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Zhong X, Peng Y, Yao C, Qing Y, Yang Q, Guo X, Xie W, Zhao M, Cai X, Zhou JG. Association of DNA methyltransferase polymorphisms with susceptibility to primary gouty arthritis. Biomed Rep 2016; 5:467-472. [PMID: 27699015 DOI: 10.3892/br.2016.746] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/27/2016] [Indexed: 01/03/2023] Open
Abstract
Gouty arthritis is the most common type of inflammatory and immune disease, and the prevalence and incidence of gout increases annually. Genetic variations in the DNA methyltransferases (DNMTs) gene have not, to the best of our knowledge, been reported to influence gene expression and to participate in the pathogenesis of gout. The aim of the present study was to investigate whether the DNMT1, DNMT3A and DNMT3B polymorphisms contribute to gout susceptibility. These polymorphisms were screened for in 336 gout patients and 306 healthy control subjects (from a South China population) for association with gout. The distribution frequencies of DNMT1 rs2228611 AA genotype (P=0.007) and A allele (P=0.002; odds ratio=1.508, 95% confidence interval=1.158-1.964) were found to be significantly increased in the gout patients when compared with those in the healthy control subjects. The rs1550117 in DNMT3A and rs2424913 in DNMT3B exhibited no significant associations with gout susceptibility between the patients and control subjects. These results demonstrated that the DNMT1 rs2228611 polymorphism may be involved in the pathogenesis of gout, while DNMT3A rs1550117 and DNMT3B rs2424913 did not show any obvious significance in the current study; thus, may not be used as risk factors to predict the susceptibility to gout. However, further studies are required to investigate the functions and regulatory mechanism of the polymorphisms of DNMTs in gout.
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Affiliation(s)
- Xiaowu Zhong
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China; Medicine Research Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China; Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan 637007, P.R. China
| | - Yuanhong Peng
- Department of Rheumatology and Immunology of the Affiliated Hospital, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Chengjiao Yao
- Medicine Research Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Yufeng Qing
- Department of Rheumatology and Immunology of the Affiliated Hospital, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Qibin Yang
- Department of Rheumatology and Immunology of the Affiliated Hospital, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China; Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan 637007, P.R. China
| | - Wenguang Xie
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China; Medicine Research Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Mingcai Zhao
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China; Medicine Research Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China; Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan 637007, P.R. China
| | - Xiaoming Cai
- Department of Biology, North Sichuan Medical College, Nanchong, Sichuan 637007, P.R. China
| | - Jing-Guo Zhou
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan 637007, P.R. China; Department of Rheumatology and Immunology of the Affiliated Hospital, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
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Weigele P, Raleigh EA. Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses. Chem Rev 2016; 116:12655-12687. [PMID: 27319741 DOI: 10.1021/acs.chemrev.6b00114] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Naturally occurring modification of the canonical A, G, C, and T bases can be found in the DNA of cellular organisms and viruses from all domains of life. Bacterial viruses (bacteriophages) are a particularly rich but still underexploited source of such modified variant nucleotides. The modifications conserve the coding and base-pairing functions of DNA, but add regulatory and protective functions. In prokaryotes, modified bases appear primarily to be part of an arms race between bacteriophages (and other genomic parasites) and their hosts, although, as in eukaryotes, some modifications have been adapted to convey epigenetic information. The first half of this review catalogs the identification and diversity of DNA modifications found in bacteria and bacteriophages. What is known about the biogenesis, context, and function of these modifications are also described. The second part of the review places these DNA modifications in the context of the arms race between bacteria and bacteriophages. It focuses particularly on the defense and counter-defense strategies that turn on direct recognition of the presence of a modified base. Where modification has been shown to affect other DNA transactions, such as expression and chromosome segregation, that is summarized, with reference to recent reviews.
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Affiliation(s)
- Peter Weigele
- Chemical Biology, New England Biolabs , Ipswich, Massachusetts 01938, United States
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Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res 2016; 44:7511-26. [PMID: 27317694 PMCID: PMC5027499 DOI: 10.1093/nar/gkw551] [Citation(s) in RCA: 452] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/03/2016] [Indexed: 12/19/2022] Open
Abstract
The 5′ m7G cap is an evolutionarily conserved modification of eukaryotic mRNA. Decades of research have established that the m7G cap serves as a unique molecular module that recruits cellular proteins and mediates cap-related biological functions such as pre-mRNA processing, nuclear export and cap-dependent protein synthesis. Only recently has the role of the cap 2′O methylation as an identifier of self RNA in the innate immune system against foreign RNA has become clear. The discovery of the cytoplasmic capping machinery suggests a novel level of control network. These new findings underscore the importance of a proper cap structure in the synthesis of functional messenger RNA. In this review, we will summarize the current knowledge of the biological roles of mRNA caps in eukaryotic cells. We will also discuss different means that viruses and their host cells use to cap their RNA and the application of these capping machineries to synthesize functional mRNA. Novel applications of RNA capping enzymes in the discovery of new RNA species and sequencing the microbiome transcriptome will also be discussed. We will end with a summary of novel findings in RNA capping and the questions these findings pose.
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Affiliation(s)
- Anand Ramanathan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - G Brett Robb
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Siu-Hong Chan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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Cloning, expression and characterization of histidine-tagged biotin synthase of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2016; 98:42-9. [PMID: 27156617 DOI: 10.1016/j.tube.2016.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/21/2016] [Accepted: 02/29/2016] [Indexed: 11/20/2022]
Abstract
The emergence of Mycobacterium tuberculosis strains that are resistant to the current anti-tuberculosis (TB) drugs necessitates a need to develop a new class of drugs whose targets are different from the current ones. M. tuberculosis biotin synthase (MtbBS) is one such target that is essential for the survival of the bacteria. In this study, MtbBS was cloned, overexpressed and purified to homogeneity for biochemical characterization. It is likely to be a dimer in its native form. Its pH and temperature optima are 8.0 and 37 °C, respectively. Km for DTB and SAM was 2.81 ± 0.35 and 9.95 ± 0.98 μM, respectively. The enzyme had a maximum velocity of 0.575 ± 0.015 μM min(-1), and a turn-over of 0.0935 min(-1). 5'-deoxyadenosine (dAH), S-(5'-Adenosyl)-l-cysteine (AdoCy) and S-(5'-Adenosyl)-l-homocysteine (AdoHcy) were competitive inhibitors of MtbBS with the following inactivation parameters: Ki = 24.2 μM, IC50 = 267.4 μM; Ki = 0.84 μM, IC50 = 9.28 μM; and Ki = 0.592 μM, IC50 = 6.54 μM for dAH, AdoCy and AdoHcy respectively. dAH could inhibit the growth of M. tuberculosis H37Ra with an MIC of 392.6 μg/ml. This information should be useful for the discovery of inhibitors of MtbBS.
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Hong S, Cheng X. DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:321-341. [PMID: 27826845 DOI: 10.1007/978-3-319-43624-1_14] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The modification of DNA bases is a classic hallmark of epigenetics. Four forms of modified cytosine-5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine-have been discovered in eukaryotic DNA. In addition to cytosine carbon-5 modifications, cytosine and adenine methylated in the exocyclic amine-N4-methylcytosine and N6-methyladenine-are other modified DNA bases discovered even earlier. Each modified base can be considered a distinct epigenetic signal with broader biological implications beyond simple chemical changes. Since 1994, crystal structures of proteins and enzymes involved in writing, reading, and erasing modified bases have become available. Here, we present a structural synopsis of writers, readers, and erasers of the modified bases from prokaryotes and eukaryotes. Despite significant differences in structures and functions, they are remarkably similar regarding their engagement in flipping a target base/nucleotide within DNA for specific recognitions and/or reactions. We thus highlight base flipping as a common structural framework broadly applied by distinct classes of proteins and enzymes across phyla for epigenetic regulations of DNA.
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Affiliation(s)
- Samuel Hong
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA. .,Molecular and Systems Pharmacology Graduate Program, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA.
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA
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Iyer LM, Zhang D, Aravind L. Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification. Bioessays 2015; 38:27-40. [PMID: 26660621 PMCID: PMC4738411 DOI: 10.1002/bies.201500104] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
While N6‐methyladenosine (m6A) is a well‐known epigenetic modification in bacterial DNA, it remained largely unstudied in eukaryotes. Recent studies have brought to fore its potential epigenetic role across diverse eukaryotes with biological consequences, which are distinct and possibly even opposite to the well‐studied 5‐methylcytosine mark. Adenine methyltransferases appear to have been independently acquired by eukaryotes on at least 13 occasions from prokaryotic restriction‐modification and counter‐restriction systems. On at least four to five instances, these methyltransferases were recruited as RNA methylases. Thus, m6A marks in eukaryotic DNA and RNA might be more widespread and diversified than previously believed. Several m6A‐binding protein domains from prokaryotes were also acquired by eukaryotes, facilitating prediction of potential readers for these marks. Further, multiple lineages of the AlkB family of dioxygenases have been recruited as m6A demethylases. Although members of the TET/JBP family of dioxygenases have also been suggested to be m6A demethylases, this proposal needs more careful evaluation. Also watch the Video Abstract.
