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Hayashi M, Wada Y, Yamamura A, Inoue H, Yamashita N, Ichimura S, Iida Y. Evaluation of the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions. Biosci Biotechnol Biochem 2024; 88:1155-1163. [PMID: 39085041 DOI: 10.1093/bbb/zbae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024]
Abstract
We previously identified M.ApeKI from Aeropyum pernix K1 as a highly thermostable DNA (cytosine-5)-methyltransferase. M.ApeKI uses the type II restriction-modification system (R-M system), among the best-studied R-M systems. Although endonucleases generally utilize Mg (II) as a cofactor, several reports have shown that MTases exhibit different reactions in the presence of metal ions. This study aim was to evaluate the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions. We evaluated the influence of metal ions on the catalytic activity and DNA binding of M.ApeKI. The catalytic activity was inhibited by Cu (II), Mg (II), Mn (II), and Zn (II), each at 5 m m. DNA binding was more strongly inhibited by 5 m m Cu (II) and 10 m m Zn (II). To our knowledge, this is the first report showing that DNA binding of type II MTase is inhibited by metal ions.
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Affiliation(s)
- Mao Hayashi
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Yoshinari Wada
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Akira Yamamura
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Hideki Inoue
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Naoya Yamashita
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Shigetoshi Ichimura
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Yasuhiro Iida
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
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2
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Yang W, Luyten Y, Reister E, Mangelson H, Sisson Z, Auch B, Liachko I, Roberts RJ, Ettwiller L. Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5 C methyltransferase specificities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603628. [PMID: 39071437 PMCID: PMC11275837 DOI: 10.1101/2024.07.15.603628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Methylation patterns in bacteria can be used to study Restriction-Modification (RM) or other defense systems with novel properties. While m4 C and m6 A methylation is well characterized mainly through PacBio sequencing, the landscape of m5 C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5 C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on viral DNA and compared to host DNA, strengthening evidence for virus-host interaction. Applied to three different microbiomes, the method unveils over 1900 motifs that were deposited in REBASE. The motifs include a novel 8-base recognition site (CAT m5 CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5 C methyltransferase specificities, providing insights to bacterial biology and biotechnological applications.
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3
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Albert P, Varga B, Ferenc G, Kiss A. Conversion of the CG specific M.MpeI DNA methyltransferase into an enzyme predominantly methylating CCA and CCC sites. Nucleic Acids Res 2024; 52:1896-1908. [PMID: 38164970 PMCID: PMC10899764 DOI: 10.1093/nar/gkad1217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
We used structure guided mutagenesis and directed enzyme evolution to alter the specificity of the CG specific bacterial DNA (cytosine-5) methyltransferase M.MpeI. Methylation specificity of the M.MpeI variants was characterized by digestions with methylation sensitive restriction enzymes and by measuring incorporation of tritiated methyl groups into double-stranded oligonucleotides containing single CC, CG, CA or CT sites. Site specific mutagenesis steps designed to disrupt the specific contacts between the enzyme and the non-substrate base pair of the target sequence (5'-CG/5'-CG) yielded M.MpeI variants with varying levels of CG specific and increasing levels of CA and CC specific MTase activity. Subsequent random mutagenesis of the target recognizing domain coupled with selection for non-CG specific methylation yielded a variant, which predominantly methylates CC dinucleotides, has very low activity on CG and CA sites, and no activity on CT sites. This M.MpeI variant contains a one amino acid deletion (ΔA323) and three substitutions (N324G, R326G and E305N) in the target recognition domain. The mutant enzyme has very strong preference for A and C in the 3' flanking position making it a CCA and CCC specific DNA methyltransferase.
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Affiliation(s)
- Pál Albert
- Laboratory of DNA-Protein Interactions, Institute of Biochemistry, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Bence Varga
- Laboratory of DNA-Protein Interactions, Institute of Biochemistry, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
- Nucleic Acid Synthesis Laboratory, Institute of Plant Biology, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
| | - Györgyi Ferenc
- Nucleic Acid Synthesis Laboratory, Institute of Plant Biology, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
| | - Antal Kiss
- Laboratory of DNA-Protein Interactions, Institute of Biochemistry, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
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4
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Liang M, Pan W, You Y, Qin X, Su H, Zhan Z, Weng S, Guo C, He J. Hypermethylated genome of a fish vertebrate iridovirus ISKNV plays important roles in viral infection. Commun Biol 2024; 7:237. [PMID: 38413759 PMCID: PMC10899263 DOI: 10.1038/s42003-024-05919-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Iridoviruses are nucleocytoplasmic large dsDNA viruses that infect invertebrates and ectothermic vertebrates. The hypermethylated genome of vertebrate iridoviruses is unique among animal viruses. However, the map and function of iridovirus genomic methylation remain unknown. Herein, the methylated genome of Infectious spleen and kidney necrosis virus (ISKNV, a fish iridovirus), and its role in viral infection, are investigated. The methylation level of ISKNV is 23.44%. The hypermethylated genome is essential for ISKNV amplification, but there is no correlation between hypermethylation and viral gene expression. The hypomethylated ISKNV (obtained via 5-Azacytidine) activates a strong immunoreaction in vitro and reduces its pathogenicity in vivo. The unmethylated viral DNA can induce a stronger immunoreaction in vitro, whereas inactivated hypomethylated ISKNV can induce a stronger immunoreaction in vivo, suggesting ISKNV may evade from immune system by increasing its genome methylation level. Our work provides new insights into the role of genome methylation in viral infection.
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Affiliation(s)
- Mincong Liang
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weiqiang Pan
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanlin You
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaowei Qin
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hualong Su
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhipeng Zhan
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shaoping Weng
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Changjun Guo
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China.
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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5
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Zhu C, Hao Z, Liu D. Reshaping the Landscape of the Genome: Toolkits for Precise DNA Methylation Manipulation and Beyond. JACS AU 2024; 4:40-57. [PMID: 38274248 PMCID: PMC10806789 DOI: 10.1021/jacsau.3c00671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 01/27/2024]
Abstract
DNA methylation plays a pivotal role in various biological processes and is highly related to multiple diseases. The exact functions of DNA methylation are still puzzling due to its uneven distribution, dynamic conversion, and complex interactions with other substances. Current methods such as chemical- and enzyme-based sequencing techniques have enabled us to pinpoint DNA methylation at single-base resolution, which necessitated the manipulation of DNA methylation at comparable resolution to precisely illustrate the correlations and causal relationships between the functions of DNA methylation and its spatiotemporal patterns. Here a perspective on the past, recent process, and future of precise DNA methylation tools is provided. Specifically, genome-wide and site-specific manipulation of DNA methylation methods is discussed, with an emphasis on their principles, limitations, applications, and future developmental directions.
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Affiliation(s)
- Chenyou Zhu
- Engineering
Research Center of Advanced Rare Earth Materials, Ministry of Education,
Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ziyang Hao
- School
of Pharmaceutical Sciences, Capital Medical
University, Beijing, 100069, PR China
| | - Dongsheng Liu
- Engineering
Research Center of Advanced Rare Earth Materials, Ministry of Education,
Department of Chemistry, Tsinghua University, Beijing 100084, China
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6
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Sergeev AV, Loiko AG, Genatullina AI, Petrov AS, Kubareva EA, Dolinnaya NG, Gromova ES. Crosstalk between G-Quadruplexes and Dnmt3a-Mediated Methylation of the c-MYC Oncogene Promoter. Int J Mol Sci 2023; 25:45. [PMID: 38203216 PMCID: PMC10779317 DOI: 10.3390/ijms25010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
The methylation of cytosines at CpG sites in DNA, carried out de novo by DNA methyltransferase Dnmt3a, is a basic epigenetic modification involved in gene regulation and genome stability. Aberrant CpG methylation in gene promoters leads to oncogenesis. In oncogene promoters, CpG sites often colocalize with guanine-rich sequences capable of folding into G-quadruplexes (G4s). Our in vitro study aimed to investigate how parallel G4s formed by a sequence derived from the c-MYC oncogene promoter region affect the activity of the Dnmt3a catalytic domain (Dnmt3a-CD). For this purpose, we designed synthetic oligonucleotide constructs: a c-MYC G4-forming oligonucleotide and linear double-stranded DNA containing an embedded stable extrahelical c-MYC G4. The topology and thermal stability of G4 structures in these DNA models were analyzed using physicochemical techniques. We showed that Dnmt3a-CD specifically binds to an oligonucleotide containing c-MYC G4, resulting in inhibition of its methylation activity. c-MYC G4 formation in a double-stranded context significantly reduces Dnmt3a-CD-induced methylation of a CpG site located in close proximity to the quadruplex structure; this effect depends on the distance between the non-canonical structure and the specific CpG site. One would expect DNA hypomethylation near the G4 structure, while regions distant from this non-canonical form would maintain a regular pattern of high methylation levels. We hypothesize that the G4 structure sequesters the Dnmt3a-CD and impedes its proper binding to B-DNA, resulting in hypomethylation and activation of c-MYC transcription.
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Affiliation(s)
- Alexander V. Sergeev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (A.V.S.); (A.G.L.); (A.I.G.); (A.S.P.); (N.G.D.); (E.S.G.)
| | - Andrei G. Loiko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (A.V.S.); (A.G.L.); (A.I.G.); (A.S.P.); (N.G.D.); (E.S.G.)
| | - Adelya I. Genatullina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (A.V.S.); (A.G.L.); (A.I.G.); (A.S.P.); (N.G.D.); (E.S.G.)
| | - Alexander S. Petrov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (A.V.S.); (A.G.L.); (A.I.G.); (A.S.P.); (N.G.D.); (E.S.G.)
