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One-carbon metabolism

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https://www.readbyqxmd.com/read/29150517/multi-omics-reveal-the-lifestyle-of-the-acidophilic-mineral-oxidizing-model-species-leptospirillum-ferriphilum-t
#1
Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor V Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum(T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum(T) DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150512/a-genetic-system-for-the-thermophilic-acetogenic-bacterium-thermoanaerobacter-kivui
#2
Mirko Basen, Irina Geiger, Laura Henke, Volker Müller
Thermoanaerobacter kivui is one of the very few thermophilic acetogenic microorganisms. It grows optimally at 66°C on sugars but also lithotrophically with H2 + CO2 or with CO, producing acetate as major product. While a genome-derived model of acetogenesis has been developed, only few physiological or biochemical experiments towards the function of important enzymes in carbon and energy metabolism have been carried out. To address this issue, we developed a method for targeted, markerless gene deletions and for integration of genes into the genome of T...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150511/sulfolobus-acidocaldarius-uptakes-pentoses-via-a-cut2-type-abc-transporter-and-metabolizes-them-through-the-aldolase-independent-weimberg-pathway
#3
Michaela Wagner, Lu Shen, Andreas Albersmeier, Nienke van der Kolk, Sujin Kim, Jaeho Cha, Christopher Bräsen, Jörn Kalinowski, Bettina Siebers, Sonja-Verena Albers
Sulfolobus spp. possess a great metabolic versatility and grow heterotrophically on various carbon sources such as different sugars and peptides. Known sugar transporters in Archaea predominantly belong to ABC transport systems. Although several ABC transporters for sugar uptake have been characterized in the crenarchaeon Sulfolobus solfataricus, only one homologue of these transporters, the maltose/maltooligomer transporter, could be identified in the closely related Sulfolobus acidocaldarius Comparison of the transcriptome of S...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29142823/investigation-of-useful-carbon-tracers-for-13-c-metabolic-flux-analysis-of-escherichia-coli-by-considering-five-experimentally-determined-flux-distributions
#4
Kousuke Maeda, Nobuyuki Okahashi, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu
The (13)C-MFA experiments require an optimal design since the precision or confidence intervals of the estimated flux levels depends on factors such as the composition of (13)C-labeled carbon sources, as well as the metabolic flux distribution of interest. In this study, useful compositions of (13)C-labeled glucose for (13)C-metabolic flux analysis ((13)C-MFA) of Escherichia coli are investigated using a computer simulation of the stable isotope labeling experiment. Following the generation of artificial mass spectra datasets of amino acid fragments using five literature-reported flux distributions of E...
December 2016: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29142288/identification-of-small-rnas-abundant-in-burkholderia-cenocepacia-biofilms-reveal-putative-regulators-with-a-potential-role-in-carbon-and-iron-metabolism
#5
Andrea Sass, Sanne Kiekens, Tom Coenye
Small RNAs play a regulatory role in many central metabolic processes of bacteria, as well as in developmental processes such as biofilm formation. Small RNAs of Burkholderia cenocepacia, an opportunistic pathogenic beta-proteobacterium, are to date not well characterised. To address that, we performed genome-wide transcriptome structure analysis of biofilm grown B. cenocepacia J2315. 41 unannotated short transcripts were identified in intergenic regions of the B. cenocepacia genome. 15 of these short transcripts, highly abundant in biofilms, widely conserved in Burkholderia sp...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29141978/cobalamin-status-from-pregnancy-to-early-childhood-lessons-from-global-experience
#6
REVIEW
Rima Obeid, Michelle Murphy, Pol Solé-Navais, Chittaranjan Yajnik
Low cobalamin intake and status during pregnancy or lactation have been linked to adverse maternal and perinatal health outcomes, whereas low cobalamin status during early childhood is associated with impaired development in children. Women who begin pregnancy with depleted stores (low or very low plasma cobalamin) will give birth to depleted infants who are likely to develop deficiency symptoms during the first few weeks or months postpartum. Newly ingested cobalamin during pregnancy and lactation (from diet or supplements) is transferred to the child and is not likely to correct cobalamin status in depleted women...
