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One carbon metabolism

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https://www.readbyqxmd.com/read/28443812/enhancing-ethanol-yields-through-d-xylose-and-l-arabinose-co-fermentation-after-construction-of-a-novel-high-efficient-l-arabinose-fermenting-saccharomyces-cerevisiae-strain
#1
Antonio Caballero, Juan Luis Ramos
Lignocellulose contains two pentose sugars, l-arabinose and d-xylose, neither of which is naturally fermented by first generation (1G) ethanol-producing Saccharomyces cerevisiae yeast. Since these sugars are inaccessible to 1G yeast, a significant percentage of the total carbon in bioethanol production from plant residues, which are used in second generation (2G) ethanol production, remains unused. Recombinant Saccharomyces cerevisiae strains capable of fermenting d-xylose are available on the market; however, there are few examples of l-arabinose-fermenting yeasts, and commercially, there are no strains capable of fermenting both d-xylose and l-arabinose because of metabolic incompatibilities when both metabolic pathways are expressed in the same cell...
April 2017: Microbiology
https://www.readbyqxmd.com/read/28442570/coordination-chemistry-controls-the-thiol-oxidase-activity-of-the-b12-trafficking-protein-cblc
#2
Zhu Li, Aranganathan Shanmuganathan, Markus Ruetz, Kazuhiro Yamada, Nicholas A Lesniak, Bernhard Kraeutler, Thomas C Brunold, Markos Koutmos, Ruma Banerjee
The cobalamin or B12 cofactor supports sulfur and one-carbon metabolism and the catabolism of odd-chain fatty acids, branched-chain amino acids and cholesterol. CblC is a B12 processing enzyme involved in an early cytoplasmic step in the cofactor trafficking pathway. It catalyzes the glutathione (GSH)-dependent dealkylation of alkylcobalamins and the reductive decyanation of cyanocobalamin. CblC from Caenorhabdiitis elegans (ceCblC) also exhibits a robust thiol oxidase activity converting reduced GSH to oxidized GSSG with concomitant scrubbing of ambient dissolved O2 The mechanism of thiol oxidation catalyzed by ceCblC is not known...
April 25, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28441628/potassium-deficiency-affects-the-carbon-nitrogen-balance-in-cotton-leaves
#3
Wei Hu, Taylor D Coomer, Dimitra A Loka, Derrick M Oosterhuis, Zhiguo Zhou
Potassium (K) plays important roles in the metabolism of carbon (C) and nitrogen (N), but studies of K deficiency affecting C-N balance are lacking. This study explored the influence of K deficiency on C-N interaction in cotton leaves by conducting a field experiment with cotton cultivar DP0912 under two K rates (K0: 0 kg K2O ha(-1) and K67: 67 kg K2O ha(-1)) and a controlled environment experiment with K-deficient solution (K1: 0 mM K(+)) and K-sufficient solution (K2: 6 mM K(+)). The results showed that leaf K content, leaf number, leaf area, boll number, reproductive dry weight and total dry weight were significant lower under K deficiency (K0 or K1)...
April 6, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28432307/arsenic-metabolism-in-high-altitude-modern-stromatolites-revealed-by-metagenomic-analysis
#4
Daniel Kurth, Ariel Amadio, Omar F Ordoñez, Virginia H Albarracín, Wolfgang Gärtner, María E Farías
Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa's stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429420/the-crystal-structure-of-a-new-o-demethylase-from-sphingobium-sp-strain-syk-6
#5
Ayaka Harada, Naofumi Kamimura, Koh Takeuchi, Hong Yang Yu, Eiji Masai, Toshiya Senda
In the cell, tetrahydrofolate derivatives with a C1 unit are utilized in various ways, such as for the synthesis of amino acids and nucleic acids. While tetrahydrofolate derivatives with the C1 unit are typically produced in the glycine cleavage system, Sphingobium sp. strain SYK-6, which can utilize lignin-derived aromatic compounds as a sole source of carbon and energy, lacks this pathway, probably due to its unique nutrient requirements. In this bacterium, tetrahydrofolate-dependent O-demethylases in catabolic pathways for lignin-derived aromatic compounds seem to be involved in the C1 metabolism...
