Methylation Reactions Research Articles

Polymer model predicts history dependent epigenetic and lamin-associated domain sizes.

The association of epigenetic markers with phase-separated genomic compartments is well known. Although correlated changes in 3D organization and epigenetics in response to stimuli have been observed, current physical models cannot explain this behavior. To tackle this problem, we develop a dynamic, reaction-based polymer model which takes input from ChIP-seq data to identify the initial active, repressed, and CTCF-associated beads on a string to represent the chromatin. The interaction potentials between different epigenetic states are tuned against known spatial distance-genomic distance relationships and show established hierarchical structures in the obtained HiC contact map. The proposed dynamics of the polymer form finite-size domains and prevent spatial domain coarsening. We further show that the dynamics succeed in maintaining epigenetic domain stability and spatial distance relations. Chromatin compaction and expansion are seen in response to epigenetic spreading through methylation and acetylation reactions, respectively, which agrees with experimental STORM imaging observations. We can also predict 3D chromatin reorganization in response to changing chromatin-lamin interactions. Lastly, we expose our system to changing stimuli and find that the genomic domains show memory-like features. The simplicity of the dynamics, along with our use of biological inputs, is a significant step forward in understanding how chromatin dynamics affect both short-term (immediate response) and long-term (memory) cellular behavior.

Characterization and novel pathway of atrazine catabolism by Agrobacterium rhizogenes AT13 and its potential for environmental bioremediation

Agrobacterium rhizogenes AT13, a novel bacterial strain that was isolated from contaminated soil, could utilize atrazine as the sole nitrogen, thereby degrading it. Optimization of the degradation reaction using a Box–Behnken design resulted in 99.94% atrazine degradation at pH 8.57, with an inoculum size of 3.10 × 109 CFU/mL and a concentration of 50 mg/L atrazine. Ultra-high performance liquid chromatography-electrospray ionization-high resolution mass spectrometry (UPLC-ESI-HRMS), liquid chromatography tandem mass spectrometry (LC-MS/MS) and high performance liquid chromatography (HPLC) analyses identified and quantified six reported metabolites and a novel metabolite (2-hydroxypropazine) from atrazine degradation by AT13. On the basis of these metabolites, we propose an atrazine degradation pathway that includes dichlorination, hydroxylation, deamination, dealkylation and methylation reactions. The toxicity of the degradation products was evaluated by Toxicity Estimation Software Tool (T.E.S.T). Bioaugmentation of atrazine-polluted soils/water with strain AT13 significantly improved the atrazine removal rate. Thus, AT13 has potential applications in bioremediation.

Methyl Donors, Epigenetic Alterations, and Brain Health: Understanding the Connection.

Methyl donors such as choline, betaine, folic acid, methionine, and vitamins B6 and B12 are critical players in the one-carbon metabolism and have neuroprotective functions. The one-carbon metabolism comprises a series of interconnected chemical pathways that are important for normal cellular functions. Among these pathways are those of the methionine and folate cycles, which contribute to the formation of S-adenosylmethionine (SAM). SAM is the universal methyl donor of methylation reactions such as histone and DNA methylation, two epigenetic mechanisms that regulate gene expression and play roles in human health and disease. Epigenetic mechanisms have been considered a bridge between the effects of environmental factors, such as nutrition, and phenotype. Studies in human and animal models have indicated the importance of the optimal levels of methyl donors on brain health and behavior across the lifespan. Imbalances in the levels of these micronutrients during critical periods of brain development have been linked to epigenetic alterations in the expression of genes that regulate normal brain function. We present studies that support the link between imbalances in the levels of methyl donors, epigenetic alterations, and stress-related disorders. Appropriate levels of these micronutrients should then be monitored at all stages of development for a healthier brain.

Methyl 3-Bromo-5-carbamoylisothiazole-4-carboxylate

Reaction of methyl 3-bromo-5-cyanoisothiazole-4-carboxylate with conc. H2SO4 gave methyl 3-bromo-5-carbamoylisothiazole-4-carboxylate in 93% yield. The compound was fully characterized.

Direct Identification of Disaccharide Structural Isomers Using Ambient Ionization Tandem Mass Spectrometry with In Situ Methylation.

