1
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Vilkaitis G, Masevičius V, Kriukienė E, Klimašauskas S. Chemical Expansion of the Methyltransferase Reaction: Tools for DNA Labeling and Epigenome Analysis. Acc Chem Res 2023; 56:3188-3197. [PMID: 37904501 PMCID: PMC10666283 DOI: 10.1021/acs.accounts.3c00471] [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: 08/09/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023]
Abstract
DNA is the genetic matter of life composed of four major nucleotides which can be further furnished with biologically important covalent modifications. Among the variety of enzymes involved in DNA metabolism, AdoMet-dependent methyltransferases (MTases) combine the recognition of specific sequences and covalent methylation of a target nucleotide. The naturally transferred methyl groups play important roles in biological signaling, but they are poor physical reporters and largely resistant to chemical derivatization. Therefore, an obvious strategy to unlock the practical utility of the methyltransferase reactions is to enable the transfer of "prederivatized" (extended) versions of the methyl group.However, previous enzymatic studies of extended AdoMet analogs indicated that the transalkylation reactions are drastically impaired as the size of the carbon chain increases. In collaborative efforts, we proposed that, akin to enhanced SN2 reactivity of allylic and propargylic systems, addition of a π orbital next to the transferable carbon atom might confer the needed activation of the reaction. Indeed, we found that MTase-catalyzed transalkylations of DNA with cofactors containing a double or a triple C-C bond in the β position occurred in a robust and sequence-specific manner. Altogether, this breakthrough approach named mTAG (methyltransferase-directed transfer of activated groups) has proven instrumental for targeted labeling of DNA and other types of biomolecules (using appropriate MTases) including RNA and proteins.Our further work focused on the propargylic cofactors and their reactions with DNA cytosine-5 MTases, a class of MTases common for both prokaryotes and eukaryotes. Here, we learned that the 4-X-but-2-yn-1-yl (X = polar group) cofactors suffered from a rapid loss of activity in aqueous buffers due to susceptibility of the triple bond to hydration. This problem was remedied by synthetically increasing the separation between X and the triple bond from one to three carbon units (6-X-hex-2-ynyl cofactors). To further optimize the transfer of the bulkier groups, we performed structure-guided engineering of the MTase cofactor pocket. Alanine replacements of two conserved residues conferred substantial improvements of the transalkylation activity with M.HhaI and three other engineered bacterial C5-MTases. Of particular interest were CpG-specific DNA MTases (M.SssI), which proved valuable tools for studies of mammalian methylomes and chemical probing of DNA function.Inspired by the successful repurposing of bacterial enzymes, we turned to more complex mammalian C5-MTases (Dnmt1, Dnmt3A, and Dnmt3B) and asked if they could ultimately lead to mTAG labeling inside mammalian cells. Our efforts to engineer mouse Dnmt1 produced a variant (Dnmt1*) that enabled efficient Dnmt1-directed deposition of 6-azide-hexynyl groups on DNA in vitro. CRISPR-Cas9 editing of the corresponding codons in the genomic Dnmt1 alleles established endogenous expression of Dnmt1* in mouse embryonic stem cells. To circumvent the poor cellular uptake of AdoMet and its analogs, we elaborated their efficient internalization by electroporation, which has finally enabled selective catalysis-dependent azide tagging of natural Dnmt1 targets in live mammalian cells. The deposited chemical groups were then exploited as "click" handles for reading adjoining sequences and precise genomic mapping of the methylation sites. These findings offer unprecedented inroads into studies of DNA methylation in a wide range of eukaryotic model systems.
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Affiliation(s)
- Giedrius Vilkaitis
- Institute
of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Viktoras Masevičius
- Institute
of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
- Institute
of Chemistry, Department of Chemistry and Geosciences, Vilnius University, LT-03225 Vilnius, Lithuania
| | - Edita Kriukienė
- Institute
of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Saulius Klimašauskas
- Institute
of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
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2
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Pradhan S, Apaydin S, Bucevičius J, Gerasimaitė R, Kostiuk G, Lukinavičius G. Sequence-specific DNA labelling for fluorescence microscopy. Biosens Bioelectron 2023; 230:115256. [PMID: 36989663 DOI: 10.1016/j.bios.2023.115256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.
