccharomyces cerevisiae) and, subsequently, for the so-called 'malolactic fermentation' (Oenococcus oeni). However, in the last decade, a relevant number of studies proposed the enological exploitation of an increasing number of species (e...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28642366/saccharomyces-cerevisiae-red1-protein-exhibits-nonhomologous-dna-end-joining-activity-and-potentiates-hop1-promoted-pairing-of-double-stranded-dna
#8
Rucha Kshirsagar, Indrajeet Ghodke, Kalappa Muniyappa
Elucidation of the function of synaptonemal complex (SC) in <Saccharomyces cerevisiae> has mainly focused on in vivo analysis of recombination-defective meiotic mutants. Consequently, significant gaps remain in the mechanistic understanding of the activities of different SC proteins and the functional relationships among them. S. cerevisiae Hop1 and Red1 are essential structural components of the SC axial/lateral elements. Previous studies have demonstrated that Hop1 is a structure-specific DNA-binding protein that exhibits high affinity for the Holliday junction, promotes DNA bridging, condensation and pairing between duplex DNA molecules...
June 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28642365/phenotypic-diagnosis-of-lineage-and-differentiation-during-sake-yeast-breeding
#9
Shinsuke Ohnuki, Hiroki Okada, Anne Friedrich, Yoichiro Kanno, Tetsuya Goshima, Hirokazu Hasuda, Masaaki Inahashi, Naoto Okazaki, Hiroyasu Tamura, Ryo Nakamura, Dai Hirata, Hisashi Fukuda, Hitoshi Shimoi, Katsuhiko Kitamoto, Daisuke Watanabe, Joseph Schacherer, Takeshi Akao, Yoshikazu Ohya
Sake yeast was developed exclusively in Japan. Its diversification during breeding remains largely uncharacterized. To evaluate the breeding processes of the sake lineage, we thoroughly investigated the phenotypes and differentiation of 27 sake yeast strains using high-dimensional, single-cell morphological phenotyping. Although the genetic diversity of the sake yeast lineage is relatively low, its morphological diversity has expanded substantially compared to that of the Saccharomyces cerevisiae species as a whole...
June 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28641210/comparative-analysis-of-polyspecificity-of-the-endogenous-trna-synthetase-of-different-expression-host-towards-photocrosslinking-amino-acids-using-an-in-silico-approach
#10
Nadarajan Saravanan Prabhu, Hyungdon Yun
Photo-induced covalent crosslinking has emerged as the powerful strategy for analyzing and characterizing the protein-protein interaction and mapping protein 3D conformations. In the last decades, a number of photocrosslinking amino acids have been reported but only a few have been efficiently utilized for photocrosslinking purposes. Recently, incorporation of diazirine containing photoactivatable analogs such as photo-methionine, photo-leucine, photo-isoleucine and photo-lysine into target proteins were accomplished in live cells (Human A549cells, HEK 293) by depleting corresponding natural amino acid and supplementing these analogs in the medium...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28641144/impact-of-saccharomyces-cerevisiae-and-torulaspora-delbrueckii-starter-cultures-on-cocoa-beans-fermentation
#11
Simonetta Visintin, Lacerda Ramos, Nara Batista, Paola Dolci, Freitas Schwan, Luca Cocolin
Aim of this work was to study the impact of mixed cultures of Saccharomyces cerevisiae and Torulaspora delbrueckii and T. delbrueckii monoculture on the fermentation process conducted on two different cocoa hybrids, PS1319 and SJ02, in Bahia, Brazil. This was performed throughout studying physico-chemical changes during the fermentation process and analyzing volatile compounds and sensory analysis of chocolates. (GTG)5-PCR fingerprinting was used to type isolates at strain level allowing to assess the implantation of the starter cultures added...
June 7, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28638833/isolation-and-abiotic-stress-resistance-analyses-of-a-catalase-gene-from-ipomoea-batatas-l-lam
#12
Bin Yong, Xiaoyan Wang, Pan Xu, Haiyan Zheng, Xueting Fei, Zixi Hong, Qinqin Ma, Yuzhi Miao, Xianghua Yuan, Yusong Jiang, Huanhuan Shao
As an indicator of the antioxidant capability of plants, catalase can detoxify reactive oxygen species (ROS) generated by environmental stresses. Sweet potato is one of the top six most important crops in the world. However, its catalases remain largely unknown. In this study, a catalase encoding gene, IbCAT2 (accession number: KY615708), was identified and cloned from sweet potato cv. Xushu 18. It contained a 1479 nucleotides' open reading frame (ORF). S-R-L, Q-K-L, and a putative calmodulin binding domain were located at the C-terminus of IbCAT2, which suggests that IbCAT2 could be a peroxisomal catalase...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28638050/de-novo-yeast-genome-assemblies-from-minion-pacbio-and-miseq-platforms
#13
Francesca Giordano, Louise Aigrain, Michael A Quail, Paul Coupland, James K Bonfield, Robert M Davies, German Tischler, David K Jackson, Thomas M Keane, Jing Li, Jia-Xing Yue, Gianni Liti, Richard Durbin, Zemin Ning
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637875/coupled-feedback-loops-control-the-stimulus-dependent-dynamics-of-the-yeast-transcription-factor-msn2
#14
Yanfei Jiang, Zohreh AkhavanAghdam, Lev S Tsimring, Nan Hao
Information about environmental stimuli often can be encoded by the dynamics of signaling molecules or transcription factors. In the yeast Saccharomyces cerevisiae, different types of stresses induce distinct nuclear translocation dynamics of the general stress-responsive transcription factor Msn2, but the underlying mechanisms remain unclear. Using deterministic and stochastic modeling, we reproduced in silico the different dynamic responses of Msn2 to glucose limitation and osmotic stress observed in vivo and found that a positive feedback loop on protein kinase A mediated by the AMP-activated protein kinase Snf1 is coupled with a negative feedback loop to generate the characteristic pulsatile dynamics of Msn2...