Carbohydrates play critically important roles in energy supply and biological functions in living systems. However, it has been a great challenge to identify saccharides and distinguish their isomers because they have highly similar structures and many possible positions for glycosidic linkages. In this work, an ambient ionization tandem mass spectrometry method was developed to characterize disaccharide structural isomers with in situ methylation. The direct analysis in real time ion source can be used to facilitate the methylation reaction of disaccharides with tetramethylammonium hydroxide. The hydroxyl groups of disaccharides can be methylated instantaneously, and the products can be ionized at the same time. The methylated product ions from full scan mass spectrometry (MS) and tandem MS can be used to distinguish a variety of disaccharide structural isomers with different glycosidic linkages, compositions, and configurations. Characteristic marker ions were discovered, and they can be used for the assignment of linkage type and identification of specific isomeric forms. The method was used for the direct identification of disaccharide isomers from real commercial products such as honey, wine, and milk without complex sample pretreatment or chromatographic separation.

Folate and Folic Acid Metabolism: A Significant Nutrient-Gene-Environment Interaction

Folate has an important metabolic role by providing one carbon units that are used for nucleotide biosynthesis and methylation reactions that are both vital for epigenetic control, genomic stability and the maintenance of health. Important not only for its availability as an essential nutrient but folate also intertwines us firmly within the environment as part of an unexpected link between light and the genome. Folate deficiency has been overcome by replacement with folic acid, taken as a supplement and/or through food fortification but is this solving one problem but risking others with the wider long-term implication of this manipulation in its potential to alter the human genome. The mandatory folic acid food fortification public health policy and implementation needs to be re-examined and possibly debated in the public arena, particularly in view of the risk of altering the human genome. Have the public been adequately informed and are there implications for the whole vitamin and mineral supplement industry?

Biosynthesis and function of microbial methylmenaquinones.

The membranous quinone/quinol pool is essential for the majority of life forms and its composition has been widely used as a biomarker in microbial taxonomy. The most abundant quinone is menaquinone (MK), which serves as an essential redox mediator in various electron transport chains of aerobic and anaerobic respiration. Several methylated derivatives of MK, designated methylmenaquinones (MMKs), have been reported to be present in members of various microbial phyla possessing either the classical MK biosynthesis pathway (Men) or the futalosine pathway (Mqn). Due to their low redox midpoint potentials, MMKs have been proposed to be specifically involved in appropriate electron transport chains of anaerobic respiration. The class C radical SAM methyltransferases MqnK, MenK and MenK2 have recently been shown to catalyse specific MK methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesise 8-MMK, 7-MMK and 7,8-dimethylmenaquinone (DMMK). MqnK, MenK and MenK2 from organisms such as Wolinella succinogenes, Adlercreutzia equolifaciens, Collinsella tanakaei, Ferrimonas marina and Syntrophus aciditrophicus have been functionally produced in Escherichia coli, enabling extensive quinone/quinol pool engineering of the native MK and 2-demethylmenaquinone (DMK). Cluster and phylogenetic analyses of available MK and MMK methyltransferase sequences revealed signature motifs that allowed the discrimination of MenK/MqnK/MenK2 family enzymes from other radical SAM enzymes and the identification of C-7-specific menaquinone methyltransferases of the MenK2 subfamily. It is envisaged that this knowledge will help to predict the methylation status of the menaquinone/menaquinol pool of any microbial species (or even a microbial community) from its (meta)genome.

Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase

S-adenosylmethionine (SAM) is a ubiquitous co-factor that serves as a donor for methylation reactions and additionally serves as a donor of other functional groups such as amino and ribosyl moieties in a variety of other biochemical reactions. Such versatility in function is enabled by the ability of SAM to be recognized by a wide variety of protein molecules that vary in their sequences and structural folds. To understand what gives rise to specific SAM binding in diverse proteins, we set out to study if there are any structural patterns at their binding sites. A comprehensive analysis of structures of the binding sites of SAM by all-pair comparison and clustering, indicated the presence of 4 different site-types, only one among them being well studied. For each site-type we decipher the common minimum principle involved in SAM recognition by diverse proteins and derive structural motifs that are characteristic of SAM binding. The presence of the structural motifs with precise three-dimensional arrangement of amino acids in SAM sites that appear to have evolved independently, indicates that these are winning arrangements of residues to bring about SAM recognition. Further, we find high similarity between one of the SAM site types and a well known ATP binding site type. We demonstrate using in vitro experiments that a known SAM binding protein, HpyAII.M1, a type 2 methyltransferase can bind and hydrolyse ATP. We find common structural motifs that explain this, further supported through site-directed mutagenesis. Observation of similar motifs for binding two of the most ubiquitous ligands in multiple protein families with diverse sequences and structural folds presents compelling evidence at the molecular level in favour of convergent evolution.