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Affiliation(s)
- Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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Dippe M, Brandt W, Rost H, Porzel A, Schmidt J, Wessjohann LA. Rationally engineered variants of S-adenosylmethionine (SAM) synthase: reduced product inhibition and synthesis of artificial cofactor homologues. Chem Commun (Camb) 2015; 51:3637-40. [PMID: 25642798 DOI: 10.1039/c4cc08478k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
S-Adenosylmethionine (SAM) synthase was engineered for biocatalytic production of SAM and long-chain analogues by rational re-design. Substitution of two conserved isoleucine residues extended the substrate spectrum of the enzyme to artificial S-alkylhomocysteines. The variants proved to be beneficial in preparative synthesis of SAM (and analogues) due to a much reduced product inhibition.
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Affiliation(s)
- M Dippe
- Leibniz-Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Weinberg 3, D-06120 Halle, Germany.
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58
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DNA adenine hypomethylation leads to metabolic rewiring in Deinococcus radiodurans. J Proteomics 2015; 126:131-9. [DOI: 10.1016/j.jprot.2015.05.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/22/2015] [Accepted: 05/30/2015] [Indexed: 12/27/2022]
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Duan F, Cui S, Song C, Dai L, Zhao X, Zhang X. Systematic evaluation of cancer risk associated with DNMT3B polymorphisms. J Cancer Res Clin Oncol 2015; 141:1205-20. [PMID: 25515408 DOI: 10.1007/s00432-014-1894-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/02/2014] [Indexed: 02/08/2023]
Abstract
PURPOSE The aim of our study is to provide a precise quantification for the association between DNA methyltransferase 3B (DNMT3B) variations (rs2424913 C/T, rs1569686 G/T, rs6087990 T/C and rs2424908 T/C) and the risk of cancer. METHODS We performed a systematic literature review and assessed the methodological quality of included case-control designed studies based on Newcastle-Ottawa Scale. Pooled odds ratios (ORs) and corresponding 95% confidence intervals (95% CIs) were calculated to assess the strengths of the associations. RESULTS We identified 34 studies for pooled analyses. Overall, the results demonstrated that rs2424913 polymorphism was significantly associated with negative cancer risk in the African population (CT vs TT: OR 0.10, 95% CI 0.02-0.63, P = 0.01; CT+CC vs TT: OR 0.14, 95% CI 0.03-0.76, P = 0.02), and the rs1569686 polymorphism was significantly associated with a subtly decreased cancer risk (GT vs TT: OR 0.80, 95% CI 0.72-0.90, P < 0.01; GT+GG vs TT: OR 0.84, 95% CI 0.76-0.94, P < 0.01), particularly in the Asian population (GT vs TT: OR 0.79, 95% CI 0.66-0.96, P < 0.01) and in colorectal cancer subgroup (G vs T: OR 0.69, 95% CI 0.54-0.88, P < 0.01). In addition, the rs6087990 polymorphism was associated with decreased risk in Asian population (T vs C: OR 0.77, 95% CI 0.62-0.96, P = 0.02). Similarly, the rs2424908 polymorphism was observed as a protective factor for cancer in the Asian population (CT+CC vs TT: OR 0.79, 95% CI 0.66-0.95, P = 0.01). CONCLUSIONS DNMT3B polymorphisms might be associated with decreased cancer risk especially in the Asian population and for colorectal cancer. Further multicentric studies are still needed to confirm the results.
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Affiliation(s)
- Fujiao Duan
- Department of Hospital Infection Management, Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou, Henan, China,
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Zhu J, Du S, Zhang J, Wang Y, Wu Q, Ni J. Polymorphism of DNA methyltransferase 3B -149C/T and cancer risk: a meta-analysis. Med Oncol 2015; 32:399. [PMID: 25433949 PMCID: PMC4247848 DOI: 10.1007/s12032-014-0399-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 11/21/2014] [Indexed: 12/15/2022]
Abstract
Published data on the association between DNA methyltransferase (DNMT) 3B -149C/T polymorphism and cancer risk remain inconclusive. To derive a more precise estimation for this association, we performed a meta-analysis of 5,903 cancer cases and 8,132 controls from 22 published case-control studies. We used odds ratios (ORs) with 95 % confidence intervals (CIs) to assess the strength of the association. Our meta-analysis suggested that DNMT3B -149C/T polymorphism was associated with the risk of head and neck cancer under heterozygote comparison (OR 0.73, 95 % CI 0.59-0.90) and dominant model (OR 1.75, 95 % CI 0.62-0.92), although no evidence of association between DNMT3B -149C/T polymorphism and cancer risk was observed as we compared in the pooled analyses (homozygote comparison: OR 0.96, 95 % CI 0.86-1.09; heterozygote comparison: OR 1.07, 95 % CI 0.86-0.32; dominant model: OR 1.03, 95 % CI 0.85-1.25; recessive model: OR 0.93, 95 % CI 0.8-1.08). More studies are needed to detect DNMT3B -149C/T polymorphism and its association with cancer in different ethnic populations incorporated with environment exposures in the susceptibility of different kinds of cancer.
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Affiliation(s)
- Jing Zhu
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Three Gorges University, Yichang, 443000 China
| | - Songtao Du
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
| | - Jiaqi Zhang
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
| | - Yingnan Wang
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
| | - Qiaoling Wu
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
| | - Jixiang Ni
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Three Gorges University, Yichang, 443000 China
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Xiang J, Luo F, Chen Y, Zhu F, Wang J. si-DNMT1 restore tumor suppressor genes expression through the reversal of DNA hypermethylation in cholangiocarcinoma. Clin Res Hepatol Gastroenterol 2014; 38:181-9. [PMID: 24361215 DOI: 10.1016/j.clinre.2013.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 11/10/2013] [Accepted: 11/15/2013] [Indexed: 02/04/2023]
Abstract
OBJECTIVE The aim of our study was to evaluate the effect of shorthairpin RNA plasmid vector knockdown of human DNA methyltransferase 1 on proliferation and the methylation status and expression of tumor suppressor genes in hilar cholangiocarcinoma. METHODS The hilar cholangiocarcinoma cell line QBC939 was utilized for this study. QBC939 cells were transfected with a shorthairpin RNA plasmid vector targeting human DNA methyltransferase 1. Control and human DNA methyltransferase 1 shorthairpin RNA plasmid vector-transfected cells were collected at different time points, and the expression levels of human DNA methyltransferase 1 and tumor suppressor genes (cyclin-dependent kinase inhibitor 2B, cyclin-dependent kinase inhibitor 2A, RAS association domain family 1, and cadherin-1) were detected by reverse transcription-polymerase chain reaction. Furthermore, interfering efficiency was confirmed by Western blotting. The methylation status of tumor suppressor genes was detected using methylation-specific polymerase chain reaction. Furthermore, the effect of human DNA methyltransferase 1 knockdown on proliferation was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. RESULTS Targeted gene knockout of human DNA methyltransferase 1 restored the expression levels of tumor suppressor genes cyclin-dependent kinase inhibitor 2B, cyclin-dependent kinase inhibitor 2A, RAS association domain family 1, and cadherin-1, indicating that the silencing of these tumor suppressor genes is associated with promoter hypermethylation. In addition, knockdown of human DNA methyltransferase 1 expression significantly inhibited the proliferation of QBC939 cells. CONCLUSIONS Targeted knockdown of human DNA methyltransferase 1 expression restores the expression levels of tumor suppressor genes, thus inhibiting the proliferation of QBC939 cells. These results may provide insight for the development of novel therapies for cholangiocarcinoma.