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3
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Malikėnas M, Masevičius V, Klimašauskas S. Synthesis of S-Adenosyl-L-Methionine Analogs with Extended Transferable Groups for Methyltransferase-Directed Labeling of DNA and RNA. Curr Protoc 2023; 3:e799. [PMID: 37327316 DOI: 10.1002/cpz1.799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
S-Adenosyl-L-methionine (AdoMet) is a ubiquitous methyl donor for a variety of biological methylation reactions catalyzed by methyltransferases (MTases). AdoMet analogs with extended propargylic chains replacing the sulfonium-bound methyl group can serve as surrogate cofactors for many DNA and RNA MTases, enabling covalent derivatization and subsequent labeling of their cognate target sites in DNA or RNA. Although AdoMet analogs with saturated aliphatic chains are less popular than propargylic ones, they can be useful for dedicated studies that require certain chemical derivatization. Here we describe synthetic procedures for the preparation of two AdoMet analogs, one with a transferable 6-azidohex-2-ynyl group (carrying an activating C≡C triple bond and a terminal azide functionality), and the other one with a transferable ethyl-2,2,2-d3 group (an isotope-labeled aliphatic moiety). Our synthetic approach is based on direct chemoselective alkylation of S-adenosyl-L-homocysteine at sulfur with a corresponding nosylate or triflate, respectively, under acidic conditions. We also describe synthetic routes to 6-azidohex-2-yn-1-ol and conversion of the alcohols to corresponding nosylate and triflate alkylators. Using these protocols, the synthetic AdoMet analogs can be prepared within 1 to 2 weeks. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 6-azidohex-2-yn-1-ol Basic Protocol 2: Synthesis of 4-nitrobenzenesulfonate Basic Protocol 3: Synthesis of trifluoromethanesulfonates Basic Protocol 4: S-Alkylation of AdoHcy with sulfonates Basic Protocol 5: Purification and characterization of AdoMet analogs.
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Affiliation(s)
- Martynas Malikėnas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Institute of Chemistry, Department of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
| | - Viktoras Masevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Institute of Chemistry, Department of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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4
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Cornelissen NV, Hoffmann A, Rentmeister A. DNA‐Methyltransferasen und AdoMet‐Analoga als Werkzeuge für die Molekularbiologie und Biotechnologie. CHEM-ING-TECH 2023. [DOI: 10.1002/cite.202200174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Nicolas V. Cornelissen
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Arne Hoffmann
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
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5
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Tomkuvienė M, Meier M, Ikasalaitė D, Wildenauer J, Kairys V, Klimašauskas S, Manelytė L. Enhanced nucleosome assembly at CpG sites containing an extended 5-methylcytosine analogue. Nucleic Acids Res 2022; 50:6549-6561. [PMID: 35648439 PMCID: PMC9226530 DOI: 10.1093/nar/gkac444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 05/05/2022] [Accepted: 05/16/2022] [Indexed: 02/01/2023] Open
Abstract
Methylation of cytosine to 5-methylcytosine (mC) at CpG sites is a prevalent reversible epigenetic mark in vertebrates established by DNA methyltransferases (MTases); the attached methyl groups can alter local structure of DNA and chromatin as well as binding of dedicated proteins. Nucleosome assembly on methylated DNA has been studied extensively, however little is known how the chromatin structure is affected by larger chemical variations in the major groove of DNA. Here, we studied the nucleosome formation in vitro on DNA containing an extended 5mC analog, 5-(6-azidohex-2-ynyl)cytosine (ahyC) installed at biological relevant CpG sites. We found that multiple ahyC residues on 80-Widom and Hsp70 promoter DNA fragments proved compatible with nucleosome assembly. Moreover, unlike mC, ahyC increases the affinity of histones to the DNA, partially altering nucleosome positioning, stability, and the action of chromatin remodelers. Based on molecular dynamics calculations, we suggest that these new features are due to increased DNA flexibility at ahyC-modified sites. Our findings provide new insights into the biophysical behavior of modified DNA and open new ways for directed design of synthetic nucleosomes.
