1
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Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator. mBio 2021; 12:mBio.03549-20. [PMID: 33688012 PMCID: PMC8092309 DOI: 10.1128/mbio.03549-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Entamoeba histolytica is a unicellular parasite that causes amebiasis. The parasite resides in the colon and feeds on the colonic microbiota. Queuosine is a naturally occurring modified ribonucleoside found in the first position of the anticodon of the transfer RNAs for Asp, Asn, His, and Tyr. Eukaryotes lack pathways to synthesize queuine, the nucleobase precursor to queuosine, and must obtain it from diet or gut microbiota. Here, we describe the effects of queuine on the physiology of the eukaryotic parasite Entamoeba histolytica, the causative agent of amebic dysentery. Queuine is efficiently incorporated into E. histolytica tRNAs by a tRNA-guanine transglycosylase (EhTGT) and this incorporation stimulates the methylation of C38 in
tRNAGUCAsp. Queuine protects the parasite against oxidative stress (OS) and antagonizes the negative effect that oxidation has on translation by inducing the expression of genes involved in the OS response, such as heat shock protein 70 (Hsp70), antioxidant enzymes, and enzymes involved in DNA repair. On the other hand, queuine impairs E. histolytica virulence by downregulating the expression of genes previously associated with virulence, including cysteine proteases, cytoskeletal proteins, and small GTPases. Silencing of EhTGT prevents incorporation of queuine into tRNAs and strongly impairs methylation of C38 in
tRNAGUCAsp, parasite growth, resistance to OS, and cytopathic activity. Overall, our data reveal that queuine plays a dual role in promoting OS resistance and reducing parasite virulence.
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2
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Müller M, Samel-Pommerencke A, Legrand C, Tuorto F, Lyko F, Ehrenhofer-Murray AE. Division of labour: tRNA methylation by the NSun2 tRNA methyltransferases Trm4a and Trm4b in fission yeast. RNA Biol 2019; 16:249-256. [PMID: 30646830 PMCID: PMC6380293 DOI: 10.1080/15476286.2019.1568819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Enzymes of the cytosine-5 RNA methyltransferase Trm4/NSun2 family methylate tRNAs at C48 and C49 in multiple tRNAs, as well as C34 and C40 in selected tRNAs. In contrast to most other organisms, fission yeast Schizosaccharomyces pombe carries two Trm4/NSun2 homologs, Trm4a (SPAC17D4.04) and Trm4b (SPAC23C4.17). Here, we have employed tRNA methylome analysis to determine the dependence of cytosine-5 methylation (m5C) tRNA methylation in vivo on the two enzymes. Remarkably, Trm4a is responsible for all C48 methylation, which lies in the tRNA variable loop, as well as for C34 in tRNALeuCAA and tRNAProCGG, which are at the anticodon wobble position. Conversely, Trm4b methylates C49 and C50, which both lie in the TΨC-stem. Thus, S. pombe show an unusual separation of activities of the NSun2/Trm4 enzymes that are united in a single enzyme in other eukaryotes like humans, mice and Saccharomyces cerevisiae. Furthermore, in vitro activity assays showed that Trm4a displays intron-dependent methylation of C34, whereas Trm4b activity is independent of the intron. The absence of Trm4a, but not Trm4b, causes a mild resistance of S. pombe to calcium chloride.
