Journal articles: 'Methyltransferases'

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Wnuk, Maciej, Piotr Slipek, Mateusz Dziedzic, and Anna Lewinska. "The Roles of Host 5-Methylcytosine RNA Methyltransferases during Viral Infections." International Journal of Molecular Sciences 21, no. 21 (October 31, 2020): 8176. http://dx.doi.org/10.3390/ijms21218176.

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Eukaryotic 5-methylcytosine RNA methyltransferases catalyze the transfer of a methyl group to the fifth carbon of a cytosine base in RNA sequences to produce 5-methylcytosine (m5C). m5C RNA methyltransferases play a crucial role in the maintenance of functionality and stability of RNA. Viruses have developed a number of strategies to suppress host innate immunity and ensure efficient transcription and translation for the replication of new virions. One such viral strategy is to use host m5C RNA methyltransferases to modify viral RNA and thus to affect antiviral host responses. Here, we summarize the latest findings concerning the roles of m5C RNA methyltransferases, namely, NOL1/NOP2/SUN domain (NSUN) proteins and DNA methyltransferase 2/tRNA methyltransferase 1 (DNMT2/TRDMT1) during viral infections. Moreover, the use of m5C RNA methyltransferase inhibitors as an antiviral therapy is discussed.

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Paul, Ligi, Donald J. Ferguson, and Joseph A. Krzycki. "The Trimethylamine Methyltransferase Gene and Multiple Dimethylamine Methyltransferase Genes of Methanosarcina barkeri Contain In-Frame and Read-Through Amber Codons." Journal of Bacteriology 182, no. 9 (May 1, 2000): 2520–29. http://dx.doi.org/10.1128/jb.182.9.2520-2529.2000.

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ABSTRACT Three different methyltransferases initiate methanogenesis from trimethylamine (TMA), dimethylamine (DMA) or monomethylamine (MMA) by methylating different cognate corrinoid proteins that are subsequently used to methylate coenzyme M (CoM). Here, genes encoding the DMA and TMA methyltransferases are characterized for the first time. A single copy of mttB, the TMA methyltransferase gene, was cotranscribed with a copy of the DMA methyltransferase gene,mtbB1. However, two other nearly identical copies ofmtbB1, designated mtbB2 and mtbB3, were also found in the genome. A 6.8-kb transcript was detected with probes to mttB and mtbB1, as well as tomtbC and mttC, encoding the cognate corrinoid proteins for DMA:CoM and TMA:CoM methyl transfer, respectively, and with probes to mttP, encoding a putative membrane protein which might function as a methylamine permease. These results indicate that these genes, found on the chromosome in the ordermtbC, mttB, mttC, mttP, and mtbB1, form a single transcriptional unit. A transcriptional start site was detected 303 or 304 bp upstream of the translational start of mtbC. The MMA, DMA, and TMA methyltransferases are not homologs; however, like the MMA methyltransferase gene, the genes encoding the DMA and TMA methyltransferases each contain a single in-frame amber codon. Each of the three DMA methyltransferase gene copies from Methanosarcina barkeri contained an amber codon at the same position, followed by a downstream UAA or UGA codon. The C-terminal residues of DMA methyltransferase purified from TMA-grown cells matched the residues predicted for the gene products of mtbB1,mtbB2, or mtbB3 if termination occurred at the UAA or UGA codon rather than the in-frame amber codon. ThemttB gene from Methanosarcina thermophilacontained a UAG codon at the same position as the M. barkeri mttB gene. The UAG codon is also present in mttBtranscripts. Thus, the genes encoding the three types of methyltransferases that initiate methanogenesis from methylamine contain in-frame amber codons that are suppressed during expression of the characterized methyltransferases.

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Ramdhan, Peter, and Chenglong Li. "Targeting Viral Methyltransferases: An Approach to Antiviral Treatment for ssRNA Viruses." Viruses 14, no. 2 (February 12, 2022): 379. http://dx.doi.org/10.3390/v14020379.

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Methyltransferase enzymes have been associated with different processes within cells and viruses. Specifically, within viruses, methyltransferases are used to form the 5′cap-0 structure for optimal evasion of the host innate immune system. In this paper, we seek to discuss the various methyltransferases that exist within single-stranded RNA (ssRNA) viruses along with their respective inhibitors. Additionally, the importance of motifs such as the KDKE tetrad and glycine-rich motif in the catalytic activity of methyltransferases is discussed.

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Jeevarajah, Dharshini, John H. Patterson, Ellen Taig, Tobias Sargeant, Malcolm J. McConville, and Helen Billman-Jacobe. "Methylation of GPLs in Mycobacterium smegmatis and Mycobacterium avium." Journal of Bacteriology 186, no. 20 (October 15, 2004): 6792–99. http://dx.doi.org/10.1128/jb.186.20.6792-6799.2004.

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ABSTRACT Several species of mycobacteria express abundant glycopeptidolipids (GPLs) on the surfaces of their cells. The GPLs are glycolipids that contain modified sugars including acetylated 6-deoxy-talose and methylated rhamnose. Four methyltransferases have been implicated in the synthesis of the GPLs of Mycobacterium smegmatis and Mycobacterium avium. A rhamnosyl 3-O-methytransferase and a fatty acid methyltransferase of M. smegmatis have been previously characterized. In this paper, we characterize the methyltransferases that are responsible for modifying the hydroxyl groups at positions 2 and 4 of rhamnose and propose the biosynthetic sequence of GPL trimethylrhamnose formation. The analysis of M. avium genes through the creation of specific mutants is technically difficult; therefore, an alternative approach to determine the function of putative methyltransferases of M. avium was undertaken. Complementation of M. smegmatis methyltransferase mutants with M. avium genes revealed that MtfC and MtfB of the latter species have 4-O-methyltransferase activity and that MtfD is a 3-O-methyltransferase which can modify rhamnose of GPLs in M. smegmatis.

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Yan, Dongsheng, Yong Zhang, Lifang Niu, Yi Yuan, and Xiaofeng Cao. "Identification and characterization of two closely related histone H4 arginine 3 methyltransferases in Arabidopsis thaliana." Biochemical Journal 408, no. 1 (October 29, 2007): 113–21. http://dx.doi.org/10.1042/bj20070786.

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Arginine methylation of histone H3 and H4 plays important roles in transcriptional regulation in eukaryotes such as yeasts, fruitflies, nematode worms, fish and mammals; however, less is known in plants. In the present paper, we report the identification and characterization of two Arabidopsis thaliana protein arginine N-methyltransferases, AtPRMT1a and AtPRMT1b, which exhibit high homology with human PRMT1. Both AtPRMT1a and AtPRMT1b methylated histone H4, H2A, and myelin basic protein in vitro. Site-directed mutagenesis of the third arginine (R3) on the N-terminus of histone H4 to lysine (H4R3N) completely abolished the methylation of histone H4. When fused to GFP (green fluorescent protein), both methyltransferases localized to the cytoplasm as well as to the nucleus. Consistent with their subcellular distribution, GST (glutathione transferase) pull-down assays revealed an interaction between the two methyltransferases, suggesting that both proteins may act together in a functional unit. In addition, we demonstrated that AtFib2 (Arabidopsis thaliana fibrillarin 2), an RNA methyltransferase, is a potential substrate for AtPRMT1a and AtPRMT1b, and, furthermore, uncovered a direct interaction between the protein methyltransferase and the RNA methyltransferase. Taken together, our findings implicate AtPRMT1a and AtPRMT1b as H4-R3 protein arginine N-methyltransferases in Arabidopsis and may be involved in diverse biological processes inside and outside the nucleus.

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Lashley, Audrey, Ryan Miller, Stephanie Provenzano, Sara-Alexis Jarecki, Paul Erba, and Vonny Salim. "Functional Diversification and Structural Origins of Plant Natural Product Methyltransferases." Molecules 28, no. 1 (December 21, 2022): 43. http://dx.doi.org/10.3390/molecules28010043.

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In plants, methylation is a common step in specialized metabolic pathways, leading to a vast diversity of natural products. The methylation of these small molecules is catalyzed by S-adenosyl-l-methionine (SAM)-dependent methyltransferases, which are categorized based on the methyl-accepting atom (O, N, C, S, or Se). These methyltransferases are responsible for the transformation of metabolites involved in plant defense response, pigments, and cell signaling. Plant natural product methyltransferases are part of the Class I methyltransferase-superfamily containing the canonical Rossmann fold. Recent advances in genomics have accelerated the functional characterization of plant natural product methyltransferases, allowing for the determination of substrate specificities and regioselectivity and further realizing the potential for enzyme engineering. This review compiles known biochemically characterized plant natural product methyltransferases that have contributed to our knowledge in the diversification of small molecules mediated by methylation steps.

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Rao, Mingzhu. "Gene Expression Profile of RNA N1-methyladenosine methyltransferases." E3S Web of Conferences 218 (2020): 03052. http://dx.doi.org/10.1051/e3sconf/202021803052.