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Affiliation(s)
- Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Markus Meier
- Biochemistry III, University of Regensburg, Regensburg, Bavaria, DE-93053, Germany
| | - Diana Ikasalaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Julia Wildenauer
- Biochemistry III, University of Regensburg, Regensburg, Bavaria, DE-93053, Germany
| | - Visvaldas Kairys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Laura Manelytė
- Biochemistry III, University of Regensburg, Regensburg, Bavaria, DE-93053, Germany
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6
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Rudenko AY, Mariasina SS, Sergiev PV, Polshakov VI. Analogs of S-Adenosyl-L-Methionine in Studies of Methyltransferases. Mol Biol 2022; 56:229-250. [PMID: 35440827 PMCID: PMC9009987 DOI: 10.1134/s002689332202011x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 01/02/2023]
Abstract
Methyltransferases (MTases) play an important role in the functioning of living systems, catalyzing the methylation reactions of DNA, RNA, proteins, and small molecules, including endogenous compounds and drugs. Many human diseases are associated with disturbances in the functioning of these enzymes; therefore, the study of MTases is an urgent and important task. Most MTases use the cofactor S‑adenosyl‑L‑methionine (SAM) as a methyl group donor. SAM analogs are widely applicable in the study of MTases: they are used in studies of the catalytic activity of these enzymes, in identification of substrates of new MTases, and for modification of the substrates or substrate linking to MTases. In this review, new synthetic analogs of SAM and the problems that can be solved with their usage are discussed.
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Affiliation(s)
- A. Yu. Rudenko
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Zelinsky Institute of Organic Chemistry, 119991 Moscow, Russia
| | - S. S. Mariasina
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - P. V. Sergiev
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - V. I. Polshakov
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
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7
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Stankevičius V, Gibas P, Masiulionytė B, Gasiulė L, Masevičius V, Klimašauskas S, Vilkaitis G. Selective chemical tracking of Dnmt1 catalytic activity in live cells. Mol Cell 2022; 82:1053-1065.e8. [PMID: 35245449 PMCID: PMC8901439 DOI: 10.1016/j.molcel.2022.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/04/2021] [Accepted: 02/01/2022] [Indexed: 12/24/2022]
Abstract
Enzymatic methylation of cytosine to 5-methylcytosine in DNA is a fundamental epigenetic mechanism involved in mammalian development and disease. DNA methylation is brought about by collective action of three AdoMet-dependent DNA methyltransferases, whose catalytic interactions and temporal interplay are poorly understood. We used structure-guided engineering of the Dnmt1 methyltransferase to enable catalytic transfer of azide tags onto DNA from a synthetic cofactor analog, Ado-6-azide, in vitro. We then CRISPR-edited the Dnmt1 locus in mouse embryonic stem cells to install the engineered codon, which, following pulse internalization of the Ado-6-azide cofactor by electroporation, permitted selective azide tagging of Dnmt1-specific genomic targets in cellulo. The deposited covalent tags were exploited as “click” handles for reading adjoining sequences and precise genomic mapping of the methylation sites. The proposed approach, Dnmt-TOP-seq, enables high-resolution temporal tracking of the Dnmt1 catalysis in mammalian cells, paving the way to selective studies of other methylation pathways in eukaryotic systems. A single alanine substitution in Dnmt1 confers catalytic transfer of extended groups Electroporation permits facile delivery of AdoMet analogs into live mammalian cells Engineered Dnmt1 adds trackable azide tags at its native target sites in cellulo Dnmt-TOP-seq enables genome-wide tracking of Dnmt1 activity in live mammalian cells
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Affiliation(s)
- Vaidotas Stankevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Povilas Gibas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Bernadeta Masiulionytė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Liepa Gasiulė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Viktoras Masevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania; Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Vilnius 03225, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania.
| | - Giedrius Vilkaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania.