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Affiliation(s)
- Martin Müller
- a Institut für Biologie, Molekulare Zellbiologie , Humboldt-Universität zu Berlin , Berlin , Germany
| | - Anke Samel-Pommerencke
- a Institut für Biologie, Molekulare Zellbiologie , Humboldt-Universität zu Berlin , Berlin , Germany
| | - Carine Legrand
- b Division of Epigenetics, DKFZ-ZMBH Alliance , German Cancer Research Center , Heidelberg , Germany
| | - Francesca Tuorto
- b Division of Epigenetics, DKFZ-ZMBH Alliance , German Cancer Research Center , Heidelberg , Germany
| | - Frank Lyko
- b Division of Epigenetics, DKFZ-ZMBH Alliance , German Cancer Research Center , Heidelberg , Germany
| | - Ann E Ehrenhofer-Murray
- a Institut für Biologie, Molekulare Zellbiologie , Humboldt-Universität zu Berlin , Berlin , Germany
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3
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Su T, Yang X, Deng JH, Huang QJ, Huang SC, Zhang YM, Zheng HM, Wang Y, Lu LL, Liu ZQ. Evodiamine, a Novel NOTCH3 Methylation Stimulator, Significantly Suppresses Lung Carcinogenesis in Vitro and in Vivo. Front Pharmacol 2018; 9:434. [PMID: 29765324 PMCID: PMC5938359 DOI: 10.3389/fphar.2018.00434] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/12/2018] [Indexed: 12/20/2022] Open
Abstract
Lung cancer is a leading cause of cancer-related deaths worldwide. NOTCH3 signaling is mainly expressed in non-small cell lung carcinoma (NSCLC), and has been proposed as a therapeutic target of NSCLC. While, few agents for preventing or treating NSCLC via targeting NOTCH3 signaling are used in modern clinical practice. Evodiamine (EVO), an alkaloid derived from Euodiae Fructus, possesses low toxicity and has long been shown to exert anti-lung cancer activity. However, the underlying anti-lung cancer mechanisms of EVO are not yet fully understood. In this study, we explored the involvement of NOTCH3 signaling in the anti-lung cancer effects of EVO. Urethane-induced lung cancer mouse model and two NSCLC cell models, A549 and H1299, were used to evaluate the in vivo and in vitro anti-lung cancer action of EVO. A DNA methyltransferase inhibitor was employed to investigate the role of NOTCH3 signaling in the anti-lung cancer effects of EVO. Results showed that EVO potently reduced tumor size and tumor numbers in mice, and inhibited NOTCH3 in the tumors. EVO also dramatically reduced cell viability, induced G2/M cell cycle arrest, inhibited cell migration and reduced stemness in cultured NSCLC cells. Mechanistic studies showed that EVO potently inhibited NOTCH3 signaling by activation of DNMTs-induced NOTCH3 methylation. Importantly, inhibition of NOTCH3 methylation in NSCLC cells diminished EVO's anti-NSCLC effects. Collectively, EVO, a novel NOTCH3 methylation stimulator, exerted potent anti-lung cancer effects partially by inhibiting NOTCH3 signaling. These findings provide new insight into the EVO's anti-NSCLC action, and suggest a potential role of EVO in lung cancer prevention and treatment.
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Affiliation(s)
- Tao Su
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xia Yang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jian-Hua Deng
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiu-Ju Huang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Su-Chao Huang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yan-Min Zhang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hong-Ming Zheng
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lin-Lin Lu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhong-Qiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
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4
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Vieira GC, D'Ávila MF, Zanini R, Deprá M, da Silva Valente VL. Evolution of DNMT2 in drosophilids: Evidence for positive and purifying selection and insights into new protein (pathways) interactions. Genet Mol Biol 2018; 41:215-234. [PMID: 29668012 PMCID: PMC5913717 DOI: 10.1590/1678-4685-gmb-2017-0056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/18/2017] [Indexed: 12/03/2022] Open
Abstract
The DNA methyltransferase 2 (DNMT2) protein is the most conserved member of the
DNA methyltransferase family. Nevertheless, its substrate specificity is still
controversial and elusive. The genomic role and determinants of DNA methylation
are poorly understood in invertebrates, and several mechanisms and associations
are suggested. In Drosophila, the only known DNMT gene is
Dnmt2. Here we present our findings from a wide search for
Dnmt2 homologs in 68 species of Drosophilidae. We
investigated its molecular evolution, and in our phylogenetic analyses the main
clades of Drosophilidae species were recovered. We tested whether the
Dnmt2 has evolved neutrally or under positive selection
along the subgenera Drosophila and Sophophora
and investigated positive selection in relation to several physicochemical
properties. Despite of a major selective constraint on Dnmt2,
we detected six sites under positive selection. Regarding the DNMT2 protein, 12
sites under positive-destabilizing selection were found, which suggests a
selection that favors structural and functional shifts in the protein. The
search for new potential protein partners with DNMT2 revealed 15 proteins with
high evolutionary rate covariation (ERC), indicating a plurality of DNMT2
functions in different pathways. These events might represent signs of molecular
adaptation, with molecular peculiarities arising from the diversity of
evolutionary histories experienced by drosophilids.
