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One carbon metabolism

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https://www.readbyqxmd.com/read/28822867/de-novo-assembly-and-characterization-of-seabass-lateolabrax-japonicus-transcriptome-and-expression-of-hepatic-genes-following-different-dietary-phosphorus-calcium-levels
#1
Kang-Le Lu, Zhong-Li Ji, Samad Rahimnejad, Chun-Xiao Zhang, Ling Wang, Kai Song
Fish farming seriously influences the aquatic environment because most dietary phosphorus (P) is excreted in the effluent. To increase the P utilization in fish, molecular techniques should be explored given the remarkable development of these techniques. Thus, to identify the candidate genes related to P utilization and molecular alterations following administration of a P-deficient diet in seabass Lateolabrax japonicus, we assessed the de novo pituitary, gill, intestine, liver, kidney, scales and vertebra transcriptomes, and we compared the expression of hepatic genes with three diets varying in P and Ca levels: diet I (0...
August 9, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28821550/crystal-structure-of-the-tetr-family-repressor-alkx-from-dietzia-sp-dq12-45-1b-implicated-in-biodegradation-of-n-alkanes
#2
Jie-Liang Liang, Yuan Gao, Zheng He, Yong Nie, Meng Wang, Jing-Hong JiangYang, Xuejun C Zhang, Wen-Sheng Shu, Xiao-Lei Wu
n-Alkanes are ubiquitous in nature and are widely used by microorganisms as carbon sources. Alkane hydroxylation by alkane monooxygenases is a critical step in the aerobic biodegradation of n-alkanes, which plays important roles in natural alkane attenuation and is used in industrial and environmental applications. The alkane oxidation operon, alkW1-alkX, in an alkane-degrading strain Dietzia sp. DQ12-45-1b, is negatively auto-regulated by the TetR family repressor, AlkX, via a product positive feedback mechanism...
August 18, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28818947/methanogenic-heterodisulfide-reductase-hdrabc-mvhagd-uses-two-noncubane-4fe-4s-clusters-for-reduction
#3
Tristan Wagner, Jürgen Koch, Ulrich Ermler, Seigo Shima
In methanogenic archaea, the carbon dioxide (CO2) fixation and methane-forming steps are linked through the heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhAGD) complex that uses flavin-based electron bifurcation to reduce ferredoxin and the heterodisulfide of coenzymes M and B. Here, we present the structure of the native heterododecameric HdrABC-MvhAGD complex at 2.15-angstrom resolution. HdrB contains two noncubane [4Fe-4S] clusters composed of fused [3Fe-4S]-[2Fe-2S] units sharing 1 iron (Fe) and 1 sulfur (S), which were coordinated at the CCG motifs...
August 18, 2017: Science
https://www.readbyqxmd.com/read/28814973/photoautotrophic-production-of-polyhydroxyalkanoates-in-a-synthetic-mixed-culture-of-synechococcus-elongatus-cscb-and-pseudomonas-putida-cscab
#4
Hannes Löwe, Karina Hobmeier, Manuel Moos, Andreas Kremling, Katharina Pflüger-Grau
BACKGROUND: One of the major challenges for the present and future generations is to find suitable substitutes for the fossil resources we rely on today. Cyanobacterial carbohydrates have been discussed as an emerging renewable feedstock in industrial biotechnology for the production of fuels and chemicals, showing promising production rates when compared to crop-based feedstock. However, intrinsic capacities of cyanobacteria to produce biotechnological compounds are limited and yields are low...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28814397/association-of-tcn2-rs1801198-c-776g-c-polymorphism-with-markers-of-one-carbon-metabolism-and-related-diseases-a-systematic-review-and-meta-analysis-of-genetic-association-studies
#5
Abderrahim Oussalah, Julien Levy, Pierre Filhine-Trésarrieu, Fares Namour, Jean-Louis Guéant
Background: Vitamin B-12 (cobalamin) deficiency may produce severe neurologic and hematologic manifestations. Approximately 20-25% of circulating cobalamin binds to transcobalamin 2 (TCN2), which is referred to as active vitamin B-12. The G allele of the TCN2 c.776G>C (rs1801198) polymorphism has been associated with a lower plasma concentration of holotranscobalamin. However, genotype association studies on rs1801198 have led to conflicting results regarding its influence on one-carbon metabolism (OCM) markers or its association with pathologic conditions...