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8
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DNA Labeling Using DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:535-562. [DOI: 10.1007/978-3-031-11454-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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9
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Rakauskaitė R, Urbanavičiūtė G, Simanavičius M, Lasickienė R, Vaitiekaitė A, Petraitytė G, Masevičius V, Žvirblienė A, Klimašauskas S. Photocage-Selective Capture and Light-Controlled Release of Target Proteins. iScience 2020; 23:101833. [PMID: 33305188 PMCID: PMC7718476 DOI: 10.1016/j.isci.2020.101833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 12/05/2022] Open
Abstract
Photochemical transformations enable exquisite spatiotemporal control over biochemical processes; however, methods for reliable manipulations of biomolecules tagged with biocompatible photo-sensitive reporters are lacking. Here we created a high-affinity binder specific to a photolytically removable caging group. We utilized chemical modification or genetically encoded incorporation of noncanonical amino acids to produce proteins with photocaged cysteine or selenocysteine residues, which were used for raising a high-affinity monoclonal antibody against a small photoremovable tag, 4,5-dimethoxy-2-nitrobenzyl (DMNB) group. Employing the produced photocage-selective binder, we demonstrate selective detection and immunoprecipitation of a variety of DMNB-caged target proteins in complex biological mixtures. This combined orthogonal strategy permits photocage-selective capture and light-controlled traceless release of target proteins for a myriad of applications in nanoscale assays. The first high-affinity monoclonal antibody specific for a popular photocaging group A new tool for selective detection of DMNB-tagged proteins in complex mixtures Enables non-covalent capture of native proteins with surface-exposed DMNB groups Orthogonal protein manipulation by photocage-selective capture and photolytic release
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Affiliation(s)
- Rasa Rakauskaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Giedrė Urbanavičiūtė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Martynas Simanavičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Rita Lasickienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Aušra Vaitiekaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Gražina Petraitytė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.,Institute of Chemistry, Department of Chemistry and Geosciences, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Viktoras Masevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.,Institute of Chemistry, Department of Chemistry and Geosciences, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Aurelija Žvirblienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
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10
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Tomkuvienė M, Ikasalaitė D, Slyvka A, Rukšėnaitė A, Ravichandran M, Jurkowski TP, Bochtler M, Klimašauskas S. Enzymatic Hydroxylation and Excision of Extended 5-Methylcytosine Analogues. J Mol Biol 2020; 432:6157-6167. [PMID: 33065111 PMCID: PMC7763475 DOI: 10.1016/j.jmb.2020.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 11/28/2022]
Abstract
Methylation of cytosine to 5-methylcytosine (mC) is a prevalent reversible epigenetic mark in vertebrates established by DNA methyltransferases (MTases); the methylation mark can be actively erased via a multi-step demethylation mechanism involving oxidation by Ten-eleven translocation (TET) enzyme family dioxygenases, excision of the latter oxidation products by thymine DNA (TDG) or Nei-like 1 (NEIL1) glycosylases followed by base excision repair to restore the unmodified state. Here we probed the activity of the mouse TET1 (mTET1) and Naegleria gruberi TET (nTET) oxygenases with DNA substrates containing extended derivatives of the 5-methylcytosine carrying linear carbon chains and adjacent unsaturated CC bonds. We found that the nTET and mTET1 enzymes were active on modified mC residues in single-stranded and double-stranded DNA in vitro, while the extent of the reactions diminished with the size of the extended group. Iterative rounds of nTET hydroxylations of ssDNA proceeded with high stereo specificity and included not only the natural alpha position but also the adjoining carbon atom in the extended side chain. The regioselectivity of hydroxylation was broken when the reactive carbon was adjoined with an sp1 or sp2 system. We also found that NEIL1 but not TDG was active with bulky TET-oxidation products. These findings provide important insights into the mechanism of these biologically important enzymatic reactions.
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Affiliation(s)
- Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Diana Ikasalaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Anton Slyvka
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Audronė Rukšėnaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | | | | | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania.