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N1-methyladenosine (m1A) is a kind of common and abundant methylation modification in eukaryotic mRNA and long-chain non-coding RNA. Nucleoside methyltransferase (MTase) of m1A is a diverse protein family, which is characterized by the presence of methyltransferases like domains and conserved S-adenosylmethionine (SAM) binding domains formed by the central sevenstranded beta-sheet structure. However, comprehensive analysis of the gene expression profile of such enzymes has not been performed to classify them according to evolutionary criteria and to guide the functional prediction. Here, we conducted extensive searches of databases to collect all members of previously identified m1A RNA methyltransferases. And we report bioinformatics studies on gene expression profile based on evolutionary analysis, sequence alignment, expression in tissues and cells within the family of RNA methyltransferases. Our analysis showed that the base modification behavior mediated by m1A RNA methyltransferases evolved from invertebrate, and the active sites of m1A RNA methyltransferases were highly conserved during the evolution from invertebrates to human. And m1A RNA methyltransferases have low tissue and cell specificity.

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Mushegian, Arcady. "Methyltransferases of Riboviria." Biomolecules 12, no. 9 (September 6, 2022): 1247. http://dx.doi.org/10.3390/biom12091247.

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Many viruses from the realm Riboviria infecting eukaryotic hosts encode protein domains with sequence similarity to S-adenosylmethionine-dependent methyltransferases. These protein domains are thought to be involved in methylation of the 5′-terminal cap structures in virus mRNAs. Some methyltransferase-like domains of Riboviria are homologous to the widespread cellular FtsJ/RrmJ-like methyltransferases involved in modification of cellular RNAs; other methyltransferases, found in a subset of positive-strand RNA viruses, have been assigned to a separate “Sindbis-like” family; and coronavirus-specific Nsp13/14-like methyltransferases appeared to be different from both those classes. The representative structures of proteins from all three groups belong to a specific variety of the Rossmann fold with a seven-stranded β-sheet, but it was unclear whether this structural similarity extends to the level of conserved sequence signatures. Here I survey methyltransferases in Riboviria and derive a joint sequence alignment model that covers all groups of virus methyltransferases and subsumes the previously defined conserved sequence motifs. Analysis of the spatial structures indicates that two highly conserved residues, a lysine and an aspartate, frequently contact a water molecule, which is located in the enzyme active center next to the methyl group of S-adenosylmethionine cofactor and could play a key role in the catalytic mechanism of the enzyme. Phylogenetic evidence indicates a likely origin of all methyltransferases of Riboviria from cellular RrmJ-like enzymes and their rapid divergence with infrequent horizontal transfer between distantly related viruses.

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BOULANGER, Marie-Chloé, Tina Branscombe MIRANDA, Steven CLARKE, Marco di FRUSCIO, Beat SUTER, Paul LASKO, and Stéphane RICHARD. "Characterization of the Drosophila protein arginine methyltransferases DART1 and DART4." Biochemical Journal 379, no. 2 (April 15, 2004): 283–89. http://dx.doi.org/10.1042/bj20031176.

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The role of arginine methylation in Drosophila melanogaster is unknown. We identified a family of nine PRMTs (protein arginine methyltransferases) by sequence homology with mammalian arginine methyltransferases, which we have named DART1 to DART9 (Drosophilaarginine methyltransferases 1–9). In keeping with the mammalian PRMT nomenclature, DART1, DART4, DART5 and DART7 are the putative homologues of PRMT1, PRMT4, PRMT5 and PRMT7. Other DART family members have a closer resemblance to PRMT1, but do not have identifiable homologues. All nine genes are expressed in Drosophila at various developmental stages. DART1 and DART4 have arginine methyltransferase activity towards substrates, including histones and RNA-binding proteins. Amino acid analysis of the methylated arginine residues confirmed that both DART1 and DART4 catalyse the formation of asymmetrical dimethylated arginine residues and they are type I arginine methyltransferases. The presence of PRMTs in D. melanogaster suggest that flies are a suitable genetic system to study arginine methylation.

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Ruszkowska, Agnieszka. "METTL16, Methyltransferase-Like Protein 16: Current Insights into Structure and Function." International Journal of Molecular Sciences 22, no. 4 (February 22, 2021): 2176. http://dx.doi.org/10.3390/ijms22042176.

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Methyltransferase-like protein 16 (METTL16) is a human RNA methyltransferase that installs m6A marks on U6 small nuclear RNA (U6 snRNA) and S-adenosylmethionine (SAM) synthetase pre-mRNA. METTL16 also controls a significant portion of m6A epitranscriptome by regulating SAM homeostasis. Multiple molecular structures of the N-terminal methyltransferase domain of METTL16, including apo forms and complexes with S-adenosylhomocysteine (SAH) or RNA, provided the structural basis of METTL16 interaction with the coenzyme and substrates, as well as indicated autoinhibitory mechanism of the enzyme activity regulation. Very recent structural and functional studies of vertebrate-conserved regions (VCRs) indicated their crucial role in the interaction with U6 snRNA. METTL16 remains an object of intense studies, as it has been associated with numerous RNA classes, including mRNA, non-coding RNA, long non-coding RNA (lncRNA), and rRNA. Moreover, the interaction between METTL16 and oncogenic lncRNA MALAT1 indicates the existence of METTL16 features specifically recognizing RNA triple helices. Overall, the number of known human m6A methyltransferases has grown from one to five during the last five years. METTL16, CAPAM, and two rRNA methyltransferases, METTL5/TRMT112 and ZCCHC4, have joined the well-known METTL3/METTL14. This work summarizes current knowledge about METTL16 in the landscape of human m6A RNA methyltransferases.

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Abeykoon, Amila H., Chien-Chung Chao, Guanghui Wang, Marjan Gucek, David C. H. Yang, and Wei-Mei Ching. "Two Protein Lysine Methyltransferases Methylate Outer Membrane Protein B from Rickettsia." Journal of Bacteriology 194, no. 23 (September 21, 2012): 6410–18. http://dx.doi.org/10.1128/jb.01379-12.

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ABSTRACTRickettsia prowazekii, the etiologic agent of epidemic typhus, is a potential biological threat agent. Its outer membrane protein B (OmpB) is an immunodominant antigen and plays roles as protective envelope and as adhesins. The observation of the correlation between methylation of lysine residues in rickettsial OmpB and bacterial virulence has suggested the importance of an enzymatic system for the methylation of OmpB. However, no rickettsial lysine methyltransferase has been characterized. Bioinformatic analysis of genomic DNA sequences ofRickettsiaidentified putative lysine methyltransferases. The genes of the potential methyltransferases were synthesized, cloned, and expressed inEscherichia coli, and expressed proteins were purified by nickel-nitrilotriacetic acid (Ni-NTA) affinity chromatography. The methyltransferase activities of the purified proteins were analyzed by methyl incorporation of radioactively labeledS-adenosylmethionine into recombinant fragments of OmpB. Two putative recombinant methyltransferases (rRP789 and rRP027-028) methylated recombinant OmpB fragments. The specific activity of rRP789 is 10- to 30-fold higher than that of rRP027-028. Western blot analysis using specific antibodies against trimethyl lysine showed that both rRP789 and rRP027-028 catalyzed trimethylation of recombinant OmpB fragments. Liquid chromatography-tandem mass spectrometry (LC/MS-MS) analysis showed that rRP789 catalyzed mono-, di-, and trimethylation of lysine, while rRP027-028 catalyzed exclusively trimethylation. To our knowledge, rRP789 and rRP027-028 are the first biochemically characterized lysine methyltransferases of outer membrane proteins from Gram-negative bacteria. The production and characterization of rickettsial lysine methyltransferases provide new tools to investigate the mechanism of methylation of OmpB, effects of methylation on the structure and function of OmpB, and development of methylated OmpB-based diagnostic assays and vaccine candidates.

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Szulik, Marta W., Kathryn Davis, Anna Bakhtina, Presley Azarcon, Ryan Bia, Emilee Horiuchi, and Sarah Franklin. "Transcriptional regulation by methyltransferases and their role in the heart: highlighting novel emerging functionality." American Journal of Physiology-Heart and Circulatory Physiology 319, no. 4 (October 1, 2020): H847—H865. http://dx.doi.org/10.1152/ajpheart.00382.2020.

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Methyltransferases are a superfamily of enzymes that transfer methyl groups to proteins, nucleic acids, and small molecules. Traditionally, these enzymes have been shown to carry out a specific modification (mono-, di-, or trimethylation) on a single, or limited number of, amino acid(s). The largest subgroup of this family, protein methyltransferases, target arginine and lysine side chains of histone molecules to regulate gene expression. Although there is a large number of functional studies that have been performed on individual methyltransferases describing their methylation targets and effects on biological processes, no analyses exist describing the spatial distribution across tissues or their differential expression in the diseased heart. For this review, we performed tissue profiling in protein databases of 199 confirmed or putative methyltransferases to demonstrate the unique tissue-specific expression of these individual proteins. In addition, we examined transcript data sets from human heart failure patients and murine models of heart disease to identify 40 methyltransferases in humans and 15 in mice, which are differentially regulated in the heart, although many have never been functionally interrogated. Lastly, we focused our analysis on the largest subgroup, that of protein methyltransferases, and present a newly emerging phenomenon in which 16 of these enzymes have been shown to play dual roles in regulating transcription by maintaining the ability to both activate and repress transcription through methyltransferase-dependent or -independent mechanisms. Overall, this review highlights a novel paradigm shift in our understanding of the function of histone methyltransferases and correlates their expression in heart disease.