August 16, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28813411/mammals-divert-endogenous-genotoxic-formaldehyde-into-one-carbon-metabolism
#6
Guillermo Burgos-Barragan, Niek Wit, Johannes Meiser, Felix A Dingler, Matthias Pietzke, Lee Mulderrig, Lucas B Pontel, Ivan V Rosado, Thomas F Brewer, Rebecca L Cordell, Paul S Monks, Christopher J Chang, Alexei Vazquez, Ketan J Patel
The folate-driven one-carbon (1C) cycle is a fundamental metabolic hub in cells that enables the synthesis of nucleotides and amino acids and epigenetic modifications. This cycle might also release formaldehyde, a potent protein and DNA crosslinking agent that organisms produce in substantial quantities. Here we show that supplementation with tetrahydrofolate, the essential cofactor of this cycle, and other oxidation-prone folate derivatives kills human, mouse and chicken cells that cannot detoxify formaldehyde or that lack DNA crosslink repair...
August 16, 2017: Nature
https://www.readbyqxmd.com/read/28812308/transcriptional-regulation-of-the-protein-kinase-a-subunits-in-saccharomyces-cerevisiae-during-fermentative-growth
#7
Fiorella Galello, Constanza Pautasso, Sol Reca, Luciana Cañonero, Paula Portela, Silvia Moreno, Silvia Rossi
Yeast cells can adapt their growth in response to the nutritional environment. Glucose is the favorite carbon source of Saccharomyces cerevisiae that prefers a fermentative metabolism despite the presence of oxygen. When glucose is consumed, the cell switches to the aerobic metabolism of ethanol, during the so-called diauxic shift. The difference between fermentative and aerobic growth is in part mediated by a regulatory mechanism called glucose repression. During glucose derepression a profound gene transcriptional reprogramming occurs and genes involved in the utilization of alternative carbon sources are expressed...
August 15, 2017: Yeast
https://www.readbyqxmd.com/read/28810182/selenium-increases-hepatic-dna-methylation-and-modulates-one-carbon-metabolism-in-the-liver-of-mice
#8
Bodo Speckmann, Sarah Schulz, Franziska Hiller, Deike Hesse, Fabian Schumacher, Burkhard Kleuser, Jürgen Geisel, Rima Obeid, Tilman Grune, Anna P Kipp
The average intake of the essential trace element selenium (Se) is below the recommendation in most European countries, possibly causing sub-optimal expression of selenoproteins. It is still unclear how a suboptimal Se status may affect health. To mimic this situation, mice were fed one of three physiologically relevant amounts of Se. We focused on the liver, the organ most sensitive to changes in the Se supply indicated by hepatic glutathione peroxidase activity. In addition, liver is the main organ for synthesis of methyl groups and glutathione via one-carbon metabolism...
July 9, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28809400/prenatal-one-carbon-metabolism-dysregulation-programs-schizophrenia-like-deficits
#9
A Alachkar, L Wang, R Yoshimura, A R Hamzeh, Z Wang, N Sanathara, S M Lee, X Xu, G W Abbott, O Civelli
The methionine-folate cycle-dependent one-carbon metabolism is implicated in the pathophysiology of schizophrenia. Since schizophrenia is a developmental disorder, we examined the effects that perturbation of the one-carbon metabolism during gestation has on mice progeny. Pregnant mice were administered methionine equivalent to double their daily intake during the last week of gestation. Their progeny (MET mice) exhibited schizophrenia-like social deficits, cognitive impairments and elevated stereotypy, decreased neurogenesis and synaptic plasticity, and abnormally reduced local excitatory synaptic connections in CA1 neurons...
August 15, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28809129/effect-of-methotrexate-vitamin-b12-on-dna-methylation-as-a-potential-factor-in-leukemia-treatment-related-neurotoxicity
#10
Victoria J Forster, Alex McDonnell, Rachel Theobald, Jill A McKay
Methotrexate (MTX) is administered to treat childhood acute lymphoblastic leukemia (ALL). It acts by inhibiting dihydrofolate reductase which reduces methyltetrahydrofolate, a key component in one carbon metabolism, thus reducing cell proliferation. Further perturbations to one carbon metabolism, such as reduced vitamin B12 levels via the use of nitrous oxide for sedation during childhood ALL treatment, may increase neurotoxicity risk. With B12 as an enzymatic cofactor, methyltetrahydrofolate is essential to produce methionine, which is critical for DNA methylation...