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11
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Discovery of an Unnatural DNA Modification Derived from a Natural Secondary Metabolite. Cell Chem Biol 2020; 28:97-104.e4. [PMID: 33053370 DOI: 10.1016/j.chembiol.2020.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/19/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Abstract
Despite widespread interest for understanding how modified bases have evolved their contemporary functions, limited experimental evidence exists for measuring how close an organism is to accidentally creating a new, modified base within the framework of its existing genome. Here, we describe the biochemical and structural basis for how a single-point mutation in E. coli's naturally occurring cytosine methyltransferase can surprisingly endow a neomorphic ability to create the unnatural DNA base, 5-carboxymethylcytosine (5cxmC), in vivo. Mass spectrometry, bacterial genetics, and structure-guided biochemistry reveal this base to be exclusively derived from the natural but sparse secondary metabolite carboxy-S-adenosyl-L-methionine (CxSAM). Our discovery of a new, unnatural DNA modification reveals insights into the substrate selectivity of DNA methyltransferase enzymes, offers a promising new biotechnological tool for the characterization of the mammalian epigenome, and provides an unexpected model for how neomorphic bases could arise in nature from repurposed host metabolites.
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12
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Ličytė J, Gibas P, Skardžiūtė K, Stankevičius V, Rukšėnaitė A, Kriukienė E. A Bisulfite-free Approach for Base-Resolution Analysis of Genomic 5-Carboxylcytosine. Cell Rep 2020; 32:108155. [DOI: 10.1016/j.celrep.2020.108155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/10/2020] [Accepted: 08/25/2020] [Indexed: 01/01/2023] Open
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13
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Huber TD, Clinger JA, Liu Y, Xu W, Miller MD, Phillips GN, Thorson JS. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes. ACS Chem Biol 2020; 15:695-705. [PMID: 32091873 DOI: 10.1021/acschembio.9b00943] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structural conservation among methyltransferases (MTs) and MT functional redundancy is a major challenge to the cellular study of individual MTs. As a first step toward the development of an alternative biorthogonal platform for MTs and other AdoMet-utilizing enzymes, we describe the evaluation of 38 human methionine adenosyltransferase II-α (hMAT2A) mutants in combination with 14 non-native methionine analogues to identify suitable bioorthogonal mutant/analogue pairings. Enabled by the development and implementation of a hMAT2A high-throughput (HT) assay, this study revealed hMAT2A K289L to afford a 160-fold inversion of the hMAT2A selectivity index for a non-native methionine analogue over the native substrate l-Met. Structure elucidation of K289L revealed the mutant to be folded normally with minor observed repacking within the modified substrate pocket. This study highlights the first example of exchanging l-Met terminal carboxylate/amine recognition elements within the hMAT2A active-site to enable non-native bioorthgonal substrate utilization. Additionally, several hMAT2A mutants and l-Met substrate analogues produced AdoMet analogue products with increased stability. As many AdoMet-producing (e.g., hMAT2A) and AdoMet-utlizing (e.g., MTs) enzymes adopt similar active-site strategies for substrate recognition, the proof of concept first generation hMAT2A engineering highlighted herein is expected to translate to a range of AdoMet-utilizing target enzymes.
