Mutational analysis of vaccinia virus mRNA cap (guanine-N7) methyltransferase reveals essential contributions of the N-terminal peptide that closes over the active site

RNA guanine-N7 methyltransferase catalyzes the third step of eukaryal mRNA capping, the transfer of a methyl group from AdoMet to GpppRNA to form m⁷GpppRNA. Mutational and crystallographic analyses of cellular and poxvirus cap methyltransferases have yielded a coherent picture of a conserved active site and determinants of substrate specificity. Models of the Michaelis complex suggest a direct in-line mechanism of methyl transfer. Because no protein contacts to the guanine-N7 nucleophile, the AdoMet methyl carbon (Cε) or the AdoHcy sulfur (Sδ) leaving group were observed in ligand-bound structures of cellular cap methyltransferase, it was initially thought that the enzyme facilitates catalysis by optimizing proximity and geometry of the donor and acceptor. However, the structure of AdoHcy-bound vaccinia virus cap methyltransferase revealed the presence of an N-terminal “lid peptide” that closes over the active site and makes multiple contacts with the substrates, including the AdoMet sulfonium. This segment is disordered in the vaccinia apoenzyme and is not visible in the available structures of cellular cap methyltransferase. Here, we conducted a mutational analysis of the vaccinia virus lid peptide (⁵⁴⁵DKFRLNPEVSYFTNKRTRG⁵⁶³) entailing in vivo and in vitro readouts of the effects of alanine and conservative substitutions. We thereby identified essential functional groups that interact with the AdoMet sulfonium (Tyr555, Phe556), the AdoMet adenine (Asn550), and the cap triphosphate bridge (Arg560, Arg562). The results suggest that van der Waals contacts of Tyr555 and Phe556 to the AdoMet Sδ and Cε atoms, and the electron-rich environment around the sulfonium, serve to stabilize the transition state of the transmethylation reaction.     

Regulation of sterol biosynthesis in sunflower by 24(R,S),25-epiminolanosterol, a novel C-24 methyl transferase inhibitor

Whereas sitosterol and 24(28)-methylene cycloartanol were competitive inhibitors (with Ki = 26 microM and 14 microM, respectively), 24(R,S)-25-epiminolanosterol was found to be a potent non-competitive inhibitor (Ki = 3.0 nM) of the S-adenosyl-L-methionine-C-24 methyl transferase from sunflower embryos. Because the ground state analog, 24(R,S)-oxidolanosterol, failed to inhibit the catalysis and 25-azalanosterol inhibited the catalysis with a Ki of 30 nM we conclude that the aziridine functions in a manner similar to the azasteriod (Rahier, A., et al., J. Biol. Chem. (1984) 259, 15215) as a transition state analog mimicking the carbonium intermediate found in the normal transmethylation reaction. Additionally, we observed that the aziridine inhibited cycloartenol metabolism (the preferred substrate for transmethylation) in cultured sunflower cells and cell growth.     

Biosynthesis of adenosyl-d-methionine and adenosyl-2-methylmethionine by Candida utilis

Supplementation of the culture medium of Candida utilis with d-methionine or 2-methyl-dl-methionine leads to intracellular synthesis of S-adenosyl-d-methionine and S-adenosyl-2-methylmethionine. The identity of the sulfonium compounds was established by tracer technique, chromatography, acid hydrolysis, and examination of the released methionine and 2-methylmethionine. In addition to the expected sulfur amino acid component, both adenosine sulfonium fractions contained S-adenosyl-l-methionine. This is explained by transmethylation of S-adenosyl-d-methionine and of S-adenosyl-2-methyl-methionine with endogenous l-homocysteine; the resulting l-methionine reacts with ATP to form S-adenosyl-l-methionine. Experiments with purified cell-free preparations of S-adenosylmethionine synthetase (EC 2.5.1.6) from C. utilis confirmed the reaction of ATP with d-methionine or 2-methyl-dl-methionine.     

