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https://www.readbyqxmd.com/read/28004936/computational-study-of-the-degradation-of-s-adenosyl-methionine-in-water
#1
Timm Lankau, Tzu Nung Kuo, Chin Hui Yu
The degradation of S-adenosyl methionine (SAM) to homoserine-γ-lactone (HSL) and methyltioadenine (MTA) in water is studied with MD simulations. The AM1 Hamiltonian is used for the quantum part and the flexible AMBER force field for the H2O molecules. The MD simulations predict the free energy barrier for the degradation reaction to be between 109 and 112 kJ mol(-1) and an overall gain in free energy of -26 kJ mol(-1). The high barrier and the low energy gain of this reaction can be linked to interactions among the carboxylate group of the SAM molecule and solvent H2O molecules, which are not observed on the product side...
January 5, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27997431/attenuation-of-genome-wide-5-methylcytosine-level-is-an-epigenetic-feature-of-cutaneous-malignant-melanomas
#2
Goran Micevic, Nicholas Theodosakis, Janis M Taube, Marcus W Bosenberg, Nemanja Rodić
Epigenetic modification of DNA, namely covalent changes of cytosine residues, plays a key role in the maintenance of inactive chromatin regions, both in health and in disease. In the vast majority of malignant melanomas, the most notable known epigenetic abnormality is the attenuation of 5-hydroxymethylcytosine (5-hmC) residues. However, it remains unknown whether a decrease in 5-hmC represents a primary defect of melanoma cancer epigenome or whether it is secondary to the loss of 5-methylcytosine (5-mC), a chemical substrate for 5-hmC...
December 16, 2016: Melanoma Research
https://www.readbyqxmd.com/read/27994001/stability-of-the-human-sperm-dna-methylome-to-folic-acid-fortification-and-short-term-supplementation
#3
D Chan, S McGraw, K Klein, L M Wallock, C Konermann, C Plass, P Chan, B Robaire, R A Jacob, C M T Greenwood, J M Trasler
STUDY QUESTION: Do short-term and long-term exposures to low-dose folic acid supplementation alter DNA methylation in sperm? SUMMARY ANSWER: No alterations in sperm DNA methylation patterns were found following the administration of low-dose folic acid supplements of 400 μg/day for 90 days (short-term exposure) or when pre-fortification of food with folic acid and post-fortification sperm samples (long-term exposure) were compared. WHAT IS KNOWN ALREADY: Excess dietary folate may be detrimental to health and DNA methylation profiles due to folate's role in one-carbon metabolism and the formation of S-adenosyl methionine, the universal methyl donor...
December 18, 2016: Human Reproduction
https://www.readbyqxmd.com/read/27986076/transcriptome-analysis-in-switchgrass-discloses-ecotype-difference-in-photosynthetic-efficiency
#4
Desalegn D Serba, Srinivasa Rao Uppalapati, Nick Krom, Shreyartha Mukherjee, Yuhong Tang, Kirankumar S Mysore, Malay C Saha
BACKGROUND: Switchgrass, a warm-season perennial grass studied as a potential dedicated biofuel feedstock, is classified into two main taxa - lowland and upland ecotypes - that differ in morphology and habitat of adaptation. But there is limited information on their inherent molecular variations. RESULTS: Transcriptome analysis by RNA-sequencing (RNA-Seq) was conducted for lowland and upland ecotypes to document their gene expression variations. Mapping of transcriptome to the reference genome (Panicum virgatum v1...
December 16, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27958669/an-orthogonal-d2-o-based-induction-system-that-provides-insights-into-d-amino-acid-pattern-formation-by-radical-s-adenosylmethionine-peptide-epimerases
#5
Brandon I Morinaka, Marjan Verest, Michael F Freeman, Muriel Gugger, Jörn Piel
Radical S-adenosyl methionine peptide epimerases (RSPEs) are an enzyme family that accomplishes regiospecific and irreversible introduction of multiple d-configured residues into ribosomally encoded peptides. Collectively, RSPEs can generate diverse epimerization patterns in a wide range of substrates. Previously, the lack of rapid methods to localize epimerized residues has impeded efforts to investigate the function and applicative potential of RSPEs. An efficient mass spectrometry-based assay is introduced that permits characterization of products generated in E...