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Affiliation(s)
- Gilberto Cavalheiro Vieira
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Marícia Fantinel D'Ávila
- Departamento de Zoologia e Ciências Biológicas, Universidade Federal de Santa Maria (UFSM), Palmeira das Missões, RS, Brazil
| | - Rebeca Zanini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Maríndia Deprá
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Vera Lúcia da Silva Valente
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Departamento de Zoologia e Ciências Biológicas, Universidade Federal de Santa Maria (UFSM), Palmeira das Missões, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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5
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Wei H, Jiang S, Chen L, He C, Wu S, Peng H. Characterization of Cytosine Methylation and the DNA Methyltransferases of Toxoplasma gondii. Int J Biol Sci 2017; 13:458-470. [PMID: 28529454 PMCID: PMC5436566 DOI: 10.7150/ijbs.18644] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/22/2017] [Indexed: 01/02/2023] Open
Abstract
DNA methylation is a key epigenetic modification which confers phenotypic plasticity and adaptation. Cyst-forming strains of Toxoplasma gondii undergo tachyzoite to bradyzoite conversion after initial acute infection of a host, and the reverse conversion may occur in immune-suppressed hosts. The formation of m5C is catalyzed by DNA methyltransferase (DNMT). We identified two functional DNA methyltransferases, TgDNMTa and TgDNMTb, in T. gondii that may mediate DNA methylation. The recombinant proteins showed intrinsic methyltransferase activity; both have higher transcription levels in bradyzoites than that in tachyzoites. We performed genome-wide analysis of DNA methylation in tachyzoites and bradyzoites. The results showed more methylation sites in bradyzoites than that in tachyzoites. The most significantly enriched GO-terms of genes with DNA methylation were associated with basal cellular processes such as energy metabolism and parasite resistance to host immunity. Tachyzoite proliferation in parasitophorous vacuoles (PV) can be inhibited by the DNA methyltransferase inhibitor 5-azacytidine, a chemical analogue of the nucleotide cytosine that can inactivate DNA methyltransferases. These findings provide the first confirmation of DNA methylation in T. gondii.
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Affiliation(s)
- Haixia Wei
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Shichen Jiang
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Longfei Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Cheng He
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Shuizhen Wu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Hongjuan Peng
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
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6
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Kaiser S, Jurkowski TP, Kellner S, Schneider D, Jeltsch A, Helm M. The RNA methyltransferase Dnmt2 methylates DNA in the structural context of a tRNA. RNA Biol 2016; 14:1241-1251. [PMID: 27819523 PMCID: PMC5699543 DOI: 10.1080/15476286.2016.1236170] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The amino acid sequence of Dnmt2 is very similar to the catalytic domains of bacterial and eukaryotic DNA-(cytosine 5)-methyltransferases, but it efficiently catalyzes tRNA methylation, while its DNA methyltransferase activity is the subject of controversial reports with rates varying between zero and very weak. By using composite nucleic acid molecules as substrates, we surprisingly found that DNA fragments, when presented as covalent DNA-RNA hybrids in the structural context of a tRNA, can be more efficiently methylated than the corresponding natural tRNA substrate. Furthermore, by stepwise development of tRNAAsp, we showed that this natural Dnmt2 substrate could be engineered to employ RNAs that act like guide RNAs in vitro. The 5’-half of tRNAAsp was able to efficiently guide methylation toward a single stranded tRNA fragment as would result from tRNA cleavage by tRNA specific nucleases. In a more artificial setting, a composite system of guide RNAs could ultimately be engineered to enable the enzyme to perform cytidine methylation on single stranded DNA in vitro.