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Affiliation(s)
- Jifeng Xiang
- Department of Hepatobiliary Sugery, The First Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China
| | - Fang Luo
- Department of Hepatobiliary Sugery, The First Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China.
| | - Yong Chen
- Department of Hepatobiliary Sugery, The First Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China
| | - Fangyu Zhu
- Department of Hepatobiliary Sugery, The First Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China
| | - Jiming Wang
- Department of Hepatobiliary Sugery, The First Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China
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Zheng Q, Zeng TT, Chen J, Liu H, Zhang H, Su J. Association between DNA methyltransferases 3B gene polymorphisms and the susceptibility to acute myeloid leukemia in Chinese Han population. PLoS One 2013; 8:e74626. [PMID: 24069326 PMCID: PMC3775800 DOI: 10.1371/journal.pone.0074626] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/06/2013] [Indexed: 02/05/2023] Open
Abstract
DNMT3B plays a crucial role in the generation of aberrant methylation during carcinogenesis. Polymorphisms in the DNMT3B gene may influence the DNA methylation enzymatic activity of DNMT3B, thereby modulating the susceptibility to AML. Thus, we investigated the association between SNPs in the DNMT3Bgene and their haplotypes with the risk of AML in the Chinese Han population. The DNMT3B genotype was determined by HRM in 317 de novo AML patients and 406 healthy control subjects matched for age and gender. Among the 5 SNPs investigated in this study, rs2424913 demonstrated no polymorphisms in the Chinese Han populations, rs1569686 and rs2424908 were significantly associated with AML risk. The GG genotype of rs1569686 was associated with increased AML risk (OR: 5.76; 95%CI: 2.60-12.73; P<0.01) compared with the TT genotype, and individuals with a G allele had a significantly increased risk (OR: 1.89; 95%CI: 1.41-2.52; P<0.01) for AML compared with those harboring a C allele, this polymorphism can predict the risk of AML in a minority of patients. While the CC genotype of rs2424908 appeared to reduce the AML risk (OR: 0.57; 95%CI: 0.36-0.91; P=0.01) compared with the TT genotype, individuals with a C allele were associated with a lower risk (OR: 0.79, 95%CI: 0.64-0.97, P=0.03) for developing AML compared with those harboring a T allele. The other 2 SNPs, rs6087990 and rs6119954, had no significant association with AML risk in the study population. The CGGT, CTAT, TGAT, and CGAT haplotypes of rs6087990, rs1569686, rs6119954, and rs2424908 appeared to significantly increase the AML risk, and the TTGC haplotype appeared to significantly reduce the risk. These results suggest that DNMT3B polymorphisms may contribute to the genetic susceptibility to AML; in particular, the G allele of rs1569686 serves as a risk factor for AML, whereas the C allele of rs2424908 represents a potential protective factor.
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Affiliation(s)
- Qin Zheng
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Ting-ting Zeng
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Jiao Chen
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Hua Liu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - He Zhang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Jun Su
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
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DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis. PLoS Pathog 2013; 9:e1003419. [PMID: 23853579 PMCID: PMC3701705 DOI: 10.1371/journal.ppat.1003419] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 04/30/2013] [Indexed: 01/07/2023] Open
Abstract
DNA methylation regulates gene expression in many organisms. In eukaryotes, DNA methylation is associated with gene repression, while it exerts both activating and repressive effects in the Proteobacteria through largely locus-specific mechanisms. Here, we identify a critical DNA methyltransferase in M. tuberculosis, which we term MamA. MamA creates N6-methyladenine in a six base pair recognition sequence present in approximately 2,000 copies on each strand of the genome. Loss of MamA reduces the expression of a number of genes. Each has a MamA site located at a conserved position relative to the sigma factor −10 binding site and transcriptional start site, suggesting that MamA modulates their expression through a shared, not locus-specific, mechanism. While strains lacking MamA grow normally in vitro, they are attenuated in hypoxic conditions, suggesting that methylation promotes survival in discrete host microenvironments. Interestingly, we demonstrate strikingly different patterns of DNA methyltransferase activity in different lineages of M. tuberculosis, which have been associated with preferences for distinct host environments and different disease courses in humans. Thus, MamA is the major functional adenine methyltransferase in M. tuberculosis strains of the Euro-American lineage while strains of the Beijing lineage harbor a point mutation that largely inactivates MamA but possess a second functional DNA methyltransferase. Our results indicate that MamA influences gene expression in M. tuberculosis and plays an important but strain-specific role in fitness during hypoxia. Tuberculosis is a disease with a devastating impact on public health, killing over 1.5 million people each year around the globe. Tuberculosis is caused by the bacterium Mycobacterium tuberculosis, which over millennia has evolved the ability to survive and persist for decades in the harsh environment inside its human host. Regulation of gene expression is critical for adaptation to stressful conditions. To successfully tackle M. tuberculosis, we therefore need to understand how it regulates its genes and responds to environmental stressors. In this work, we report the first investigation of the role of DNA methylation in gene regulation and stress response in M. tuberculosis. We have found that DNA methylation is important for survival of hypoxia, a stress condition present in human infections, and furthermore that DNA methylation affects the expression of several genes. In contrast to methylation-regulation systems reported in other bacteria, in which the effects of methylation vary from one gene to the next, M. tuberculosis appears to use a concerted mechanism to influence multiple genes. Our findings identify a novel mechanism by which M. tuberculosis modulates gene expression in response to stress.
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Abstract
In prokaryotes, alteration in gene expression was observed with the modification of DNA, especially DNA methylation. Such changes are inherited from generation to generation with no alterations in the DNA sequence and represent the epigenetic signal in prokaryotes. DNA methyltransferases are enzymes involved in DNA modification and thus in epigenetic regulation of gene expression. DNA methylation not only affects the thermodynamic stability of DNA, but also changes its curvature. Methylation of specific residues on DNA can affect the protein-DNA interactions. DNA methylation in prokaryotes regulates a number of physiological processes in the bacterial cell including transcription, DNA mismatch repair and replication initiation. Significantly, many reports have suggested a role of DNA methylation in regulating the expression of a number of genes in virulence and pathogenesis thus, making DNA methlytransferases novel targets for the designing of therapeutics. Here, we summarize the current knowledge about the influence of DNA methylation on gene regulation in different bacteria, and on bacterial virulence.
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Affiliation(s)
- Ritesh Kumar
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India,
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65
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Yang XX, He XQ, Li FX, Wu YS, Gao Y, Li M. Risk-association of DNA methyltransferases polymorphisms with gastric cancer in the Southern Chinese population. Int J Mol Sci 2012; 13:8364-8378. [PMID: 22942708 PMCID: PMC3430239 DOI: 10.3390/ijms13078364] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 06/20/2012] [Accepted: 06/27/2012] [Indexed: 01/10/2023] Open
Abstract
DNA hypomethylation and/or hypermethylation are presumed to be early events in carcinogenesis, and one or more DNA methyltransferases (DNMTs) have been suggested to play roles in carcinogenesis of gastric cancer (GC). However, there have been no systematic studies regarding the association between DNMT gene polymorphisms and GC risk. Here, we examined the associations of 16 single nucleotide polymorphisms (SNPs) from DNMT1 (rs2114724, rs2228611, rs2228612, rs8101866, rs16999593), DNMT2 (rs11695471, rs11254413), DNMT3A (rs1550117, rs11887120, rs13420827, rs13428812, rs6733301), DNMT3B (rs2424908, rs2424913, rs6087990) and DNMT3L (rs113593938) with GC in the Southern Chinese population. We assessed the associations of these 16 SNPs with GC in a case-control study that consisted of 242 GC cases and 294 controls, using the Sequenom MALDI-TOF-MS platform. Association analyses based on the χ2 test and binary logistic regression were performed to determine the odds ratio (OR) and 95% confidence interval (95%CI) for each SNP. We found that rs16999593 in DNMT1, rs11254413 in DNMT2 and rs13420827 in DNMT3A were significantly associated with GC susceptibility (OR 1.45, 0.15, 0.66, respectively; 95% CI 1.00–2.11, p = 0.047; 0.08–0.27, p < 0.01; 0.45–0.97, p = 0.034, respectively, overdominant model). These results suggested that DNMT1, DNMT2 and DNMT3A may play important roles in GC carcinogenesis. However, further studies are required to elucidate the mechanism.
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Affiliation(s)
- Xue-Xi Yang
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China; E-Mails: (X.-X.Y.); (F.-X.L.); (Y.-S.W.); (Y.G.)
| | - Xuan-Qiu He
- The First Clinical College, Southern Medical University, Guangzhou 510515, China; E-Mail:
| | - Fen-Xia Li
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China; E-Mails: (X.-X.Y.); (F.-X.L.); (Y.-S.W.); (Y.G.)
| | - Ying-Song Wu
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China; E-Mails: (X.-X.Y.); (F.-X.L.); (Y.-S.W.); (Y.G.)
| | - Yang Gao
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China; E-Mails: (X.-X.Y.); (F.-X.L.); (Y.-S.W.); (Y.G.)
| | - Ming Li
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China; E-Mails: (X.-X.Y.); (F.-X.L.); (Y.-S.W.); (Y.G.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-20-61648550; Fax: +86-20-61648554
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66
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Matje DM, Reich NO. Molecular drivers of base flipping during sequence-specific DNA methylation. Chembiochem 2012; 13:1574-7. [PMID: 22730226 DOI: 10.1002/cbic.201200104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Indexed: 11/07/2022]
Abstract
One step at a time: Substrates containing nucleotide analogues lacking sequence-specific contacts to the C5 methyltransferase M.HhaI were used to probe the role of individual interactions in effecting conformational transitions during base flipping. A segregation of duties, that is, specific recognition and chemomechanical force for base flipping and active site assembly, within the enzyme is confirmed.