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (A.V.S.); (A.G.L.); (A.I.G.); (A.S.P.); (N.G.D.); (E.S.G.)
| | - Elizaveta S. Gromova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (A.V.S.); (A.G.L.); (A.I.G.); (A.S.P.); (N.G.D.); (E.S.G.)
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7
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Zhou J, Horton JR, Kaur G, Chen Q, Li X, Mendoza F, Wu T, Blumenthal RM, Zhang X, Cheng X. Biochemical and structural characterization of the first-discovered metazoan DNA cytosine-N4 methyltransferase from the bdelloid rotifer Adineta vaga. J Biol Chem 2023; 299:105017. [PMID: 37414145 PMCID: PMC10406627 DOI: 10.1016/j.jbc.2023.105017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
Much is known about the generation, removal, and roles of 5-methylcytosine (5mC) in eukaryote DNA, and there is a growing body of evidence regarding N6-methyladenine, but very little is known about N4-methylcytosine (4mC) in the DNA of eukaryotes. The gene for the first metazoan DNA methyltransferase generating 4mC (N4CMT) was reported and characterized recently by others, in tiny freshwater invertebrates called bdelloid rotifers. Bdelloid rotifers are ancient, apparently asexual animals, and lack canonical 5mC DNA methyltransferases. Here, we characterize the kinetic properties and structural features of the catalytic domain of the N4CMT protein from the bdelloid rotifer Adineta vaga. We find that N4CMT generates high-level methylation at preferred sites, (a/c)CG(t/c/a), and low-level methylation at disfavored sites, exemplified by ACGG. Like the mammalian de novo 5mC DNA methyltransferase 3A/3B (DNMT3A/3B), N4CMT methylates CpG dinucleotides on both DNA strands, generating hemimethylated intermediates and eventually fully methylated CpG sites, particularly in the context of favored symmetric sites. In addition, like DNMT3A/3B, N4CMT methylates non-CpG sites, mainly CpA/TpG, though at a lower rate. Both N4CMT and DNMT3A/3B even prefer similar CpG-flanking sequences. Structurally, the catalytic domain of N4CMT closely resembles the Caulobacter crescentus cell cycle-regulated DNA methyltransferase. The symmetric methylation of CpG, and similarity to a cell cycle-regulated DNA methyltransferase, together suggest that N4CMT might also carry out DNA synthesis-dependent methylation following DNA replication.
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Affiliation(s)
- Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Qin Chen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xuwen Li
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Fabian Mendoza
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tao Wu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA.
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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8
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Abstract
DNA-editing enzymes perform chemical reactions on DNA nucleobases. These reactions can change the genetic identity of the modified base or modulate gene expression. Interest in DNA-editing enzymes has burgeoned in recent years due to the advent of clustered regularly interspaced short palindromic repeat-associated (CRISPR-Cas) systems, which can be used to direct their DNA-editing activity to specific genomic loci of interest. In this review, we showcase DNA-editing enzymes that have been repurposed or redesigned and developed into programmable base editors. These include deaminases, glycosylases, methyltransferases, and demethylases. We highlight the astounding degree to which these enzymes have been redesigned, evolved, and refined and present these collective engineering efforts as a paragon for future efforts to repurpose and engineer other families of enzymes. Collectively, base editors derived from these DNA-editing enzymes facilitate programmable point mutation introduction and gene expression modulation by targeted chemical modification of nucleobases.
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Affiliation(s)
- Kartik L Rallapalli
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA;
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA;
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9
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Gao Q, Lu S, Wang Y, He L, Wang M, Jia R, Chen S, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Mao S, Ou X, Sun D, Tian B, Cheng A. Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria. Front Microbiol 2023; 14:1129437. [PMID: 37032876 PMCID: PMC10073500 DOI: 10.3389/fmicb.2023.1129437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
Epigenetics modulates expression levels of various important genes in both prokaryotes and eukaryotes. These epigenetic traits are heritable without any change in genetic DNA sequences. DNA methylation is a universal mechanism of epigenetic regulation in all kingdoms of life. In bacteria, DNA methylation is the main form of epigenetic regulation and plays important roles in affecting clinically relevant phenotypes, such as virulence, host colonization, sporulation, biofilm formation et al. In this review, we survey bacterial epigenomic studies and focus on the recent developments in the structure, function, and mechanism of several highly conserved bacterial DNA methylases. These methyltransferases are relatively common in bacteria and participate in the regulation of gene expression and chromosomal DNA replication and repair control. Recent advances in sequencing techniques capable of detecting methylation signals have enabled the characterization of genome-wide epigenetic regulation. With their involvement in critical cellular processes, these highly conserved DNA methyltransferases may emerge as promising targets for developing novel epigenetic inhibitors for biomedical applications.
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Affiliation(s)
- Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Shuwei Lu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuwei Wang
- Key Laboratory of Livestock and Poultry Provenance Disease Research in Mianyang, Sichuan, China
| | - Longgui He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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10
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Mattei AL, Bailly N, Meissner A. DNA methylation: a historical perspective. Trends Genet 2022; 38:676-707. [DOI: 10.1016/j.tig.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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11
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Furuta Y, Miura F, Ichise T, Nakayama SMM, Ikenaka Y, Zorigt T, Tsujinouchi M, Ishizuka M, Ito T, Higashi H. A GCDGC-specific DNA (cytosine-5) methyltransferase that methylates the GCWGC sequence on both strands and the GCSGC sequence on one strand. PLoS One 2022; 17:e0265225. [PMID: 35312710 PMCID: PMC8936443 DOI: 10.1371/journal.pone.0265225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
5-Methylcytosine is one of the major epigenetic marks of DNA in living organisms. Some bacterial species possess DNA methyltransferases that modify cytosines on both strands to produce fully-methylated sites or on either strand to produce hemi-methylated sites. In this study, we characterized a DNA methyltransferase that produces two sequences with different methylation patterns: one methylated on both strands and another on one strand. M.BatI is the orphan DNA methyltransferase of Bacillus anthracis coded in one of the prophages on the chromosome. Analysis of M.BatI modified DNA by bisulfite sequencing revealed that the enzyme methylates the first cytosine in sequences of 5ʹ-GCAGC-3ʹ, 5ʹ-GCTGC-3ʹ, and 5ʹ-GCGGC-3ʹ, but not of 5ʹ-GCCGC-3ʹ. This resulted in the production of fully-methylated 5ʹ-GCWGC-3ʹ and hemi-methylated 5ʹ-GCSGC-3ʹ. M.BatI also showed toxicity when expressed in E. coli, which was caused by a mechanism other than DNA modification activity. Homologs of M.BatI were found in other Bacillus species on different prophage like regions, suggesting the spread of the gene by several different phages. The discovery of the DNA methyltransferase with unique modification target specificity suggested unrevealed diversity of target sequences of bacterial cytosine DNA methyltransferase.
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Affiliation(s)
- Yoshikazu Furuta
- Division of Infection and Immunity, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- * E-mail:
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Takahiro Ichise
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Shouta M. M. Nakayama
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshinori Ikenaka
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Tuvshinzaya Zorigt
- Division of Infection and Immunity, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mai Tsujinouchi
- Division of Infection and Immunity, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mayumi Ishizuka
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Hideaki Higashi
- Division of Infection and Immunity, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
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12
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Wang J, Catania S, Wang C, de la Cruz MJ, Rao B, Madhani HD, Patel DJ. Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance. Mol Cell 2022; 82:1186-1198.e6. [PMID: 35202575 PMCID: PMC8956514 DOI: 10.1016/j.molcel.2022.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 10/19/2022]
Abstract
Epigenetic evolution occurs over million-year timescales in Cryptococcus neoformans and is mediated by DNMT5, the first maintenance type cytosine methyltransferase identified in the fungal or protist kingdoms, the first dependent on adenosine triphosphate (ATP), and the most hemimethyl-DNA-specific enzyme known. To understand these novel properties, we solved cryo-EM structures of CnDNMT5 in three states. These studies reveal an elaborate allosteric cascade in which hemimethylated DNA binding first activates the SNF2 ATPase domain by a large rigid body rotation while the target cytosine partially flips out of the DNA duplex. ATP binding then triggers striking structural reconfigurations of the methyltransferase catalytic pocket to enable cofactor binding, completion of base flipping, and catalysis. Bound unmethylated DNA does not open the catalytic pocket and is instead ejected upon ATP binding, driving high fidelity. This unprecedented chaperone-like, enzyme-remodeling role of the SNF2 ATPase domain illuminates how energy is used to enable faithful epigenetic memory.
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Affiliation(s)
- Juncheng Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Sandra Catania
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chongyuan Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - M Jason de la Cruz
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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13
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Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:1-19. [DOI: 10.1007/978-3-031-11454-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Evaluation of the Properties of the DNA Methyltransferase from Aeropyrum pernix K1. Microbiol Spectr 2021; 9:e0018621. [PMID: 34585946 PMCID: PMC8557920 DOI: 10.1128/spectrum.00186-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Little is known regarding the DNA methyltransferases (MTases) in hyperthermophilic archaea. In this study, we focus on an MTase from Aeropyrum pernix K1, a hyperthermophilic archaeon that is found in hydrothermal vents and whose optimum growth temperature is 90°C to 95°C. From genomic sequence analysis, A. pernix K1 has been predicted to have a restriction-modification system (R-M system). The restriction endonuclease from A. pernix K1 (known as ApeKI from New England BioLabs Inc. [catalog code R06435]) has been described previously, but the properties of the MTase from A. pernix K1 (M.ApeKI) have not yet been clarified. Thus, we demonstrated the properties of M.ApeKI. In this study, M.ApeKI was expressed in Escherichia coli strain JM109 and affinity purified using its His tag. The recognition sequence of M.ApeKI was determined by methylation activity and bisulfite sequencing (BS-seq). High-performance liquid chromatography (HPLC) was used to detect the position of the methyl group in methylated cytosine. As a result, it was clarified that M.ApeKI adds the methyl group at the C-5 position of the second cytosine in 5'-GCWGC-3'. Moreover, we also determined that the MTase optimum temperature was over 70°C and that it is strongly tolerant to high temperatures. M.ApeKI is the first highly thermostable DNA (cytosine-5)-methyltransferase to be evaluated by experimental evidence. IMPORTANCE In general, thermophilic bacteria with optimum growth temperatures over or equal to 60°C have been predicted to include only N4-methylcytosine or N6-methyladenine as methylated bases in their DNA, because 5-methylcytosine is susceptible to deamination by heat. However, from this study, A. pernix K1, with an optimum growth temperature at 95°C, was demonstrated to produce a DNA (cytosine-5)-methyltransferase. Thus, A. pernix K1 presumably has 5-methylcytosine in its DNA and may produce an original repair system for the expected C-to-T mutations. M.ApeKI was demonstrated to be tolerant to high temperatures; thus, we expect that M.ApeKI may be valuable for the development of a novel analysis system or epigenetic editing tool.