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Goll, Mary Grace, Finn Kirpekar, Keith A. Maggert, Jeffrey A. Yoder, Chih-Lin Hsieh, Xiaoyu Zhang, Kent G. Golic, Steven E. Jacobsen, and Timothy H. Bestor. "Methylation of tRNAAsp by the DNA Methyltransferase Homolog Dnmt2." Science 311, no. 5759 (January 20, 2006): 395–98. http://dx.doi.org/10.1126/science.1120976.

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The sequence and the structure of DNA methyltransferase-2 (Dnmt2) bear close affinities to authentic DNA cytosine methyltransferases. A combined genetic and biochemical approach revealed that human DNMT2 did not methylate DNA but instead methylated a small RNA; mass spectrometry showed that this RNA is aspartic acid transfer RNA (tRNAAsp) and that DNMT2 specifically methylated cytosine 38 in the anticodon loop. The function of DNMT2 is highly conserved, and human DNMT2 protein restored methylation in vitro to tRNAAsp from Dnmt2-deficient strains of mouse, Arabidopsis thaliana, and Drosophila melanogaster in a manner that was dependent on preexisting patterns of modified nucleosides. Indirect sequence recognition is also a feature of eukaryotic DNA methyltransferases, which may have arisen from a Dnmt2-like RNA methyltransferase.

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Ashihara, Hiroshi. "Biosynthetic Pathways of Purine and Pyridine Alkaloids in Coffee Plants." Natural Product Communications 11, no. 7 (July 2016): 1934578X1601100. http://dx.doi.org/10.1177/1934578x1601100742.

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Caffeine (1,3,7- N-trimethylxanthine) and trigonelline (1 N-methylnicotinic acid) are major alkaloids in coffee plants. The key enzymes involved in the biosynthesis of these compounds are very closely related N-methyltransferases belonging to the motif B’ family of methyltransferases. The major biosynthetic pathways of caffeine and trigonelline are summarized in this review, including new evidence obtained from recombinant enzymes. In addition, precursor supply pathways are discussed with newly obtained results. Transgenic plants produced by the modification of the expression of N-methyltransferase genes are also introduced.

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Li, Jinmei, Shenglei Feng, Xixiang Ma, Shuiqiao Yuan, and Xiaoli Wang. "METTL21A, a Non-Histone Methyltransferase, Is Dispensable for Spermatogenesis and Male Fertility in Mice." International Journal of Molecular Sciences 23, no. 4 (February 9, 2022): 1942. http://dx.doi.org/10.3390/ijms23041942.

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Protein methyltransferases play various physiological and pathological roles through methylating histone and non-histone targets. Many histone methyltransferases have been reported to regulate the development of spermatogenic cells. However, the specific function of non-histone methyltransferases during spermatogenesis remains unclear. In this study, we found that METTL21A, a non-histone methyltransferase, is highly expressed in mouse testes. In order to elucidate the role of METTL21A in spermatogenesis, we generated a Mettl21a global knockout mouse model using CRISPR/Cas9 technology. Unexpectedly, our results showed that knockout males are fertile without apparent defects in the processes of male germ cell development, including spermatogonial differentiation, meiosis, and sperm maturation. Furthermore, the ablation of METTL21A does not affect the expression and localization of its known targeting proteins in testes. Together, our data demonstrated that METTL21A is not essential for mouse spermatogenesis and male fertility.

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Falnes, Pål Ø., Magnus E. Jakobsson, Erna Davydova, Angela Ho, and Jędrzej Małecki. "Protein lysine methylation by seven-β-strand methyltransferases." Biochemical Journal 473, no. 14 (July 12, 2016): 1995–2009. http://dx.doi.org/10.1042/bcj20160117.

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Lysine methylation is an important post-translational protein modification, and a number of novel lysine-specific protein methyltransferases belonging to the seven-β-strand methyltransferase family have recently been discovered. This article provides a comprehensive review of this group of enzymes.

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Woodcock, Clayton B., John R. Horton, Xing Zhang, Robert M. Blumenthal, and Xiaodong Cheng. "Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences." Nucleic Acids Research 48, no. 18 (May 26, 2020): 10034–44. http://dx.doi.org/10.1093/nar/gkaa446.

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Abstract S-adenosyl-l-methionine dependent methyltransferases catalyze methyl transfers onto a wide variety of target molecules, including DNA and RNA. We discuss a family of methyltransferases, those that act on the amino groups of adenine or cytosine in DNA, have conserved motifs in a particular order in their amino acid sequence, and are referred to as class beta MTases. Members of this class include M.EcoGII and M.EcoP15I from Escherichia coli, Caulobacter crescentus cell cycle–regulated DNA methyltransferase (CcrM), the MTA1-MTA9 complex from the ciliate Oxytricha, and the mammalian MettL3-MettL14 complex. These methyltransferases all generate N6-methyladenine in DNA, with some members having activity on single-stranded DNA as well as RNA. The beta class of methyltransferases has a unique multimeric feature, forming either homo- or hetero-dimers, allowing the enzyme to use division of labor between two subunits in terms of substrate recognition and methylation. We suggest that M.EcoGII may represent an ancestral form of these enzymes, as its activity is independent of the nucleic acid type (RNA or DNA), its strandedness (single or double), and its sequence (aside from the target adenine).

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Mashhoon, Neda, Cynthia Pruss, Michael Carroll, Paul H. Johnson, and Norbert O. Reich. "Selective Inhibitors of Bacterial DNA Adenine Methyltransferases." Journal of Biomolecular Screening 11, no. 5 (April 28, 2006): 497–510. http://dx.doi.org/10.1177/1087057106287933.

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The authors describe the discovery and characterization of several structural classes of small-molecule inhibitors of bacterial DNA adenine methyltransferases. These enzymes are essential for bacterial virulence (DNA adenine methyltransferase [DAM]) and cell viability (cell cycle–regulated methyltransferase [CcrM]). Using a novel high-throughput fluorescence-based assay and recombinant DAM and CcrM, the authors screened a diverse chemical library. They identified 5 major structural classes of inhibitors composed of more than 350 compounds: cyclopentaquinolines, phenyl vinyl furans, pyrimidine-diones, thiazolidine-4-ones, and phenyl-pyrroles. DNA binding assays were used to identify compounds that interact directly with DNA. Potent compounds selective for the bacterial target were identified, whereas other compounds showed greater selectivity for the mammalian DNA cytosine methyltransferase, Dnmt1. Enzyme inhibition analysis identified mechanistically distinct compounds that interfered with DNA or cofactor binding. Selected compounds demonstrated cell-based efficacy. These small-molecule DNA methyltransferase inhibitors provide useful reagents to probe the role of DNA methylation and may form the basis of developing novel antibiotics.

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Goričan, Larisa, Tomaž Büdefeld, Helena Čelešnik, Matija Švagan, Boštjan Lanišnik, and Uroš Potočnik. "Gene Expression Profiles of Methyltransferases and Demethylases Associated with Metastasis, Tumor Invasion, CpG73 Methylation, and HPV Status in Head and Neck Squamous Cell Carcinoma." Current Issues in Molecular Biology 45, no. 6 (May 27, 2023): 4632–46. http://dx.doi.org/10.3390/cimb45060294.

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Epigenetic studies on the role of DNA-modifying enzymes in HNSCC tumorigenesis have focused on a single enzyme or a group of enzymes. To acquire a more comprehensive insight into the expression profile of methyltransferases and demethylases, in the present study, we examined the mRNA expression of the DNA methyltransferases DNMT1, DNMT3A, and DNMT3B, the DNA demethylases TET1, TET2, TET3, and TDG, and the RNA methyltransferase TRDMT1 by RT-qPCR in paired tumor–normal tissue samples from HNSCC patients. We characterized their expression patterns in relation to regional lymph node metastasis, invasion, HPV16 infection, and CpG73 methylation. Here, we show that tumors with regional lymph node metastases (pN+) exhibited decreased expression of DNMT1, 3A and 3B, and TET1 and 3 compared to non-metastatic tumors (pN0), suggesting that metastasis requires a distinct expression profile of DNA methyltransferases/demethylases in solid tumors. Furthermore, we identified the effect of perivascular invasion and HPV16 on DNMT3B expression in HNSCC. Finally, the expression of TET2 and TDG was inversely correlated with the hypermethylation of CpG73, which has previously been associated with poorer survival in HNSCC. Our study further confirms the importance of DNA methyltransferases and demethylases as potential prognostic biomarkers as well as molecular therapeutic targets for HNSCC.