April 20, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28429316/c2-metabolism-in-euglena
#6
Masami Nakazawa
Euglenoids are able to assimilate fatty acids and alcohols with various carbon-chain lengths, and ethanol is known to be one of the best carbon sources to support the growth of Euglena gracilis. Ethanol is first oxidized to acetate by the sequential reactions of alcohol dehydrogenase and acetaldehyde dehydrogenase in the mitochondria, and then converted to acetyl coenzyme A (acetyl-CoA). Acetyl-CoA is metabolized through the glyoxylate cycle which is a modified tricarboxylic acid (TCA) cycle in which isocitrate lyase (ICL) and malate synthase (MS) function to bypass the two decarboxylation steps of the TCA cycle, enabling the net synthesis of carbohydrates from C2 compounds...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28427325/global-analysis-of-protein-lysine-succinylation-profiles-in-common-wheat
#7
Yumei Zhang, Guangyuan Wang, Limin Song, Ping Mu, Shu Wang, Wenxing Liang, Qi Lin
BACKGROUND: Protein lysine succinylation is an important post-translational modification and plays a critical regulatory role in almost every aspects of cell metabolism in both eukaryotes and prokaryotes. Common wheat is one of the major global cereal crops. However, to date, little is known about the functions of lysine succinylation in this plant. Here, we performed a global analysis of lysine succinylation in wheat and examined its overlap with lysine acetylation. RESULTS: In total, 330 lysine succinylated modification sites were identified in 173 proteins...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28425205/engineering-the-xylose-catabolizing-dahms-pathway-for-production-of-poly-d-lactate-co-glycolate-and-poly-d-lactate-co-glycolate-co-d-2-hydroxybutyrate-in-escherichia-coli
#8
So Young Choi, Won Jun Kim, Seung Jung Yu, Si Jae Park, Sung Gap Im, Sang Yup Lee
Poly(lactate-co-glycolate), PLGA, is a representative synthetic biopolymer widely used in medical applications. Recently, we reported one-step direct fermentative production of PLGA and its copolymers by metabolically engineered Escherichia coli from xylose and glucose. In this study, we report development of metabolically engineered E. coli strains for the production of PLGA and poly(d-lactate-co-glycolate-co-d-2-hydroxybutyrate) having various monomer compositions from xylose as a sole carbon source. To achieve this, the metabolic flux towards Dahms pathway was modulated using five different synthetic promoters for the expression of Caulobacter crescentus XylBC...
April 19, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28424769/folates-in-plants-research-advances-and-progress-in-crop-biofortification
#9
REVIEW
Vera Gorelova, Lars Ambach, Fabrice Rébeillé, Christophe Stove, Dominique Van Der Straeten
Folates, also known as B9 vitamins, serve as donors and acceptors in one-carbon (C1) transfer reactions. The latter are involved in synthesis of many important biomolecules, such as amino acids, nucleic acids and vitamin B5. Folates also play a central role in the methyl cycle that provides one-carbon groups for methylation reactions. The important functions fulfilled by folates make them essential in all living organisms. Plants, being able to synthesize folates de novo, serve as an excellent dietary source of folates for animals that lack the respective biosynthetic pathway...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28424186/circulating-concentrations-of-biomarkers-and-metabolites-related-to-vitamin-status-one-carbon-and-the-kynurenine-pathways-in-us-nordic-asian-and-australian-populations
#10
Øivind Midttun, Despoina Theofylaktopoulou, Adrian McCann, Anouar Fanidi, David C Muller, Klaus Meyer, Arve Ulvik, Wei Zheng, Xiao-Ou Shu, Yong-Bing Xiang, Ross Prentice, Cynthia A Thomson, Mary Pettinger, Graham G Giles, Allison Hodge, Qiuyin Cai, William J Blot, Jie Wu, Mikael Johansson, Johan Hultdin, Kjell Grankvist, Victoria L Stevens, Marjorie L McCullough, Stephanie J Weinstein, Demetrius Albanes, Arnulf Langhammer, Kristian Hveem, Marit Næss, Howard D Sesso, J Michael Gaziano, Julie E Buring, I-Min Lee, Gianluca Severi, Xuehong Zhang, Jiali Han, Meir J Stampfer, Stephanie A Smith-Warner, Anne Zeleniuch-Jacquotte, Loic le Marchand, Jian-Min Yuan, Lesley M Butler, Woon-Puay Koh, Renwei Wang, Yu-Tang Gao, Ulrika Ericson, Emily Sonestedt, Regina G Ziegler, Neal D Freedman, Kala Visvanathan, Miranda R Jones, Caroline Relton, Paul Brennan, Mattias Johansson, Per M Ueland
Background: Circulating concentrations of biomarkers that are related to vitamin status vary by factors such as diet, fortification, and supplement use. Published biomarker concentrations have also been influenced by the variation across laboratories, which complicates a comparison of results from different studies.Objective: We robustly and comprehensively assessed differences in biomarkers that are related to vitamin status across geographic regions.Design: The trial was a cross-sectional study in which we investigated 38 biomarkers that are related to vitamin status and one-carbon and tryptophan metabolism in serum and plasma from 5314 healthy control subjects representing 20 cohorts recruited from the United States, Nordic countries, Asia, and Australia, participating in the Lung Cancer Cohort Consortium...