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15
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Anton BP, Roberts RJ. Beyond Restriction Modification: Epigenomic Roles of DNA Methylation in Prokaryotes. Annu Rev Microbiol 2021; 75:129-149. [PMID: 34314594 DOI: 10.1146/annurev-micro-040521-035040] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The amount of bacterial and archaeal genome sequence and methylome data has greatly increased over the last decade, enabling new insights into the functional roles of DNA methylation in these organisms. Methyltransferases (MTases), the enzymes responsible for DNA methylation, are exchanged between prokaryotes through horizontal gene transfer and can function either as part of restriction-modification systems or in apparent isolation as single (orphan) genes. The patterns of DNA methylation they confer on the host chromosome can have significant effects on gene expression, DNA replication, and other cellular processes. Some processes require very stable patterns of methylation, resulting in conservation of persistent MTases in a particular lineage. Other processes require patterns that are more dynamic yet more predictable than what is afforded by horizontal gene transfer and gene loss, resulting in phase-variable or recombination-driven MTase alleles. In this review, we discuss what is currently known about the functions of DNA methylation in prokaryotes in light of these evolutionary patterns. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Brian P Anton
- New England Biolabs, Ipswich, Massachusetts 01938, USA; ,
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16
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Phage-encoded ten-eleven translocation dioxygenase (TET) is active in C5-cytosine hypermodification in DNA. Proc Natl Acad Sci U S A 2021; 118:2026742118. [PMID: 34155108 PMCID: PMC8256090 DOI: 10.1073/pnas.2026742118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chemical tailoring of canonical bases expands the functionality of DNA in the same manner that posttranscriptional and -translational modifications enhance functional diversity in RNA and proteins. We describe the activities of ten-eleven translocation dioxygenase (TET)-like iron(II)- and 2-oxo-glutarate–dependent 5mC dioxygenases that are encoded by several bacteriophages to enable hypermodification of C5-methyl cytosine bases in their DNA. Phage TETs act on methylation marks deposited within GpC sequences by functionally-associated cytosine 5-methyltransferases. The hydroxymethyl groups installed are further elaborated by tailoring enzymes, thereby decorating the phage DNA with diverse, complex modifications. These modifications are predicted to have protective roles against host defenses during viral infection. TET/JBP (ten-eleven translocation/base J binding protein) enzymes are iron(II)- and 2-oxo-glutarate–dependent dioxygenases that are found in all kingdoms of life and oxidize 5-methylpyrimidines on the polynucleotide level. Despite their prevalence, few examples have been biochemically characterized. Among those studied are the metazoan TET enzymes that oxidize 5-methylcytosine in DNA to hydroxy, formyl, and carboxy forms and the euglenozoa JBP dioxygenases that oxidize thymine in the first step of base J biosynthesis. Both enzymes have roles in epigenetic regulation. It has been hypothesized that all TET/JBPs have their ancestral origins in bacteriophages, but only eukaryotic orthologs have been described. Here we demonstrate the 5mC-dioxygenase activity of several phage TETs encoded within viral metagenomes. The clustering of these TETs in a phylogenetic tree correlates with the sequence specificity of their genomically cooccurring cytosine C5-methyltransferases, which install the methyl groups upon which TETs operate. The phage TETs favor Gp5mC dinucleotides over the 5mCpG sites targeted by the eukaryotic TETs and are found within gene clusters specifying complex cytosine modifications that may be important for DNA packaging and evasion of host restriction.
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17
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Khrabrova DA, Yakubovskaya MG, Gromova ES. AML-Associated Mutations in DNA Methyltransferase DNMT3A. BIOCHEMISTRY (MOSCOW) 2021; 86:307-318. [PMID: 33838631 DOI: 10.1134/s000629792103007x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In mammals, DNA methylation is an essential epigenetic modification necessary for the maintenance of genome stability, regulation of gene expression, and other processes. Carcinogenesis is accompanied by multiple changes in the DNA methylation pattern and DNA methyltransferase (DNMT) genes; these changes are often associated with poor disease prognosis. Human DNA methyltransferase DNMT3A is responsible for de novo DNA methylation. Missense mutations in the DNMT3A gene occur frequently at the early stages of tumor development and are often observed in hematologic malignances, especially in acute myeloid leukemia (AML), with a prevalence of the R882H mutation. This mutation is the only one that has been extensively studied using both model DNA substrates and cancer cell lines. Biochemical characterization of other DNMT3A mutants is necessary to assess their potential effects on the DNMT3A functioning. In this review, we describe DNMT3A mutations identified in AML with special emphasis on the missense mutations in the DNMT3A catalytic domain. The impact of R882H and less common missense mutations on the DNMT3A activity toward model DNA substrates and in cancer cell lines is discussed together with the underlying molecular mechanisms. Understanding general features of these mechanisms will be useful for further development of novel approaches for early diagnostics of hematologic diseases and personalized cancer therapy.
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Affiliation(s)
- Dariya A Khrabrova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Marianna G Yakubovskaya
- Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, 115478, Russia
| | - Elizaveta S Gromova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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18
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Molaro A, Malik HS, Bourc'his D. Dynamic Evolution of De Novo DNA Methyltransferases in Rodent and Primate Genomes. Mol Biol Evol 2021; 37:1882-1892. [PMID: 32077945 PMCID: PMC7306680 DOI: 10.1093/molbev/msaa044] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transcriptional silencing of retrotransposons via DNA methylation is paramount for mammalian fertility and reproductive fitness. During germ cell development, most mammalian species utilize the de novo DNA methyltransferases DNMT3A and DNMT3B to establish DNA methylation patterns. However, many rodent species deploy a third enzyme, DNMT3C, to selectively methylate the promoters of young retrotransposon insertions in their germline. The evolutionary forces that shaped DNMT3C’s unique function are unknown. Using a phylogenomic approach, we confirm here that Dnmt3C arose through a single duplication of Dnmt3B that occurred ∼60 Ma in the last common ancestor of muroid rodents. Importantly, we reveal that DNMT3C is composed of two independently evolving segments: the latter two-thirds have undergone recurrent gene conversion with Dnmt3B, whereas the N-terminus has instead evolved under strong diversifying selection. We hypothesize that positive selection of Dnmt3C is the result of an ongoing evolutionary arms race with young retrotransposon lineages in muroid genomes. Interestingly, although primates lack DNMT3C, we find that the N-terminus of DNMT3A has also evolved under diversifying selection. Thus, the N-termini of two independent de novo methylation enzymes have evolved under diversifying selection in rodents and primates. We hypothesize that repression of young retrotransposons might be driving the recurrent innovation of a functional domain in the N-termini on germline DNMT3s in mammals.
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Affiliation(s)
- Antoine Molaro
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA
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19
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Chen X, Xu X, Shen X, Li H, Zhu C, Chen R, Munir N, Zhang Z, Chen Y, Xuhan X, Lin Y, Lai Z. Genome-wide investigation of DNA methylation dynamics reveals a critical role of DNA demethylation during the early somatic embryogenesis of Dimocarpus longan Lour. TREE PHYSIOLOGY 2020; 40:1807-1826. [PMID: 32722792 DOI: 10.1093/treephys/tpaa097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 05/23/2023]
Abstract
DNA methylation plays essential roles in gene regulation, chromatin structure stability, gene imprinting, X chromosome inactivation and embryonic development. However, the dynamics and functions of DNA methylation during the early stage of longan (Dimocarpus longan) somatic embryogenesis (SE) are still unclear. In this study, we carried out whole genome bisulphite sequencing and transcriptome sequencing analyses for embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC) and globular embryos (GE) in an early SE system. At a global level, the DNA 5-methylcytosine content in EC, ICpEC and GE was 24.59, 19.65 and 19.74%, respectively, suggesting a global decrease in DNA methylation from EC to ICpEC and then a slight increase from ICpEC to GE. Differentially methylated region (DMR) analysis showed that hypomethylation mainly occurred in CHH contexts. Gene ontology and Kyoto encyclopedia of genes and genomes analysis of hypomethylated-CHH-DMR-associated genes revealed that zein biosynthesis, fatty acid biosynthesis, circadian rhythm and mitophagy pathways were involved in longan early SE. Expression patterns of DNA methyltransferase and demethylase genes during longan early SE suggested that the decrease in DNA methylation was probably regulated by DNA methyltransferase genes and the DNA demethylase gene REPRESSOR OF SILENCING 1 (ROS1). The correlation between DNA hypomethylation and gene expression revealed that decreased DNA methylation did not cause extensive changes in gene expression during early longan SE and that gene expression may be affected by methylation changes in gene and downstream regions. Inhibiting DNA methylation with 5-azacytidine treatment in EC promoted the formation of GE and enhanced the capability of longan SE. Our results suggest that DNA demethylation has important roles in longan SE development.