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Affiliation(s)
- Douglas M Matje
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106-9510, USA
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67
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DNA extraction method with improved efficiency and specificity using DNA methyltransferase and “click” chemistry. Anal Biochem 2012; 425:169-74. [DOI: 10.1016/j.ab.2012.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 03/20/2012] [Accepted: 03/21/2012] [Indexed: 11/22/2022]
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68
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Malygin EG, Hattman S. DNA methyltransferases: mechanistic models derived from kinetic analysis. Crit Rev Biochem Mol Biol 2012; 47:97-193. [PMID: 22260147 DOI: 10.3109/10409238.2011.620942] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The sequence-specific transfer of methyl groups from donor S-adenosyl-L-methionine (AdoMet) to certain positions of DNA-adenine or -cytosine residues by DNA methyltransferases (MTases) is a major form of epigenetic modification. It is virtually ubiquitous, except for some notable exceptions. Site-specific methylation can be regarded as a means to increase DNA information capacity and is involved in a large spectrum of biological processes. The importance of these functions necessitates a deeper understanding of the enzymatic mechanism(s) of DNA methylation. DNA MTases fall into one of two general classes; viz. amino-MTases and [C5-cytosine]-MTases. Amino-MTases, common in prokaryotes and lower eukaryotes, catalyze methylation of the exocyclic amino group of adenine ([N6-adenine]-MTase) or cytosine ([N4-cytosine]-MTase). In contrast, [C5-cytosine]-MTases methylate the cyclic carbon-5 atom of cytosine. Characteristics of DNA MTases are highly variable, differing in their affinity to their substrates or reaction products, their kinetic parameters, or other characteristics (order of substrate binding, rate limiting step in the overall reaction). It is not possible to present a unifying account of the published kinetic analyses of DNA methylation because different authors have used different substrate DNAs and/or reaction conditions. Nevertheless, it would be useful to describe those kinetic data and the mechanistic models that have been derived from them. Thus, this review considers in turn studies carried out with the most consistently and extensively investigated [N6-adenine]-, [N4-cytosine]- and [C5-cytosine]-DNA MTases.
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Affiliation(s)
- Ernst G Malygin
- Institute of Molecular Biology, State Research Center of Virology and Biotechnology Vector, Novosibirsk, Russia
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69
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Drozdz M, Piekarowicz A, Bujnicki JM, Radlinska M. Novel non-specific DNA adenine methyltransferases. Nucleic Acids Res 2011; 40:2119-30. [PMID: 22102579 PMCID: PMC3299994 DOI: 10.1093/nar/gkr1039] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The mom gene of bacteriophage Mu encodes an enzyme that converts adenine to N6-(1-acetamido)-adenine in the phage DNA and thereby protects the viral genome from cleavage by a wide variety of restriction endonucleases. Mu-like prophage sequences present in Haemophilus influenzae Rd (FluMu), Neisseria meningitidis type A strain Z2491 (Pnme1) and H. influenzae biotype aegyptius ATCC 11116 do not possess a Mom-encoding gene. Instead, at the position occupied by mom in Mu they carry an unrelated gene that encodes a protein with homology to DNA adenine N6-methyltransferases (hin1523, nma1821, hia5, respectively). Products of the hin1523, hia5 and nma1821 genes modify adenine residues to N6-methyladenine, both in vitro and in vivo. All of these enzymes catalyzed extensive DNA methylation; most notably the Hia5 protein caused the methylation of 61% of the adenines in λ DNA. Kinetic analysis of oligonucleotide methylation suggests that all adenine residues in DNA, with the possible exception of poly(A)-tracts, constitute substrates for the Hia5 and Hin1523 enzymes. Their potential ‘sequence specificity’ could be summarized as AB or BA (where B = C, G or T). Plasmid DNA isolated from Escherichia coli cells overexpressing these novel DNA methyltransferases was resistant to cleavage by many restriction enzymes sensitive to adenine methylation.
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Affiliation(s)
- Marek Drozdz
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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70
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Lalrempuia R, Müller-Bunz H, Albrecht M. Methyltransferase Activity of an Iridium Center with Methylpyridinium as Methylene Source. Angew Chem Int Ed Engl 2011; 50:9969-72. [DOI: 10.1002/anie.201104073] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Indexed: 11/06/2022]
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71
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Lalrempuia R, Müller-Bunz H, Albrecht M. Methyltransferase-Aktivität eines Iridiumzentrums mit Methylpyridinium als Methylenquelle. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201104073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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72
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Bao Q, He B, Pan Y, Tang Z, Zhang Y, Qu L, Xu Y, Zhu C, Tian F, Wang S. Genetic variation in the promoter of DNMT3B is associated with the risk of colorectal cancer. Int J Colorectal Dis 2011; 26:1107-12. [PMID: 21519807 DOI: 10.1007/s00384-011-1199-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/11/2011] [Indexed: 02/04/2023]
Abstract
PURPOSE DNA methyltransferase-3B (DNMT3B) plays an important role in the generation of aberrant methylation in carcinogenesis. Polymorphisms of the DNMT3B gene may influence DNMT3B enzyme activity on DNA methylation, thereby modulating the susceptibility to colorectal cancer (CRC). METHODS The polymorphisms in the promoter region of the DNMT3B gene [-149C>T (rs2424913) and -579G>T (rs1569686)] were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and a total of 544 CRC patients and 533 age- and sex-matched healthy controls were enrolled in the case-control study. RESULTS The results showed that the -579G allele was associated with a significantly decreased risk of CRC (adjusted OR, 0.50; 95%CI, 0.35-0.72; P = 0.0002) when compared with the -579TT genotype. However, the DNMT3B-149CT genotype was not associated with the risk of CRC (adjusted OR, 0.48; 95%CI, 0.18-1.30; P = 0.151). In addition, stratification analysis revealed that the increased risk was predominant in both colon cancer and rectal cancer showing no effect of primary occurrence site. CONCLUSION Our research demonstrated the -579G allele was a potential protective factor for the occurrence of CRC.
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Affiliation(s)
- Qian Bao
- Department of Life Sciences, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China.
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Abstract
Gastric cancer (GC) is a world health burden, ranging as the second cause of cancer death worldwide. Etiologically, GC arises not only from the combined effects of environmental factors and susceptible genetic variants but also from the accumulation of genetic and epigenetic alterations. In the last years, molecular oncobiology studies brought to light a number of genes that are implicated in gastric carcinogenesis. This review is intended to focus on the recently described basic aspects that play key roles in the process of gastric carcinogenesis. Genetic variants of the genes IL-10, IL-17, MUC1, MUC6, DNMT3B, SMAD4, and SERPINE1 have been reported to modify the risk of developing GC. Several genes have been newly associated with gastric carcinogenesis, both through oncogenic activation (GSK3β, CD133, DSC2, P-Cadherin, CDH17, CD168, CD44, metalloproteinases MMP7 and MMP11, and a subset of miRNAs) and through tumor suppressor gene inactivation mechanisms (TFF1, PDX1, BCL2L10, XRCC, psiTPTE-HERV, HAI-2, GRIK2, and RUNX3). It also addressed the role of the inflammatory mediator cyclooxygenase-2 (COX-2) in the process of gastric carcinogenesis and its importance as a potential molecular target for therapy.