April 19, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28424096/metabolic-and-proteomic-analyses-of-product-selectivity-and-redox-regulation-in-clostridium-pasteurianum-grown-on-glycerol-under-varied-iron-availability
#11
Christin Groeger, Wei Wang, Wael Sabra, Tyll Utesch, An-Ping Zeng
BACKGROUND: Clostridium pasteurianum as an emerging new microbial cell factory can produce both n-butanol (BuOH) and 1,3-propanediol (1,3-PDO), and the pattern of product formation changes significantly with the composition of the culture medium. Among others iron content in the medium was shown to strongly affect the products selectivity. However, the mechanism behind this metabolic regulation is still unclear. For a better understanding of such metabolic regulation and for process optimization, we carried out fermentation experiments under either iron excess or iron limitation conditions, and performed metabolic, stoichiometric and proteomic analyses...
April 19, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28421040/isolation-and-molecular-characterization-of-novel-chlorpyrifos-and-3-5-6-trichloro-2-pyridinol-degrading-bacteria-from-sugarcane-farm-soils
#12
Smriti Rayu, Uffe N Nielsen, Loïc Nazaries, Brajesh K Singh
Chlorpyrifos (CP) is one of the most widely used organophosphate pesticides in agriculture worldwide, but its extensive use has led to the contamination of various soil and water systems. Microbial bioremediation is considered to be one of the most viable options for the removal of CP from the environment; however, little is known about the soil bacterial diversity that degrade CP. Sequential soil and liquid culture enrichments enabled the isolation of bacterial CP degraders with sequence homologies to Xanthomonas sp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28418785/metabolomics-analysis-of-the-osteogenic-differentiation-of-umbilical-cord-blood-mesenchymal-stem-cells-reveals-differential-sensitivity-to-osteogenic-agents
#13
Michail E Klontzas, Spyros I Vernardis, Manolis Heliotis, Eleftherios Tsiridis, Athanasios Mantalaris
Mesenchymal stem cells (MSCs) of fetal origin, such as umbilical cord blood MSCs (UCB MSCs), have emerged as a promising cell source for musculoskeletal tissue regeneration because of their higher proliferation potential, lack of donor site morbidity, and their off-the-shelf potential. MSCs differentiated toward the osteogenic lineage exhibit a specific metabolic phenotype characterized by reliance to oxidative phosphorylation for energy production and reduced glycolytic rates. Currently, limited information exists on the metabolic transitions at different stages of the osteogenic process after osteoinduction with different agents...
April 18, 2017: Stem Cells and Development
https://www.readbyqxmd.com/read/28413444/functional-photosystem-i-maintains-proper-energy-balance-during-nitrogen-depletion-in-chlamydomonas-reinhardtii-promoting-triacylglycerol-accumulation
#14
Mahmoud Gargouri, Philip D Bates, Jeong-Jin Park, Helmut Kirchhoff, David R Gang
BACKGROUND: Nutrient deprivation causes significant stress to the unicellular microalga, Chlamydomonas reinhardtii, which responds by significantly altering its metabolic program. Following N deprivation, the accumulation of starch and triacylglycerols (TAGs) is significantly altered following massive reprogramming of cellular metabolism. One protein that was found to change dramatically and early to this stress was TAB2, a photosystem I (PSI) translation initiation factor, whose transcript and protein levels increased significantly after only 30 min of N deprivation...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28411369/comparison-of-equine-platelet-function-and-survival-in-whole-blood-collected-in-acid-citrate-dextrose-solution-or-citrate-phosphate-dextrose-adenine-solution
#15
Rana Bozorgmanesh, Julie W Sutton-Burges, Fern Tablin
BACKGROUND: Equine whole blood collection and storage methods have been evaluated to assess red blood cell viability; however, platelet (PLT) viability has not been comprehensively assessed. OBJECTIVES: The purpose of the study was to compare viability of PLTs collected in whole blood into 2 different anticoagulants. METHODS: Whole blood from 6 healthy adult Thoroughbred horses was collected into citrate-phosphate-dextrose-adenine (CPDA) or acid-citrate-dextrose (ACD)...