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van Tran, Nhan, Felix G. M. Ernst, Ben R. Hawley, Christiane Zorbas, Nathalie Ulryck, Philipp Hackert, Katherine E. Bohnsack, et al. "The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112." Nucleic Acids Research 47, no. 15 (July 22, 2019): 7719–33. http://dx.doi.org/10.1093/nar/gkz619.

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Abstract N6-methyladenosine (m6A) has recently been found abundantly on messenger RNA and shown to regulate most steps of mRNA metabolism. Several important m6A methyltransferases have been described functionally and structurally, but the enzymes responsible for installing one m6A residue on each subunit of human ribosomes at functionally important sites have eluded identification for over 30 years. Here, we identify METTL5 as the enzyme responsible for 18S rRNA m6A modification and confirm ZCCHC4 as the 28S rRNA modification enzyme. We show that METTL5 must form a heterodimeric complex with TRMT112, a known methyltransferase activator, to gain metabolic stability in cells. We provide the first atomic resolution structure of METTL5–TRMT112, supporting that its RNA-binding mode differs distinctly from that of other m6A RNA methyltransferases. On the basis of similarities with a DNA methyltransferase, we propose that METTL5–TRMT112 acts by extruding the adenosine to be modified from a double-stranded nucleic acid.

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Savic, Miloje, S. Sunita, Natalia Zelinskaya, Pooja M. Desai, Rachel Macmaster, Kellie Vinal, and Graeme L. Conn. "30S Subunit-Dependent Activation of the Sorangium cellulosum So ce56 Aminoglycoside Resistance-Conferring 16S rRNA Methyltransferase Kmr." Antimicrobial Agents and Chemotherapy 59, no. 5 (March 2, 2015): 2807–16. http://dx.doi.org/10.1128/aac.00056-15.

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ABSTRACTMethylation of bacterial 16S rRNA within the ribosomal decoding center confers exceptionally high resistance to aminoglycoside antibiotics. This resistance mechanism is exploited by aminoglycoside producers for self-protection while functionally equivalent methyltransferases have been acquired by human and animal pathogenic bacteria. Here, we report structural and functional analyses of theSorangium cellulosumSo ce56 aminoglycoside resistance-conferring methyltransferase Kmr. Our results demonstrate that Kmr is a 16S rRNA methyltransferase acting at residue A1408 to confer a canonical aminoglycoside resistance spectrum inEscherichia coli. Kmr possesses a class I methyltransferase core fold but with dramatic differences in the regions which augment this structure to confer substrate specificity in functionally related enzymes. Most strikingly, the region linking core β-strands 6 and 7, which forms part of theS-adenosyl-l-methionine (SAM) binding pocket and contributes to base flipping by the m1A1408 methyltransferase NpmA, is disordered in Kmr, correlating with an exceptionally weak affinity for SAM. Kmr is unexpectedly insensitive to substitutions of residues critical for activity of other 16S rRNA (A1408) methyltransferases and also to the effects of by-product inhibition byS-adenosylhomocysteine (SAH). Collectively, our results indicate that adoption of a catalytically competent Kmr conformation and binding of the obligatory cosubstrate SAM must be induced by interaction with the 30S subunit substrate.

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Jin, Lu, Fei Ye, Dan Zhao, Shijie Chen, Kongkai Zhu, Mingyue Zheng, Ren-Wang Jiang, Hualiang Jiang, and Cheng Luo. "Metadynamics Simulation Study on the Conformational Transformation of HhaI Methyltransferase: An Induced-Fit Base-Flipping Hypothesis." BioMed Research International 2014 (2014): 1–13. http://dx.doi.org/10.1155/2014/304563.

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DNA methyltransferases play crucial roles in establishing and maintenance of DNA methylation, which is an important epigenetic mark. Flipping the target cytosine out of the DNA helical stack and into the active site of protein provides DNA methyltransferases with an opportunity to access and modify the genetic information hidden in DNA. To investigate the conversion process of base flipping in the HhaI methyltransferase (M.HhaI), we performed different molecular simulation approaches on M.HhaI-DNA-S-adenosylhomocysteine ternary complex. The results demonstrate that the nonspecific binding of DNA to M.HhaI is initially induced by electrostatic interactions. Differences in chemical environment between the major and minor grooves determine the orientation of DNA. Gln237 at the target recognition loop recognizes the GCGC base pair from the major groove side by hydrogen bonds. In addition, catalytic loop motion is a key factor during this process. Our study indicates that base flipping is likely to be an “induced-fit” process. This study provides a solid foundation for future studies on the discovery and development of mechanism-based DNA methyltransferases regulators.

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Jeong, Pil-Soo, Bo-Woong Sim, Soo-Hyun Park, Min Ju Kim, Hyo-Gu Kang, Tsevelmaa Nanjidsuren, Sanghoon Lee, Bong-Seok Song, Deog-Bon Koo, and Sun-Uk Kim. "Chaetocin Improves Pig Cloning Efficiency by Enhancing Epigenetic Reprogramming and Autophagic Activity." International Journal of Molecular Sciences 21, no. 14 (July 8, 2020): 4836. http://dx.doi.org/10.3390/ijms21144836.

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Efficient epigenetic reprogramming is crucial for the in vitro development of mammalian somatic cell nuclear transfer (SCNT) embryos. The aberrant levels of histone H3 lysine 9 trimethylation (H3K9me3) is an epigenetic barrier. In this study, we evaluated the effects of chaetocin, an H3K9me3-specific methyltransferase inhibitor, on the epigenetic reprogramming and developmental competence of porcine SCNT embryos. The SCNT embryos showed abnormal levels of H3K9me3 at the pronuclear, two-cell, and four-cell stages compared to in vitro fertilized embryos. Moreover, the expression levels of H3K9me3-specific methyltransferases (suv39h1 and suv39h2) and DNA methyltransferases (DNMT1, DNMT3a, and DNMT3b) were higher in SCNT embryos. Treatment with 0.5 nM chaetocin for 24 h after activation significantly increased the developmental competence of SCNT embryos in terms of the cleavage rate, blastocyst formation rate, hatching rate, cell number, expression of pluripotency-related genes, and cell survival rate. In particular, chaetocin enhanced epigenetic reprogramming by reducing the H3K9me3 and 5-methylcytosine levels and restoring the abnormal expression of H3K9me3-specific methyltransferases and DNA methyltransferases. Chaetocin induced autophagic activity, leading to a significant reduction in maternal mRNA levels in embryos at the pronuclear and two-cell stages. These findings revealed that chaetocin enhanced the developmental competence of porcine SCNT embryos by regulating epigenetic reprogramming and autophagic activity and so could be used to enhance the production of transgenic pigs for biomedical research.

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McKeever, M., A. Molloy, D. G. Weir, P. B. Young, D. G. Kennedy, S. Kennedy, and J. M. Scott. "An Abnormal Methylation Ratio Induces Hypomethylation In Vitro in the Brain of Pig and Man, But Not in Rat." Clinical Science 88, no. 1 (January 1, 1995): 73–79. http://dx.doi.org/10.1042/cs0880073.

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1. The ratio of the methyl donor, S-adenosylmethionine, to the co-product, S-adenosylhomocysteine (the methylation ratio) is known to control the activity of methyltransferases in tissues. Inactivation of the vitamin B12-dependent enzyme, methionine synthase, reduces the methylation ratio in rats and pigs in vivo. 2. We have determined the effect that such alterations have on neural protein ‘O’ and ‘N’ methyltransferases using an in vitro assay in rats, pigs and humans in the presence of the normal methylation ratio and the abnormal methylation ratios found experimentally in vivo in rats and pigs. 3. The methylation ratio found in the neural tissues of vitamin B12-inactivated pigs significantly inhibits the protein methyltransferases of pigs and humans. 4. By contrast, the altered methylation ratio found in vitamin B12-inactivated rats only marginally inhibits the equivalent rat methyltransferases. 5. This is consistent with the induction of a myelopathy by such treatment in pigs and humans, but not in the rat. 6. Dietary supplements of methionine given to vitamin B12-inactivated pigs have been shown to prevent the myelopathy in vivo by both elevating the neural S-adenosylmethionine level and resetting the methylation ratio. We find in our in vitro assay that these events reinstate the methyltransferase activity to near normal levels, thus explaining its protective effect in vivo.

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McGann, Patrick, Sarah Chahine, Darius Okafor, Ana C. Ong, Rosslyn Maybank, Yoon I. Kwak, Kerry Wilson, Michael Zapor, Emil Lesho, and Mary Hinkle. "Detecting 16S rRNA Methyltransferases in Enterobacteriaceae by Use of Arbekacin." Journal of Clinical Microbiology 54, no. 1 (November 4, 2015): 208–11. http://dx.doi.org/10.1128/jcm.02642-15.

