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One carbon metabolism

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https://www.readbyqxmd.com/read/28338685/prebiotic-synthesis-of-phosphoenol-pyruvate-by-%C3%AE-phosphorylation-controlled-triose-glycolysis
#1
Adam J Coggins, Matthew W Powner
Phosphoenol pyruvate is the highest-energy phosphate found in living organisms and is one of the most versatile molecules in metabolism. Consequently, it is an essential intermediate in a wide variety of biochemical pathways, including carbon fixation, the shikimate pathway, substrate-level phosphorylation, gluconeogenesis and glycolysis. Triose glycolysis (generation of ATP from glyceraldehyde 3-phosphate via phosphoenol pyruvate) is among the most central and highly conserved pathways in metabolism. Here, we demonstrate the efficient and robust synthesis of phosphoenol pyruvate from prebiotic nucleotide precursors, glycolaldehyde and glyceraldehyde...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28334792/gwas-identifies-population-specific-new-regulatory-variants-in-fut6-associated-with-plasma-b12-concentrations-in-indians
#2
Suraj S Nongmaithem, Charudatta V Joglekar, Ghattu V Krishnaveni, Sirazul A Sahariah, Meraj Ahmad, Swetha Ramachandran, Meera Gandhi, Harsha Chopra, Anand Pandit, Ramesh D Potdar, Caroline Hd Fall, Chittaranjan S Yajnik, Giriraj R Chandak
Vitamin B12 is an important cofactor in one-carbon metabolism whose dysregulation is associated with various clinical conditions. Indians have a high prevalence of B12 deficiency but little is known about the genetic determinants of circulating B12 concentrations in Indians. We performed a genome-wide association study in 1001 healthy participants in the Pune Maternal Nutrition Study (PMNS), replication studies in 3418 individuals from other Indian cohorts and by meta-analysis identified new variants, rs3760775 (p = 1...
February 27, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28326310/cardiopulmonary-response-during-whole-body-vibration-training-in-patients-with-severe-copd
#3
Rainer Gloeckl, Petra Richter, Sandra Winterkamp, Michael Pfeifer, Christoph Nell, Jeffrey W Christle, Klaus Kenn
Several studies in patients with chronic obstructive pulmonary disease (COPD) have shown that whole-body vibration training (WBVT) has beneficial effects on exercise capacity. However, the acute cardiopulmonary demand during WBVT remains unknown and was therefore investigated in this study. Ten patients with severe COPD (forced expiratory volume in 1 s: 38±8% predicted) were examined on two consecutive days. On day one, symptom-limited cardiopulmonary exercise testing was performed on a cycle ergometer. The next day, six bouts of repeated squat exercises were performed in random order for one, two or three minutes either with or without WBVT while metabolic demands were simultaneously measured...
January 2017: ERJ Open Research
https://www.readbyqxmd.com/read/28314724/impact-of-seasonal-hypoxia-on-activity-and-community-structure-of-chemolithoautotrophic-bacteria-in-a-coastal-sediment
#4
Yvonne A Lipsewers, Diana Vasquez-Cardenas, Dorina Seitaj, Regina Schauer, Silvia Hidalgo Martinez, Jaap S Sinninghe Damsté, Filip J R Meysman, Laura Villanueva, Henricus T S Boschker
Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyze these reoxidation reactions, is rarely studied. Here we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28302759/preclinical-evaluation-of-11-c-sarcosine-as-a-substrate-of-proton-coupled-amino-acid-transporters-and-first-human-application-in-prostate-cancer
#5
Morand Piert, Xia Shao, David M Raffel, Mathew S Davenport, Jeffrey Montgomery, Lakshmi Kunju, Brian G Hockley, Javed Siddiqui, Peter J H Scott, Arul Chinnaiyan, Thekkelnaycke Rajandiran
Sarcosine is a known substrate of proton-coupled amino acid transporters (PAT), which are overexpressed in selected tissues and solid tumors. Sarcosine, an N-methyl derivative of the amino acid glycine and a metabolic product of choline, plays an important role for prostate cancer aggressiveness and progression. Methods: Carbon-11 radiolabeled sarcosine ((11)C-sarcosine) was tested as a new positron emission tomography (PET) imaging probe in comparison with (11)C-choline in two prostate cancer tumor xenograft models (DU-145 and PC-3)...