June 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28637810/mcclintock-an-integrated-pipeline-for-detecting-transposable-element-insertions-in-whole-genome-shotgun-sequencing-data
#15
Michael G Nelson, Raquel S Linheiro, Casey M Bergman
Transposable element (TE) insertions are among the most challenging type of variants to detect in genomic data because of their repetitive nature and complex mechanisms of replication. Nevertheless, the recent availability of large resequencing datasets has spurred development of many new methods to detect TE insertions in whole genome shotgun sequences. Here we report an integrated bioinformatics pipeline for the detection of TE insertions in whole genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods...
June 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28637712/shrinking-daughters-rlm1-dependent-g1-s-checkpoint-maintains-saccharomyces-cerevisiae-daughter-cell-size-and-viability
#16
Sarah Piccirillo, Deepshikha Neog, David Spade, J David Van Horn, LeAnn M Tiede-Lewis, Sarah L Dallas, Tamas Kapros, Saul M Honigberg
The Rlm1 transcription factor is a target of the cell-wall integrity pathway. We report that an rlm1Δ; mutant grown on a non-fermentable carbon source at low osmolarity forms cell groups in which a mother cell is surrounded by smaller "satellite daughter" cells. Mother cells in these groups progressed through repeated rounds of cell division with normal rates of bud growth and genetic stability; however, these cells underwent precocious START relative to wild-type mothers. Thus, once activated, Rlm1 delays the transition from G1 to S, a mechanism we term the CW/START checkpoint...
June 21, 2017: Genetics
https://www.readbyqxmd.com/read/28637443/trichoderma-virens-%C3%AE-glucosidase-i-bgli-gene-expression-in-saccharomyces-cerevisiae-including-docking-and-molecular-dynamics-studies
#17
Gammadde Hewa Ishan Maduka Wickramasinghe, Pilimathalawe Panditharathna Attanayake Mudiyanselage Samith Indika Rathnayake, Naduviladath Vishvanath Chandrasekharan, Mahindagoda Siril Samantha Weerasinghe, Ravindra Lakshman Chundananda Wijesundera, Wijepurage Sandhya Sulochana Wijesundera
BACKGROUND: Cellulose, a linear polymer of β 1-4, linked glucose, is the most abundant renewable fraction of plant biomass (lignocellulose). It is synergistically converted to glucose by endoglucanase (EG) cellobiohydrolase (CBH) and β-glucosidase (BGL) of the cellulase complex. BGL plays a major role in the conversion of randomly cleaved cellooligosaccharides into glucose. As it is well known, Saccharomyces cerevisiae can efficiently convert glucose into ethanol under anaerobic conditions...
June 21, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28637248/expression-and-comparison-of-codon-optimised-aspergillus-tubingensis-amylase-variants-in-saccharomyces-cerevisiae
#18
Rosemary A Cripwell, Shaunita H Rose, Willem H van Zyl
The expression of codon optimised genes is a popular genetic engineering approach for the production of industrially relevant proteins. This study investigates and compares the expression of codon optimised and codon adapted amylase variants. The Aspergillus tubingensis raw starch hydrolysing α-amylase (amyA) and glucoamylase (glaA) encoding genes were redesigned using synonymous codons and expressed in S. cerevisiae Y294. Codon optimisation to favour S. cerevisiae codon bias resulted in a decrease in extracellular enzyme activity of 72% (30...
June 15, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28637241/the-chromatin-remodeling-complex-swi-snf-regulates-splicing-of-meiotic-transcripts-in-saccharomyces-cerevisiae
#19
Srivats Venkataramanan, Stephen Douglass, Anoop R Galivanche, Tracy L Johnson
Despite its relatively streamlined genome, there are important examples of regulated RNA splicing in Saccharomyces cerevisiae, such as splicing of meiotic transcripts. Like other eukaryotes, S. cerevisiae undergoes a dramatic reprogramming of gene expression during meiosis, including regulated splicing of a number of crucial meiosis-specific RNAs. Splicing of a subset of these is dependent upon the splicing activator Mer1. Here we show a crucial role for the chromatin remodeler Swi/Snf in regulation of splicing of meiotic genes and find that the complex affects meiotic splicing in two ways...
May 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637236/the-ribosome-assembly-gene-network-is-controlled-by-the-feedback-regulation-of-transcription-elongation
#20
Fernando Gómez-Herreros, Thanasis Margaritis, Olga Rodríguez-Galán, Vicent Pelechano, Victoria Begley, Gonzalo Millán-Zambrano, Macarena Morillo-Huesca, Mari Cruz Muñoz-Centeno, José E Pérez-Ortín, Jesús de la Cruz, Frank C P Holstege, Sebastián Chávez
Ribosome assembly requires the concerted expression of hundreds of genes, which are transcribed by all three nuclear RNA polymerases. Transcription elongation involves dynamic interactions between RNA polymerases and chromatin. We performed a synthetic lethal screening in Saccharomyces cerevisiae with a conditional allele of SPT6, which encodes one of the factors that facilitates this process. Some of these synthetic mutants corresponded to factors that facilitate pre-rRNA processing and ribosome biogenesis...
June 15, 2017: Nucleic Acids Research
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