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16S rRNA methyltransferases confer resistance to most aminoglycosides, but discriminating their activity from that of aminoglycoside-modifying enzymes (AMEs) is challenging using phenotypic methods. We demonstrate that arbekacin, an aminoglycoside refractory to most AMEs, can rapidly detect 16S methyltransferase activity inEnterobacteriaceaewith high specificity using the standard disk susceptibility test.

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Corrêa, Laís L., Marta A. Witek, Natalia Zelinskaya, Renata C. Picão, and Graeme L. Conn. "Heterologous Expression and Functional Characterization of the Exogenously Acquired Aminoglycoside Resistance Methyltransferases RmtD, RmtD2, and RmtG." Antimicrobial Agents and Chemotherapy 60, no. 1 (November 9, 2015): 699–702. http://dx.doi.org/10.1128/aac.02482-15.

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ABSTRACTThe exogenously acquired 16S rRNA methyltransferases RmtD, RmtD2, and RmtG were cloned and heterologously expressed inEscherichia coli, and the recombinant proteins were purified to near homogeneity. Each methyltransferase conferred an aminoglycoside resistance profile consistent with m7G1405 modification, and this activity was confirmed byinvitro30S methylation assays. Analyses of protein structure and interaction withS-adenosyl-l-methionine suggest that the molecular mechanisms of substrate recognition and catalysis are conserved across the 16S rRNA (m7G1405) methyltransferase family.

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Tirot, Louis, Pauline E. Jullien, and Mathieu Ingouff. "Evolution of CG Methylation Maintenance Machinery in Plants." Epigenomes 5, no. 3 (September 14, 2021): 19. http://dx.doi.org/10.3390/epigenomes5030019.

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Cytosine methylation is an epigenetic mark present in most eukaryotic genomes that contributes to the regulation of gene expression and the maintenance of genome stability. DNA methylation mostly occurs at CG sequences, where it is initially deposited by de novo DNA methyltransferases and propagated by maintenance DNA methyltransferases (DNMT) during DNA replication. In this review, we first summarize the mechanisms maintaining CG methylation in mammals that involve the DNA Methyltransferase 1 (DNMT1) enzyme and its cofactor, UHRF1 (Ubiquitin-like with PHD and RING Finger domain 1). We then discuss the evolutionary conservation and diversification of these two core factors in the plant kingdom and speculate on potential functions of novel homologues typically observed in land plants but not in mammals.

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Husain, Nilofer, Karolina L. Tkaczuk, Rajesh T. Shenoy, Katarzyna H. Kaminska, Sonja Čubrilo, Gordana Maravić-Vlahoviček, Janusz M. Bujnicki, and J. Sivaraman. "Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m 7 G methyltransferases." Nucleic Acids Research 38, no. 12 (February 27, 2010): 4120–32. http://dx.doi.org/10.1093/nar/gkq122.

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Abstract Sgm (Sisomicin-gentamicin methyltransferase) from antibiotic-producing bacterium Micromonospora zionensis is an enzyme that confers resistance to aminoglycosides like gentamicin and sisomicin by specifically methylating G1405 in bacterial 16S rRNA. Sgm belongs to the aminoglycoside resistance methyltransferase (Arm) family of enzymes that have been recently found to spread by horizontal gene transfer among disease-causing bacteria. Structural characterization of Arm enzymes is the key to understand their mechanism of action and to develop inhibitors that would block their activity. Here we report the structure of Sgm in complex with cofactors S-adenosylmethionine (AdoMet) and S-adenosylhomocysteine (AdoHcy) at 2.0 and 2.1 Å resolution, respectively, and results of mutagenesis and rRNA footprinting, and protein-substrate docking. We propose the mechanism of methylation of G1405 by Sgm and compare it with other m 7 G methyltransferases, revealing a surprising diversity of active sites and binding modes for the same basic reaction of RNA modification. This analysis can serve as a stepping stone towards developing drugs that would specifically block the activity of Arm methyltransferases and thereby re-sensitize pathogenic bacteria to aminoglycoside antibiotics.

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L. Aishwarya, K. V., P. V. Geetha, M. Shanthi, and S. Uma. "Co occurrence of two 16S rRNA methyltrasferases along with NDM and OXA 48 like carbapenamases on a single plasmid in Klebsiella pneumoniae." Journal of Laboratory Physicians 11, no. 04 (October 2019): 305–11. http://dx.doi.org/10.4103/jlp.jlp_59_19.

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Abstract BACKGROUND: The carbapenemase-encoding genes, bla NDM- and bla OXA-48 - like , confer resistance to all the known beta-lactams and are encountered along with other beta-lactamase-encoding genes and/or 16S ribosomal RNA (rRNA)-methylating genes. The co-occurrence of bla NDM and bla OXA-48 - like on a single plasmid is a rare occurrence. AIM AND OBJECTIVE: The purpose of the study was to characterize the plasmids in Klebsiella pneumoniae isolates producing 16S rRNA methyltransferase along with bla NDM , bla OXA-48-like , and other resistance encoding genes. MATERIALS AND METHODS: One-hundred and seventeen K. pneumoniae clinical isolates which were resistant to aminoglycosides were collected. Polymerase chain reaction-based screening for 16S rRNA methyltransferase genes armA, rmtB, and rmtC; carbapenamase genes bla NDM , bla OXA-48-like , bla IMP, bla VIM, and bla KPC ; and other resistance genes such as bla TEM, bla SHV, bla CTX-M , and qnr (A, B, and S) determinants acc (6') Ib-cr was performed. Conjugation experiment was carried out for seven isolates that anchored bla NDM and bla OXA-48-like along with any one of the 16S rRNA methyltransferases. The plasmid-based replicon typing for different plasmid-incompatible (Inc) group was performed on the conjugatively transferable plasmids. RESULTS: Among the 16S rRNA methyltransferases, armA was more predominant. bla NDM and bla OXA-48 -like were present in 56 (47.86%) and 22 (18.80%) isolates, respectively. Out of seven isolates which were conjugatively transferable, only four had bla NDM and bla OXA-48 - like on the same plasmid and they belonged to Inc N and A/C replicon. Three isolates co-harbored 16S rRNA methyltransferases armA, rmtB, and rmtC, and out of the them, one isolate harbored two 16S rRNA methyltransferases armA and rmtB, on the single-plasmid replicon A/C. CONCLUSION: This is the first report revealing the coexistence of bla NDM and bla OXA-48 - like co-harboring two 16S rRNA methylases on a single conjugative plasmid replicon belonging to incompatibility group A/C.

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Filonov, V. L., M. A. Khomutov, A. V. Sergeev, A. L. Khandazhinskaya, S. N. Kochetkov, E. S. Gromova, and A. R. Khomutov. "Interaction of DNA Methyltransferase Dnmt3a with Phosphorus Analogs of S-Adenosylmethionine and S-Adenosylhomocysteine." Molecular Biology 57, no. 4 (August 2023): 747–54. http://dx.doi.org/10.1134/s0026893323040064.

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Abstract Enzymatic methyltransferase reactions are of crucial importance for cell metabolism. S-Adenosyl-L-methionine (AdoMet) is a main donor of the methyl group. DNA, RNA, proteins, and low-molecular-weight compounds are substrates of methyltransferases. In mammals, DNA methyltransferase Dnmt3a de novo methylates the C5 position of cytosine residues in CpG sequences in DNA. The methylation pattern is one of the factors that determine the epigenetic regulation of gene expression. Here, interactions with the catalytic domain of Dnmt3a was for the first time studied for phosphonous and phosphonic analogs of AdoMet and S-adenosyl-L-homocysteine (AdoHcy), in which the carboxyl group was substituted for respective phosphorus-containing group. These AdoMet analogs were shown to be substrates of Dnmt3a, and the methylation efficiency was only halved as compared with that of natural AdoMet. Both phosphorus-containing analogs of AdoHcy, which is a natural methyltransferase inhibitor, showed similar inhibitory activities toward Dnmt3a and were approximately four times less active than AdoHcy. The finding that the phosphonous and phosphonic analogs are similar in activity was quite unexpected because the geometry and charge of their phosphorus-containing groups differ substantially. The phosphorus-containing analogs of AdoMet and AdoHcy are discussed as promising tools for investigation of methyltransferases.

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Gutierrez, Belen, Jose A. Escudero, Alvaro San Millan, Laura Hidalgo, Laura Carrilero, Cristina M. Ovejero, Alfonso Santos-Lopez, Daniel Thomas-Lopez, and Bruno Gonzalez-Zorn. "Fitness Cost and Interference of Arm/Rmt Aminoglycoside Resistance with the RsmF Housekeeping Methyltransferases." Antimicrobial Agents and Chemotherapy 56, no. 5 (February 13, 2012): 2335–41. http://dx.doi.org/10.1128/aac.06066-11.