Mannich bases derivatives of 2-Phenyl-5-Benzimidazole sulfonic acid; Synthesis, Characterization, Computational studies and Biological evaluation

A new series of N-Mannich bases of 2-Phenyl-5-benzimidazole sulfonic acid have been synthesized through amino methylation reaction with secondary amines. The two moieties were held together through a methylene bridge, which comes from formaldehyde (Formalin Solution 37%) used in the reaction. Chemical structures of the newly synthesized compounds have been confirmed using FT-IR, 1HNMR and 13CNMR. Different in vitro assays including Anti-oxidant, Enzyme inhibition, Anti-microbial and Cytotoxicity assay were performed to evaluate the biological potential with reference to the standard drug. Among the synthesized library, compound 3a shows maximum alpha-glucosidase inhibition with an IC50 value of 66.66 μg/ml, compound 3d was found most toxic with LC50 value of 10.17 μg/ml. ADME evaluation studies were performed with the help of Molinspiration online software. Docking calculations were also performed. Given the importance of the nucleus involved, the synthesized compound might find extensive medicinal applications as reported in the literature.

Evaluation of Plasma Homocysteine Levels in Type II Diabetes and Hypertensive Patients Attending University of Port Harcourt Teaching Hospital, Nigeria

Background: Homocysteine is an important non-protein amino acid, very useful in all methylation reactions occurring in the body as the precursor of the sole methyl group donor S-Adenosyl-methionine (SAM). However, elevated plasma homocysteine levels have been reported to contribute to epithelial damage leading to coronary artery disease and other metabolic syndromes. This study was aimed at evaluating the concentration of plasma homocysteine in diabetics and hypertensive patients in Port Harcourt, Nigeria. Methods: The study population included 60 Type II diabetes mellitus and Hypertensivesubjectsas group (I), 60 Type II diabetes mellitus and Normotensive subjects as group (II), 60 Hypertensive subjects as group (III), and 60 healthy subjects as control group within the age range of 30 - 70 years. An enzyme-linked immunosorbent assay (ELISA) method was used to quantitatively measure homocysteine in the serum sample, glycated haemoglobin were determined quantitatively using sandwich immunodetection and blood pressure was determined using mercury sphygnanometer. Statistics: The statistical analysis was done using GraphPad Prism version 9.4.1, and statistical significance was determined by a P < 0.05. Results: The results showed significantly higher plasma homocysteine levels in diabetics and hypertensive comorbidity patients when compared to healthy controls, P < 0.013. There was also a significant increase in plasma homocysteine levels in the comorbidity and hypertensives single morbidity, P < 0.0001 and also diabetes single morbidity, but there was no significant difference from the levels in the diabetics and hypertensives single morbidity. Furthermore, there was no significant difference between groups in terms of age range or duration of diagnosis. Conclusion: Our result shows an increase in plasma homocysteine levels in diabetics and hypertensives when compared to controls, and comorbidity instigates a higher increase in plasma levels when compared with the single morbidity.

ReACT (redox-activated chemical tagging) chemistry enables direct derivatization and fluorescence detection of S-adenosyl-L-homocysteine (SAH).

S-Adenosyl-L-homocysteine (SAH) is a universal byproduct and product inhibitor of the methyltransferase-catalyzed methylation reaction. Here based on ReACT (redox-activated chemical tagging) chemistry, direct derivatization and fluorescence measurement of SAH were achieved with features such as mild reaction conditions and simple operation.

Cu-Catalyzed Methylenation of Alcohols with N-Methyl Amide as a Sustainable Methylene Reagent

Herein, we report a new approach to methylenation of alcohols using N-methyl amide as a sustainable methylene reagent; the N-methyl delivers the methylene group. This new reagent is easily prepared and stable to both air and moisture. Furthermore, the final byproduct of this methylene reagent can be recycled in excellent yields and then reused in methylenation reactions upon treating with CH3I.

Characterization of ginsenoside structural isomers from mixtures using in situ methylation with direct analysis in real-time ionization tandem mass spectrometry

Characterization of structural isomers of bioactive molecules is important for recognizing their functions, but it has been challenging due to their highly similar structures. As the main bioactive constituents of Panax ginseng, ginsenosides have different structural isomers attributed to the aglycone structure and glycosylation sites as well as stereochemistry of sugar groups attached. This work demonstrated a simple and robust in situ methylation reaction with tetramethylammonium hydroxide (TMAH) using ambient ionization source of direct analysis in real time (DART) to characterize saponin structural isomers. The DART ion source provides favorable conditions to methylate hydroxyl groups of ginsenoside instantaneously with TMAH, and it can ionize the methylated products at the same time. Methylated ginsenoside stereoisomers even with subtle structure differences generated very different mass signals from full-scan MS and tandem MS. High-resolution mass spectrometry aided the assignment of molecular structures of the various precursor and fragment ions from different ginsenosides, which provided structural information for both the aglycone skeleton and the sugar moieties in ginsenosides. The presented method was successfully used for the identification of ginsenosides in Panax ginseng, and saponin isomers were characterized without the need for chromatographic separation and/or tedious offline sample pretreatment.