S-Adenosylmethionine

S-Adenosyl-Lmethionine (SAM) is an important molecule in normal cell function and survival. SAM is utilized by three key metabolic pathways: transmethylation; transsulfuration; and polyamine synthesis. In transmethylation reactions, the methyl group of SAM is donated to a large variety of acceptor substrates including DNA, phospholipids and proteins. Thus, interference of these reactions can affect a wide spectrum of processes ranging from gene expression to membrane fluidity. In transsulfuration, the sulfur atom of the SAM is converted via a series of enzymatic steps to cysteine, a precursor of taurine and glutathione, a major cellular anti-oxidant. Polyamines are required for normal cell growth. Given the importance of SAM in tissue function, it is not surprising that this molecule is being investigated as a possible therapeutic agent for the treatment of various clinical disorders.     

Synthesis of S-adenosyl-L-methionine analogs and their use for sequence-specific transalkylation of DNA by methyltransferases

Here we describe a one-step synthetic procedure for the preparation of S-adenosyl-L-methionine (AdoMet) analogs with extended carbon chains replacing the methyl group. These AdoMet analogs function as efficient cofactors for DNA methyltransferases (MTases), and we provide a protocol for sequence-specific transfer of extended side chains from these AdoMet analogs to DNA by DNA MTases. Direct chemoselective allylation or propargylation of S-adenosyl-L-homocysteine (AdoHcy) at sulfur is achieved under the acidic conditions needed to protect other nucleophilic positions in AdoHcy. The unsaturated bonds in beta position to the sulfonium center of the resulting AdoMet analogs are designed to stabilize the transition state formed upon DNA MTase-catalyzed nucleophilic attack at the carbon next to the sulfonium center and lead to efficient transfer of the extended side chains to DNA. Using these protocols, sequence-specific functionalized DNA can be obtained within one to two weeks.     

Regulation of methyl group metabolism in lactating ewes

The effect of lactation on a number of enzymes involved in transmethylation reactions and the secretion of major methyl compounds into milk have been examined in sheep. The activities of hepatic phospholipid methyltransferase and 5-methyltetrahydrofolate-homocysteine methyltransferase were significantly higher in lactating ewes, compared with those in non-lactating ewes, while the activity of both hepatic and pancreatic glycine methyltransferase was significantly lower in the lactating state. No differences were observed in the activities of hepatic guanidoacetate methyltransferase, betaine-homocysteine methyltransferase and cystathionine beta-synthase on lactation. These results suggest that the extra demand for methyl groups for the secretion of methyl compounds in the milk is facilitated by enhancing the rate of de novo methyl group synthesis and lowering the rate of physiologically nonessential methylation.     

Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues

S-Adenosyl-l-methionine (AdoMet or SAM)-dependent methyltransferases (MTase) catalyze the transfer of the activated methyl group from AdoMet to specific positions in DNA, RNA, proteins and small biomolecules. This natural methylation reaction can be expanded to a wide variety of alkylation reactions using synthetic cofactor analogues. Replacement of the reactive sulfonium center of AdoMet with an aziridine ring leads to cofactors which can be coupled with DNA by various DNA MTases. These aziridine cofactors can be equipped with reporter groups at different positions of the adenine moiety and used for Sequence-specific Methyltransferase-Induced Labeling of DNA (SMILing DNA). As a typical example we give a protocol for biotinylation of pBR322 plasmid DNA at the 5’-ATCGAT-3’ sequence with the DNA MTase M.BseCI and the aziridine cofactor 6BAz in one step. Extension of the activated methyl group with unsaturated alkyl groups results in another class of AdoMet analogues which are used for methyltransferase-directed Transfer of Activated Groups (mTAG). Since the extended side chains are activated by the sulfonium center and the unsaturated bond, these cofactors are called double-activated AdoMet analogues. These analogues not only function as cofactors for DNA MTases, like the aziridine cofactors, but also for RNA, protein and small molecule MTases. They are typically used for enzymatic modification of MTase substrates with unique functional groups which are labeled with reporter groups in a second chemical step. This is exemplified in a protocol for fluorescence labeling of histone H3 protein. A small propargyl group is transferred from the cofactor analogue SeAdoYn to the protein by the histone H3 lysine 4 (H3K4) MTase Set7/9 followed by click labeling of the alkynylated histone H3 with TAMRA azide. MTase-mediated labeling with cofactor analogues is an enabling technology for many exciting applications including identification and functional study of MTase substrates as well as DNA genotyping and methylation detection.     