December 13, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27939670/identification-and-characterization-of-a-catechol-o-methyltransferase-cdna-in-the-catfish-heteropneustes-fossilis-tissue-sex-and-seasonal-variations-and-effects-of-gonadotropin-and-2-hydroxyestradiol-17%C3%AE-on-mrna-expression
#6
R Chaube, A Rawat, R M Inbaraj, J Bobe, Y Guiguen, A Fostier, K P Joy
Catechol-O-methyltransferase (COMT) is involved in the methylation and inactivation of endogenous and xenobiotic catechol compounds, and serves as a common biochemical link in the catecholamine and catecholestrogen metabolism. Studies on cloning, sequencing and function characterization comt gene in lower vertebrates like fish are fewer. In the present study, a full-length comt cDNA of 1442bp with an open-reading frame (ORF) of 792bp, and start codon (ATG) at nucleotide 162 and stop codon (TAG) at nucleotide 953 was isolated and characterized in the stinging catfish Heteropneustes fossilis (accession No...
December 8, 2016: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/27877178/an-s-adenosyl-methionine-synthetase-sams-gene-from-andropogon-virginicus-l-confers-aluminum-stress-tolerance-and-facilitates-epigenetic-gene-regulation-in-arabidopsis-thaliana
#7
Bunichi Ezaki, Aiko Higashi, Norie Nanba, Takumi Nishiuchi
Candidate clones which conferred Al tolerance to yeast transformants (TFs) were obtained from a cDNA library derived from a highly Al-tolerant poaceae, Andropogon virginicus L. One such clone, AL3A-4, encoded an S-adenosyl methionine synthetase (SAMS) gene. A full-length cDNA was obtained by 5'-RACE, designated AvSAMS1, and introduced into Arabidopsis thaliana to investigate its biological functions under Al stress. Two TF plant lines both showed higher tolerance than the Col-0 ecotype (non-TF) not only for Al stress, but also for Cu, Pb, Zn and diamide stresses, suggesting the AvSAMS1 was a multiple tolerance gene...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27834868/steric-clash-in-the-set-domain-of-histone-methyltransferase-nsd1-as-a-cause-of-sotos-syndrome-and-its-genetic-heterogeneity-in-a-brazilian-cohort
#8
Kyungsoo Ha, Priya Anand, Jennifer A Lee, Julie R Jones, Chong Ae Kim, Debora Romeo Bertola, Jonathan D J Labonne, Lawrence C Layman, Wolfgang Wenzel, Hyung-Goo Kim
Most histone methyltransferases (HMTase) harbor a predicted Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain, which transfers a methyl group to a lysine residue in their substrates. Mutations of the SET domains were reported to cause intellectual disability syndromes such as Sotos, Weaver, or Kabuki syndromes. Sotos syndrome is an overgrowth syndrome with intellectual disability caused by haploinsufficiency of the nuclear receptor binding SET domain protein 1 (NSD1) gene, an HMTase at 5q35.2-35.3. Here, we analyzed NSD1 in 34 Brazilian Sotos patients and identified three novel and eight known mutations...
November 9, 2016: Genes
https://www.readbyqxmd.com/read/27827847/programmed-effects-in-neurobehavior-and-antioxidative-physiology-in-zebrafish-embryonically-exposed-to-cadmium-observations-and-hypothesized-adverse-outcome-pathway-framework
#9
Sander Ruiter, Josefine Sippel, Manon C Bouwmeester, Tobias Lommelaars, Piet Beekhof, Hennie M Hodemaekers, Frank Bakker, Evert-Jan van den Brandhof, Jeroen L A Pennings, Leo T M van der Ven
Non-communicable diseases (NCDs) are a major cause of premature mortality. Recent studies show that predispositions for NCDs may arise from early-life exposure to low concentrations of environmental contaminants. This developmental origins of health and disease (DOHaD) paradigm suggests that programming of an embryo can be disrupted, changing the homeostatic set point of biological functions. Epigenetic alterations are a possible underlying mechanism. Here, we investigated the DOHaD paradigm by exposing zebrafish to subtoxic concentrations of the ubiquitous contaminant cadmium during embryogenesis, followed by growth under normal conditions...