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Affiliation(s)
- Steffen Kaiser
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
| | - Tomasz P Jurkowski
- b Institute of Biochemistry, Faculty of Chemistry, University Stuttgart , Stuttgart , Germany
| | - Stefanie Kellner
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
| | - Dirk Schneider
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
| | - Albert Jeltsch
- b Institute of Biochemistry, Faculty of Chemistry, University Stuttgart , Stuttgart , Germany
| | - Mark Helm
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
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7
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Müller M, Hartmann M, Schuster I, Bender S, Thüring KL, Helm M, Katze JR, Nellen W, Lyko F, Ehrenhofer-Murray AE. Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine. Nucleic Acids Res 2015; 43:10952-62. [PMID: 26424849 PMCID: PMC4678861 DOI: 10.1093/nar/gkv980] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/17/2015] [Indexed: 01/13/2023] Open
Abstract
Dnmt2 enzymes are cytosine-5 methyltransferases that methylate C38 of several tRNAs. We report here that the activities of two Dnmt2 homologs, Pmt1 from Schizosaccharomyces pombe and DnmA from Dictyostelium discoideum, are strongly stimulated by prior queuosine (Q) modification of the substrate tRNA. In vivo tRNA methylation levels were stimulated by growth of cells in queuine-containing medium; in vitro Pmt1 activity was enhanced on Q-containing RNA; and queuine-stimulated in vivo methylation was abrogated by the absence of the enzyme that inserts queuine into tRNA, eukaryotic tRNA-guanine transglycosylase. Global analysis of tRNA methylation in S. pombe showed a striking selectivity of Pmt1 for tRNA(Asp) methylation, which distinguishes Pmt1 from other Dnmt2 homologs. The present analysis also revealed a novel Pmt1- and Q-independent tRNA methylation site in S. pombe, C34 of tRNA(Pro). Notably, queuine is a micronutrient that is scavenged by higher eukaryotes from the diet and gut microflora. This work therefore reveals an unanticipated route by which the environment can modulate tRNA modification in an organism.
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Affiliation(s)
- Martin Müller
- Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Mark Hartmann
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | | | - Sebastian Bender
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Kathrin L Thüring
- Institut für Pharmakologie und Biochemie, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Mark Helm
- Institut für Pharmakologie und Biochemie, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Jon R Katze
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Wolfgang Nellen
- Abteilung für Genetik, Universität Kassel, 34132 Kassel, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
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8
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Haag S, Warda AS, Kretschmer J, Günnigmann MA, Höbartner C, Bohnsack MT. NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs. RNA (NEW YORK, N.Y.) 2015; 21:1532-43. [PMID: 26160102 PMCID: PMC4536315 DOI: 10.1261/rna.051524.115] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 06/01/2015] [Indexed: 05/04/2023]
Abstract
Many cellular RNAs require modification of specific residues for their biogenesis, structure, and function. 5-methylcytosine (m(5)C) is a common chemical modification in DNA and RNA but in contrast to the DNA modifying enzymes, only little is known about the methyltransferases that establish m(5)C modifications in RNA. The putative RNA methyltransferase NSUN6 belongs to the family of Nol1/Nop2/SUN domain (NSUN) proteins, but so far its cellular function has remained unknown. To reveal the target spectrum of human NSUN6, we applied UV crosslinking and analysis of cDNA (CRAC) as well as chemical crosslinking with 5-azacytidine. We found that human NSUN6 is associated with tRNAs and acts as a tRNA methyltransferase. Furthermore, we uncovered tRNA(Cys) and tRNA(Thr) as RNA substrates of NSUN6 and identified the cytosine C72 at the 3' end of the tRNA acceptor stem as the target nucleoside. Interestingly, target recognition in vitro depends on the presence of the 3'-CCA tail. Together with the finding that NSUN6 localizes to the cytoplasm and largely colocalizes with marker proteins for the Golgi apparatus and pericentriolar matrix, our data suggest that NSUN6 modifies tRNAs in a late step in their biogenesis.