Intensification of interesterification of sustainable feedstock as mahua oil for biodiesel production

ABSTRACT In the current work, the ultrasonic horn induced cavitation was used as an intensification approach for the production of fatty acid methyl esters (FAME), i.e. biodiesel and triacetin as a by-product from the reaction of mahua oil selected as sustainable feedstock and methyl acetate (MA). The effects of process variables like reaction temperature, mahua oil to methyl acetate molar ratio, reaction time, catalyst loading, duty cycle, and power on yield of FAME have been studied and the results elucidated best conditions for maximum fatty acid methyl ester yield of 96% as time of 50 min, temperature of 50C, molar ratio of 1:8, duty cycle of 40%, ultrasonic power of 70 W and catalyst loading of 1 wt%. For conventional approach based on only stirring, the yield was 61% under otherwise similar conditions. Kinetic study was performed to estimate the order of reaction and the activation energy. It was shown that the kinetics was well fitted to first-order reaction and activation energy was observed as 25.9 kJ/mol. The study revealed the effective application of ultrasonic horn in intensification of biodiesel production using interesterification reaction resulting in considerably higher yield of FAME.

Regioselective and Scalable Total Synthesis of Licochalcone C and Related Licoagrochalcones

AbstractA novel efficient method for the synthesis of licochalcone C in good yield on up to 30 g scale was developed. The reaction sequence included relied on the directed ortho‐metalation (DOM) of bis‐O‐MOM‐protected resorcinol for the regioselective C‐prenylation, followed by metalation‐formylation, selective O‐deprotection of a hydroxyl group located between the formyl and prenyl groups, its methylation, and aldol reaction with p‐hydroxyacetophenone. Synthesis of structurally related retrochalcones, i.e., licoagrochalcones B, C, and D, was also proposed.

Arylene Diimide Derivatives as Anolyte Materials with Two-Electron Storage for Ultrastable Neutral Aqueous Organic Redox Flow Batteries

Arylene Diimide Derivatives as Anolyte Materials with Two-Electron Storage for Ultrastable Neutral Aqueous Organic Redox Flow Batteries

Arginine Methylation of the PGC-1α C-Terminus Is Temperature-Dependent.

We set out to determine whether the C-terminus (amino acids 481-798) of peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α, UniProt Q9UBK2), a regulatory metabolic protein involved in mitochondrial biogenesis, and respiration, is an arginine methyltransferase substrate. Arginine methylation by protein arginine methyltransferases (PRMTs) alters protein function and thus contributes to various cellular processes. In addition to confirming methylation of the C-terminus by PRMT1 as described in the literature, we have identified methylation by another member of the PRMT family, PRMT7. We performed in vitro methylation reactions using recombinant mammalian PRMT7 and PRMT1 at 37, 30, 21, 18, and 4 °C. Various fragments of PGC-1α corresponding to the C-terminus were used as substrates, and the methylation reactions were analyzed by fluorography and mass spectrometry to determine the extent of methylation throughout the substrates, the location of the methylated PGC-1α arginine residues, and finally, whether temperature affects the deposition of methyl groups. We also employed two prediction programs, PRmePRed and MePred-RF, to search for putative methyltransferase sites. Methylation reactions show that arginine residues R548 and R753 in PGC-1α are methylated at or below 30 °C by PRMT7, while methylation by PRMT1 was detected at these same residues at 30 °C. Computational approaches yielded additional putative methylarginine sites, indicating that since PGC-1α is an intrinsically disordered protein, additional methylated arginine residues have yet to be experimentally verified. We conclude that temperature affects the extent of arginine methylation, with more methylation by PRMT7 occurring below physiological temperature, uncovering an additional control point for PGC-1α.

METTL3 Regulates the Inflammatory Response in CPB2 Toxin-Exposed IPEC-J2 Cells through the TLR2/NF-κB Signaling Pathway.