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Affiliation(s)
- Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xu Shen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hansheng Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- School of Resources and Chemical Engineering, Sanming University, Sanming 365000, China
| | - Chen Zhu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rongzhu Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Nigarish Munir
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xu Xuhan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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20
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Mankai H, Wende W, Slama N, Ayed A, Roberts RJ, Limam F. Biochemical and molecular characterization of a restriction endonuclease Tvu2HI from Thermoactinomyces vulgaris 2H and study of its R-M system. Int J Biol Macromol 2020; 164:3105-3113. [PMID: 32835801 DOI: 10.1016/j.ijbiomac.2020.08.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/08/2020] [Accepted: 08/19/2020] [Indexed: 11/16/2022]
Abstract
A bacterial strain 2H isolated from soil and identified as Thermoactinomyces vulgaris produce a potent Type II restriction endonuclease activity that has been extracted by a PEG/dextran aqueous two-phase system. Optimal temperature for the restriction endonuclease activity was 55-65°C. Specific DNA cleavage was obtained at pH range 7-10 and 10-20mM MgCl2. Restriction cleavage analysis followed by sequencing confirms GG^CC as the recognition sequence. This enzyme, named Tvu2HI, is a thermostable isoschizomer of the mesophilic prototype restriction endonuclease HaeIII. Sequencing of the complete Thermoactinomyces vulgaris 2H genome revealed the presence of two adjacent ORFs coding for the restriction endonuclease Tvu2HI and the corresponding methyltransferase; an ORF coding for a putative Vsr nicking enzyme was found close to those coding for the Tvu2HI restriction-modification system. Phylogenetic analysis based on sequence alignment suggests a common origin of Tvu2HI R-M system with HaeIII-like R-M systems. This is the first investigation dealing with a Type II restriction endonuclease identified in a natural isolate of the genus Thermoactinomyces.
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Affiliation(s)
- Houda Mankai
- Laboratory of Bioactive Substances, Center of Biotechnology of Borj Cedria, BP-901, Hammam-lif 2050, Tunisia; University of Tunis-El Manar, Campus Universitaire Farhat Hached, BP-94 Rommana, 1068 Tunis, Tunisia
| | - Wolfgang Wende
- Institute of Biochemistry, Justus Liebig University, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Nedra Slama
- Laboratory of Bioactive Substances, Center of Biotechnology of Borj Cedria, BP-901, Hammam-lif 2050, Tunisia
| | - Ameni Ayed
- Laboratory of Bioactive Substances, Center of Biotechnology of Borj Cedria, BP-901, Hammam-lif 2050, Tunisia
| | | | - Ferid Limam
- Laboratory of Bioactive Substances, Center of Biotechnology of Borj Cedria, BP-901, Hammam-lif 2050, Tunisia.
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21
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Woodcock CB, Horton JR, Zhang X, Blumenthal RM, Cheng X. Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences. Nucleic Acids Res 2020; 48:10034-10044. [PMID: 32453412 PMCID: PMC7544214 DOI: 10.1093/nar/gkaa446] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 01/09/2023] Open
Abstract
S-adenosyl-l-methionine dependent methyltransferases catalyze methyl transfers onto a wide variety of target molecules, including DNA and RNA. We discuss a family of methyltransferases, those that act on the amino groups of adenine or cytosine in DNA, have conserved motifs in a particular order in their amino acid sequence, and are referred to as class beta MTases. Members of this class include M.EcoGII and M.EcoP15I from Escherichia coli, Caulobacter crescentus cell cycle-regulated DNA methyltransferase (CcrM), the MTA1-MTA9 complex from the ciliate Oxytricha, and the mammalian MettL3-MettL14 complex. These methyltransferases all generate N6-methyladenine in DNA, with some members having activity on single-stranded DNA as well as RNA. The beta class of methyltransferases has a unique multimeric feature, forming either homo- or hetero-dimers, allowing the enzyme to use division of labor between two subunits in terms of substrate recognition and methylation. We suggest that M.EcoGII may represent an ancestral form of these enzymes, as its activity is independent of the nucleic acid type (RNA or DNA), its strandedness (single or double), and its sequence (aside from the target adenine).
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Affiliation(s)
- Clayton B Woodcock
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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22
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Woodcock CB, Horton JR, Zhou J, Bedford MT, Blumenthal RM, Zhang X, Cheng X. Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA. Nucleic Acids Res 2020; 48:10329-10341. [PMID: 32663306 PMCID: PMC7544203 DOI: 10.1093/nar/gkaa604] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022] Open
Abstract
The recently characterized mammalian writer (methyltransferase) and eraser (demethylase) of the DNA N6-methyladenine (N6mA) methyl mark act on single-stranded (ss) and transiently-unpaired DNA. As YTH domain-containing proteins bind N6mA-containing RNA in mammalian cells, we investigated whether mammalian YTH domains are also methyl mark readers of N6mA DNA. Here, we show that the YTH domain of YTHDC1 (known to localize in the nucleus) binds ssDNA containing N6mA, with a 10 nM dissociation constant. This binding is stronger by a factor of 5 than in an RNA context, tested under the same conditions. However, the YTH domains of YTHDF2 and YTHDF1 (predominantly cytoplasmic) exhibited the opposite effect with ∼1.5-2× stronger binding to ssRNA containing N6mA than to the corresponding DNA. We determined two structures of the YTH domain of YTHDC1 in complex with N6mA-containing ssDNA, which illustrated that YTHDC1 binds the methylated adenine in a single-stranded region flanked by duplexed DNA. We discuss the hypothesis that the writer-reader-eraser of N6mA-containining ssDNA is associated with maintaining genome stability. Structural comparison of YTH and SRA domains (the latter a DNA 5-methylcytosine reader) revealed them to be diverse members of a larger family of DNA/RNA modification readers, apparently having originated from bacterial modification-dependent restriction enzymes.
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Affiliation(s)
- Clayton B Woodcock
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Genome-Wide Identification of Epigenetic Regulators in Quercus suber L. Int J Mol Sci 2020; 21:ijms21113783. [PMID: 32471127 PMCID: PMC7313042 DOI: 10.3390/ijms21113783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022] Open
Abstract
Modifications of DNA and histones, including methylation and acetylation, are critical for the epigenetic regulation of gene expression during plant development, particularly during environmental adaptation processes. However, information on the enzymes catalyzing all these modifications in trees, such as Quercus suber L., is still not available. In this study, eight DNA methyltransferases (DNA Mtases) and three DNA demethylases (DDMEs) were identified in Q. suber. Histone modifiers involved in methylation (35), demethylation (26), acetylation (8), and deacetylation (22) were also identified in Q. suber. In silico analysis showed that some Q. suber DNA Mtases, DDMEs and histone modifiers have the typical domains found in the plant model Arabidopsis, which might suggest a conserved functional role. Additional phylogenetic analyses of the DNA and histone modifier proteins were performed using several plant species homologs, enabling the classification of the Q. suber proteins. A link between the expression levels of each gene in different Q. suber tissues (buds, flowers, acorns, embryos, cork, and roots) with the functions already known for their closest homologs in other species was also established. Therefore, the data generated here will be important for future studies exploring the role of epigenetic regulators in this economically important species.
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Ehsan M, Gadahi JA, Liu T, Lu M, Wang Y, Hasan MW, Haseeb M, Yan R, Xu L, Song X, Zhu XQ, Li X. Identification of a novel methyltransferase-type 12 protein from Haemonchus contortus and its effects on functions of goat PBMCs. Parasit Vectors 2020; 13:154. [PMID: 32228657 PMCID: PMC7106832 DOI: 10.1186/s13071-020-04028-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/17/2020] [Indexed: 01/06/2023] Open
Abstract
Background Methyltransferases (MTFs) are broad range of enzymes, which are ubiquitously expressed in diverse organisms ranging from bacteria to animals. MTFs proteins have been associated with various biological/cellular processes including transcriptional regulation, subcellular protein and RNA localization, signal transduction and DNA-damage repair. However, the role of MTFs in immune mechanism during host–parasite interaction has not been addressed yet. Results An open reading frame (764 bp) of methyltransferase-type 12 gene of H. contortus denoted as HcMTF-12, was successfully cloned using reverse transcriptase-polymerase chain reaction (RT-PCR) followed by prokaryotic expression in Escherichia coli BL21 (DE3 strain). The recombinant HcMTF-12 protein (rHcMTF-12) was about 47 kDa along with a fusion vector protein of 18 kDa. Immunoblot results identified the native protein MTF-12 with antibodies produced in rats against rHcMT-12, whereas rHcMTF-12 protein was recognized with sera of goat experimentally infected with H. contortus. Immunohistochemical analysis revealed that the native MTF-12 protein was mainly located in the periphery (cuticle) of parasite sections as well as within the pharynx and intestinal region. An immunofluorescence assay validated that rHcMTF-12 attached to the surface of goat PBMCs. Furthermore, the cytokines transcription of IL-2, IFN-γ and IL-4 transcripts of PBMCs incubated with rHcMTF-12 were enhanced in a dose-dependent manner. The secretion of TGF-β1 and IL-10 was significantly decreased. However, IL-6 production was not significantly different as compared to the control groups. Moreover, the migration activity and nitric oxide (NO) production by PBMCs were induced considerably, whereas the proliferation of PBMCs cells was negatively affected when incubated with the rHcMTF-12 protein. Conclusions Our findings suggest that HcMTF-12 significantly mediated the functions of PBMCs, and it might be a potential candidate for therapeutic interventions against haemonchosis.![]()
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Affiliation(s)
- Muhammad Ehsan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People's Republic of China.,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Javaid A Gadahi
- Department of Veterinary Parasitology, Sindh Agriculture University Tandojam, Hyderabad, Pakistan
| | - Tingqi Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Mingmin Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yujian Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Muhammad W Hasan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Muhammad Haseeb
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Ruofeng Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Lixin Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xiaokai Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People's Republic of China
| | - Xiangrui Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
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25
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Functional Analysis of DNMT3A DNA Methyltransferase Mutations Reported in Patients with Acute Myeloid Leukemia. Biomolecules 2019; 10:biom10010008. [PMID: 31861499 PMCID: PMC7022712 DOI: 10.3390/biom10010008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/30/2022] Open
Abstract
In mammals, DNA methylation is necessary for the maintenance of genomic stability, gene expression regulation, and other processes. During malignant diseases progression, changes in both DNA methylation patterns and DNA methyltransferase (MTase) genes are observed. Human de novo MTase DNMT3A is most frequently mutated in acute myeloid leukemia (AML) with a striking prevalence of R882H mutation, which has been extensively studied. Here, we investigate the functional role of the missense mutations (S714C, R635W, R736H, R771L, P777R, and F752V) found in the catalytic domain of DNMT3A in AML patients. These were accordingly mutated in the murine Dnmt3a catalytic domain (S124C, R45W, R146H, R181L, P187R, and F162V) and in addition, one-site CpG-containing DNA substrates were used as a model system. The 3–15-fold decrease (S124C and P187R) or complete loss (F162V, R45W, and R146H) of Dnmt3a-CD methylation activity was observed. Remarkably, Pro 187 and Arg 146 are not located at or near the Dnmt3a functional motives. Regulatory protein Dnmt3L did not enhance the methylation activity of R45W, R146H, P187R, and F162V mutants. The key steps of the Dnmt3a-mediated methylation mechanism, including DNA binding and transient covalent intermediate formation, were examined. There was a complete loss of DNA-binding affinity for R45W located in the AdoMet binding region and for R146H. Dnmt3a mutants studied in vitro suggest functional impairment of DNMT3A during pathogenesis.