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Affiliation(s)
- Sara Haag
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Ahmed S Warda
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Jens Kretschmer
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Manuel A Günnigmann
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, 37077 Göttingen, Germany
| | - Markus T Bohnsack
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, 37073 Göttingen, Germany
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9
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Shanmugam R, Aklujkar M, Schäfer M, Reinhardt R, Nickel O, Reuter G, Lovley DR, Ehrenhofer-Murray A, Nellen W, Ankri S, Helm M, Jurkowski TP, Jeltsch A. The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu. Nucleic Acids Res 2014; 42:6487-96. [PMID: 24711368 PMCID: PMC4041430 DOI: 10.1093/nar/gku256] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Dnmt2 enzymes are conserved in eukaryotes, where they methylate C38 of tRNA-Asp with high activity. Here, the activity of one of the very few prokaryotic Dnmt2 homologs from Geobacter species (GsDnmt2) was investigated. GsDnmt2 was observed to methylate tRNA-Asp from flies and mice. Unexpectedly, it had only a weak activity toward its matching Geobacter tRNA-Asp, but methylated Geobacter tRNA-Glu with good activity. In agreement with this result, we show that tRNA-Glu is methylated in Geobacter while the methylation is absent in tRNA-Asp. The activities of Dnmt2 enzymes from Homo sapiens, Drosophila melanogaster, Schizosaccharomyces pombe and Dictyostelium discoideum for methylation of the Geobacter tRNA-Asp and tRNA-Glu were determined showing that all these Dnmt2s preferentially methylate tRNA-Asp. Hence, the GsDnmt2 enzyme has a swapped transfer ribonucleic acid (tRNA) specificity. By comparing the different tRNAs, a characteristic sequence pattern was identified in the variable loop of all preferred tRNA substrates. An exchange of two nucleotides in the variable loop of murine tRNA-Asp converted it to the corresponding variable loop of tRNA-Glu and led to a strong reduction of GsDnmt2 activity. Interestingly, the same loss of activity was observed with human DNMT2, indicating that the variable loop functions as a specificity determinant in tRNA recognition of Dnmt2 enzymes.
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Affiliation(s)
| | - Muktak Aklujkar
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA
| | - Matthias Schäfer
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | | | - Olaf Nickel
- Institute of Biology, Developmental Genetics, Martin Luther University Halle, 06120 Halle, Germany
| | - Gunter Reuter
- Institute of Biology, Developmental Genetics, Martin Luther University Halle, 06120 Halle, Germany
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA
| | | | - Wolfgang Nellen
- Department of Genetics, University of Kassel, 34132 Kassel, Germany
| | - Serge Ankri
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany
| | - Tomasz P Jurkowski
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
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10
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Militello KT, Chen LM, Ackerman SE, Mandarano AH, Valentine EL. A map of 5-methylcytosine residues in Trypanosoma brucei tRNA revealed by sodium bisulfite sequencing. Mol Biochem Parasitol 2014; 193:122-6. [PMID: 24389163 DOI: 10.1016/j.molbiopara.2013.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 01/10/2023]
Abstract
In protozoan parasites, there is little information on the presence of covalent RNA modifications which comprise the epitranscriptome. Therefore, we determined if T. brucei tRNA(Asp(GUC)), tRNA(Gly(GCC)), tRNA(Val(AAC)), and tRNA(Tyr(GUA)) contain 5-methylcytosines via RNA bisulfite sequencing. Most tRNAs examined have at least one 5-methylcytosine at the variable region-TψC junction. Only tRNA(Gly(GCC)) displayed methylation of C40 in the anticodon stem, and there was partial methylation at this site. There is no evidence for methylation of C38 in the anticodon loop in the tRNAs analyzed. Analysis of tRNA(Tyr(GUA)) demonstrates that both unspliced and spliced molecules contain C48 methylation, indicating tRNA cytosine methylation can precede tRNA splicing. Overall, our data indicate that T. brucei tRNAs contain 5-methylcytosine residues in some, but potentially not all standard eukaryotic positions. The levels of cytosine methylation of different T. brucei tRNAs vary, suggesting the presence of a mechanism for methylation control.