S-adenosylmethionine conformations in solution and in protein complexes: conformational influences of the sulfonium group

S-Adenosylmethionine (AdoMet) and other sulfonium ions play central roles in the metabolism of all organisms. The conformational preferences of AdoMet and two other biologically important sulfonium ions, S-methylmethionine and dimethylsulfonioproprionic acid, have been investigated by NMR and computational studies. Molecular mechanics parameters for the sulfonium center have been developed for the AMBER force field to permit analysis of NMR results and to enable comparison of the relative energies of the different conformations of AdoMet that have been found in crystal structures of complexes with proteins. S-Methylmethionine and S-dimethylsulfonioproprionate adopt a variety of conformations in aqueous solution; a conformation with an electrostatic interaction between the sulfonium sulfur and the carboxylate group is not noticeably favored, in contrast to the preferred conformation found by in vacuo calculations. Nuclear Overhauser effect measurements and computational results for AdoMet indicate a predominantly anti conformation about the glycosidic bond with a variety of conformations about the methionyl C(alpha)-C(beta) and C(beta)-C(gamma) bonds. An AdoMet conformation in which the positively charged sulfonium sulfur is near an electronegative oxygen in the ribose ring is common. Comparisons of NMR results for AdoMet with those for the uncharged S-adenosylhomocysteine and 5'-methylthioadenosine, and the anionic ATP, indicate that the solution conformations are not dictated mainly by molecular charge. In 20 reported structures of AdoMet.protein complexes, both anti and syn glycosidic torsional angles are found. The methionyl group typically adopts an extended conformation in complexes with enzymes that transfer the methyl group from the sulfonium center, but is more folded in complexes with proteins that do not catalyze reactions involving the sulfur and which can use the sulfonium sulfur solely as a binding site. The conformational energies of AdoMet in these crystal structures are comparable to those found for AdoMet in solution. The sulfonium sulfur is in van der Waals contact with a protein heteroatom in the structures of four proteins, which reflects an energetically favorable contact. Interactions of the sulfonium with aromatic rings are rarely observed.     

Dinosterol side chain biosynthesis in a marine dinoflagellate, Crypthecodinium cohnii

The heterotrophic dinofiagellate, Crypthecodinium cohnii, cultured in a nutrient medium containing methionine-[CD₃] incorporated deuterium into the newly synthesized 4α-monomethyl compound dinosterol (4α,23,24-trimethylcholest-22-en-3β-ol). The MS fragmentation pattern indicated that the C-23 methyl group contained three deuterium atoms and was introduced intact by transmethylation from methionine. The C-24 methyl group contained only two deuterium atoms which is consistent with the production of a 24-methylenesterol intermediate which is subsequently reduced to give the 24-methyl side chain. Mechanisms are proposed to account for the production of the dinosterol side chain.     

Transfer of the methyl group of methionine to choline and to tRNA in the honeybee Apis mellifica L.

Contrary to some previous reports on the absence of biological transmethylation reactions in some insect species, the transfer of the methyl group of methionine-methyl 14C leading to choline and to methylated bases in tRNA was shown in the honeybee Apis mellifica. The addition of antibiotics to the food of the insect does not diminish the incorporation of radioactivity, proving that intestinal bacteria are not responsible for the methylation reactions observed.     

Molecular insights of SAH enzyme catalysis and implication for inhibitor design

Biological transmethylation reaction is a key step in the duplication of virus life cycle, in which S-adenosylmethionine plays as the methyl donor. The product of this reactions, S-adenosylhomocysteine (AdoHcy) inhibits the transmethylation process. AdoHcy is hydrolysed to adenosine and L-homocysteine by the action of S-adenosylhomocysteine hydrolase (SAH). Thus the virus life cycle should be cut off once the action of SAH is inhibited. Our study was focussed on the discovery of potential inhibitor against SAH. We performed a similarity search in Traditional Chinese Medicine Database and retrieved 17 hits with high similarity. After that we virtually docked the 17 compounds as well as the natural substrates to the hydrolase using Autodock 3.0.1 software. Then we discussed about the mechanism of the inhibition reaction, followed by proposing the potential inhibitors by comparing best docked solutions and possible modification for the best inhibitors.     