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Affiliation(s)
- Tyler D. Huber
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | - Yang Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | | | | | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
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14
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Sirasunthorn N, Jailwala A, Gerber A, Comstock LR. Evaluation of
N
‐Mustard Analogues of
S
‐Adenosyl‐L‐methionine with Eukaryotic DNA Methyltransferase 1. ChemistrySelect 2019. [DOI: 10.1002/slct.201902940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Nichanun Sirasunthorn
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
| | - Anuj Jailwala
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
| | - Anna Gerber
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
| | - Lindsay R. Comstock
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
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15
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Deen J, Wang S, Van Snick S, Leen V, Janssen K, Hofkens J, Neely RK. A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA. Nucleic Acids Res 2019; 46:e64. [PMID: 29546351 PMCID: PMC6009647 DOI: 10.1093/nar/gky184] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/02/2018] [Indexed: 12/13/2022] Open
Abstract
The methyltransferase enzymes can be applied to deliver a range of modifications to pre-determined sites on large DNA molecules with exceptional specificity and efficiency. To date, however, a limited number of modifications have been delivered in this way because of the complex chemical synthesis that is needed to produce a cofactor analogue carrying a specific function, such as a fluorophore. Here, we describe a method for the direct transfer of a series of functional compounds (seven fluorescent dyes, biotin and polyethylene glycol) to the DNA duplex. Our approach uses a functional cofactor analogue, whose final preparative step is performed alongiside the DNA modification reaction in a single pot, with no purification needed. We show that fluorophore conjugation efficiency in these mixtures is significantly improved compared to two-step labeling approaches. Our experiments highlight the remarkable malleability and selectivity of the methyltransferases tested. Additional analysis using high resolution localization of the fluorophore distribution indicates that target sites for the methyltransferase are predominantly labeled on a single strand of their palindromic site and that a small and randomly-distributed probability of off-site labeling exists.
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Affiliation(s)
- Jochem Deen
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Su Wang
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Sven Van Snick
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Volker Leen
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Kris Janssen
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Johan Hofkens
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Robert K Neely
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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16
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Ganesan A. Epigenetic drug discovery: a success story for cofactor interference. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0069. [PMID: 29685973 DOI: 10.1098/rstb.2017.0069] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2017] [Indexed: 02/06/2023] Open
Abstract
Within the past two decades, seven epigenetic drugs have received regulatory approval and numerous other candidates are currently in clinical trials. Among the epigenetic targets are the writer and eraser enzymes that are, respectively, responsible for the reversible introduction and removal of structural modifications in the nucleosome. This review discusses the progress achieved in the design and development of inhibitors against the key writer and eraser pairs: DNA methyltransferases and Tet demethylases; lysine/arginine methyltransferases and lysine demethylases; and histone acetyltransferases and histone deacetylases. A common theme for the successful inhibition of these enzymes in a potent and selective manner is the targeting of the cofactors present in the active site, namely zinc and iron cations, S-adenosylmethione, nicotinamide adenine dinucleotide, flavin adenine dinucleotide and acetyl Coenzyme A.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- A Ganesan
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK .,Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg im Breisgau, Germany
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17
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Ge J, Zhao Y, Li C, Jie G. Versatile Electrochemiluminescence and Electrochemical “On–Off” Assays of Methyltransferases and Aflatoxin B1 Based on a Novel Multifunctional DNA Nanotube. Anal Chem 2019; 91:3546-3554. [DOI: 10.1021/acs.analchem.8b05362] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Junjun Ge
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People’s Republic of China
| | - Yu Zhao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People’s Republic of China
| | - Chunli Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People’s Republic of China
| | - Guifen Jie
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People’s Republic of China
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18
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Islam K. The Bump-and-Hole Tactic: Expanding the Scope of Chemical Genetics. Cell Chem Biol 2018; 25:1171-1184. [PMID: 30078633 PMCID: PMC6195450 DOI: 10.1016/j.chembiol.2018.07.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/13/2018] [Accepted: 07/02/2018] [Indexed: 12/15/2022]
Abstract
Successful mapping of the human genome has sparked a widespread interest in deciphering functional information encoded in gene sequences. However, because of the high degree of conservation in sequences along with topological and biochemical similarities among members of a protein superfamily, uncovering physiological role of a particular protein has been a challenging task. Chemical genetic approaches have made significant contributions toward understanding protein function. One such effort, dubbed the bump-and-hole approach, has convincingly demonstrated that engineering at the protein-small molecule interface constitutes a powerful method for elucidating the function of a specific gene product. By manipulating the steric component of protein-ligand interactions in a complementary manner, an orthogonal system is developed to probe a specific enzyme-cofactor pair without interference from related members. This article outlines current efforts to expand the approach for diverse protein classes and their applications. Potential future innovations to address contemporary biological problems are highlighted as well.