August 15, 2017: Epigenomics
https://www.readbyqxmd.com/read/28804512/engineering-shewanella-oneidensis-enables-xylose-fed-microbial-fuel-cell
#11
Feng Li, Yuanxiu Li, Liming Sun, Xiaofei Li, Changji Yin, Xingjuan An, Xiaoli Chen, Yao Tian, Hao Song
BACKGROUND: The microbial fuel cell (MFC) is a green and sustainable technology for electricity energy harvest from biomass, in which exoelectrogens use metabolism and extracellular electron transfer pathways for the conversion of chemical energy into electricity. However, Shewanella oneidensis MR-1, one of the most well-known exoelectrogens, could not use xylose (a key pentose derived from hydrolysis of lignocellulosic biomass) for cell growth and power generation, which limited greatly its practical applications...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28803187/reinforcing-carbon-fixation-co2-reduction-replacing-and-supporting-carboxylation
#12
REVIEW
Charles Ar Cotton, Christian Edlich-Muth, Arren Bar-Even
Carbon dioxide enters the biosphere via one of two mechanisms: carboxylation, in which CO2 is attached to an existing metabolite, or reduction, in which CO2 is converted to formate or carbon monoxide before further assimilation. Here, we focus on the latter mechanism which usually receives less attention. To better understand the possible advantages of the 'reduction-first' approach, we compare the two general strategies according to the kinetics of the CO2-capturing enzymes, and the resource consumption of the subsequent pathways...
August 10, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28794205/the-human-serum-metabolome-of-vitamin-b-12-deficiency-and-repletion-and-associations-with-neurological-function-in-elderly-adults
#13
Alex Brito, Dmitry Grapov, Johannes Fahrmann, Danielle Harvey, Ralph Green, Joshua W Miller, Sergey N Fedosov, Setareh Shahab-Ferdows, Daniela Hampel, Theresa L Pedersen, Oliver Fiehn, John W Newman, Ricardo Uauy, Lindsay H Allen
Background: The specific metabolomic perturbations that occur in vitamin B-12 deficiency, and their associations with neurological function, are not well characterized.Objective: We sought to characterize the human serum metabolome in subclinical vitamin B-12 deficiency and repletion.Methods: A before-and-after treatment study provided 1 injection of 10 mg vitamin B-12 (with 100 mg pyridoxine and 100 mg thiamin) to 27 community-dwelling elderly Chileans (∼74 y old) with vitamin B-12 deficiency, as evaluated with serum vitamin B-12, total plasma homocysteine (tHcy), methylmalonic acid (MMA), and holotranscobalamin...
August 9, 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28793223/constraint-and-contingency-pervade-the-emergence-of-novel-phenotypes-in-complex-metabolic-systems
#14
Sayed-Rzgar Hosseini, Andreas Wagner
An evolutionary constraint is a bias or limitation in phenotypic variation that a biological system produces. We know examples of such constraints, but we have no systematic understanding about their extent and causes for any one biological system. We here study metabolisms, genomically encoded complex networks of enzyme-catalyzed biochemical reactions, and the constraints they experience in bringing forth novel phenotypes that allow survival on novel carbon sources. Our computational approach does not limit us to analyzing constrained variation in any one organism, but allows us to quantify constraints experienced by any metabolism...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28789930/commentary-on-an-integrated-metabolic-atlas-of-clear-cell-renal-cell-carcinoma-hakimi-aa-reznik-e-lee-ch-creighton-cj-brannon-ar-luna-a-aksoy-ba-liu-em-shen-r-lee-w-chen-y-stirdivant-sm-russo-p-chen-yb-tickoo-sk-reuter-ve-cheng-eh-sander-c-hsieh-jj-cancer-cell
#15
Byron H Lee
Dysregulated metabolism is a hallmark of cancer, manifested through alterations in metabolites. We performed metabolomic profiling on 138 matched clear cell renal cell carcinoma (ccRCC)/normal tissue pairs and found that ccRCC is characterized by broad shifts in central carbon metabolism, one-carbon metabolism, and antioxidant response. Tumor progression and metastasis were associated with metabolite increases in glutathione and cysteine/methionine metabolism pathways. We develop an analytic pipeline and visualization tool (metabolograms) to bridge the gap between TCGA transcriptomic profiling and our metabolomic data, which enables us to assemble an integrated pathway-level metabolic atlas and to demonstrate discordance between transcriptome and metabolome...