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ABSTRACTArm/Rmt methyltransferases have emerged recently in pathogenic bacteria as enzymes that confer high-level resistance to 4,6-disubstituted aminoglycosides through methylation of the G1405 residue in the 16S rRNA (like ArmA and RmtA to -E). In prokaryotes, nucleotide methylations are the most common type of rRNA modification, and they are introduced posttranscriptionally by a variety of site-specific housekeeping enzymes to optimize ribosomal function. Here we show that while the aminoglycoside resistance methyltransferase RmtC methylates G1405, it impedes methylation of the housekeeping methyltransferase RsmF at position C1407, a nucleotide that, like G1405, forms part of the aminoglycoside binding pocket of the 16S rRNA. To understand the origin and consequences of this phenomenon, we constructed a series of in-frame knockout and knock-in mutants ofEscherichia coli, corresponding to the genotypesrsmF+, ΔrsmF,rsmF+rmtC+, and ΔrsmF rmtC+. When analyzed for the antimicrobial resistance pattern, the ΔrsmFbacteria had a decreased susceptibility to aminoglycosides, including 4,6- and 4,5-deoxystreptamine aminoglycosides, showing that the housekeeping methylation at C1407 is involved in intrinsic aminoglycoside susceptibility inE. coli. Competition experiments between the isogenicE. colistrains showed that, contrary to expectation, acquisition ofrmtCdoes not entail a fitness cost for the bacterium. Finally, matrix-assisted laser desorption ionization (MALDI) mass spectrometry allowed us to determine that RmtC methylates the G1405 residue not only in presence but also in the absence of aminoglycoside antibiotics. Thus, the coupling between housekeeping and acquired methyltransferases subverts the methylation architecture of the 16S rRNA but elicits Arm/Rmt methyltransferases to be selected and retained, posing an important threat to the usefulness of aminoglycosides worldwide.

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Mattheakis, L. C., W. H. Shen, and R. J. Collier. "DPH5, a methyltransferase gene required for diphthamide biosynthesis in Saccharomyces cerevisiae." Molecular and Cellular Biology 12, no. 9 (September 1992): 4026–37. http://dx.doi.org/10.1128/mcb.12.9.4026-4037.1992.

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A mutant of Saccharomyces cerevisiae defective in the S-adenosylmethionine (AdoMet)-dependent methyltransferase step of diphthamide biosynthesis was selected by intracellular expression of the F2 fragment of diphtheria toxin (DT) and shown to belong to complementation group DPH5. The DPH5 gene was cloned, sequenced, and found to encode a 300-residue protein with sequence similarity to bacterial AdoMet:uroporphyrinogen III methyltransferases, enzymes involved in cobalamin (vitamin B12) biosynthesis. Both DPH5 and AdoMet:uroporphyrinogen III methyltransferases lack sequence motifs commonly found in other methyltransferases and may represent a new family of AdoMet:methyltransferases. The DPH5 protein was produced in Escherichia coli and shown to be active in methylation of elongation factor 2 partially purified from the dph5 mutant. A null mutation of the chromosomal DPH5 gene did not affect cell viability, in agreement with other studies indicating that diphthamide is not required for cell survival. The dph5 null mutant survived expression of three enzymically attenuated DT fragments but was killed by expression of fully active DT fragment A. Consistent with these results, elongation factor 2 from the dph5 null mutant was found to have weak ADP-ribosyl acceptor activity, which was detectable only in the presence of high concentrations of fragment A.

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Veit, Katharina, Claudia Ehlers, and Ruth A. Schmitz. "Effects of Nitrogen and Carbon Sources on Transcription of Soluble Methyltransferases in Methanosarcina mazei Strain Gö1." Journal of Bacteriology 187, no. 17 (September 1, 2005): 6147–54. http://dx.doi.org/10.1128/jb.187.17.6147-6154.2005.

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ABSTRACT The methanogenic archaeon Methanosarcina mazei strain Gö1 uses versatile carbon sources and is able to fix molecular nitrogen with methanol as carbon and energy sources. Here, we demonstrate that when growing on trimethylamine (TMA), nitrogen fixation does not occur, indicating that ammonium released during TMA degradation is sufficient to serve as a nitrogen source and represses nif gene induction. We further report on the transcriptional regulation of soluble methyltransferases, which catalyze the initial step of methylamine consumption by methanogenesis, in response to different carbon and nitrogen sources. Unexpectedly, we obtained conclusive evidence that transcription of the mtmB2C2 operon, encoding a monomethylamine (MMA) methyltransferase and its corresponding corrinoid protein, is highly increased under nitrogen limitation when methanol serves as a carbon source. In contrast, transcription of the homologous mtmB1C1 operon is not affected by the nitrogen source but appears to be increased when TMA is the sole carbon and energy source. In general, transcription of operons encoding dimethylamine (DMA) and TMA methyltransferases and methylcobalamine:coenzyme M methyltransferases is not regulated in response to the nitrogen source. However, in all cases transcription of one of the homologous operons or genes is increased by TMA or its degradation products DMA and MMA.

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Mattheakis, L. C., W. H. Shen, and R. J. Collier. "DPH5, a methyltransferase gene required for diphthamide biosynthesis in Saccharomyces cerevisiae." Molecular and Cellular Biology 12, no. 9 (September 1992): 4026–37. http://dx.doi.org/10.1128/mcb.12.9.4026.

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A mutant of Saccharomyces cerevisiae defective in the S-adenosylmethionine (AdoMet)-dependent methyltransferase step of diphthamide biosynthesis was selected by intracellular expression of the F2 fragment of diphtheria toxin (DT) and shown to belong to complementation group DPH5. The DPH5 gene was cloned, sequenced, and found to encode a 300-residue protein with sequence similarity to bacterial AdoMet:uroporphyrinogen III methyltransferases, enzymes involved in cobalamin (vitamin B12) biosynthesis. Both DPH5 and AdoMet:uroporphyrinogen III methyltransferases lack sequence motifs commonly found in other methyltransferases and may represent a new family of AdoMet:methyltransferases. The DPH5 protein was produced in Escherichia coli and shown to be active in methylation of elongation factor 2 partially purified from the dph5 mutant. A null mutation of the chromosomal DPH5 gene did not affect cell viability, in agreement with other studies indicating that diphthamide is not required for cell survival. The dph5 null mutant survived expression of three enzymically attenuated DT fragments but was killed by expression of fully active DT fragment A. Consistent with these results, elongation factor 2 from the dph5 null mutant was found to have weak ADP-ribosyl acceptor activity, which was detectable only in the presence of high concentrations of fragment A.

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Piechulla, Birgit, Nancy Magnus, Marie Chantal Lemfack, and Stephan Von Reuss. "Neue Klasse von Methyltransferasen mit Zyklisierungsaktivität." BIOspektrum 27, no. 1 (February 2021): 31–33. http://dx.doi.org/10.1007/s12268-021-1506-8.

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AbstractMicroorganisms release small volatile metabolites with unique structures, e. g. the polymethylated homosesquiterpene sodorifen from Serratia plymuthica. Two unusual enzymes with novel features are involved in its biosynthesis, a C-methyltransferase with cyclization activity and a terpene synthase that accepts a non-canonical monocyclic C16 substrate. The novel class of methyltransferases represents an alternative route that enlarges terpene diversity.

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Bestor, Timothy H., and Gregory L. Verdine. "DNA methyltransferases." Current Opinion in Cell Biology 6, no. 3 (June 1994): 380–89. http://dx.doi.org/10.1016/0955-0674(94)90030-2.

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Lerouge, I., C. Verreth, J. Michiels, R. W. Carlson, A. Datta, M. Y. Gao, and J. Vanderleyden. "Three Genes Encoding for Putative Methyl- and Acetyltransferases Map Adjacent to the wzm and wzt Genes and Are Essential for O-Antigen Biosynthesis in Rhizobium etli CE3." Molecular Plant-Microbe Interactions® 16, no. 12 (December 2003): 1085–93. http://dx.doi.org/10.1094/mpmi.2003.16.12.1085.

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The elucidation of the structure of the O-antigen of Rhizo-bium etli CE3 predicts that the R. etli CE3 genome must contain genes encoding acetyl- and methyltransferases to confer the corresponding modifications to the O-antigen. We identified three open reading frames (ORFs) upstream of wzm, encoding the membrane component of the O-antigen transporter and located in the lpsα-region of R. etli CE3. The ORFs encode two putative acetyltransferases with similarity to the CysE-LacA-LpxA-NodL family of acetyl-transferases and one putative methyltransferase with sequence motifs common to a wide range of S-adenosyl-L-methionine-dependent methyltransferases. Mutational analysis of the ORFs encoding the putative acetyltrans-ferases and methyltransferase revealed that the acetyl and methyl decorations mediated by these specific enzymes are essential for O-antigen synthesis. Composition analysis and high performance anion exchange chromatography analysis of the lipopolysaccharides (LPSs) of the mutants show that all of these LPSs contain an intact core region and lack the O-antigen polysaccharide. The possible role of these transferases in the decoration of the O-antigen of R. etli is discussed.