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Affiliation(s)
- Carlos Resende
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
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74
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Kumar A, Saigal K, Malhotra K, Sinha KM, Taneja B. Structural and functional characterization of Rv2966c protein reveals an RsmD-like methyltransferase from Mycobacterium tuberculosis and the role of its N-terminal domain in target recognition. J Biol Chem 2011; 286:19652-61. [PMID: 21474448 PMCID: PMC3103344 DOI: 10.1074/jbc.m110.200428] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 03/24/2011] [Indexed: 11/06/2022] Open
Abstract
Nine of ten methylated nucleotides of Escherichia coli 16 S rRNA are conserved in Mycobacterium tuberculosis. All the 10 different methyltransferases are known in E. coli, whereas only TlyA and GidB have been identified in mycobacteria. Here we have identified Rv2966c of M. tuberculosis as an ortholog of RsmD protein of E. coli. We have shown that rv2966c can complement rsmD-deleted E. coli cells. Recombinant Rv2966c can use 30 S ribosomes purified from rsmD-deleted E. coli as substrate and methylate G966 of 16 S rRNA in vitro. Structure determination of the protein shows the protein to be a two-domain structure with a short hairpin domain at the N terminus and a C-terminal domain with the S-adenosylmethionine-MT-fold. We show that the N-terminal hairpin is a minimalist functional domain that helps Rv2966c in target recognition. Deletion of the N-terminal domain prevents binding to nucleic acid substrates, and the truncated protein fails to carry out the m(2)G966 methylation on 16 S rRNA. The N-terminal domain also binds DNA efficiently, a property that may be utilized under specific conditions of cellular growth.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Histones/chemistry
- Histones/genetics
- Histones/metabolism
- Methylation
- Mycobacterium tuberculosis/enzymology
- Mycobacterium tuberculosis/genetics
- Protein Structure, Tertiary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Structure-Activity Relationship
- tRNA Methyltransferases/chemistry
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- Atul Kumar
- From the Institute of Genomics and Integrative Biology (Council of Scientific and Industrial Research), Mall Road, Delhi University Campus, Delhi 110007 and
| | - Kashyap Saigal
- the Institute of Molecular Medicine, 254, Okhla Industrial Estate, Phase III, New Delhi 110020 India
| | - Ketan Malhotra
- the Institute of Molecular Medicine, 254, Okhla Industrial Estate, Phase III, New Delhi 110020 India
| | - Krishna Murari Sinha
- the Institute of Molecular Medicine, 254, Okhla Industrial Estate, Phase III, New Delhi 110020 India
| | - Bhupesh Taneja
- From the Institute of Genomics and Integrative Biology (Council of Scientific and Industrial Research), Mall Road, Delhi University Campus, Delhi 110007 and
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75
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A nucleotide insertion between two adjacent methyltransferases in Helicobacter pylori results in a bifunctional DNA methyltransferase. Biochem J 2011; 433:487-95. [PMID: 21110832 DOI: 10.1042/bj20101668] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Helicobacter pylori has a dynamic R-M (restriction-modification) system. It is capable of acquiring new R-M systems from the environment in the form of DNA released from other bacteria or other H. pylori strains. Random mutations in R-M genes can result in non-functional R-M systems or R-M systems with new properties. hpyAVIAM and hpyAVIBM are two solitary DNA MTase (methyltransferase) genes adjacent to each other and lacking a cognate restriction enzyme gene in H. pylori strain 26695. Interestingly, in an Indian strain D27, hpyAVIAM-hpyAVIBM encodes a single bifunctional polypeptide due to insertion of a nucleotide just before the stop codon of hpyAVIBM and, when a similar mutation was made in hpyAVIAM-hpyAVIBM from strain 26695, a functional MTase with an N-terminal C⁵-cytosine MTase domain and a C-terminal N⁶-adenine MTase domain was constructed. Mutations in the AdoMet (S-adenosylmethionine)-binding motif or in the catalytic motif of M.HpyAVIA or M.HpyAVIB selectively abrogated the C⁵-cytosine or N⁶-adenine methylation activity of M.HpyAVIA-M.HpyAVIB fusion protein. The present study highlights the ability of H. pylori to evolve genes with unique functions and thus generate variability. For organisms such as H. pylori, which have a small genome, these adaptations could be important for their survival in the hostile host environment.
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76
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Banerjee A, Rao DN. Functional analysis of an acid adaptive DNA adenine methyltransferase from Helicobacter pylori 26695. PLoS One 2011; 6:e16810. [PMID: 21347417 PMCID: PMC3036652 DOI: 10.1371/journal.pone.0016810] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 01/13/2011] [Indexed: 11/18/2022] Open
Abstract
HP0593 DNA-(N(6)-adenine)-methyltransferase (HP0593 MTase) is a member of a Type III restriction-modification system in Helicobacter pylori strain 26695. HP0593 MTase has been cloned, overexpressed and purified heterologously in Escherichia coli. The recognition sequence of the purified MTase was determined as 5'-GCAG-3'and the site of methylation was found to be adenine. The activity of HP0593 MTase was found to be optimal at pH 5.5. This is a unique property in context of natural adaptation of H. pylori in its acidic niche. Dot-blot assay using antibodies that react specifically with DNA containing m6A modification confirmed that HP0593 MTase is an adenine-specific MTase. HP0593 MTase occurred as both monomer and dimer in solution as determined by gel-filtration chromatography and chemical-crosslinking studies. The nonlinear dependence of methylation activity on enzyme concentration indicated that more than one molecule of enzyme was required for its activity. Analysis of initial velocity with AdoMet as a substrate showed that two molecules of AdoMet bind to HP0593 MTase, which is the first example in case of Type III MTases. Interestingly, metal ion cofactors such as Co(2+), Mn(2+), and also Mg(2+) stimulated the HP0593 MTase activity. Preincubation and isotope partitioning analyses clearly indicated that HP0593 MTase-DNA complex is catalytically competent, and suggested that DNA binds to the MTase first followed by AdoMet. HP0593 MTase shows a distributive mechanism of methylation on DNA having more than one recognition site. Considering the occurrence of GCAG sequence in the potential promoter regions of physiologically important genes in H. pylori, our results provide impetus for exploring the role of this DNA MTase in the cellular processes of H. pylori.
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Affiliation(s)
- Arun Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Desirazu N. Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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Farrar CE, Siu KKW, Howell PL, Jarrett JT. Biotin synthase exhibits burst kinetics and multiple turnovers in the absence of inhibition by products and product-related biomolecules. Biochemistry 2010; 49:9985-96. [PMID: 20961145 DOI: 10.1021/bi101023c] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Biotin synthase (BS) is a member of the "SAM radical" superfamily of enzymes, which catalyze reactions in which the reversible or irreversible oxidation of various substrates is coupled to the reduction of the S-adenosyl-l-methionine (AdoMet) sulfonium to generate methionine and 5'-deoxyadenosine (dAH). Prior studies have demonstrated that these products are modest inhibitors of BS and other members of this enzyme family. In addition, the in vivo catalytic activity of Escherichia coli BS requires expression of 5'-methylthioadenosine/S-adenosyl-l-homocysteine nucleosidase, which hydrolyzes 5'-methylthioadenosine (MTA), S-adenosyl-l-homocysteine (AdoHcy), and dAH. In the present work, we confirm that dAH is a modest inhibitor of BS (K(i) = 20 μM) and show that cooperative binding of dAH with excess methionine results in a 3-fold enhancement of this inhibition. However, with regard to the other substrates of MTA/AdoHcy nucleosidase, we demonstrate that AdoHcy is a potent inhibitor of BS (K(i) ≤ 650 nM) while MTA is not an inhibitor. Inhibition by both dAH and AdoHcy likely accounts for the in vivo requirement for MTA/AdoHcy nucleosidase and may help to explain some of the experimental disparities between various laboratories studying BS. In addition, we examine possible inhibition by other AdoMet-related biomolecules present as common contaminants in commercial AdoMet preparations and/or generated during an assay, as well as by sinefungin, a natural product that is a known inhibitor of several AdoMet-dependent enzymes. Finally, we examine the catalytic activity of BS with highly purified AdoMet in the presence of MTAN to relieve product inhibition and present evidence suggesting that the enzyme is half-site active and capable of undergoing multiple turnovers in vitro.
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Affiliation(s)
- Christine E Farrar
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
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78
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Aranda J, Roca M, López-Canut V, Tuñón I. Theoretical study of the catalytic mechanism of DNA-(N4-cytosine)-methyltransferase from the bacterium Proteus vulgaris. J Phys Chem B 2010; 114:8467-73. [PMID: 20524651 DOI: 10.1021/jp911036w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper the reaction mechanism for methylation of cytosine at the exocyclic N4 position catalyzed by M.PvuII has been explored by means of hybrid quantum mechanics/molecular mechanics (QM/MM) methods. A reaction model was prepared by placing a single cytosine base in the active site of the enzyme. In this model the exocyclic amino group of the base establishes hydrogen bond interactions with the hydroxyl oxygen atom of Ser53 and the carbonyl oxygen atom of Pro54. The reaction mechanism involves a direct methyl transfer from AdoMet to the N4 atom and a proton transfer from this atom to Ser53, which in turn transfers a proton to Asp96. Different timings for the proton transfers and methylation steps have been explored at the AM1/MM and B3LYP/MM levels including localization and characterization of stationary structures. At our best estimate the reaction proceeds by means of a simultaneous but asynchronous proton transfer from Ser53 to Asp96 and from N4 of cytosine to Ser53 followed by a direct methyl transfer from AdoMet to the exocyclic N4 of cytosine.
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Affiliation(s)
- Juan Aranda
- Departament de Química Física, Universitat de València, Spain
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79
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Bheemanaik S, Sistla S, Krishnamurthy V, Arathi S, Desirazu NR. Kinetics of Methylation by EcoP1I DNA Methyltransferase. Enzyme Res 2010; 2010:302731. [PMID: 21048863 PMCID: PMC2962900 DOI: 10.4061/2010/302731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Accepted: 06/21/2010] [Indexed: 11/20/2022] Open
Abstract
EcoP1I DNA MTase (M.EcoP1I), an N6-adenine MTase from bacteriophage P1, is a part of the EcoP1I restriction-modification (R-M) system which belongs to the Type III R-M system. It recognizes the sequence 5′-AGACC-3′ and methylates the internal adenine. M.EcoP1I requires Mg2+ for the transfer of methyl groups to DNA. M.EcoP1I is shown to exist as dimer in solution, and even at high salt concentrations (0.5 M) the dimeric M.EcoP1I does not dissociate into monomers suggesting a strong interaction between the monomer subunits. Preincubation and isotope partitioning studies with M.EcoP1I indicate a kinetic mechanism where the duplex DNA binds first followed by AdoMet. Interestingly, M.EcoP1I methylates DNA substrates in the presence of Mn2+ and Ca2+ other than Mg2+ with varying affinities. Amino acid analysis and methylation assays in the presence of metal ions suggest that M.EcoP1I has indeed two metal ion-binding sites [358ID(x)n … ExK401 and 600DxDxD604 motif]. EcoP1I DNA MTase catalyzes the transfer of methyl groups using a distributive mode of methylation on DNA containing more than one recognition site. A chemical modification of EcoP1I DNA MTase using N-ethylmaleimide resulted in an irreversible inactivation of enzyme activity suggesting the possible role of cysteine residues in catalysis.