November 2017: Advances in Nutrition
https://www.readbyqxmd.com/read/29141214/partitioning-of-one-carbon-units-in-folate-and-methionine-metabolism-is-essential-for-neural-tube-closure
#7
Kit-Yi Leung, Yun Jin Pai, Qiuying Chen, Chloe Santos, Enrica Calvani, Sonia Sudiwala, Dawn Savery, Markus Ralser, Steven S Gross, Andrew J Copp, Nicholas D E Greene
Abnormal folate one-carbon metabolism (FOCM) is implicated in neural tube defects (NTDs), severe malformations of the nervous system. MTHFR mediates unidirectional transfer of methyl groups from the folate cycle to the methionine cycle and, therefore, represents a key nexus in partitioning one-carbon units between FOCM functional outputs. Methionine cycle inhibitors prevent neural tube closure in mouse embryos. Similarly, the inability to use glycine as a one-carbon donor to the folate cycle causes NTDs in glycine decarboxylase (Gldc)-deficient embryos...
November 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/29140980/prokaryotic-diversity-and-biogeochemical-characteristics-of-benthic-microbial-ecosystems-at-la-brava-a-hypersaline-lake-at-salar-de-atacama-chile
#8
Maria Eugenia Farias, Maria Cecilia Rasuk, Kimberley L Gallagher, Manuel Contreras, Daniel Kurth, Ana Beatriz Fernandez, Daniel Poiré, Fernando Novoa, Pieter T Visscher
Benthic microbial ecosystems of Laguna La Brava, Salar de Atacama, a high altitude hypersaline lake, were characterized in terms of bacterial and archaeal diversity, biogeochemistry, (including O2 and sulfide depth profiles and mineralogy), and physicochemical characteristics. La Brava is one of several lakes in the Salar de Atacama where microbial communities are growing in extreme conditions, including high salinity, high solar insolation, and high levels of metals such as lithium, arsenic, magnesium, and calcium...
2017: PloS One
https://www.readbyqxmd.com/read/29137071/a-comparative-study-of-biological-and-metabolic-biomarkers-between-healthy-individuals-and-patients-with-acne-vulgaris-a-cross-sectional-study-protocol
#9
Kyuseok Kim, Injin Ha, Eunok Kim, Kyunglee Kim
Acne is a multifactorial dermatosis, which is influenced not only by hormones but also by the biochemical relationship between them and the pilosebaceous unit. Inflammatory cytokines, chemokines, active oxygen, and zinc are known to be associated with the development of acne. Further, steroid metabolism is known as one of the important factors related to sebum secretion and comedone formation in acne. However, there is a lack of studies comparing these human biomarkers between healthy individuals and patients with acne...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29135286/vitamin-b12-supplementation-influences-methylation-of-genes-associated-with-type-2-diabetes-and-its-intermediate-traits
#10
Dilip K Yadav, Smeeta Shrestha, Karen A Lillycrop, Charu V Joglekar, Hong Pan, Joanna D Holbrook, Caroline Hd Fall, Chittaranjan S Yajnik, Giriraj R Chandak
AIM: To investigate the effect of B12 and/or folic acid supplementation on genome-wide DNA methylation. METHODS: We performed Infinium HumanMethylation450 BeadChip (Zymo Research, CA, USA) assay in children supplemented with B12 and/or folic acid (n = 12 in each group) and investigated the functional mechanism of selected differentially methylated loci. RESULTS: We noted significant methylation changes postsupplementation in B12 (589 differentially methylated CpGs and 2892 regions) and B12 + folic acid (169 differentially methylated CpGs and 3241 regions) groups...