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26
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Schmitz RJ, Lewis ZA, Goll MG. DNA Methylation: Shared and Divergent Features across Eukaryotes. Trends Genet 2019; 35:818-827. [PMID: 31399242 DOI: 10.1016/j.tig.2019.07.007] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/01/2019] [Accepted: 07/15/2019] [Indexed: 02/02/2023]
Abstract
Chemical modification of nucleotide bases in DNA provides one mechanism for conveying information in addition to the genetic code. 5-methylcytosine (5mC) represents the most common chemically modified base in eukaryotic genomes. Sometimes referred to simply as DNA methylation, in eukaryotes 5mC is most prevalent at CpG dinucleotides and is frequently associated with transcriptional repression of transposable elements. However, 5mC levels and distributions are variable across phylogenies, and emerging evidence suggests that the functions of DNA methylation may be more diverse and complex than was previously appreciated. We summarize the current understanding of DNA methylation profiles and functions in different eukaryotic lineages.
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Affiliation(s)
- Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Zachary A Lewis
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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Murray IA, Morgan RD, Luyten Y, Fomenkov A, Corrêa IR, Dai N, Allaw MB, Zhang X, Cheng X, Roberts RJ. The non-specific adenine DNA methyltransferase M.EcoGII. Nucleic Acids Res 2019; 46:840-848. [PMID: 29228259 PMCID: PMC5778455 DOI: 10.1093/nar/gkx1191] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/16/2017] [Indexed: 01/26/2023] Open
Abstract
We describe the cloning, expression and characterization of the first truly non-specific adenine DNA methyltransferase, M.EcoGII. It is encoded in the genome of the pathogenic strain Escherichia coli O104:H4 C227–11, where it appears to reside on a cryptic prophage, but is not expressed. However, when the gene encoding M.EcoGII is expressed in vivo - using a high copy pRRS plasmid vector and a methylation–deficient E. coli host—extensive in vivo adenine methylation activity is revealed. M.EcoGII methylates adenine residues in any DNA sequence context and this activity extends to dA and rA bases in either strand of a DNA:RNA-hybrid oligonucleotide duplex and to rA bases in RNAs prepared by in vitro transcription. Using oligonucleotide and bacteriophage M13mp18 virion DNA substrates, we find that M.EcoGII also methylates single-stranded DNA in vitro and that this activity is only slightly less robust than that observed using equivalent double-stranded DNAs. In vitro assays, using purified recombinant M.EcoGII enzyme, demonstrate that up to 99% of dA bases in duplex DNA substrates can be methylated thereby rendering them insensitive to cleavage by multiple restriction endonucleases. These properties suggest that the enzyme could also be used for high resolution mapping of protein binding sites in DNA and RNA substrates.
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Affiliation(s)
- Iain A Murray
- New England Biolabs, 240 County Road, Ipswich, MA 01983, USA
| | | | - Yvette Luyten
- New England Biolabs, 240 County Road, Ipswich, MA 01983, USA
| | - Alexey Fomenkov
- New England Biolabs, 240 County Road, Ipswich, MA 01983, USA
| | - Ivan R Corrêa
- New England Biolabs, 240 County Road, Ipswich, MA 01983, USA
| | - Nan Dai
- New England Biolabs, 240 County Road, Ipswich, MA 01983, USA
| | - Mohammed B Allaw
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Xiong T, Rohm D, Workman RE, Roundtree L, Novina CD, Timp W, Ostermeier M. Protein engineering strategies for improving the selective methylation of target CpG sites by a dCas9-directed cytosine methyltransferase in bacteria. PLoS One 2018; 13:e0209408. [PMID: 30562388 PMCID: PMC6298699 DOI: 10.1371/journal.pone.0209408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/05/2018] [Indexed: 12/22/2022] Open
Abstract
Mammalian gene expression is a complex process regulated in part by CpG methylation. The ability to target methylation for de novo gene regulation could have therapeutic and research applications. We have previously developed a dCas9-MC/MN protein for targeting CpG methylation. dCas9-MC/MN is composed of an artificially split M.SssI methyltransferase (MC/MN), with the MC fragment fused to a nuclease-null CRISPR/Cas9 (dCas9). Guide RNAs directed dCas9-MC/MN to methylate target sites in E. coli and human cells but also caused some low-level off-target methylation. Here, in E. coli, we show that shortening the dCas9-MC linker increases methylation of CpG sites located at select distances from the dCas9 binding site. Although a shortened linker decreased methylation of other CpGs proximal to the target site, it did not reduce off-target methylation of more distant CpG sites. Instead, targeted mutagenesis of the methyltransferase's DNA binding domain, designed to reduce DNA affinity, significantly and preferentially reduced methylation of such sites.
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Affiliation(s)
- Tina Xiong
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Dahlia Rohm
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Rachael E. Workman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Lauren Roundtree
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Carl D. Novina
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
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Ramírez V, González B, López A, Castelló MJ, Gil MJ, Zheng B, Chen P, Vera P. A 2'-O-Methyltransferase Responsible for Transfer RNA Anticodon Modification Is Pivotal for Resistance to Pseudomonas syringae DC3000 in Arabidopsis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1323-1336. [PMID: 29975160 DOI: 10.1094/mpmi-06-18-0148-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Transfer RNA (tRNA) is the most highly modified class of RNA species in all living organisms. Recent discoveries have revealed unprecedented complexity in the tRNA chemical structures, modification patterns, regulation, and function, suggesting that each modified nucleoside in tRNA may have its own specific function. However, in plants, our knowledge of the role of individual tRNA modifications and how they are regulated is very limited. In a genetic screen designed to identify factors regulating disease resistance in Arabidopsis, we identified SUPPRESSOR OF CSB3 9 (SCS9). Our results reveal SCS9 encodes a tRNA methyltransferase that mediates the 2'-O-ribose methylation of selected tRNA species in the anticodon loop. These SCS9-mediated tRNA modifications enhance susceptibility during infection with the virulent bacterial pathogen Pseudomonas syringae DC3000. Lack of such tRNA modification, as observed in scs9 mutants, specifically dampens plant resistance against DC3000 without compromising the activation of the salicylic acid signaling pathway or the resistance to other biotrophic pathogens. Our results support a model that gives importance to the control of certain tRNA modifications for mounting an effective disease resistance in Arabidopsis toward DC3000 and, therefore, expands the repertoire of molecular components essential for an efficient disease resistance response.