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Rowe, Sebastian J., Ryan J. Mecaskey, Mohamed Nasef, Rachel C. Talton, Rory E. Sharkey, Joshua C. Halliday, and Jack A. Dunkle. "Shared requirements for key residues in the antibiotic resistance enzymes ErmC and ErmE suggest a common mode of RNA recognition." Journal of Biological Chemistry 295, no. 51 (October 5, 2020): 17476–85. http://dx.doi.org/10.1074/jbc.ra120.014280.

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Erythromycin-resistance methyltransferases are SAM dependent Rossmann fold methyltransferases that convert A2058 of 23S rRNA to m62A2058. This modification sterically blocks binding of several classes of antibiotics to 23S rRNA, resulting in a multidrug-resistant phenotype in bacteria expressing the enzyme. ErmC is an erythromycin resistance methyltransferase found in many Gram-positive pathogens, whereas ErmE is found in the soil bacterium that biosynthesizes erythromycin. Whether ErmC and ErmE, which possess only 24% sequence identity, use similar structural elements for rRNA substrate recognition and positioning is not known. To investigate this question, we used structural data from related proteins to guide site-saturation mutagenesis of key residues and characterized selected variants by antibiotic susceptibility testing, single turnover kinetics, and RNA affinity–binding assays. We demonstrate that residues in α4, α5, and the α5-α6 linker are essential for methyltransferase function, including an aromatic residue on α4 that likely forms stacking interactions with the substrate adenosine and basic residues in α5 and the α5-α6 linker that likely mediate conformational rearrangements in the protein and cognate rRNA upon interaction. The functional studies led us to a new structural model for the ErmC or ErmE-rRNA complex.

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Zhang, Jianyu, and Judith P. Klinman. "Convergent Mechanistic Features between the Structurally DiverseN- andO-Methyltransferases: GlycineN-Methyltransferase and CatecholO-Methyltransferase." Journal of the American Chemical Society 138, no. 29 (July 18, 2016): 9158–65. http://dx.doi.org/10.1021/jacs.6b03462.

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40

Vale, Filipa F., and Jorge M. B. Vítor. "Genomic Methylation: a Tool for Typing Helicobacter pylori Isolates." Applied and Environmental Microbiology 73, no. 13 (May 4, 2007): 4243–49. http://dx.doi.org/10.1128/aem.00199-07.

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ABSTRACT The genome sequences of three Helicobacter pylori strains revealed an abundant number of putative restriction and modification (R-M) systems within a small genome (1.60 to 1.67 Mb). Each R-M system includes an endonuclease that cleaves a specific DNA sequence and a DNA methyltransferase that methylates either adenosine or cytosine within the same DNA sequence. These are believed to be a defense mechanism, protecting bacteria from foreign DNA. They have been classified as selfish genetic elements; in some instances it has been shown that they are not easily lost from their host cell. Possibly because of this phenomenon, the H. pylori genome is very rich in R-M systems, with considerable variation in potential recognition sequences. For this reason the protective aspect of the methyltransferase gene has been proposed as a tool for typing H. pylori isolates. We studied the expression of H. pylori methyltransferases by digesting the genomic DNAs of 50 strains with 31 restriction endonucleases. We conclude that methyltransferase diversity is sufficiently high to enable the use of the genomic methylation status as a typing tool. The stability of methyltransferase expression was assessed by comparing the methylation status of genomic DNAs from strains that were isolated either from the same patient at different times or from different stomach locations (antrum and corpus). We found a group of five methyltransferases common to all tested strains. These five may be characteristic of the genetic pool analyzed, and their biological role may be important in the host/bacterium interaction.

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Hsieh, Chih-Lin. "In Vivo Activity of Murine De Novo Methyltransferases, Dnmt3a and Dnmt3b." Molecular and Cellular Biology 19, no. 12 (December 1, 1999): 8211–18. http://dx.doi.org/10.1128/mcb.19.12.8211.

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ABSTRACT The putative de novo methyltransferases, Dnmt3a and Dnmt3b, were reported to have weak methyltransferase activity in methylating the 3′ long terminal repeat of Moloney murine leukemia virus in vitro. The activity of these enzymes was evaluated in vivo, using a stable episomal system that employs plasmids as targets for DNA methylation in human cells. De novo methylation of a subset of the CpG sites on the stable episomes is detected in human cells overexpressing the murine Dnmt3a or Dnmt3b1 protein. This de novo methylation activity is abolished when the cysteine in the P-C motif, which is the catalytic site of cytosine methyltransferases, is replaced by a serine. The pattern of methylation on the episome is nonrandom, and different regions of the episome are methylated to different extents. Furthermore, Dnmt3a also methylates the sequence methylated by Dnmt3a on the stable episome in the corresponding chromosomal target. Overexpression of human DNMT1 or murine Dnmt3b does not lead to the same pattern or degree of de novo methylation on the episome as overexpression of murine Dnmt3a. This finding suggests that these three enzymes may have different targets or requirements, despite the fact that weak de novo methyltransferase activity has been demonstrated in vitro for all three enzymes. It is also noteworthy that both Dnmt3a and Dnmt3b proteins coat the metaphase chromosomes while displaying a more uniform pattern in the nucleus. This is the first evidence that Dnmt3a and Dnmt3b have de novo methyltransferase function in vivo and the first indication that the Dnmt3a and Dnmt3b proteins may have preferred target sites.

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Fuks, F. "The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase." Nucleic Acids Research 31, no. 9 (May 1, 2003): 2305–12. http://dx.doi.org/10.1093/nar/gkg332.

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Konttinen, Olivia, Jason Carmody, Sarath Pathuri, Kyle Anderson, Xiaofeng Zhou, and Norbert Reich. "Cell cycle regulated DNA methyltransferase: fluorescent tracking of a DNA strand-separation mechanism and identification of the responsible protein motif." Nucleic Acids Research 48, no. 20 (October 14, 2020): 11589–601. http://dx.doi.org/10.1093/nar/gkaa844.

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Abstract DNA adenine methylation by Caulobacter crescentus Cell Cycle Regulated Methyltransferase (CcrM) is an important epigenetic regulator of gene expression. The recent CcrM-DNA cocrystal structure shows the CcrM dimer disrupts four of the five base pairs of the (5′-GANTC-3′) recognition site. We developed a fluorescence-based assay by which Pyrrolo-dC tracks the strand separation event. Placement of Pyrrolo-dC within the DNA recognition site results in a fluorescence increase when CcrM binds. Non-cognate sequences display little to no fluorescence changes, showing that strand separation is a specificity determinant. Conserved residues in the C-terminal segment interact with the phospho-sugar backbone of the non-target strand. Replacement of these residues with alanine results in decreased methylation activity and changes in strand separation. The DNA recognition mechanism appears to occur with the Type II M.HinfI DNA methyltransferase and an ortholog of CcrM, BabI, but not with DNA methyltransferases that lack the conserved C-terminal segment. The C-terminal segment is found broadly in N4/N6-adenine DNA methyltransferases, some of which are human pathogens, across three Proteobacteria classes, three other phyla and in Thermoplasma acidophilum, an Archaea. This Pyrrolo-dC strand separation assay should be useful for the study of other enzymes which likely rely on a strand separation mechanism.

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Siddaway, Robert, Laura Canty, Sanja Pajovic, Etienne Coyaud, Scott Milos, Stefanie-Grace Sbergio, Evan Lubanszky, et al. "EPCO-16. ONCOHISTONE INTERACTOME PROFILING UNCOVERS MECHANISMS OF CHROMATIN DISRUPTION AND IDENTIFIES POTENTIAL THERAPEUTIC TARGETS IN PEDIATRIC HIGH-GRADE GLIOMA." Neuro-Oncology 23, Supplement_6 (November 2, 2021): vi5. http://dx.doi.org/10.1093/neuonc/noab196.015.

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Abstract Mutations in histone H3 at amino acids 27 (H3K27M) and 34 (H3G34R) occur with high-frequency in pediatric high-grade glioma. H3K27M mutations have been shown to lead to global disruption of H3K27me3 through dominant negative PRC2 inhibition with accompanying gains in H3K36me3, while H3G34R mutations lead to local losses of H3K36me3 through inhibition of SETD2. However, the mechanism of action of these mutants on the broader landscape of chromatin-associated proteins remains unknown. Importantly, proteins with differential associations with oncohistones could be targeted therapeutically. Here we profiled the interactomes of the H3.1K27M, H3.3K27M and H3.3G34R oncohistones using BioID to gain an unbiased measure of their interaction landscapes. Among the differential interactors all 3 mutants lost interaction with H3K9 methyltransferases, while H3G34R also had reduced interaction with DNA methyltransferases accompanied by genome-wide DNA hypomethylation. In contrast, H3K27M mutants had increased association with transcription factors, consistent with the activation of transcription induced by the global loss of H3K27me3. H3K9me3 was reduced in H3K27M-containing nucleosomes, and cis-H3K9 methylation was required for H3K27M to exert its effect on global H3K27me3. Depletion of H3K9 methyltransferases with shRNA or treatment with H3K9 methyltransferase inhibitors was lethal to H3.1K27M, H3.3K27M and H3.3G34R mutant pHGG cell lines, underscoring the importance of H3K9 methylation for oncohistone-mutant gliomas and suggesting it could make an attractive therapeutic target.