August 5, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28776272/concurrent-metabolism-of-pentose-and-hexose-sugars-by-the-polyextremophile-alicyclobacillus-acidocaldarius
#16
Brady D Lee, William A Apel, Linda C DeVeaux, Peter P Sheridan
Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette-type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A...
August 3, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28776040/grf10-and-bas1-regulate-transcription-of-adenylate-and-one-carbon-biosynthesis-genes-and-affect-virulence-in-the-human-fungal-pathogen-candida-albicans
#17
Tanaporn Wangsanut, Anup K Ghosh, Peter G Metzger, William A Fonzi, Ronda J Rolfes
Candida albicans is an opportunistic human fungal pathogen that causes superficial fungal infections and lethal systemic infections. To colonize and establish infections, C. albicans coordinates the expression of virulence and metabolic genes. Previous work showed that the homeodomain transcription factor Grf10 is required for formation of hyphae, a virulence factor. Here we report global gene expression analysis of a grf10Δ strain using a DNA microarray and identify genes for de novo adenylate biosynthesis (ADE genes), one-carbon metabolism, and a nucleoside permease (NUP)...
July 2017: MSphere
https://www.readbyqxmd.com/read/28770393/association-of-neural-tube-defects-with-gene-polymorphisms-in-one-carbon-metabolic-pathway
#18
Lirong Cao, Yizheng Wang, Ruiping Zhang, Liang Dong, Hualei Cui, Yulian Fang, Linsheng Zhao, Ouyan Shi, Chunquan Cai
PURPOSE: Neural tube defects (NTDs) are common congenital malformations. In this study, we aimed to explore the association between single nucleotide polymorphisms (SNPs) related to one-carbon metabolism (OCM) and NTDs in Han population of Northern China. METHODS: A case-control study was conducted in 152 children with NTDs and 169 controls. Twenty-nine SNPs in five genes were genotyped by Sequenom MassARRAY technology, and haplotype analysis was done by Haploview4...
August 2, 2017: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/28770367/carbon-catabolite-regulation-in-streptomyces-new-insights-and-lessons-learned
#19
REVIEW
Alba Romero-Rodríguez, Diana Rocha, Beatriz Ruiz-Villafán, Silvia Guzmán-Trampe, Nidia Maldonado-Carmona, Melissa Vázquez-Hernández, Augusto Zelarayán, Romina Rodríguez-Sanoja, Sergio Sánchez
One of the most significant control mechanisms of the physiological processes in the genus Streptomyces is carbon catabolite repression (CCR). This mechanism controls the expression of genes involved in the uptake and utilization of alternative carbon sources in Streptomyces and is mostly independent of the phosphoenolpyruvate phosphotransferase system (PTS). CCR also affects morphological differentiation and the synthesis of secondary metabolites, although not all secondary metabolite genes are equally sensitive to the control by the carbon source...
September 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28768179/mtorc1-regulates-mitochondrial-integrated-stress-response-and-mitochondrial-myopathy-progression
#20
Nahid A Khan, Joni Nikkanen, Shuichi Yatsuga, Christopher Jackson, Liya Wang, Swagat Pradhan, Riikka Kivelä, Alberto Pessia, Vidya Velagapudi, Anu Suomalainen
Mitochondrial dysfunction elicits various stress responses in different model systems, but how these responses relate to each other and contribute to mitochondrial disease has remained unclear. Mitochondrial myopathy (MM) is the most common manifestation of adult-onset mitochondrial disease and shows a multifaceted tissue-specific stress response: (1) transcriptional response, including metabolic cytokines FGF21 and GDF15; (2) remodeling of one-carbon metabolism; and (3) mitochondrial unfolded protein response...
August 1, 2017: Cell Metabolism
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