March 16, 2017: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/28301476/classification-and-adaptive-behavior-prediction-of-children-with-autism-spectrum-disorder-based-upon-multivariate-data-analysis-of-markers-of-oxidative-stress-and-dna-methylation
#6
Daniel P Howsmon, Uwe Kruger, Stepan Melnyk, S Jill James, Juergen Hahn
The number of diagnosed cases of Autism Spectrum Disorders (ASD) has increased dramatically over the last four decades; however, there is still considerable debate regarding the underlying pathophysiology of ASD. This lack of biological knowledge restricts diagnoses to be made based on behavioral observations and psychometric tools. However, physiological measurements should support these behavioral diagnoses in the future in order to enable earlier and more accurate diagnoses. Stepping towards this goal of incorporating biochemical data into ASD diagnosis, this paper analyzes measurements of metabolite concentrations of the folate-dependent one-carbon metabolism and transulfuration pathways taken from blood samples of 83 participants with ASD and 76 age-matched neurotypical peers...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28295011/increased-dosage-of-aox1-promoter-regulated-expression-cassettes-leads-to-transcription-attenuation-of-the-methanol-metabolism-in-pichia-pastoris
#7
Elena Cámara, Nils Landes, Joan Albiol, Brigitte Gasser, Diethard Mattanovich, Pau Ferrer
The methanol-regulated alcohol oxidase promoter (PAOX1) of Pichia pastoris is one of the strongest promoters for heterologous gene expression in this methylotrophic yeast. Although increasing gene dosage is one of the most common strategies to increase recombinant protein productivities, the increase of gene dosage of Rhizopus oryzae lipase (ROL) in P. pastoris has been previously shown to reduce cell growth, lipase production and substrate consumption in high-copy strains. To better assess that physiological response, transcriptomics analysis was performed of a subset of strains with 1 to 15 ROL copies...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28293216/comparative-genome-analysis-of-three-thiocyanate-oxidizing-thioalkalivibrio-species-isolated-from-soda-lakes
#8
Tom Berben, Lex Overmars, Dimitry Y Sorokin, Gerard Muyzer
Thiocyanate is a C1 compound containing carbon, nitrogen, and sulfur. It is a (by)product in a number of natural and industrial processes. Because thiocyanate is toxic to many organisms, including humans, its removal from industrial waste streams is an important problem. Although a number of bacteria can use thiocyanate as a nitrogen source, only a few can use it as an electron donor. There are two distinct pathways to use thiocyanate: (i) the "carbonyl sulfide pathway," which has been extensively studied, and (ii) the "cyanate pathway," whose key enzyme, thiocyanate dehydrogenase, was recently purified and studied...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28289836/prokaryotic-abundance-and-activity-in-permafrost-of-the-northern-victoria-land-and-upper-victoria-valley-antarctica
#9
Rosabruna La Ferla, Maurizio Azzaro, Luigi Michaud, Gabriella Caruso, Angelina Lo Giudice, Rodolfo Paranhos, Anderson S Cabral, Antonella Conte, Alessandro Cosenza, Giovanna Maimone, Maria Papale, Alessandro Ciro Rappazzo, Mauro Guglielmin
Victoria Land permafrost harbours a potentially large pool of cold-affected microorganisms whose metabolic potential still remains underestimated. Three cores (BC-1, BC-2 and BC-3) drilled at different depths in Boulder Clay (Northern Victoria Land) and one sample (DY) collected from a core in the Dry Valleys (Upper Victoria Valley) were analysed to assess the prokaryotic abundance, viability, physiological profiles and potential metabolic rates. The cores drilled at Boulder Clay were a template of different ecological conditions (different temperature regime, ice content, exchanges with atmosphere and with liquid water) in the same small basin while the Dry Valleys site was very similar to BC-2 conditions but with a complete different geological history and ground ice type...
March 13, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28289085/the-small-protein-sgrt-controls-transport-activity-of-the-glucose-specific-phosphotransferase-system
#10
Chelsea R Lloyd, Seongjin Park, Jingyi Fei, Carin K Vanderpool
The bacterial small RNA (sRNA) SgrS has been a fruitful model for discovery of novel RNA-based regulatory mechanisms and new facets of bacterial physiology and metabolism. SgrS is one of only a few characterized dual-function sRNAs. SgrS can control gene expression post-transcriptionally via sRNA-mRNA base pairing interactions. Its second function is coding for the small protein SgrT. Previous work demonstrated that both functions contribute to relief of growth inhibition caused by glucose-phosphate stress, a condition characterized by disrupted glycolytic flux and accumulation of sugar-phosphates...