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Affiliation(s)
- Vicente Ramírez
- 1 Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, Valencia, Spain
| | - Beatriz González
- 1 Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, Valencia, Spain
| | - Ana López
- 1 Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, Valencia, Spain
- 2 Institute for Translational Plant and Soil Biology, Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, U.K
| | - Maria Jose Castelló
- 1 Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, Valencia, Spain
| | - Maria José Gil
- 1 Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, Valencia, Spain
| | - Bo Zheng
- 3 College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China; and
| | - Peng Chen
- 4 National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, HuaZhong Agricultural University, Wuhan, China
| | - Pablo Vera
- 1 Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, Valencia, Spain
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Larsen K, Kristensen KK, Callesen H. DNA methyltransferases and tRNA methyltransferase DNMT2 in developing pig brain - expression and promoter methylation. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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31
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Albert P, Varga B, Zsibrita N, Kiss A. Circularly permuted variants of two CG-specific prokaryotic DNA methyltransferases. PLoS One 2018; 13:e0197232. [PMID: 29746549 PMCID: PMC5944983 DOI: 10.1371/journal.pone.0197232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/27/2018] [Indexed: 01/06/2023] Open
Abstract
The highly similar prokaryotic DNA (cytosine-5) methyltransferases (C5-MTases) M.MpeI and M.SssI share the specificity of eukaryotic C5-MTases (5'-CG), and can be useful research tools in the study of eukaryotic DNA methylation and epigenetic regulation. In an effort to improve the stability and solubility of complementing fragments of the two MTases, genes encoding circularly permuted (CP) variants of M.MpeI and M.SssI were created, and cloned in a plasmid vector downstream of an arabinose-inducible promoter. MTase activity of the CP variants was tested by digestion of the plasmids with methylation-sensitive restriction enzymes. Eleven of the fourteen M.MpeI permutants and six of the seven M.SssI permutants had detectable MTase activity as indicated by the full or partial protection of the plasmid carrying the cpMTase gene. Permutants cp62M.MpeI and cp58M.SssI, in which the new N-termini are located between conserved motifs II and III, had by far the highest activity. The activity of cp62M.MpeI was comparable to the activity of wild-type M.MpeI. Based on the location of the split sites, the permutants possessing MTase activity can be classified in ten types. Although most permutation sites were designed to fall outside of conserved motifs, and the MTase activity of the permutants measured in cell extracts was in most cases substantially lower than that of the wild-type enzyme, the high proportion of circular permutation topologies compatible with MTase activity is remarkable, and is a new evidence for the structural plasticity of C5-MTases. A computer search of the REBASE database identified putative C5-MTases with CP arrangement. Interestingly, all natural circularly permuted C5-MTases appear to represent only one of the ten types of permutation topology created in this work.
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Affiliation(s)
- Pál Albert
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Bence Varga
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Nikolett Zsibrita
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Antal Kiss
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
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Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT. Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing. Genes (Basel) 2018; 9:genes9030129. [PMID: 29495512 PMCID: PMC5867850 DOI: 10.3390/genes9030129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 12/31/2022] Open
Abstract
DNA methyltransferases (MTases), which catalyze the methylation of adenine and cytosine bases in DNA, can occur in bacteria and archaea alongside cognate restriction endonucleases (REases) in restriction-modification (RM) systems or independently as orphan MTases. Although DNA methylation and MTases have been well-characterized in bacteria, research into archaeal MTases has been limited. A previous study examined the genomic DNA methylation patterns (methylome) of the halophilic archaeon Haloferax volcanii, a model archaeal system which can be easily manipulated in laboratory settings, via single-molecule real-time (SMRT) sequencing and deletion of a putative MTase gene (HVO_A0006). In this follow-up study, we deleted other putative MTase genes in H. volcanii and sequenced the methylomes of the resulting deletion mutants via SMRT sequencing to characterize the genes responsible for DNA methylation. The results indicate that deletion of putative RM genes HVO_0794, HVO_A0006, and HVO_A0237 in a single strain abolished methylation of the sole cytosine motif in the genome (Cm4TAG). Amino acid alignments demonstrated that HVO_0794 shares homology with characterized cytosine CTAG MTases in other organisms, indicating that this MTase is responsible for Cm4TAG methylation in H. volcanii. The CTAG motif has high density at only one of the origins of replication, and there is no relative increase in CTAG motif frequency in the genome of H. volcanii, indicating that CTAG methylation might not have effectively taken over the role of regulating DNA replication and mismatch repair in the organism as previously predicted. Deletion of the putative Type I RM operon rmeRMS (HVO_2269-2271) resulted in abolished methylation of the adenine motif in the genome (GCAm6BN₆VTGC). Alignments of the MTase (HVO_2270) and site specificity subunit (HVO_2271) demonstrate homology with other characterized Type I MTases and site specificity subunits, indicating that the rmeRMS operon is responsible for adenine methylation in H. volcanii. Together with HVO_0794, these genes appear to be responsible for all detected methylation in H. volcanii, even though other putative MTases (HVO_C0040, HVO_A0079) share homology with characterized MTases in other organisms. We also report the construction of a multi-RM deletion mutant (ΔRM), with multiple RM genes deleted and with no methylation detected via SMRT sequencing, which we anticipate will be useful for future studies on DNA methylation in H. volcanii.
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Affiliation(s)
- Matthew Ouellette
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA.
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA.
| | - Jessica Lajoie
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA.
| | - Andrea M Makkay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA.
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA.
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Lyko F. The DNA methyltransferase family: a versatile toolkit for epigenetic regulation. Nat Rev Genet 2017; 19:81-92. [PMID: 29033456 DOI: 10.1038/nrg.2017.80] [Citation(s) in RCA: 830] [Impact Index Per Article: 118.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The DNA methyltransferase (DNMT) family comprises a conserved set of DNA-modifying enzymes that have a central role in epigenetic gene regulation. Recent studies have shown that the functions of the canonical DNMT enzymes - DNMT1, DNMT3A and DNMT3B - go beyond their traditional roles of establishing and maintaining DNA methylation patterns. This Review analyses how molecular interactions and changes in gene copy numbers modulate the activity of DNMTs in diverse gene regulatory functions, including transcriptional silencing, transcriptional activation and post-transcriptional regulation by DNMT2-dependent tRNA methylation. This mechanistic diversity enables the DNMT family to function as a versatile toolkit for epigenetic regulation.
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Affiliation(s)
- Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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Abstract
Epigenetic mechanisms play important roles in properly occurring mammalian oogenesis. One of these mechanisms is DNA methylation adding a methyl group to the fifth carbon atom of the cytosine residues using S-adenosyl-L-methionine as a methyl donor. DNA methylation generally takes place at cytosine-phosphate-guanine (CpG) dinucleotide sites and rarely occurs at cytosine-phosphate-thymine (CpT), cytosine-phosphate-adenine (CpA), or cytosine-phosphate-cytosine sites, known as non-CpG sites. Basically, two different DNA methylation processes are identified: de novo methylation and maintenance methylation. While the de novo methylation functions in methylation of unmethylated DNA strands, maintenance methylation is capable of methylating hemi-methylated DNA strands following DNA replication. Both DNA methylation processes are catalyzed by special DNA methyltransferase (DNMT) enzymes. To date, five different DNMTs have been identified: DNMT1, DNMT3A, DNMT3B, DNMT3L, and DNMT2. In this chapter, we focus particularly on temporal and spatial expression of DNMTs in mammalian oocytes and granulosa cells.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, School of Medicine, Akdeniz University, Campus, 07070, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, School of Medicine, Akdeniz University, Campus, 07070, Antalya, Turkey.
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35
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Ashapkin VV, Kutueva LI, Vanyushin BF. Dnmt2 is the most evolutionary conserved and enigmatic cytosine DNA methyltransferase in eukaryotes. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416030029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lukashevich OV, Cherepanova NA, Jurkovska RZ, Jeltsch A, Gromova ES. Conserved motif VIII of murine DNA methyltransferase Dnmt3a is essential for methylation activity. BMC BIOCHEMISTRY 2016; 17:7. [PMID: 27001594 PMCID: PMC4802922 DOI: 10.1186/s12858-016-0064-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/02/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Dnmt3a is a DNA methyltransferase that establishes de novo DNA methylation in mammals. The structure of the Dnmt3a C-terminal domain is similar to the bacterial M. HhaI enzyme, a well-studied prokaryotic DNA methyltransferase. No X-ray structure is available for the complex of Dnmt3a with DNA and the mechanistic details of DNA recognition and catalysis by mammalian Dnmts are not completely understood. RESULTS Mutant variants of the catalytic domain of the murine Dnmt3a carrying substitutions of highly conserved N167, R200, and R202 have been generated by site directed mutagenesis and purified. Their methylation activity, DNA binding affinity, ability to flip the target cytosine out of the DNA double helix and covalent complex formation with DNA have been examined. Substitutions of N167 lead to reduced catalytic activity and reduced base flipping. Catalytic activity, base flipping, and covalent conjugate formation were almost completely abolished for the mutant enzymes with substitutions of R200 or R202. CONCLUSIONS We conclude that R202 plays a similar role in catalysis in Dnmt3a-CD as R232 in M.SssI and R165 in M.HhaI, which could be positioning of the cytosine for nucleophilic attack by a conserved Cys. R200 of Dnmt3a-CD is important in both catalysis and cytosine flipping. Both conserved R200 and R202 are involved in creating and stabilizing of the transient covalent intermediate of the methylation reaction. N167 might contribute to the positioning of the residues from the motif VI, but does not play a direct role in catalysis.
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Affiliation(s)
- Olga V Lukashevich
- Department of Chemistry, Moscow State University, 119991, Moscow, Russia
| | | | - Renata Z Jurkovska
- BioMedX Innovation Center, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom RR, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, Rubin EM, Korlach J, Pennacchio LA, Roberts RJ. The Epigenomic Landscape of Prokaryotes. PLoS Genet 2016; 12:e1005854. [PMID: 26870957 PMCID: PMC4752239 DOI: 10.1371/journal.pgen.1005854] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/19/2016] [Indexed: 11/18/2022] Open
Abstract
DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active ‘orphan’ MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems. DNA methylation is a chemical modification of DNA present in many prokaryotic genomes. The best-known role of DNA methylation is as a component of restriction-modification systems. In these systems, restriction enzymes target foreign DNA for cleavage, while DNA methylation protects the host genome from destruction. Studies in a handful of organisms show that DNA methylation may also act independently of restriction systems and function in genome regulation. However, a lack of technologies has limited the study of DNA methylation to a small number of organisms, and the broader patterns and functions of DNA methylation remain unknown. Here we use SMRT-sequencing to determine the genome wide DNA methylation patterns of more than 200 diverse bacteria and archaea. We show that DNA methylation is pervasive and present in more than 90% of studied organisms. Analysis of this data enabled annotation of the specific DNA binding sites of more than 600 restriction systems, revealing their extraordinary diversity. Strikingly, we observed widespread DNA methylation in the absence of restriction systems. Analyses of these patterns reveal that they are conserved through evolution, and likely function in genome regulation. Thus DNA methylation may play a far wider function in prokaryotic genome biology than was previously supposed.