Clostridium perfringens beta2 (CPB2) toxin is one of the main pathogenic toxins produced by Clostridium perfringens, which causes intestinal diseases in animals and humans. The N6-methyladenosine (m6A) modification is the most common reversible modification in eukaryotic disease processes. Methyltransferase-like 3 (METTL3) regulates immunity and inflammatory responses induced by the bacterial infections in animals. However, METTL3's involvement in CPB2-treated intestinal porcine epithelial cell line-J2 (IPEC-J2) remains unclear. In the current study, we used methylated RNA immunoprecipitation-quantitative polymerase chain reaction, Western blotting and immunofluorescence assay to determine the role of METTL3 in CPB2-exposed IPEC-J2 cells. The findings revealed that m6A and METTL3 levels were increased in CPB2 treated IPEC-J2 cells. Functionally, METTL3 overexpression promoted the release of inflammatory factors, increased cytotoxicity, decreased cell viability and disrupted tight junctions between cells, while the knockdown of METTL3 reversed these results. Furthermore, METTL3 was involved in the inflammatory response of IPEC-J2 cells by activating the TLR2/NF-κB signaling pathway through regulating TLR2 m6A levels. In conclusion, METTL3 overexpression triggered the TLR2/NF-κB signaling pathway and promoted CPB2-induced inflammatory responses in IPEC-J2 cells. These findings may provide a new strategy for the prevention and treatment of diarrhea caused by Clostridium perfringens.

Exploratory Metabolomics Underscores the Folate Enzyme ALDH1L1 as a Regulator of Glycine and Methylation Reactions.

Folate (vitamin B9) is involved in one-carbon transfer reactions and plays a significant role in nucleic acid synthesis and control of cellular proliferation, among other key cellular processes. It is now recognized that the role of folates in different stages of carcinogenesis is complex, and more research is needed to understand how folate reactions become dysregulated in cancers and the metabolic consequences that occur as a result. ALDH1L1 (cytosolic 10-formyltetrahydrofolate dehydrogenase), an enzyme of folate metabolism expressed in many tissues, is ubiquitously downregulated in cancers and is not expressed in cancer cell lines. The RT4 cell line (derived from papillary bladder cancer) which expresses high levels of ALDH1L1 represents an exception, providing an opportunity to explore the metabolic consequences of the loss of this enzyme. We have downregulated this protein in RT4 cells (shRNA driven knockdown or CRISPR driven knockout) and compared metabolomes of ALDH1L1-expressing and -deficient cells to determine if metabolic changes linked to the loss of this enzyme might provide proliferative and/or survival advantages for cancer cells. In this study, cell extracts were analyzed using Ultra High Performance Liquid Chromatography High Resolution Mass Spectrometry (UHPLC-HR-MS). A total of 13,339 signals were identified or annotated using an in-house library and public databases. Supervised and unsupervised multivariate analysis revealed metabolic differences between RT4 cells and ALDH1L1-deficient clones. Glycine (8-fold decrease) and metabolites derived from S-adenosylmethionine utilizing pathways were significantly decreased in the ALDH1L1-deficient clones, compared with RT4 cells. Other changes linked to ALDH1L1 downregulation include decreased levels of amino acids, Krebs cycle intermediates, and ribose-5-phosphate, and increased nicotinic acid. While the ALDH1L1-catalyzed reaction is directly linked to glycine biosynthesis and methyl group flux, its overall effect on cellular metabolism extends beyond immediate metabolic pathways controlled by this enzyme.

Inherited genetic effects on arsenic metabolism: A comparison of effects on arsenic species measured in urine and in blood.

Inorganic arsenic (iAs) is a carcinogen, and chronic exposure is associated with adverse health outcomes, including cancer and cardiovascular disease. Consumed iAs can undergo two methylation reactions catalyzed by arsenic methyltransferase (AS3MT), producing monomethylated and dimethylated forms of arsenic (MMA and DMA). Methylation of iAs helps facilitate excretion of arsenic in urine, with DMA composing the majority of arsenic species excreted. Past studies have identified genetic variation in the AS3MT (10q24.32) and FTCD (21q22.3) regions associated with arsenic metabolism efficiency (AME), measured as the proportion of each species present in urine (iAs%, MMA%, and DMA%), but their association with arsenic species present in blood has not been examined. We use data from three studies nested within the Health Effects and Longitudinal Study (HEALS)-the Nutritional Influences on Arsenic Toxicity Study, the Folate and Oxidative Stress study, and the Folic Acid and Creatine Trial-to examine the association of previously identified genetic variants with arsenic species in both urine and blood of 334 individuals. We confirm that the genetic variants in AS3MT and FTCD known to effect arsenic species composition in urine (an excreted byproduct of metabolism) have similar effects on arsenic species in blood (a tissue type that directly interacts with many organs, including those prone to arsenic toxicity). This consistency we observe provides further support for the hypothesis the AME SNPs identified to date impact the efficiency of arsenic metabolism and elimination, thereby influencing internal dose of arsenic and the dose delivered to toxicity-prone organs and tissues.