November 2, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27826834/bacterial-dna-methylation-and-methylomes
#10
Josep Casadesús
Formation of C5-methylcytosine, N4-methylcytosine, and N6-methyladenine in bacterial genomes is postreplicative and involves transfer of a methyl group from S-adenosyl-methionine to a base embedded in a specific DNA sequence context. Most bacterial DNA methyltransferases belong to restriction-modification systems; in addition, "solitary" or "orphan" DNA methyltransferases are frequently found in the genomes of bacteria and phage. Base methylation can affect the interaction of DNA-binding proteins with their cognate sites, either by a direct effect (e...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27822545/proteome-remodeling-in-response-to-sulfur-limitation-in-candidatus-pelagibacter-ubique
#11
Daniel P Smith, Carrie D Nicora, Paul Carini, Mary S Lipton, Angela D Norbeck, Richard D Smith, Stephen J Giovannoni
The alphaproteobacterium "Candidatus Pelagibacter ubique" strain HTCC1062 and most other members of the SAR11 clade lack genes for assimilatory sulfate reduction, making them dependent on organosulfur compounds that occur naturally in seawater. To investigate how these cells adapt to sulfur limitation, batch cultures were grown in defined medium containing either limiting or nonlimiting amounts of dimethylsulfoniopropionate (DMSP) as the sole sulfur source. Protein and mRNA expression were measured before, during, and after the transition from exponential growth to stationary phase...
July 2016: MSystems
https://www.readbyqxmd.com/read/27814539/study-on-formation-of-2-4-6-trichloroanisole-by-microbial-o-methylation-of-2-4-6-trichlorophenol-in-lake-water
#12
Kejia Zhang, Zhang Luo, Tuqiao Zhang, Minmin Mao, Jie Fu
To explore the mechanisms and influence factors on the production of 2,4,6-trichloroanisole (2,4,6-TCA) in surface waters, the 2,4,6-TCA formation potential (FP) test was conducted by incubating the real lake water with the addition of 2,4,6-trichlorophenol (2,4,6-TCP) precursor. Besides bacteria and fungi, two common cyanobacteria and algae species, i.e., Chlorella vulgaris and Anabaena flos-aquae, have been proved to have strong capabilities to produce 2,4,6-TCA, which may contribute the high 2,4,6-TCA FP (152...
December 2016: Environmental Pollution
https://www.readbyqxmd.com/read/27727432/s-adenosyl-methionine-same-for-depression-in-adults
#13
REVIEW
Ilaria Galizia, Lucio Oldani, Karine Macritchie, Erica Amari, Dominic Dougall, Tessa N Jones, Raymond W Lam, Guido Jacopo Massei, Lakshmi N Yatham, Allan H Young
BACKGROUND: Depression is a recurrent illness with high rates of chronicity, treatment-resistance and significant economic impact. There is evidence in the literature that S-adenosyl methionine (SAMe), a naturally occurring compound in the human body, has antidepressant efficacy. This product may be an important addition to the armamentarium of antidepressant agents. OBJECTIVES: To assess the effects of SAMe in comparison with placebo or antidepressants for the treatment of depression in adults...
October 10, 2016: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/27717843/homology-modeling-of-homo-sapiens-lipoic-acid-synthase-substrate-docking-and-insights-on-its-binding-mode
#14
Ezhilarasi Krishnamoorthy, Sameer Hassan, Luke Elizabeth Hanna, Indira Padmalayam, Rama Rajaram, Vijay Viswanathan
Lipoic acid synthase (LIAS) is an iron-sulfur cluster mitochondrial enzyme which catalyzes the final step in the de novo pathway for the biosynthesis of lipoic acid, a potent antioxidant. Recently there has been significant interest in its role in metabolic diseases and its deficiency in LIAS expression has been linked to conditions such as diabetes, atherosclerosis and neonatal-onset epilepsy, suggesting a strong inverse correlation between LIAS reduction and disease status. In this study we use a bioinformatics approach to predict its structure, which would be helpful to understanding its role...
October 4, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27689866/chemical-proteomic-profiling-of-human-methyltransferases
#15
Benjamin D Horning, Radu M Suciu, Darian A Ghadiri, Olesya A Ulanovskaya, Megan L Matthews, Kenneth M Lum, Keriann M Backus, Steven J Brown, Hugh Rosen, Benjamin F Cravatt
Methylation is a fundamental mechanism used in Nature to modify the structure and function of biomolecules, including proteins, DNA, RNA, and metabolites. Methyl groups are predominantly installed into biomolecules by a large and diverse class of S-adenosyl methionine (SAM)-dependent methyltransferases (MTs), of which there are ∼200 known or putative members in the human proteome. Deregulated MT activity contributes to numerous diseases, including cancer, and several MT inhibitors are in clinical development...