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80
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Madhusoodanan UK, Rao DN. Diversity of DNA methyltransferases that recognize asymmetric target sequences. Crit Rev Biochem Mol Biol 2010; 45:125-45. [PMID: 20184512 DOI: 10.3109/10409231003628007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases usually recognize palindromic DNA sequences and add a methyl group to the target base (either adenine or cytosine) on both strands. However, there are a number of MTases that recognize asymmetric target sequences and differ in their subunit organization. In a bacterial cell, after each round of replication, the substrate for any MTase is hemimethylated DNA, and it therefore needs only a single methylation event to restore the fully methylated state. This is in consistent with the fact that most of the DNA MTases studied exist as monomers in solution. Multiple lines of evidence suggest that some DNA MTases function as dimers. Further, functional analysis of many restriction-modification systems showed the presence of more than one or fused MTase genes. It was proposed that presence of two MTases responsible for the recognition and methylation of asymmetric sequences would protect the nascent strands generated during DNA replication from cognate restriction endonuclease. In this review, MTases recognizing asymmetric sequences have been grouped into different subgroups based on their unique properties. Detailed characterization of these unusual MTases would help in better understanding of their specific biological roles and mechanisms of action. The rapid progress made by the genome sequencing of bacteria and archaea may accelerate the identification and study of species- and strain-specific MTases of host-adapted bacteria and their roles in pathogenic mechanisms.
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81
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Chiou CS, Li HY, Tung SK, Chen CY, Teng CH, Shu JC, Tseng JT, Hsu CY, Chen CC. Identification of prophage gene z2389 in Escherichia coli EDL933 encoding a DNA cytosine methyltransferase for full protection of NotI sites. Int J Med Microbiol 2010; 300:296-303. [DOI: 10.1016/j.ijmm.2009.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 10/27/2009] [Accepted: 11/15/2009] [Indexed: 10/20/2022] Open
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82
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Chung KY, Dong H, Chao AT, Shi PY, Lescar J, Lim SP. Higher catalytic efficiency of N-7-methylation is responsible for processive N-7 and 2′-O methyltransferase activity in dengue virus. Virology 2010; 402:52-60. [DOI: 10.1016/j.virol.2010.03.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 12/30/2009] [Accepted: 03/03/2010] [Indexed: 01/06/2023]
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83
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Ta HM, Kim KK. Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA methyltransferase, in complex with S-adenosyl-L-methionine. Protein Sci 2010; 19:617-24. [PMID: 20052680 DOI: 10.1002/pro.319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Streptococcus pneumoniae Sp1610, a Class-I fold S-adenosylmethionine (AdoMet)-dependent methyltransferase, is a member of the COG2384 family in the Clusters of Orthologous Groups database, which catalyzes the methylation of N(1)-adenosine at position 22 of bacterial tRNA. We determined the crystal structure of Sp1610 in the ligand-free and the AdoMet-bound forms at resolutions of 2.0 and 3.0 A, respectively. The protein is organized into two structural domains: the N-terminal catalytic domain with a Class I AdoMet-dependent methyltransferase fold, and the C-terminal substrate recognition domain with a novel fold of four alpha-helices. Observations of the electrostatic potential surface revealed that the concave surface located near the AdoMet binding pocket was predominantly positively charged, and thus this was predicted to be an RNA binding area. Based on the results of sequence alignment and structural analysis, the putative catalytic residues responsible for substrate recognition are also proposed.
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Affiliation(s)
- Hai Minh Ta
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
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84
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Hu J, Fan H, Liu D, Zhang S, Zhang F, Xu H. DNMT3B promoter polymorphism and risk of gastric cancer. Dig Dis Sci 2010; 55:1011-6. [PMID: 19517237 DOI: 10.1007/s10620-009-0831-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2008] [Accepted: 04/30/2009] [Indexed: 12/15/2022]
Abstract
To investigate the association of single-nucleotide polymorphism (SNP) in DNA methyltransferase 3B (DNMT3B) gene and the risk of gastric cancer (GC), we detected -149C>T and -579G>T in the promoter region of the DNMT3B gene by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing analysis. The DNMT3B genotype was determined in 259 gastric cancer patients and 262 healthy controls that were frequency matched for age and gender. Results showed that individuals with at least one -579G allele were also at significantly decreased risk of gastric cancer [odds ratio (OR), 0.43; 95% confidence interval (CI) 0.26-0.72] compared with those having a -579TT genotype. The -149C>T genotype distribution was irrelevant to the risk of gastric cancer (OR, 1.49; 95% CI, 0.17-17.94) in the studied Chinese population. In addition, data suggested that DNMT3B genetic polymorphism varied among different races, ethnic groups, and geographic areas.
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Affiliation(s)
- Jiabo Hu
- Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, 210009, Nanjing, Jiangsu, China
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85
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Kumar R, Mukhopadhyay AK, Rao DN. Characterization of an N6 adenine methyltransferase from Helicobacter pylori strain 26695 which methylates adjacent adenines on the same strand. FEBS J 2010; 277:1666-83. [PMID: 20180846 DOI: 10.1111/j.1742-4658.2010.07593.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genomic sequences of Helicobacter pylori strains 26695, J99, HPAGI and G27 have revealed an abundance of restriction and modification genes. hp0050, which encodes an N(6) adenine DNA methyltransferase, was cloned, overexpressed and purified to near homogeneity. It recognizes the sequence 5'-GRRG-3' (where R is A or G) and, most intriguingly, methylates both adenines when R is A (5'-GAAG-3'). Kinetic analysis suggests a nonprocessive (repeated-hit) mechanism of methylation in which HP0050 methyltransferase methylates one adenine at a time in the sequence 5'-GAAG-3'. This is the first report of an N(6) adenine DNA methyltransferase that methylates two adjacent residues on the same strand. Interestingly, HP0050 homologs from two clinical strains of H. pylori (PG227 and 128) methylate only 5'-GAGG-3' compared with 5'-GRRG-3' in strain 26695. HP0050 methyltransferase is highly conserved as it is present in more than 90% of H. pylori strains. Inactivation of hp0050 in strain PG227 resulted in poor growth, suggesting its role in the biology of H. pylori. Collectively, these findings provide impetus for exploring the role(s) of this conserved DNA methyltransferase in the cellular processes of H. pylori.
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Affiliation(s)
- Ritesh Kumar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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86
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The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes. Nat Rev Microbiol 2010; 8:196-206. [PMID: 20140025 DOI: 10.1038/nrmicro2283] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In several host-adapted pathogens, phase variation has been found to occur in genes that encode methyltransferases associated with type III restriction-modification systems. It was recently shown that in the human pathogens Haemophilus influenzae, Neisseria gonorrhoeae and Neisseria meningitidis phase variation of a type III DNA methyltransferase, encoded by members of the mod gene family, regulates the expression of multiple genes. This novel genetic system has been termed the 'phasevarion' (phase-variable regulon). The wide distribution of phase-variable mod family genes indicates that this may be a common strategy used by host-adapted bacterial pathogens to randomly switch between distinct cell types.
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87
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Hou YM, Perona JJ. Stereochemical mechanisms of tRNA methyltransferases. FEBS Lett 2009; 584:278-86. [PMID: 19944101 DOI: 10.1016/j.febslet.2009.11.075] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 11/18/2009] [Accepted: 11/19/2009] [Indexed: 12/31/2022]
Abstract
Methylation of tRNA on the four canonical bases adds structural complexity to the molecule, and improves decoding specificity and efficiency. While many tRNA methylases are known, detailed insight into the catalytic mechanism is only available in a few cases. Of interest among all tRNA methylases is the structural basis for nucleotide selection, by which the specificity is limited to a single site, or broadened to multiple sites. General themes in catalysis include the basis for rate acceleration at highly diverse nucleophilic centers for methyl transfer, using S-adenosylmethionine as a cofactor. Studies of tRNA methylases have also yielded insights into molecular evolution, particularly in the case of enzymes that recognize distinct structures to perform identical reactions at the same target nucleotide.
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Affiliation(s)
- Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th St., Philadelphia, PA 19107, USA.