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Affiliation(s)
- Matthew J. Blow
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- * E-mail: (MJB); (RJR)
| | - Tyson A. Clark
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Chris G. Daum
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Adam M. Deutschbauer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Alexey Fomenkov
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Roxanne Fries
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jeff Froula
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Dongwan D. Kang
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Rex R. Malmstrom
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Richard D. Morgan
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Janos Posfai
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Kanwar Singh
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Axel Visel
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Kelly Wetmore
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Zhiying Zhao
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Edward M. Rubin
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Len A. Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Richard J. Roberts
- New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail: (MJB); (RJR)
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Jurkowska RZ, Jeltsch A. Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:1-17. [DOI: 10.1007/978-3-319-43624-1_1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Minarovits J, Banati F, Szenthe K, Niller HH. Epigenetic Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 879:1-25. [DOI: 10.1007/978-3-319-24738-0_1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Abstract
The DNA of Escherichia coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases, and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during the repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and the regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation, although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential, and, in C. crescentus, it is important for temporal gene expression, which, in turn, is required for coordinating chromosome initiation, replication, and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage, decrease transformation frequency in certain bacteria, and decrease the stability of short direct repeats and are necessary for site-directed mutagenesis and to probe eukaryotic structure and function.
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Maier JAH, Albu RF, Jurkowski TP, Jeltsch A. Investigation of the C-terminal domain of the bacterial DNA-(adenine N6)-methyltransferase CcrM. Biochimie 2015; 119:60-7. [PMID: 26475175 DOI: 10.1016/j.biochi.2015.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/11/2015] [Indexed: 01/30/2023]
Abstract
CcrM-related DNA-(adenine N6)-methyltransferases play very important roles in the biology of Caulobacter crescentus and other alpha-proteobacteria. These enzymes methylate GANTC sequences, but the molecular mechanism by which they recognize their target sequence is unknown. We carried out multiple sequence alignments and noticed that CcrM enzymes contain a conserved C-terminal domain (CTD) which is not present in other DNA-(adenine N6)-methyltransferases and we show here that deletion of this part abrogates catalytic activity and DNA binding of CcrM. A mutational study identified 7 conserved residues in the CTD (out of 13 tested), mutation of which led to a strong reduction in catalytic activity. All of these mutants showed altered DNA binding, but no change in AdoMet binding and secondary structure. Some mutants exhibited reduced DNA binding, but others showed an enhanced DNA binding. Moreover, we show that CcrM does not specifically bind to DNA containing GANTC sequences. Taken together, these findings suggest that the specific CcrM-DNA complex undergoes a conformational change, which is endergonic but essential for catalytic activity and this step is blocked by some of the mutations. Moreover, our data indicate that the CTD of CcrM is involved in DNA binding and recognition. This suggests that the CTD functions as target recognition domain of CcrM and, therefore, CcrM can be considered the first example of a δ-type DNA-(adenine N6)-methyltransferase identified so far.
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Affiliation(s)
- Johannes A H Maier
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - Razvan F Albu
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - Tomasz P Jurkowski
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany.
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Ramírez V, Gonzalez B, López A, Castelló MJ, Gil MJ, Zheng B, Chen P, Vera P. Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity. PLoS Genet 2015; 11:e1005586. [PMID: 26492405 PMCID: PMC4619653 DOI: 10.1371/journal.pgen.1005586] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/16/2015] [Indexed: 12/20/2022] Open
Abstract
tRNA is the most highly modified class of RNA species, and modifications are found in tRNAs from all organisms that have been examined. Despite their vastly different chemical structures and their presence in different tRNAs, occurring in different locations in tRNA, the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent discoveries have revealed unprecedented complexity in the modification patterns of tRNA, their regulation and function, suggesting that each modified nucleoside in tRNA may have its own specific function. However, in plants, our knowledge on the role of individual tRNA modifications and how they are regulated is very limited. In a genetic screen designed to identify factors regulating disease resistance and activation of defenses in Arabidopsis, we identified SUPPRESSOR OF CSB3 9 (SCS9). Our results reveal SCS9 encodes a tRNA methyltransferase that mediates the 2´-O-ribose methylation of selected tRNA species in the anticodon loop. These SCS9-mediated tRNA modifications enhance during the course of infection with the bacterial pathogen Pseudomonas syringae DC3000, and lack of such tRNA modification, as observed in scs9 mutants, severely compromise plant immunity against the same pathogen without affecting the salicylic acid (SA) signaling pathway which regulates plant immune responses. Our results support a model that gives importance to the control of certain tRNA modifications for mounting an effective immune response in Arabidopsis, and therefore expands the repertoire of molecular components essential for an efficient disease resistance response. Numerous studies revealed the existence of nearly 110 ribonucleoside structures incorporated as post-transcriptional modifications in tRNA, with 25–30 modifications present in any one organism. Emerging evidence points to the critical role of tRNA modifications in various cellular responses to stimuli, including transcription of stress response genes and control of cell viability and growth. The primary function of tRNA modifications, and in particular tRNA methylations, are linked to different steps in protein synthesis including stabilization of tRNA structures, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. Furthermore, tRNA methylations are involved in the RNA quality control system and regulation of tRNA localization in the cell, all of which affect translation rate, but modifications in the anti-codon, which exhibit important roles in decoding mRNA are particularly important. We identified that the SCS9 gene from Arabidopsis encodes a tRNA 2´-O-ribose methyltransferase homologous to the TRM7 methyltransferase from yeast. We identify that SCS9 is crucial for the 2´-O-ribose methylation of nucleotides 32 and 34 of the tRNAs anticodon loop of certain tRNA molecules. We show that SCS9 is required for effectiveness of plant immunity and suggest the importance of precise tRNA modifications in this process.
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Affiliation(s)
- Vicente Ramírez
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Beatriz Gonzalez
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Ana López
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Valencia, Spain
| | - María José Castelló
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Valencia, Spain
| | - María José Gil
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Bo Zheng
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Peng Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, HuaZhong Agricultural University, Wuhan, China
| | - Pablo Vera
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Valencia, Spain
- * E-mail:
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Uysal F, Akkoyunlu G, Ozturk S. Dynamic expression of DNA methyltransferases (DNMTs) in oocytes and early embryos. Biochimie 2015; 116:103-13. [PMID: 26143007 DOI: 10.1016/j.biochi.2015.06.019] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/26/2015] [Indexed: 11/26/2022]
Abstract
Epigenetic mechanisms play critical roles in oogenesis and early embryo development in mammals. One of these epigenetic mechanisms, DNA methylation is accomplished through the activities of DNA methyltransferases (DNMTs), which are responsible for adding a methyl group to the fifth carbon atom of the cytosine residues within cytosine-phosphate-guanine (CpG) and non-CpG dinuclotide sites. Five DNMT enzymes have been identified in mammals including DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMT3L. They function in two different methylation processes: maintenance and de novo. For maintenance methylation, DNMT1 preferentially transfers methyl groups to the hemi-methylated DNA strands following DNA replication. However, for de novo methylation activities both DNMT3A and DNMT3B function in the methylation of the unmodified cytosine residues. Although DNMT3L indirectly contributes to de novo methylation process, DNMT2 enables the methylation of the cytosine 38 in the anticodon loop of aspartic acid transfer RNA and does not methylate DNA. In this review article, we have evaluated and discussed the existing published studies to characterize the spatial and temporal expression patterns of the DNMTs in mouse, bovine and human oocytes and early embryos. We have also reviewed the effects of in vitro culture conditions (serum abundance and glucose concentration), aging, superovulation, vitrification, and somatic cell nuclear transfer technology on the dynamics of DNMTs.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Antalya, Turkey
| | - Gokhan Akkoyunlu
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Antalya, Turkey.
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Dallas LJ, Jha AN. Applications of biological tools or biomarkers in aquatic biota: A case study of the Tamar estuary, South West England. MARINE POLLUTION BULLETIN 2015; 95:618-633. [PMID: 25817310 DOI: 10.1016/j.marpolbul.2015.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 02/15/2015] [Accepted: 03/09/2015] [Indexed: 06/04/2023]
Abstract
Biological systems are the ultimate recipients of pollutant-induced damage. Consequently, our traditional reliance on analytical tools is not enough to assess ecosystem health. Biological responses or biomarkers are therefore also considered to be important tools for environmental hazard and risk assessments. Due to historical mining, other anthropogenic activities, and its conservational importance (e.g. NATURA sites, SACs), the Tamar estuary in South West England is an ideal environment in which to examine applications of such biological tools. This review presents a thorough and critical evaluation of the different biological tools used in the Tamar estuary thus far, while also discussing future perspectives for biomarker studies from a global perspective. In particular, we focus on the challenges which hinder applications of biological tools from being more readily incorporated into regulatory frameworks, with the aim of enabling both policymakers and primary stakeholders to maximise the environmental relevance and regulatory usefulness of such tools.
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Affiliation(s)
- Lorna J Dallas
- School of Biological Sciences, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK
| | - Awadhesh N Jha
- School of Biological Sciences, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK.