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Jayaram, Hariharan, Dominik Hoelper, Siddhant U. Jain, Nico Cantone, Stefan M. Lundgren, Florence Poy, C. David Allis, Richard Cummings, Steven Bellon, and Peter W. Lewis. "S-adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3." Proceedings of the National Academy of Sciences 113, no. 22 (May 16, 2016): 6182–87. http://dx.doi.org/10.1073/pnas.1605523113.

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Lysine to methionine (K-to-M) mutations in genes encoding histone H3 are thought to drive a subset of pediatric brain and bone cancers. These high-frequency K-to-M mutations occur at sites of methylation on histone H3, and tumors containing the mutant histones exhibit a global loss of specific histone methylation marks. Previous studies showed that K-to-M mutant histones, also known as oncohistones, are potent orthosteric inhibitors of specific Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain methyltransferases. However, the biochemical and biophysical details of the interaction between K-to-M mutant histones and the respective SET domain methyltransferases are currently unknown. Here, we use the histone H3K9-directed methyltransferase G9a as a model to explore the mechanism of inhibition by K-to-M oncohistones. X-ray cocrystal structures revealed that the K9M residue of histone H3 occupies the active site cavity of G9a, and kinetic analysis indicates competitive inhibition of G9a by histone H3K9M. Additionally, we find that the cofactor S-adenosyl methionine (SAM) is necessary for stable interaction between G9a and H3K9M histone. Consistent with the formation of a ternary complex, we find that the inhibitory peptide is uncompetitive with regard to SAM. These data and others indicate that K-to-M oncohistones promote global loss of specific lysine methylation through sequestration and inhibition of SAM-bound SET domain methyltransferases.

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Harro, Carly, Jairo Perez-Sanz, Tara Lee Costich, Kyle K. Payne, Carmen Maria Anadon Galindo, Ricardo A. Chaurio Gonzalez, Subir Biswas, et al. "SATB1 as a novel therapeutic target for methyltransferase inhibitors against Cutaneous T Cell Lymphoma." Journal of Immunology 204, no. 1_Supplement (May 1, 2020): 154.8. http://dx.doi.org/10.4049/jimmunol.204.supp.154.8.

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Abstract Cutaneous T cell lymphoma (CTCL) is a clinically unmet need. Using conditional knockout mice, we found that ablation of the genomic organizer Special AT rich sequence binding protein 1 (Satb1) induces a progressively fatal lymphoma characterized by mature, skin homing, Notch activated CD4 and CD8 T cells. Mechanistically, Satb1 restrains Stat5 phosphorylation and the expression of skin homing chemokine receptors in mature T cells. Notably, SUV39H1 and 2 methyltransferase dependent epigenetic repression of SATB1 is universally found in human Sezary Syndrome, but not other peripheral T cell malignancies. Accordingly, H3K27 and H3K9 trimethylation occlude the SATB1 promoter in Sezary cells. Inhibition of SUV39H1 and 2 methyltransferases with novel drugs, unlike EZH2 inhibition, restores SATB1 expression, selectively abrogating the growth of primary Sezary cells more effectively than Romidepsin. Therefore, SATB1 acts as a tumor suppressor in mature T cells upon NOTCH1 deregulation, and inhibition of methyltransferases that silence SATB1 could address an unmet need for patients with mycosis fungoides and Sezary syndrome.

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Mansfield, Kyle D. "RNA Binding by the m6A Methyltransferases METTL16 and METTL3." Biology 13, no. 6 (May 29, 2024): 391. http://dx.doi.org/10.3390/biology13060391.

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Methyltransferases are a wide-ranging, yet well-conserved, class of molecules that have been found to modify a wide variety of substrates. Interest in RNA methylation has surged in recent years with the identification of the major eukaryotic mRNA m6A methyltransferase METTL3. METTL16 has also been identified as an RNA m6A methyltransferase; however, much less is known about its targets and actions. Interestingly, in addition to their catalytic activities, both METTL3 and METTL16 also have “methylation-independent” functions, including translational regulation, which have been discovered. However, evidence suggests that METTL16’s role as an RNA-binding protein may be more significant than is currently recognized. In this review, we will introduce RNA methylation, specifically m6A, and the enzymes responsible for its deposition. We will discuss the varying roles that these enzymes perform and delve deeper into their RNA targets and possible roles as methylation-independent RNA binding proteins. Finally, we will touch upon the many open questions still remaining.

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Kostyushev, D. S., A. P. Zueva, S. A. Brezgin, A. D. Lipatnikov, V. N. Simirskii, D. Glebe, E. V. Volchkova, G. A. Shipulin, and V. P. Chulanov. "Overexpression of DNA-methyltransferases in persistency of cccDNA pool in chronic hepatitis B." Terapevticheskii arkhiv 89, no. 11 (November 15, 2017): 21–26. http://dx.doi.org/10.17116/terarkh2017891121-26.

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Aim. To define the role of DNA-methyltransferases of type 1 and type 3A in hepatitis B viral cycle. Materials and methods. Human hepatoma cells HepG2 with stable expression of 1.1-mer HBV genome were transfected with vectors encoding DNA-methyltransferase 1 (DNMT1), DNA-methyltransferase 3A (DNMT3A) or were co-transfected with these vectors. Total HBV DNA copy number, relative expression of pregenomic RNA (pgRNA), S-protein-encoding RNA (S-RNA) and cccDNA were analyzed by quantitative and semi-quantitative real-time PCR-analysis with TaqMan probes for assessment of DNMTs-mediated effects on HBV. Results. DNMT1 and DNMT3A suppress HBV transcription and replication, though to different magnitude. cccDNA pool is enlarged statistically significantly ≈2-fold (P

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Fokina, A. S., A. S. Karyagina, I. S. Rusinov, D. M. Moshensky, S. A. Spirin, and A. V. Alexeevski. "Evolution of restriction-modification systems with one restriction endonuclease and two DNA methyltransferases." Биохимия 88, no. 2 (February 15, 2023): 285–94. http://dx.doi.org/10.31857/s0320972523020082.

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Some restriction-modification systems contain two DNA methyltransferases. In the present work, we have classified such systems according to the families of catalytic domains present in restriction endonucleases and both DNA methyltransferases. The evolution of restriction-modification systems of one class was studied in detail. Systems in this class include an endonuclease with a NOV_C family domain and two DNA methyltransferases, both with DNA_methylase family domains. The phylogenetic tree of DNA methyltransferases from systems of this class consists of two clades of the same size. Two DNA methyltransferases of each restriction-modification system of the class belong to different clades. This indicates independent evolution of the two methyltransferases. We detected multiple cross-species horizontal transfers of systems as a whole, as well as cases of gene transfer between systems.

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Nosrati, Meisam, Debayan Dey, Atousa Mehrani, Sarah E. Strassler, Natalia Zelinskaya, Eric D. Hoffer, Scott M. Stagg, Christine M. Dunham, and Graeme L. Conn. "Functionally critical residues in the aminoglycoside resistance-associated methyltransferase RmtC play distinct roles in 30S substrate recognition." Journal of Biological Chemistry 294, no. 46 (October 8, 2019): 17642–53. http://dx.doi.org/10.1074/jbc.ra119.011181.

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Methylation of the small ribosome subunit rRNA in the ribosomal decoding center results in exceptionally high-level aminoglycoside resistance in bacteria. Enzymes that methylate 16S rRNA on N7 of nucleotide G1405 (m7G1405) have been identified in both aminoglycoside-producing and clinically drug-resistant pathogenic bacteria. Using a fluorescence polarization 30S-binding assay and a new crystal structure of the methyltransferase RmtC at 3.14 Å resolution, here we report a structure-guided functional study of 30S substrate recognition by the aminoglycoside resistance-associated 16S rRNA (m7G1405) methyltransferases. We found that the binding site for these enzymes in the 30S subunit directly overlaps with that of a second family of aminoglycoside resistance-associated 16S rRNA (m1A1408) methyltransferases, suggesting that both groups of enzymes may exploit the same conserved rRNA tertiary surface for docking to the 30S. Within RmtC, we defined an N-terminal domain surface, comprising basic residues from both the N1 and N2 subdomains, that directly contributes to 30S-binding affinity. In contrast, additional residues lining a contiguous adjacent surface on the C-terminal domain were critical for 16S rRNA modification but did not directly contribute to the binding affinity. The results from our experiments define the critical features of m7G1405 methyltransferase–substrate recognition and distinguish at least two distinct, functionally critical contributions of the tested enzyme residues: 30S-binding affinity and stabilizing a binding-induced 16S rRNA conformation necessary for G1405 modification. Our study sets the scene for future high-resolution structural studies of the 30S-methyltransferase complex and for potential exploitation of unique aspects of substrate recognition in future therapeutic strategies.

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Journal articles on the topic 'Methyltransferases'

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