November 14, 2017: Epigenomics
https://www.readbyqxmd.com/read/29133450/resurrecting-ancestral-genes-in-bacteria-to-interpret-ancient-biosignatures
#11
Betul Kacar, Lionel Guy, Eric Smith, John Baross
Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29129471/higher-intake-of-fish-and-fat-is-associated-with-lower-plasma-s-adenosylhomocysteine-a-cross-sectional-study
#12
Mads V Lind, Lotte Lauritzen, Oluf Pedersen, Henrik Vestergaard, Ken D Stark, Torben Hansen, Alastair B Ross, Mette Kristensen
Several B-vitamins act as co-factors in one-carbon metabolism, a pathway that plays a central role in several chronic diseases. However, there is a lack of knowledge of how diet affects markers in one-carbon metabolism. The aim of this study was to explore dietary patterns and components associated with one-carbon metabolites. We hypothesized that intake of whole-grains and fish would be associated with lower Hcy, and higher SAM:SAH ratio due to their nutrient content. We assessed dietary information using a four-day dietary record in 118 men and women with features of the metabolic syndrome...
October 2, 2017: Nutrition Research
https://www.readbyqxmd.com/read/29123071/samtor-is-an-s-adenosylmethionine-sensor-for-the-mtorc1-pathway
#13
Xin Gu, Jose M Orozco, Robert A Saxton, Kendall J Condon, Grace Y Liu, Patrycja A Krawczyk, Sonia M Scaria, J Wade Harper, Steven P Gygi, David M Sabatini
mTOR complex 1 (mTORC1) regulates cell growth and metabolism in response to multiple environmental cues. Nutrients signal via the Rag guanosine triphosphatases (GTPases) to promote the localization of mTORC1 to the lysosomal surface, its site of activation. We identified SAMTOR, a previously uncharacterized protein, which inhibits mTORC1 signaling by interacting with GATOR1, the GTPase activating protein (GAP) for RagA/B. We found that the methyl donor S-adenosylmethionine (SAM) disrupts the SAMTOR-GATOR1 complex by binding directly to SAMTOR with a dissociation constant of approximately 7 μM...
November 10, 2017: Science
https://www.readbyqxmd.com/read/29121255/adipocyte-expression-of-slc19a1-links-dna-hypermethylation-to-adipose-tissue-inflammation-and-insulin-resistance
#14
Paul Petrus, Lucia Bialesova, Antonio Checa, Alastair Kerr, Shama Naz, Jesper Bäckdahl, Ana Gracia, Sofia Toft, Karin Dahlman-Wright, Per Hedén, Ingrid Dahlman, Craig E Wheelock, Peter Arner, Niklas Mejhert, Hui Gao, Mikael Rydén
Context: Insulin resistance (IR) is promoted by a chronic low-grade inflammation in white adipose tissue (WAT). The latter may be regulated through epigenetic mechanisms such as DNA-methylation. The one carbon cycle (1CC) is a central metabolic process governing DNA-methylation. Objective: To identify adipocyte-expressed 1CC genes linked to WAT inflammation, IR and their causal role. Design: Cohort study. Setting: Outpatient academic clinic...
November 7, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29116537/critical-analysis-of-excessive-utilization-of-crude-protein-in-ruminants-ration-impact-on-environmental-ecosystem-and-opportunities-of-supplementation-of-limiting-amino-acids-a-review
#15
Imtiaz Hussain Raja Abbasi, Farzana Abbasi, Mohamed E Abd El-Hack, Mervat A Abdel-Latif, Rab N Soomro, Khawar Hayat, Mohamed A E Mohamed, Bello M Bodinga, Junhu Yao, Yangchun Cao
Protein quality plays a key role than quantity in growth, production, and reproduction of ruminants. Application of high concentration of dietary crude protein (CP) did not balance the proportion of these limiting amino acids (AA) at duodenal digesta of high producing dairy cow. Thus, dietary supplementation of rumen-protected AA is recommended to sustain the physiological, productive, and reproductive performance of ruminants. Poor metabolism of high CP diets in rumen excretes excessive nitrogen (N) through urine and feces in the environment...