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Affiliation(s)
- Kabirul Islam
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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19
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Tomkuvienė M, Mickutė M, Vilkaitis G, Klimašauskas S. Repurposing enzymatic transferase reactions for targeted labeling and analysis of DNA and RNA. Curr Opin Biotechnol 2018; 55:114-123. [PMID: 30296696 DOI: 10.1016/j.copbio.2018.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 12/16/2022]
Abstract
Produced as linear biopolymers from four major types of building blocks, DNA and RNA are further furnished with a range of covalent modifications. Despite the impressive specificity of natural enzymes, the transferred groups are often poor reporters and not amenable to further derivatization. Therefore, strategies based on repurposing some of these enzymatic reactions to accept derivatized versions of the transferrable groups have been exploited. By far the most widely used are S-adenosylmethionine-dependent methyltransferases, which along with several other nucleic acids modifying enzymes offer a broad selection of tagging chemistries and molecular features on DNA and RNA that can be targeted in vitro and in vivo. Engineered enzymatic reactions have been implemented in validated DNA sequencing-based protocols for epigenome analysis. The utility of chemo-enzymatic labeling is further enhanced with recent advances in physical detection of individual reporter groups on DNA using super resolution microscopy and nanopore sensing enabling single-molecule multiplex analysis of genetic and epigenetic marks in minute samples. Altogether, a number of new powerful techniques are currently in use or on the verge of real benchtop applications as research tools or next generation diagnostics.
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Affiliation(s)
- Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Milda Mickutė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Giedrius Vilkaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania.
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20
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Heimes M, Kolmar L, Brieke C. Efficient cosubstrate enzyme pairs for sequence-specific methyltransferase-directed photolabile caging of DNA. Chem Commun (Camb) 2018; 54:12718-12721. [DOI: 10.1039/c8cc05913f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Efficient and selective methyltransferase-catalyzed transfer of photolabile groups onto DNA enables photoregulation of gene expression and can be performed even in the presence of AdoMet.
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Affiliation(s)
- Michael Heimes
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- D-69120 Heidelberg
- Germany
| | - Leonie Kolmar
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- D-69120 Heidelberg
- Germany
| | - Clara Brieke
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- D-69120 Heidelberg
- Germany
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21
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Zhou X, Zhao M, Duan X, Guo B, Cheng W, Ding S, Ju H. Collapse of DNA Tetrahedron Nanostructure for "Off-On" Fluorescence Detection of DNA Methyltransferase Activity. ACS APPLIED MATERIALS & INTERFACES 2017; 9:40087-40093. [PMID: 29111659 DOI: 10.1021/acsami.7b13551] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
As a potential detection technique, highly rigid and versatile functionality of DNA tetrahedron nanostructures is often used in biosensing systems. In this work, a novel multifunctional nanostructure has been developed as an "off-on" fluorescent probe for detection of target methyltransferase by integrating the elements of DNA tetrahedron, target recognition, and dual-labeled reporter. This sensing system is initially in an "OFF" state owing to the close proximity of fluorophores and quenchers. After the substrate is recognized by target methyltransferase, the DNA tetrahedron can be methylated to produce methylated DNA sites. These sites can be recognized and cut by the restriction endonuclease DpnI to bring about the collapse of the DNA tetrahedron, which leads to the separation of the dual-labeled reporters from the quenchers, and thus the recovery of fluorescence signal to produce an "ON" state. The proposed DNA tetrahedron-based sensing method can detect Dam methyltransferase in the range of 0.1-90 U mL-1 with a detection limit of 0.045 U mL-1 and shows good specificity and reproducibility for detection of Dam methyltransferase in a real sample. It has been successfully applied for screening various methylation inhibitors. Thus, this work possesses a promising prospect for detection of DNA methyltransfrase in the field of clinical diagnostics.