A coupled spectrophotometric enzyme assay for methyltransferases

Adenosine deaminase (EC 3.5.4.4), purified from Aspergillus oryzae, is active in deaminating S-adenosylhomocysteine and its related thioethers, whereas the related sulfonium compound, S-adenosylmethionine, is not deaminated. By taking advantage of the different reactivity of the two compounds, a coupled optical enzyme assay for methyl transfer reactions has been developed. The amount of Ado-Hcy formed is calculated from the decrease in optical density at 265 nm, after addition of an excess of adenosine deaminase. The validity of the method has been tested with three purified enzymes, i.e., homocysteine methyltransferase, histamine methylase, and acetylserotonin methyltransferase. Some kinetic constants of these enzymes have been obtained. The procedure is highly accurate, reproducible, and relatively simple compared to the conventional radio-chemical methods currently in use.     

Methyl group metabolism in sheep

1. Sheep have a very low intake of methyl nutrients in the post-ruminant state, due to the almost complete degradation of dietary choline by rumen microorganisms, the lack of dietary creatine and the relatively low content of methionine in microbial proteins. 2. Methylneogenesis provides a major source of labile methyl groups in post-ruminant sheep and impairment of the methylneogenesis leads to a marked reduction of the labile methyl pool. 3. S-Adenosylmethionine (AdoMet) metabolism via transmethylation is most active in sheep liver and pancreas and is regulated by the availability of methionine and intracellular ratios of AdoMet to S-adenosylhomocysteine (AdoHcy). 4. Adaptive mechanisms which arise as a consequence of the poor methyl nutrition in post-ruminant sheep are a marked reduction of labile methyl catabolism and an increase in the capacity of methylneogenesis.     

Comparison of three GC/MS methodologies for the analysis of fatty acids in Sinorhizobium meliloti: development of a micro-scale, one-vial method

Three protocols for fatty acid analysis in Sinorhizobium meliloti were improved by the addition of a number of standards/controls and a silylation step which allowed the determination of recoveries, extents of conversion of lipids to fatty acid methyl esters (FAMEs) and extents of side reactions. Basic hydrolysis followed by acid-catalyzed methylation and transmethylation with sodium methoxide, were the best for the analysis of 3-hydroxy- and cyclopropane fatty acids, respectively. A micro-scale, one-vial method that employed sodium methoxide/methanol was equally efficient and on a 1000-fold smaller scale than standard methods. Because this method avoids aqueous extractions, 3-hydroxybutanoic acid was detected as its trimethylsilyloxy methyl ester along with FAMEs.     

Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases

S-Adenosyl-L-methionine (AdoMet) is the major methyl donor for biological methylation reactions catalyzed by methyltransferases. We report the first chemical synthesis of AdoMet analogs with extended carbon chains replacing the methyl group and their evaluation as cofactors for all three classes of DNA methyltransferases. Extended groups containing a double or triple bond in the beta position to the sulfonium center were transferred onto DNA in a catalytic and sequence-specific manner, demonstrating a high utility of such synthetic cofactors for targeted functionalization of biopolymers.     

The rate of transmethylation in mouse liver as measured by trapping S-adenosylhomocysteine

Periodate-oxidized adenosine has previously been shown to be a potent inhibitor in vitro of S-adenosylhomocysteine hydrolase (E.C. 3.3.1.1). This paper describes the inhibition of this enzyme in liver following injection of mice with periodate-oxidized adenosine. A maximally effective dose of 100 nmol/g of this compound causes liver S-adenosylhomocysteine to increase from 12 to 600 nmol/g within 30 min. This accumulation of S-adenosylhomocysteine provides an estimate of the rates of transmethylation, as well as adenosine and homocysteine production, as being at least 20 nmol/min/g liver. A doubling of S-adenosylmethionine in the liver of mice treated with periodate-oxidized adenosine suggests that the high levels of S-adenosylhomocysteine inhibit some transmethylation reactions.     