November 8, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29116430/microaerophilic-alkane-degradation-in-pseudomonas-extremaustralis-a-transcriptomic-and-physiological-approach
#16
Paula M Tribelli, Leticia Rossi, Martiniano M Ricardi, Maria Gomez-Lozano, Søren Molin, Laura J Raiger Iustman, Nancy I Lopez
Diesel fuel is one of the most important sources of hydrocarbon contamination worldwide. Its composition consists of a complex mixture of n-alkanes, branched alkanes and aromatic compounds. Hydrocarbon degradation in Pseudomonas species has been mostly studied under aerobic conditions; however, a dynamic spectrum of oxygen availability can be found in the environment. Pseudomonas extremaustralis, an Antarctic bacterium isolated from a pristine environment, is able to degrade diesel fuel and presents a wide microaerophilic metabolism...
November 7, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29107179/uptake-and-metabolism-of-water-borne-progesterone-by-the-mussel-mytilus-spp-mollusca
#17
Tamar I Schwarz, Ioanna Katsiadaki, Benjamin H Maskrey, Alexander P Scott
Previous studies have shown that mussels can pick up 17β-estradiol [E2] and testosterone [T] from water, metabolize them and conjugate them to fatty acids (esterification), leading to their accumulation in tissue. A key requirement for the esterification process is that a steroid must have a 'reactive' hydroxyl group to conjugate to a fatty acid (which in T, and probably E2, is the β-hydroxyl group on carbon 17). Progesterone (P) lacks any hydroxyl groups and theoretically cannot be esterified and hence should not accumulate in mussels in the same way as E2 or T...
October 26, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29105249/mimicking-microbial-interactions-under-nitrate-reducing-conditions-in-an-anoxic-bioreactor-enrichment-of-novel-nitrospirae-bacteria-distantly-related-to-thermodesulfovibrio
#18
Arslan Arshad, Paula Dalcin Martins, Jeroen Frank, Mike S M Jetten, Huub J M Op den Camp, Cornelia U Welte
Microorganisms are main drivers of the sulfur, nitrogen and carbon biogeochemical cycles. These element cycles are interconnected by the activity of different guilds in e.g. sediments or wastewater treatment systems. Here, we investigated a nitrate-reducing microbial community in a laboratory-scale bioreactor model that closely mimicked estuary or brackish sediment conditions. The bioreactor simultaneously consumed sulfide, methane and ammonium at the expense of nitrate. Ammonium oxidation occurred solely by the activity of anammox bacteria identified as Candidatus Scalindua brodae and Ca...
November 3, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29103702/improving-safety-of-a-live-attenuated-edwardsiella-ictaluri-vaccine-against-enteric-septicemia-of-catfish-and-evaluation-of-efficacy
#19
Seong Won Nho, Hossam Abdelhamed, Attila Karsi, Mark L Lawrence
Edwardsiella ictaluri is a Gram-negative facultative intracellular pathogen causing enteric septicemia of channel catfish (ESC). Our recent work indicated that tricarboxylic acid cycle and one-carbon metabolism are critical pathways for E. ictaluri virulence. Although single and double gene deletions in these pathways resulted in safe and efficacious vaccines for use in catfish fingerlings, vaccine trials in catfish fry showed safety concerns. Therefore, we aimed to improve the safety of these mutants by constructing two triple mutant combinations...
October 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/29102294/anaerobic-biodegradation-of-benzo-a-pyrene-by-a-novel-cellulosimicrobium-cellulans-cws2-isolated-from-polycyclic-aromatic-hydrocarbon-contaminated-soil
#20
Wei Qin, Fuqiang Fan, Yi Zhu, Xiaolong Huang, Aizhong Ding, Xiang Liu, Junfeng Dou
Cellulosimicrobium cellulans CWS2, a novel strain capable of utilizing benzo(a)pyrene (BaP) as the sole carbon and energy source under nitrate-reducing conditions, was isolated from PAH-contaminated soil. Temperature and pH significantly affected BaP biodegradation, and the strain exhibited enhanced biodegradation ability at temperatures above 30°C and between pH 7 and 10. The highest BaP removal rate (78.8%) was observed in 13 days when the initial BaP concentration was 10mg/L, and the strain degraded BaP at constant rate even at a higher concentration (50mg/L)...
October 12, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
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