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Affiliation(s)
- Kevin T Militello
- State University of New York at Geneseo, Department of Biology, 1 College Circle, Geneseo, NY 14454, United States.
| | - Leanne M Chen
- State University of New York at Geneseo, Department of Biology, 1 College Circle, Geneseo, NY 14454, United States
| | - Sarah E Ackerman
- State University of New York at Geneseo, Department of Biology, 1 College Circle, Geneseo, NY 14454, United States
| | - Alexandra H Mandarano
- State University of New York at Geneseo, Department of Biology, 1 College Circle, Geneseo, NY 14454, United States
| | - Erika L Valentine
- State University of New York at Geneseo, Department of Biology, 1 College Circle, Geneseo, NY 14454, United States
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11
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Schulz EC, Roth HM, Ankri S, Ficner R. Structure analysis of Entamoeba histolytica DNMT2 (EhMeth). PLoS One 2012; 7:e38728. [PMID: 22737219 PMCID: PMC3380923 DOI: 10.1371/journal.pone.0038728] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/14/2012] [Indexed: 11/25/2022] Open
Abstract
In eukaryotes, DNA methylation is an important epigenetic modification that is generally involved in gene regulation. Methyltransferases (MTases) of the DNMT2 family have been shown to have a dual substrate specificity acting on DNA as well as on three specific tRNAs (tRNAAsp, tRNAVal, tRNAGly). Entamoeba histolytica is a major human pathogen, and expresses a single DNA MTase (EhMeth) that belongs to the DNMT2 family and shows high homology to the human enzyme as well as to the bacterial DNA MTase M.HhaI. The molecular basis for the recognition of the substrate tRNAs and discrimination of non-cognate tRNAs is unknown. Here we present the crystal structure of the cytosine-5-methyltransferase EhMeth at a resolution of 2.15 Å, in complex with its reaction product S-adenosyl-L-homocysteine, revealing all parts of a DNMT2 MTase, including the active site loop. Mobility shift assays show that in vitro the full length tRNA is required for stable complex formation with EhMeth.
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Affiliation(s)
- Eike C. Schulz
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Heide M. Roth
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Serge Ankri
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Ralf Ficner
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
- * E-mail:
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Rajendran G, Shanmuganandam K, Bendre A, Muzumdar D, Mujumdar D, Goel A, Shiras A. Epigenetic regulation of DNA methyltransferases: DNMT1 and DNMT3B in gliomas. J Neurooncol 2011; 104:483-94. [PMID: 21229291 DOI: 10.1007/s11060-010-0520-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 12/21/2010] [Indexed: 02/08/2023]
Abstract
The role of epigenetics and significance of aberrant gene regulation in etiology of cancer is a well-established phenomenon. The hallmark of cancer epigenetics is aberrant DNA methylation consisting of global hypomethylation and regional hypermethylation of tumor suppressor genes (TSGs) by DNA methyltransferases (DNMTs). In mammals, DNA methylation is catalyzed by DNMTs encoded by DNMT1, DNMT3A, and DNMT3B. Interestingly, little is known about variation in the methylation status of epigenetic regulators themselves in gliomas. Here, we report significant overexpression of DNMT1 and DNMT3B. A study of the methylation status and histone modifications at the promoter region of DNA methyltransferase I (DNMT1) gene revealed an unmethylated DNA promoter, similar to that detected in normal brain tissues. However, a differential histone code with distinct euchromatin marks--AcH3, AcH4, and H3k4me2--was specifically detected in tumors, unlike in normal brain tissues, which were found predominantly enriched with heterochromatin marks such as H3K9me2 and H3K27me3. In contrast, a differential methylation pattern of DNMT3B gene promoter occurred in glioma tumors, wherein it was found hypomethylated. Transcriptional silencing by CpG island methylation is a prevalent mechanism for inactivation of TSGs. Inhibiting DNMTs by 5-azacytidine (DNMT inhibitor) treatment led to significant inhibition of expression of DNMT1 and DNMT3B and enhanced expression of TSGs such as PTEN and p21 analyzed in this study. Our studies have identified effects of increased presence of DNMTs on inhibition of tumor suppressors that are epigenetically silenced in gliomas, thereby leading to aberrant regulation of cell cycle progression and failure to maintain genomic stability.
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