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88
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Homology modeling and molecular dynamics simulations of HgiDII methyltransferase in complex with DNA and S-adenosyl-methionine: catalytic mechanism and interactions with DNA. J Mol Model 2009; 16:1213-22. [PMID: 20033464 DOI: 10.1007/s00894-009-0632-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 11/23/2009] [Indexed: 10/20/2022]
Abstract
M.HgiDII is a methyltransferase (MTase) from Herpetosiphon giganteus that recognizes the sequence GTCGAC. This enzyme belongs to a group of MTases that share a high degree of amino acid similarity, albeit none of them has been thoroughly characterized. To study the catalytic mechanism of M.HgiDII and its interactions with DNA, we performed molecular dynamics simulations with a homology model of M.HgiDII complexed with DNA and S-adenosyl-methionine. Our results indicate that M.HgiDII may not rely only on Glu119 to activate the cytosine ring, which is an early step in the catalysis of cytosine methylation; apparently, Arg160 and Arg162 may also participate in the activation by interacting with cytosine O2. Another residue from the catalytic site, Val118, also played a relevant role in the catalysis of M.HgiDII. Val118 interacted with the target cytosine and kept water molecules from accessing the region of the catalytic pocket where Cys79 interacts with cytosine, thus preventing water-mediated disruption of interactions in the catalytic site. Specific recognition of DNA was mediated mainly by amino acids of the target recognition domain, although some amino acids (loop 80-88) of the catalytic domain may also contribute to DNA recognition. These interactions involved direct contacts between M.HgiDII and DNA, as well as indirect contacts through water bridges. Additionally, analysis of sequence alignments with closely related MTases helped us to identify a motif in the TRD of M.HgiDII that may be relevant to specific DNA recognition.
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89
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Yadav VP, Mandal PK, Rao DN, Bhattacharya S. Characterization of the restriction enzyme-like endonuclease encoded by the Entamoeba histolytica non-long terminal repeat retrotransposon EhLINE1. FEBS J 2009; 276:7070-82. [DOI: 10.1111/j.1742-4658.2009.07419.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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90
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Selisko B, Peyrane FF, Canard B, Alvarez K, Decroly E. Biochemical characterization of the (nucleoside-2'O)-methyltransferase activity of dengue virus protein NS5 using purified capped RNA oligonucleotides (7Me)GpppAC(n) and GpppAC(n). J Gen Virol 2009; 91:112-21. [PMID: 19776234 DOI: 10.1099/vir.0.015511-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The flavivirus RNA genome contains a conserved cap-1 structure, (7Me)GpppA(2'OMe)G, at the 5' end. Two mRNA cap methyltransferase (MTase) activities involved in the formation of the cap, the (guanine-N7)- and the (nucleoside-2'O)-MTases (2'O-MTase), reside in a single domain of non-structural protein NS5 (NS5MTase). This study reports on the biochemical characterization of the 2'O-MTase activity of NS5MTase of dengue virus (NS5MTase(DV)) using purified, short, capped RNA substrates ((7Me)GpppAC(n) or GpppAC(n)). NS5MTase(DV) methylated both types of substrate exclusively at the 2'O position. The efficiency of 2'O-methylation did not depend on the methylation of the N7 position. Using (7Me)GpppAC(n) and GpppAC(n) substrates of increasing chain lengths, it was found that both NS5MTase(DV) 2'O activity and substrate binding increased before reaching a plateau at n=5. Thus, the cap and 6 nt might define the interface providing efficient binding of enzyme and substrate. K(m) values for (7Me)GpppAC(5) and the co-substrate S-adenosyl-L-methionine (AdoMet) were determined (0.39 and 3.26 microM, respectively). As reported for other AdoMet-dependent RNA and DNA MTases, the 2'O-MTase activity of NS5MTase(DV) showed a low turnover of 3.25x10(-4) s(-1). Finally, an inhibition assay was set up and tested on GTP and AdoMet analogues as putative inhibitors of NS5MTase(DV), which confirmed efficient inhibition by the reaction product S-adenosyl-homocysteine (IC(50) 0.34 microM) and sinefungin (IC(50) 0.63 microM), demonstrating that the assay is sufficiently sensitive to conduct inhibitor screening and characterization assays.
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Affiliation(s)
- Barbara Selisko
- Laboratoire d'Architecture et Fonction des Macromolécules Biologiques, UMR 6098, Centre National de la Recherche Scientifique and Université de la Méditerranée Aix-Marseille I et II, Marseille, France.
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91
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Coffin SR, Reich NO. Escherichia coli DNA adenine methyltransferase: intrasite processivity and substrate-induced dimerization and activation. Biochemistry 2009; 48:7399-410. [PMID: 19580332 DOI: 10.1021/bi9008006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylation of GATC sites in Escherichia coli by DNA adenine methyltransferase (EcoDam) is essential for proper DNA replication timing, gene regulation, and mismatch repair. The low cellular concentration of EcoDam and the high number of GATC sites in the genome (approximately 20000) support the reliance on methylation efficiency-enhancing strategies such as extensive intersite processivity. Here, we present evidence that EcoDam has evolved other unique mechanisms of activation not commonly observed with restriction-modification methyltransferases. EcoDam dimerizes on short, synthetic DNA, resulting in enhanced catalysis; however, dimerization is not observed on large genomic DNA where the potential for intersite processive methylation precludes any dimerization-dependent activation. An activated form of the enzyme is apparent on large genomic DNA and can also be achieved with high concentrations of short, synthetic substrates. We suggest that this activation is inherent on polymeric DNA where either multiple GATC sites are available for methylation or the partitioning of the enzyme onto nonspecific DNA is favored. Unlike other restriction-modification methyltransferases, EcoDam carries out intrasite processive catalysis whereby the enzyme-DNA complex methylates both strands of an unmethylated GATC site prior to dissociation from the DNA. This occurs with short 21 bp oligonucleotides and is highly dependent upon salt concentrations. Kinetic modeling which invokes enzyme activation by both dimerization and excess substrate provides mechanistic insights into key regulatory checkpoints for an enzyme involved in multiple, diverse biological pathways.
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Affiliation(s)
- Stephanie R Coffin
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA
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92
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Coffin SR, Reich NO. Escherichia coli DNA adenine methyltransferase: the structural basis of processive catalysis and indirect read-out. J Biol Chem 2009; 284:18390-400. [PMID: 19419959 PMCID: PMC2709375 DOI: 10.1074/jbc.m109.005876] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 04/08/2009] [Indexed: 11/06/2022] Open
Abstract
We have investigated the structural basis of processive GATC methylation by the Escherichia coli DNA adenine methyltransferase, which is critical in chromosome replication and mismatch repair. We determined the contribution of the orthologically conserved phosphate interactions involving residues Arg(95), Asn(126), Asn(132), Arg(116), and Lys(139), which directly contact the DNA outside the cognate recognition site (GATC) to processive catalysis, and that of residue Arg(137), which is not conserved and contacts the DNA backbone within the GATC sequence. Alanine substitutions at the conserved positions have large impacts on processivity yet do not impact k(cat)/K(m)(DNA) or DNA affinity (K(D)(DNA)). However, these mutants cause large preferences for GATC sites varying in flanking sequences when considering the pre-steady state efficiency constant k(chem)/K(D)(DNA). These changes occur mainly at the level of the methylation rate constant, which results in the observed decreases in processive catalysis. Thus, processivity and catalytic efficiency (k(cat)/K(m)(DNA)) are uncoupled in these mutants. These results reveal that the binding energy involved in DNA recognition contributes to the assembly of the active site rather than tight binding. Furthermore, the conserved residues (Arg(95), Asn(126), Asn(132), and Arg(116)) repress the modulation of the response of the enzyme to flanking sequence effects. Processivity impacted mutants do not show substrate-induced dimerization as is observed for the wild type enzyme. This study describes the structural means by which an enzyme that does not completely enclose its substrate has evolved to achieve processive catalysis, and how interactions with DNA flanking the recognition site alter this processivity.
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Affiliation(s)
| | - Norbert O. Reich
- From the Department of Chemistry and Biochemistry and
- the Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510
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93
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Estabrook RA, Nguyen TT, Fera N, Reich NO. Coupling sequence-specific recognition to DNA modification. J Biol Chem 2009; 284:22690-6. [PMID: 19497854 DOI: 10.1074/jbc.m109.015966] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Enzymes that modify DNA are faced with significant challenges in specificity for both substrate binding and catalysis. We describe how single hydrogen bonds between M.HhaI, a DNA cytosine methyltransferase, and its DNA substrate regulate the positioning of a peptide loop which is approximately 28 A away. Stopped-flow fluorescence measurements of a tryptophan inserted into the loop provide real-time observations of conformational rearrangements. These long-range interactions that correlate with substrate binding and critically, enzyme turnover, will have broad application to enzyme specificity and drug design for this medically relevant class of enzymes.