April 14, 2017: Veterinary Clinical Pathology
https://www.readbyqxmd.com/read/28409450/method-for-measurement-of-peroxisomal-very-long-chain-fatty-acid-beta-oxidation-and-de-novo-c26-0-synthesis-activity-in-living-cells-using-stable-isotope-labeled-docosanoic-acid
#16
Malu-Clair van de Beek, Inge M E Dijkstra, Stephan Kemp
Peroxisomes are present in virtually every eukaryotic cell type with the exception of the mature erythrocyte. In higher eukaryotes, one of the main functions of peroxisomes is lipid metabolism by means of beta-oxidation of very long-chain fatty acids (VLCFA; ≥22 carbon atoms). A dysfunction in peroxisomal VLCFA beta-oxidation results in elevated VLCFA levels in cells, tissue, and plasma. Here, we describe a straightforward and sensitive method to measure peroxisomal beta-oxidation capacity in living cells using stable-isotope labeled docosanoic acid (D3-C22:0)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28401465/metabolism-of-pyrene-through-phthalic-acid-pathway-by-enriched-bacterial-consortium-composed-of-pseudomonas-burkholderia-and-rhodococcus-pbr
#17
Sagar Vaidya, Kunal Jain, Datta Madamwar
Polycyclic aromatic hydrocarbons (PAHs) are highly recalcitrant compounds due to their high hydrophobicity and tendency to partition in organic phase of soils. Pyrene is a high-molecular weight PAH, which has human health concerns. In the present study, a bacterial consortium, PBR, was developed from a long-term polluted site, viz., Amlakhadi, Ankleshwar, Gujarat, for effective degradation of pyrene. The consortium effectively metabolized pyrene as a sole source of carbon and energy. The consortium comprised three bacterial species, Pseudomonas sp...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28400561/a-hybrid-stochastic-model-of-folate-mediated-one-carbon-metabolism-effect-of-the-common-c677t-mthfr-variant-on-de-novo-thymidylate-biosynthesis
#18
Karla Misselbeck, Luca Marchetti, Martha S Field, Marco Scotti, Corrado Priami, Patrick J Stover
Folate-mediated one-carbon metabolism (FOCM) is an interconnected network of metabolic pathways, including those required for the de novo synthesis of dTMP and purine nucleotides and for remethylation of homocysteine to methionine. Mouse models of folate-responsive neural tube defects (NTDs) indicate that impaired de novo thymidylate (dTMP) synthesis through changes in SHMT expression is causative in folate-responsive NTDs. We have created a hybrid computational model comprised of ordinary differential equations and stochastic simulation...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28396257/b-vitamin-and-choline-supplementation-increases-neuroplasticity-and-recovery-after-stroke
#19
Nafisa M Jadavji, Joshua T Emmerson, Amanda J MacFarlane, William G Willmore, Patrice D Smith
Folates are B-vitamins that play an important role in brain function. Dietary and genetic deficiencies in folate metabolism result in elevated levels of homocysteine which have been linked to increased risk of developing a stroke. Reducing levels of homocysteine before or after a stroke through B-vitamin supplementation has been a focus of many clinical studies, however, the results remain inconsistent. Animal model systems provide a powerful mechanism to study and understand functional impact and mechanisms through which supplementation affects stroke recovery...
April 7, 2017: Neurobiology of Disease
https://www.readbyqxmd.com/read/28390506/diversity-of-opportunistic-black-fungi-on-babassu-coconut-shells-a-rich-source-of-esters-and-hydrocarbons
#20
Mariana M F Nascimento, Vania A Vicente, Juliana V M Bittencourt, Jane Mary L Gelinski, Francesc X Prenafeta-Boldú, Maycoll Romero-Güiza, Gheniffer Fornari, Renata R Gomes, Germana D Santos, A H G Gerrits Van Den Ende, Conceição D M P S de Azevedo, G Sybren De Hoog
The present study assessed the diversity of black yeast-like fungi present on babassu coconut shells, a substrate rich in lipids and several volatile organic compounds (VOCs) including aromatic hydrocarbons. Using different isolation methods, one-hundred-six isolates were obtained and were identified by ITS sequencing as members of the genera Exophiala, Cladophialophora, Veronaea, and Rhinocladiella. Two novel species were discovered. Eight strains were selected for assessing their ability to grow on toluene and phenyl acetate as the sole carbon and energy source...
May 2017: Fungal Biology
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