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Genetic Stabilization of the Drug-Resistant PMEN1 Pneumococcus Lineage by Its Distinctive DpnIII Restriction-Modification System. mBio 2015; 6:e00173. [PMID: 26081630 PMCID: PMC4471560 DOI: 10.1128/mbio.00173-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The human pathogen Streptococcus pneumoniae (pneumococcus) exhibits a high degree of genomic diversity and plasticity. Isolates with high genomic similarity are grouped into lineages that undergo homologous recombination at variable rates. PMEN1 is a pandemic, multidrug-resistant lineage. Heterologous gene exchange between PMEN1 and non-PMEN1 isolates is directional, with extensive gene transfer from PMEN1 strains and only modest transfer into PMEN1 strains. Restriction-modification (R-M) systems can restrict horizontal gene transfer, yet most pneumococcal strains code for either the DpnI or DpnII R-M system and neither limits homologous recombination. Our comparative genomic analysis revealed that PMEN1 isolates code for DpnIII, a third R-M system syntenic to the other Dpn systems. Characterization of DpnIII demonstrated that the endonuclease cleaves unmethylated double-stranded DNA at the tetramer sequence 5′ GATC 3′, and the cognate methylase is a C5 cytosine-specific DNA methylase. We show that DpnIII decreases the frequency of recombination under in vitro conditions, such that the number of transformants is lower for strains transformed with unmethylated DNA than in those transformed with cognately methylated DNA. Furthermore, we have identified two PMEN1 isolates where the DpnIII endonuclease is disrupted, and phylogenetic work by Croucher and colleagues suggests that these strains have accumulated genomic differences at a higher rate than other PMEN1 strains. We propose that the R-M locus is a major determinant of genetic acquisition; the resident R-M system governs the extent of genome plasticity. Pneumococcus is one of the most important community-acquired bacterial pathogens. Pneumococcal strains can develop resistance to antibiotics and to serotype vaccines by acquiring genes from other strains or species. Thus, genomic plasticity is associated with strain adaptability and pneumococcal success. PMEN1 is a widespread and multidrug-resistant highly pathogenic pneumococcal lineage, which has evolved over the past century and displays a relatively stable genome. In this study, we characterize DpnIII, a restriction-modification (R-M) system that limits recombination. DpnIII is encountered in the PMEN1 lineage, where it replaces other R-M systems that do not decrease plasticity. Our hypothesis is that this genomic region, where different pneumococcal lineages code for variable R-M systems, plays a role in the fine-tuning of the extent of genomic plasticity. It is possible that well-adapted lineages such as PMEN1 have a mechanism to increase genomic stability, rather than foster genomic plasticity.
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Yang SX, Guo C, Xu M, Sun JT, Hong XY. Sex-dependent activity of de novo methyltransferase 3 (Tudnmt3) in the two-spotted mite, Tetranychus urticae Koch. INSECT MOLECULAR BIOLOGY 2014; 23:743-753. [PMID: 25055993 DOI: 10.1111/imb.12120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
DNA methylation is an epigenetic mechanism for regulating developmental and other important processes in eukaryotes. Several components of the DNA methylation machinery have been identified, such as DNA methyltransferases. However, little is known about DNA methyltransferases in chelicerates, which is the second largest arthropod group. Epigenetics are expected to have a crucial role in the metabolism and development of this group. Here, we investigated the role of DNA methyltransferase 3 in the development of Tetranychus urticae Koch. In silico analyses clearly showed that this enzyme possesses the necessary conserved motifs for the catalytic activity of de novo methylation of DNA. Real-time PCR revealed that T. urticae de novo methyltransferase 3 (Tudnmt3) is expressed ubiquitously and throughout the life cycle of the two-spotted spider mite. However, the pattern of Tudnmt3 expression was sex-dependent during the adult stage. Whole in situ hybridization provided supportive evidence that Tudnmt3 is linked to the differentiation of the gonads in adult females and males. Methylation-sensitive amplification polymorphism analyses of 119 loci showed that the status of DNA methylation is partially different between adult females and males, raising the possibility that this sex-dependent DNA methylation pattern is mediated by different methylation activity of Tudnmt3.
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Affiliation(s)
- S-X Yang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Cinelli T, Moscetti I, Marchi G. PsasM2I, a type II restriction-modification system in Pseudomonas savastanoi pv. savastanoi: differential distribution of carrier strains in the environment and the evolutionary history of homologous RM systems in the Pseudomonas syringae complex. MICROBIAL ECOLOGY 2014; 68:842-858. [PMID: 25008981 DOI: 10.1007/s00248-014-0451-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/19/2014] [Indexed: 06/03/2023]
Abstract
A type II restriction-modification system was found in a native plasmid of Pseudomonas savastanoi pv. savastanoi MLLI2. Functional analysis of the methyltransferase showed that the enzyme acts by protecting the DNA sequence CTGCAG from cleavage. Restriction endonuclease expression in recombinant Escherichia coli cells resulted in mutations in the REase sequence or transposition of insertion sequence 1A in the coding sequence, preventing lethal gene expression. Population screening detected homologous RM systems in other P. savastanoi strains and in the Pseudomonas syringae complex. An epidemiological survey carried out by sampling olive and oleander knots in two Italian regions showed an uneven diffusion of carrier strains, whose presence could be related to a selective advantage in maintaining the RM system in particular environments or subpopulations. Moreover, carrier strains can coexist in the same orchards, plants, and knot tissues with non-carriers, revealing unexpected genetic variability on a very small spatial scale. Phylogenetic analysis of the RM system and housekeeping gene sequences in the P. syringae complex demonstrated the ancient acquisition of the RM systems. However, the evolutionary history of the gene complex also showed the involvement of horizontal gene transfer between related strains and recombination events.
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Affiliation(s)
- Tamara Cinelli
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente (DISPAA), Sezione di Patologia Vegetale ed Entomologia, Università degli Studi di Firenze, Piazzale delle Cascine 28, 50144, Firenze, Italy,
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Qian Y, Xi Y, Cheng B, Zhu S. Genome-wide identification and expression profiling of DNA methyltransferase gene family in maize. PLANT CELL REPORTS 2014; 33:1661-72. [PMID: 24950734 DOI: 10.1007/s00299-014-1645-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/05/2014] [Accepted: 06/05/2014] [Indexed: 05/10/2023]
Abstract
In this study, we identified eight DNA MTase genes in maize and the diversity of expression patterns of them was presented by EST mining, microarray and semi-quantitative expression profile analyses. DNA methylation plays a pivotal role in promoting genomic stability through diverse biological processes including regulation of gene expression during development and chromatin organization. Although this important biological process is mainly regulated by several conserved Cytosine-5 DNA methyltransferases encoded by a smaller multigene family in plants, investigation of the plant C5-MTase-encoding gene family will serve to elucidate the epigenetic mechanism diversity in plants. Recently, genome-wide identification and evolutionary analyses of the C5-MTase-encoding gene family have been characterized in multiple plant species including Arabidopsis, rice, carrot and wheat. However, little is known regarding the C5-MTase-encoding genes in the entire maize genome. Here, genome-wide identification and expression profile analyses of maize C5-MTase-encoding genes (ZmMETs) were performed from the latest version of the maize (B73) genome. Phylogenetic analysis indicated that the orthologs from the three species (maize, Arabidopsis and rice) were categorized into four classes. Chromosomal location of these genes revealed that they are unevenly distributed on 6 of all 10 chromosomes with three chromosomal/segmental duplication events, suggesting that gene duplication played a key role in expansion of the maize C5-MTase-encoding gene family. Furthermore, EST expression data mining, microarray data and semi-quantitative expression profile analyses detected in the leaves by two different abiotic stress treatments have demonstrated that these genes had temporal and spatial expression pattern and exhibited different expression levels in stress treatments, suggesting that functional diversification of ZmMET genes family. Overall, our study will serve to present signification insights to explore the plant C5-MTase-encoding gene expression and function and also be beneficial for future experimental research to further unravel the mechanisms of epigenetic regulation in plants.
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Affiliation(s)
- Yexiong Qian
- Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000, China,
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Abstract
DNA methylation is one of the best characterized epigenetic modifications. In mammals it is involved in various biological processes including the silencing of transposable elements, regulation of gene expression, genomic imprinting, and X-chromosome inactivation. This article describes how DNA methylation serves as a cellular memory system and how it is dynamically regulated through the action of the DNA methyltransferase (DNMT) and ten eleven translocation (TET) enzymes. Its role in the regulation of gene expression, through its interplay with histone modifications, is also described, and its implication in human diseases discussed. The exciting areas of investigation that will likely become the focus of research in the coming years are outlined in the summary.
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Affiliation(s)
- En Li
- China Novartis Institutes for BioMedical Research, Pudong New Area, Shanghai 201203, China
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Abstract
The 1952 observation of host-induced non-hereditary variation in bacteriophages by Salvador Luria and Mary Human led to the discovery in the 1960s of modifying enzymes that glucosylate hydroxymethylcytosine in T-even phages and of genes encoding corresponding host activities that restrict non-glucosylated phage DNA: rglA and rglB (restricts glucoseless phage). In the 1980’s, appreciation of the biological scope of these activities was dramatically expanded with the demonstration that plant and animal DNA was also sensitive to restriction in cloning experiments. The rgl genes were renamed mcrA and mcrBC (modified cytosine restriction). The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I–III. A third Escherichia coli enzyme, mrr (modified DNA rejection and restriction) recognizes both methylcytosine and methyladenine. In recent years, the universe of modification-dependent enzymes has expanded greatly. Technical advances allow use of Type IV enzymes to study epigenetic mechanisms in mammals and plants. Type IV enzymes recognize modified DNA with low sequence selectivity and have emerged many times independently during evolution. Here, we review biochemical and structural data on these proteins, the resurgent interest in Type IV enzymes as tools for epigenetic research and the evolutionary pressures on these systems.
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Affiliation(s)
- Wil A M Loenen
- Leiden University Medical Center, P.O. Box 9600 2300RC Leiden, The Netherlands and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
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