October 12, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27648579/a-histone-h3k9m-mutation-traps-histone-methyltransferase-clr4-to-prevent-heterochromatin-spreading
#16
Chun-Min Shan, Jiyong Wang, Ke Xu, Huijie Chen, Jia-Xing Yue, Stuart Andrews, James J Moresco, John R Yates, Peter L Nagy, Liang Tong, Songtao Jia
Histone lysine-to-methionine (K-to-M) mutations are associated with multiple cancers, and they function in a dominant fashion to block the methylation of corresponding lysines on wild type histones. However, their mechanisms of function are controversial. Here we show that in fission yeast, introducing the K9M mutation into one of the three histone H3 genes dominantly blocks H3K9 methylation on wild type H3 across the genome. In addition, H3K9M enhances the interaction of histone H3 tail with the H3K9 methyltransferase Clr4 in a SAM (S-adenosyl-methionine)-dependent manner, and Clr4 is trapped at nucleation sites to prevent its spreading and the formation of large heterochromatin domains...
September 20, 2016: ELife
https://www.readbyqxmd.com/read/27594595/s-adenosyl-methionine-in-the-therapy-of-depression-and-other-psychiatric-disorders
#17
Nataša Karas Kuželički
Preclinical Research S-adenosyl methionine (SAM) is a major methyl donor and as such exerts its influence on CNS function through methylation reactions, such as methylation of several catecholamine moiety-containing neurotransmitters, epigenetic changes through methylation of DNA, RNA, RNA-binding proteins and histones, and phospholipid methylation. Based on available evidence, SAM is currently recommended as a next-step (second-line) treatment option following inadequate treatment response to a first-line antidepressant...
November 2016: Drug Development Research
https://www.readbyqxmd.com/read/27571175/methyl-transfer-by-substrate-signaling-from-a-knotted-protein-fold
#18
Thomas Christian, Reiko Sakaguchi, Agata P Perlinska, Georges Lahoud, Takuhiro Ito, Erika A Taylor, Shigeyuki Yokoyama, Joanna I Sulkowska, Ya-Ming Hou
Proteins with knotted configurations, in comparison with unknotted proteins, are restricted in conformational space. Little is known regarding whether knotted proteins have sufficient dynamics to communicate between spatially separated substrate-binding sites. TrmD is a bacterial methyltransferase that uses a knotted protein fold to catalyze methyl transfer from S-adenosyl methionine (AdoMet) to G37-tRNA. The product, m(1)G37-tRNA, is essential for life and maintains protein-synthesis reading frames. Using an integrated approach of structural, kinetic, and computational analysis, we show that the structurally constrained TrmD knot is required for its catalytic activity...
October 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27562259/the-physiology-and-habitat-of-the-last-universal-common-ancestor
#19
Madeline C Weiss, Filipa L Sousa, Natalia Mrnjavac, Sinje Neukirchen, Mayo Roettger, Shijulal Nelson-Sathi, William F Martin
The concept of a last universal common ancestor of all cells (LUCA, or the progenote) is central to the study of early evolution and life's origin, yet information about how and where LUCA lived is lacking. We investigated all clusters and phylogenetic trees for 6.1 million protein coding genes from sequenced prokaryotic genomes in order to reconstruct the microbial ecology of LUCA. Among 286,514 protein clusters, we identified 355 protein families (∼0.1%) that trace to LUCA by phylogenetic criteria. Because these proteins are not universally distributed, they can shed light on LUCA's physiology...
2016: Nature Microbiology
https://www.readbyqxmd.com/read/27552169/modulation-of-conformational-equilibria-in-the-s-adenosylmethionine-sam-ii-riboswitch-by-sam-mg-2-and-trimethylamine-n-oxide
#20
Peter McPhie, Patrick Brown, Bin Chen, Theodore K Dayie, Allen P Minton
The dependence of the conformation of the S-adenosylmethionine (SAM) II riboswitch on the concentration of added Mg(2+) ions and SAM, individually and in mixtures, was monitored by circular dichroism (CD) spectroscopy and by measurement of the diffusion coefficient. The results are analyzed in the context of two complementary quantitative models, both of which are consistent with a single underlying physical model. Magnesium binding sites in the open state have an affinity on average higher than the affinity of those in the compact state, but formation of the compact state is accompanied by an increase in the number of binding sites...
September 13, 2016: Biochemistry
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