March 13, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28286551/systems-analysis-of-ethanol-production-in-the-genetically-engineered-cyanobacterium-synechococcus-sp-pcc-7002
#11
Joachim Kopka, Stefanie Schmidt, Frederik Dethloff, Nadin Pade, Susanne Berendt, Marco Schottkowski, Nico Martin, Ulf Dühring, Ekaterina Kuchmina, Heike Enke, Dan Kramer, Annegret Wilde, Martin Hagemann, Alexandra Friedrich
BACKGROUND: Future sustainable energy production can be achieved using mass cultures of photoautotrophic microorganisms, which are engineered to synthesize valuable products directly from CO2 and sunlight. As cyanobacteria can be cultivated in large scale on non-arable land, these phototrophic bacteria have become attractive organisms for production of biofuels. Synechococcus sp. PCC 7002, one of the cyanobacterial model organisms, provides many attractive properties for biofuel production such as tolerance of seawater and high light intensities...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28285855/insights-in-the-regulation-of-the-degradation-of-pahs-in-novosphingobium-sp-hr1a-and-utilization-of-this-regulatory-system-as-a-tool-for-the-detection-of-pahs
#12
Ana Segura, Verónica Hernández-Sánchez, Silvia Marqués, Lázaro Molina
Novosphingobium sp. HR1a is able to grow using diverse polycyclic aromatic hydrocarbons (PAHs) as the sole carbon sources. We have identified two transposons that contain genes encoding several ring-hydroxylating dioxygenases and we have demonstrated the crucial role of one of these dioxygenases in the PAH metabolism in this strain; a mutant in the large subunit of this dioxygenase was unable to growth with 2-, 3-, or 4-rings aromatic hydrocarbons. Using a construction of lacZ gene fused with the pathway promoter, we determined that the expression of the dioxygenase gene was specifically induced in the presence of some PAHs and intermediates of their metabolic pathway...
March 9, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28280926/enhanced-detoxification-of-arsenic-under-carbon-starvation-a-new-insight-into-microbial-arsenic-physiology
#13
Vinod S Nandre, Sachin P Bachate, Rahul C Salunkhe, Aditi V Bagade, Yogesh S Shouche, Kisan M Kodam
Nutrient availability in nature influenced the microbial ecology and behavior present in existing environment. In this study, we have focused on isolation of arsenic-oxidizing cultures from arsenic devoid environment and studied effect of carbon starvation on rate of arsenite oxidation. In spite of the absence of arsenic, a total of 40 heterotrophic, aerobic, arsenic-transforming bacterial strains representing 18 different genera were identified. Nineteen bacterial species were isolated from tannery effluent and twenty-one from tannery soil...
March 10, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28276134/deterministic-influences-exceed-dispersal-effects-on-hydrologically-connected-microbiomes
#14
Emily B Graham, Alex R Crump, Charles T Resch, Sarah Fansler, Evan Arntzen, David W Kennedy, Jim K Fredrickson, James C Stegen
Subsurface groundwater-surface water mixing zones (hyporheic zones) have enhanced biogeochemical activity, but assembly processes governing subsurface microbiomes remain a critical uncertainty in understanding hyporheic biogeochemistry. To address this obstacle, we investigated (a) biogeographical patterns in attached and waterborne microbiomes across three hydrologically-connected, physicochemically-distinct zones (inland hyporheic, nearshore hyporheic, and river); (b) assembly processes that generated these patterns; (c) groups of organisms that corresponded to deterministic changes in the environment; and (d) correlations between these groups and hyporheic metabolism...
March 9, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28266642/abundant-iron-and-sulfur-oxidizers-in-the-stratified-sediment-of-a-eutrophic-freshwater-reservoir-with-annual-cyanobacterial-blooms
#15
Long Jin, Chang Soo Lee, Chi-Yong Ahn, Hyung-Gwan Lee, Sanghyup Lee, Hyeon Ho Shin, Dhongil Lim, Hee-Mock Oh
The microbial community in eutrophic freshwater sediment was investigated from a 67-cm-deep sediment core collected from the Daechung Reservoir in South Korea, where cyanobacterial blooms have occurred annually for the past 30 years. The majority of core sediments were characterized by dark-grayish, fine-grained mud with abundant gas-escaped and thinly laminated layers. Intervals of summer and winter seasons were represented by periodic peaks of geochemical profiles of parameters such as grain size and relative carbon mass ratios to various nutrients such as nitrogen, sulfur, and phosphorus...