Cytolysis of nucleated cells by complement: inhibition of membrane-transmethylation enhances cell death by C5b-9

Inhibition of transmethylation, i.e., enzymatic transfer of methyl groups to phosphatidyl ethanolamine resulting in generation and translocation of phosphatidyl choline, enhances the killing of nucleated cells by complement. Furthermore, under complement attack, transmethylation measured as incorporation of [3H]methyl groups into phosphatidyl choline is enhanced, suggesting that transmethylation functions as a membrane defense mechanism either by increasing the phosphatidyl choline synthesis or by transducing a signal that might trigger another membrane repair process.     

Myosin light chain kinase binding to plastic

Methionine-81 and/or -8 of the transmembrane sialoglycoprotein, glycophorin A, have been specifically alkylated with ¹³CH₃I to produce the sulfonium ion derivatives [S-[¹³C]methylmethionine-8]glycophorin A and [S-[¹³C]methylmethionine-8 and -81]glycophorin A. ¹³C NMR spectra of these species show that the resonances of the methyl groups of the modified glycophorins occur at 26.1 ppm downfield from Me₄Si. A spin-lattice relaxation time of 0.4 was observed for the ¹³C-enriched methyl resonances of the sulfonium ion derivatives of Met-8 and -81, which corresponds to an effective correlation time of < 2× 10^?10 s. Demethylation of the 2 glycophorin A sulfonium ion species with 2-mercaptoethanol produces native glycophorin A which now has the ε-carbon of the methionine residue(s) 45% isotopically enriched. The ε-carbon of Met-8 was found to occur at 15.7 ppm downfield from Me₄Si whereas the ε-carbon of Met-81 exhibited an unusual chemical shift of 2.0 ppm downfield from Me₄Si. The spin-lattice relaxation time of both resonances was found to be ～0.3 s.     

MAT2A promotes porcine adipogenesis by mediating H3K27me3 at Wnt10b locus and repressing Wnt/β-catenin signaling

Methionine adenosyltransferase (MAT) is a critical biological enzyme and that can catalyze L-met and ATP to form S-adenosylmethionine (SAM), which is acted as a biological methyl donor in transmethylation reactions involving histone methylation. However, the regulatory effect of methionine adenosyltransferase2A (MAT2A) and its associated methyltransferase activity on adipogenesis is still unclear. In this study, we investigate the effect of MAT2A on adipogenesis and its potential mechanism on histone methylation during porcine preadipocyte differentiation. We demonstrated that overexpression of MAT2A promoted lipid accumulation and significantly up-regulated the levels of adipogenic marker genes including PPARγ, SREBP-1c, and aP2. Whereas, knockdown of MAT2A or inhibition MATII enzyme activity inhibited lipid accumulation and down-regulated the expression of the above-mentioned genes. Mechanistic studies revealed that MAT2A interacted with histone-lysine N-methyltransferase Ezh2 and was recruited to Wnt10b promoter to repress its expression by promoting H3K27 methylation. Additionally, MAT2A interacted with MafK protein and was recruited to MARE element at Wnt10b gene. The catalytic activity of MAT2A as well as its interacting factor-MAT2B, was required for Wnt10b repression and supplying SAM for methyltransferases. Moreover, MAT2A suppressed Wnt10b expression and further inhibited Wnt/β-catenin signaling to promote adipogenesis.     

Biochemical characterization of an l-methionine-enriched mutant of a methylotrophic yeast,Candida boidinii

The effects of an ethionine-resistant mutation in a methylotrophic yeast, Candida boidinii, were studied. In mutant strain E500-78 (ethionine-resistant), SAM synthetase activity was low and was only slightly repressed by l-methionine. Formyltetrahydrofolate synthetase and serine hydroxymethyltransferase were involved in synthesis of the methyl group of l-methionine. The activities of the methyl group transferring enzymes and homocysteine transmethylation were repressed by l-methionine in the wild type strain, but not in the mutant. The activities of the methyl group transferring enzymes were markedly stimulated when the mutant was grown in methanol medium.