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Affiliation(s)
- R August Estabrook
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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94
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Furmanek-Blaszk B, Boratynski R, Zolcinska N, Sektas M. M1.MboII and M2.MboII type IIS methyltransferases: different specificities, the same target. MICROBIOLOGY-SGM 2009; 155:1111-1121. [PMID: 19332813 DOI: 10.1099/mic.0.025023-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Methylation of a base in a specific DNA sequence protects the DNA from nucleolytic cleavage by restriction enzymes recognizing the same sequence. The MboII restriction-modification (R-M) system of Moraxella bovis ATCC 10900 consists of a restriction endonuclease gene and two methyltransferase genes. The enzymes encoded by this system recognize an asymmetrical sequence 5'-GAAGA-3'/3'-CTTCT-5'. M1.MboII modifies the last adenine in the recognition sequence 5'-GAAGA-3' to N(6)-methyladenine. A second methylase, M2.MboII, was cloned and purified to electrophoretic homogeneity using a four-step chromatographic procedure. It was demonstrated that M2.MboII modifies the internal cytosine in the recognition sequence 3'-CTTCT-5', yielding N(4)-methylcytosine, and moreover is able to methylate single-stranded DNA. The protein exists in solution as a monomer of molecular mass 30 000+/-1000 Da under denaturing conditions. Divalent cations (Ca(2+), Mg(2+), Mn(2+) and Zn(2+)) inhibit M2.MboII methylation activity. It was found that the isomethylomer M2.NcuI from Neisseria cuniculi ATCC 14688 behaves in the same manner. Functional analysis showed that the complete MboII R-M system, consisting of two methyltransferases genes and the mboIIR gene, is the most stable and the least harmful to bacterial cells.
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Affiliation(s)
| | - Robert Boratynski
- Department of Microbiology, University of Gdansk, 80-822 Gdansk, Kladki 24, Poland
| | - Natalia Zolcinska
- Department of Microbiology, University of Gdansk, 80-822 Gdansk, Kladki 24, Poland
| | - Marian Sektas
- Department of Microbiology, University of Gdansk, 80-822 Gdansk, Kladki 24, Poland
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95
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Goto-Ito S, Ito T, Ishii R, Muto Y, Bessho Y, Yokoyama S. Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5. Proteins 2009; 72:1274-89. [PMID: 18384044 DOI: 10.1002/prot.22019] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methylation of the N1 atom of guanosine at position 37 in tRNA, the position 3'-adjacent to the anticodon, generates the modified nucleoside m(1)G37. In archaea and eukaryotes, m(1)G37 synthesis is catalyzed by tRNA(m(1)G37)methyltransferase (archaeal or eukaryotic Trm5, a/eTrm5). Here we report the crystal structure of archaeal Trm5 (aTrm5) from Methanocaldococcus jannaschii (formerly known as Methanococcus jannaschii) in complex with the methyl donor analogue at 2.2 A resolution. The crystal structure revealed that the entire protein is composed of three structural domains, D1, D2, and D3. In the a/eTrm5 primary structures, D2 and D3 are highly conserved, while D1 is not conserved. The D3 structure is the Rossmann fold, which is the hallmark of the canonical class-I methyltransferases. The a/eTrm5-defining domain, D2, exhibits structural similarity to some class-I methyltransferases. In contrast, a DALI search with the D1 structure yielded no structural homologues. In the crystal structure, D3 contacts both D1 and D2. The residues involved in the D1:D3 interactions are not conserved, while those participating in the D2:D3 interactions are well conserved. D1 and D2 do not contact each other, and the linker between them is disordered. aTrm5 fragments corresponding to the D1 and D2-D3 regions were prepared in a soluble form. The NMR analysis of the D1 fragment revealed that D1 is well folded by itself, and it did not interact with either the D2-D3 fragment or the tRNA. The NMR analysis of the D2-D3 fragment revealed that it is well folded, independently of D1, and that it interacts with tRNA. Furthermore, the D2-D3 fragment was as active as the full-length enzyme for tRNA methylation. The positive charges on the surface of D2-D3 may be involved in tRNA binding. Therefore, these findings suggest that the interaction between D1 and D3 is not persistent, and that the D2-D3 region plays the major role in tRNA methylation.
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Affiliation(s)
- Sakurako Goto-Ito
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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96
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Stutes M, Tran S, DeMorrow S. Genetic and epigenetic changes associated with cholangiocarcinoma: from DNA methylation to microRNAs. World J Gastroenterol 2008. [PMID: 18161915 DOI: 10.3748/wjg.13.6465] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cholangiocarcinomas are malignant epithelial liver tumors arising from the intra- and extra-hepatic bile ducts. Little is known about the molecular development of this disease, and very few effective treatment options are available. Thus, prognosis is poor. Genetic and epigenetic changes play an integral role in the neoplastic transformation of human cells to their malignant counterparts. This review summarizes some of the more prevalent genetic alterations (by microRNA expression) and epigenetic changes (hypermethylation of specific gene promoters) that are thought to contribute to the carcinogenic process in cholangiocarcinoma.
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Affiliation(s)
- Monique Stutes
- Division of Research and Education, Scott & White Hospital, Temple, TX 76504, USA
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97
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Ding WJ, Fang JY, Chen XY, Peng YS. The expression and clinical significance of DNA methyltransferase proteins in human gastric cancer. Dig Dis Sci 2008; 53:2083-9. [PMID: 18253830 DOI: 10.1007/s10620-007-0145-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Accepted: 11/24/2007] [Indexed: 02/06/2023]
Abstract
This study investigates the varied expression of DNA methyltransferase (DNMT) proteins in gastric cancer (GC) and their relationship with the biological behavior of the tissues. Immunohistochemistry was used to detect the expression of the 3 DNMTs in gastric tissues. We discovered that the positive rates of DNMT1, DNMT3a, and DNMT3b expression in GC tissues were 81.6%, 81.6%, and 68.4%, respectively, and they were significantly higher than those of both para-cancerous (39.5%, 50%, and 44.7%) and normal tissues (10.5%, 10.5%, and 7.9%). DNMT1 was well distributed in the cytoplasm and nuclei of tumor cells or glands, while DNMT3a and 3b were well distributed only in the cytoplasm, as shown by staining a dark brown color. A significant correlation between the DNMT1 and DNMT3a proteins (P < 0.01), a low correlation between DNMT3a and DNMT3b (P < 0.05), and no correlation between DNMT1 and DNMT3b (P > 0.05) were observed. DNMT1 protein expression exhibited no correlation with age, lymphnode metastasis, and also tumor differentiation, but it may have had a correlation with gender. The DNMT3 family was not associated with these factors. Therefore, DNMT overexpression is involved in gastric tumorigenesis, but there is no correlation between the DNMTs and the biological behaviors of tissues.
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Affiliation(s)
- Wen-Jin Ding
- Shanghai Jiao-Tong University School of Medicine Renji Hospital, Shanghai Institute of Digestive Disease, Shanghai, China
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98
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Morita R, Ishikawa H, Nakagawa N, Kuramitsu S, Masui R. Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8. Proteins 2008; 73:259-64. [DOI: 10.1002/prot.22158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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99
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Coffin SR, Reich NO. Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences. J Biol Chem 2008; 283:20106-16. [PMID: 18502761 DOI: 10.1074/jbc.m802502200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli DNA adenine methyltransferase (EcoDam) methylates the N-6 position of the adenine in the sequence 5'-GATC-3' and plays vital roles in gene regulation, mismatch repair, and DNA replication. It remains unclear how the small number of critical GATC sites involved in the regulation of replication and gene expression are differentially methylated, whereas the approximately 20,000 GATCs important for mismatch repair and dispersed throughout the genome are extensively methylated. Our prior work, limited to the pap regulon, showed that methylation efficiency is controlled by sequences immediately flanking the GATC sites. We extend these studies to include GATC sites involved in diverse gene regulatory and DNA replication pathways as well as sites previously shown to undergo differential in vivo methylation but whose function remains to be assigned. EcoDam shows no change in affinity with variations in flanking sequences derived from these sources, but methylation kinetics varied 12-fold. A-tracts immediately adjacent to the GATC site contribute significantly to these differences in methylation kinetics. Interestingly, only when the poly(A) is located 5' of the GATC are the changes in methylation kinetics revealed. Preferential methylation is obscured when two GATC sites are positioned on the same DNA molecule, unless both sites are surrounded by large amounts of nonspecific DNA. Thus, facilitated diffusion and sequences immediately flanking target sites contribute to higher order specificity for EcoDam; we suggest that the diverse biological roles of the enzyme are in part regulated by these two factors, which may be important for other enzymes that sequence-specifically modify DNA.
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Affiliation(s)
- Stephanie R Coffin
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
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100
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Kornblatt JA, Zhou JM, Ibrahim RK. Structure-activity relationships of wheat flavone O-methyltransferase - a homodimer of convenience. FEBS J 2008; 275:2255-66. [DOI: 10.1111/j.1742-4658.2008.06377.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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