March 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28265051/comparative-genomics-uncovers-the-prolific-and-distinctive-metabolic-potential-of-the-cyanobacterial-genus-moorea
#16
Tiago Leao, Guilherme Castelão, Anton Korobeynikov, Emily A Monroe, Sheila Podell, Evgenia Glukhov, Eric E Allen, William H Gerwick, Lena Gerwick
Cyanobacteria are major sources of oxygen, nitrogen, and carbon in nature. In addition to the importance of their primary metabolism, some cyanobacteria are prolific producers of unique and bioactive secondary metabolites. Chemical investigations of the cyanobacterial genus Moorea have resulted in the isolation of over 190 compounds in the last two decades. However, preliminary genomic analysis has suggested that genome-guided approaches can enable the discovery of novel compounds from even well-studied Moorea strains, highlighting the importance of obtaining complete genomes...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28263314/widespread-distribution-of-encapsulin-nanocompartments-reveals-functional-diversity
#17
Tobias W Giessen, Pamela A Silver
Cells organize and regulate their metabolism via membrane- or protein-bound organelles. In this way, incompatible processes can be spatially separated and controlled. In prokaryotes, protein-based compartments are used to sequester harmful reactions and store useful compounds. These protein compartments play key roles in various metabolic and ecological processes, ranging from iron homeostasis to carbon fixation. One of the newest types of protein organelle are encapsulin nanocompartments. They are able to encapsulate specific protein cargo and are proposed to be involved in redox-related processes...
March 6, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28259896/the-one-carbon-metabolism-pathway-highlights-therapeutic-targets-for-gastrointestinal-cancer-review
#18
Masamitsu Konno, Ayumu Asai, Koichi Kawamoto, Naohiro Nishida, Taroh Satoh, Yuichiro Doki, Masaki Mori, Hideshi Ishii
After the initial use of anti-folates for treatment of malignancies, folate metabolism has emerged as a rational diagnostic and therapeutic target in gastrointestinal cancer. The one-carbon metabolic pathway, which comprises three critical reactions (i.e., folate and methionine cycles), underlies this effect in conjunction with the trans-sulfuration pathway. Understanding of the one-carbon metabolism pathway has served to unravel the link between the causes and effects of cancer phenotypes leading to several seminal discoveries such as that of diadenosine tri-phosphate hydrolase, microRNAs, 5-FU and, more recently, trifluridine...
February 20, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28257867/cobalamin-supplementation-during-in%C3%A2-vitro-maturation-improves-developmental-competence-of-sheep-oocytes
#19
Federica Zacchini, Paola Toschi, Grazyna Ewa Ptak
Pregnancies obtained by Assisted Reproductive Technologies are at higher risk of miscarriage than those obtained naturally. Previously, we reported impaired placental vascular development of in vitro produced (IVP) sheep embryos and defective DNA methylation in the placentae of those embryos. One reason behind these observed defects may be an impaired One Carbon Metabolism (OCM) The present study was performed to test the hypothesis that Cobalamin (Vitamin B12, an important OCM co-factor) supplementation during IVM corrects DNA methylation of IVP embryos and, consequently, ameliorates placental vasculogenesis...
April 15, 2017: Theriogenology
https://www.readbyqxmd.com/read/28256129/quantification-of-chemotaxis-related-alkane-accumulation-in-acinetobacter-baylyi-using-raman-microspectroscopy
#20
Hanbing Li, Francis Luke Martin, Dayi Zhang
Alkanes are one of the most widespread contaminants in the natural environment, primarily as a consequence of biological synthesis and oil spills. Many indigenous microbes metabolize alkanes, and the chemotaxis and accumulation in some strains has been identified. For the first time, we apply Raman microspectroscopy to identify such chemotaxis-related affinity, and quantify the alkane concentrations via spectral alterations. Raman spectral alterations were only found for the alkane chemo-attractant bacteria Acinetobacter baylyi ADP1, not for Pseudomonas fluorescence, which exhibits limited chemotaxis toward alkane...
March 16, 2017: Analytical Chemistry
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