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Affiliation(s)
- Xiaoyan Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
- Department of Clinical Laboratory, The Affiliated Hospital of Medical College, Qingdao University , Qingdao 266101, China
| | - Min Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Xiaolei Duan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Bin Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University , Chongqing 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Huangxian Ju
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
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22
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Deen J, Vranken C, Leen V, Neely RK, Janssen KPF, Hofkens J. Methyltransferase-Directed Labeling of Biomolecules and its Applications. Angew Chem Int Ed Engl 2017; 56:5182-5200. [PMID: 27943567 PMCID: PMC5502580 DOI: 10.1002/anie.201608625] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Indexed: 01/01/2023]
Abstract
Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S-adenosyl-l-Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly-activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet-dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.
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Affiliation(s)
- Jochem Deen
- Laboratory of Nanoscale BiologySchool of Engineering, EPFL, STI IBI-STI LBEN BM 5134 (Bâtiment BM)Station 17CH-1015LausanneSwitzerland
| | - Charlotte Vranken
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Volker Leen
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Robert K. Neely
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Kris P. F. Janssen
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Johan Hofkens
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
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23
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Deen J, Vranken C, Leen V, Neely RK, Janssen KPF, Hofkens J. Die Methyltransferase-gesteuerte Markierung von Biomolekülen und ihre Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201608625] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jochem Deen
- Laboratory of Nanoscale Biology; School of Engineering, EPFL, STI IBI-STI LBEN BM 5134 (Bâtiment BM); Station 17 CH-1015 Lausanne Schweiz
| | - Charlotte Vranken
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Volker Leen
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Robert K. Neely
- School of Chemistry; University of Birmingham; Edgbaston Birmingham B15 2TT Großbritannien
| | - Kris P. F. Janssen
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Johan Hofkens
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
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24
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Engineering and Directed Evolution of DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [PMID: 27826849 DOI: 10.1007/978-3-319-43624-1_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
DNA methyltransferases (MTases) constitute an attractive target for protein engineering, thus opening the road to new ways of manipulating DNA in a unique and selective manner. Here, we review various aspects of MTase engineering, both methodological and conceptual, and also discuss future directions and challenges. Bacterial MTases that are part of restriction/modification (R/M) systems offer a convenient way for the selection of large gene libraries, both in vivo and in vitro. We review these selection methods, their strengths and weaknesses, and also the prospects for new selection approaches that will enable the directed evolution of mammalian DNA methyltransferases (Dnmts). We explore various properties of MTases that may be subject to engineering. These include engineering for higher stability and soluble expression (MTases, including bacterial ones, are prone to misfolding), engineering of the DNA target specificity, and engineering for the usage of S-adenosyl-L-methionine (AdoMet) analogs. Directed evolution of bacterial MTases also offers insights into how these enzymes readily evolve in nature, thus yielding MTases with a huge spectrum of DNA target specificities. Engineering for alternative cofactors, on the other hand, enables modification of DNA with various groups other than methyl and thus can be employed to map and redirect DNA epigenetic modifications.
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25
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Abstract
S-Adenosyl-L-methionine (SAM) is a sulfonium molecule with a structural hybrid of methionine and adenosine. As the second largest cofactor in the human body, its major function is to serve as methyl donor for SAM-dependent methyltransferases (MTases). The resultant transmethylation of biomolecules constitutes a significant biochemical mechanism in epigenetic regulation, cellular signaling, and metabolite degradation. Recently, numerous SAM analogs have been developed as synthetic cofactors to transfer the activated groups on MTase substrates for downstream ligation and identification. Meanwhile, new compounds built upon or derived from the SAM scaffold have been designed and tested as selective inhibitors for important MTase targets. Here, we summarized the recent development and application of SAM analogs as chemical biology tools for MTases.
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Affiliation(s)
- Jing Zhang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
| | - Yujun George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
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26
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Masevičius V, Nainytė M, Klimašauskas S. Synthesis of S-Adenosyl-L-Methionine Analogs with Extended Transferable Groups for Methyltransferase-Directed Labeling of DNA and RNA. ACTA ACUST UNITED AC 2016; 64:1.36.1-1.36.13. [PMID: 26967468 DOI: 10.1002/0471142700.nc0136s64] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
S-Adenosyl-L-methionine (AdoMet) is a ubiquitous methyl donor for a variety of biological methylation reactions catalyzed by methyltransferases (MTases). AdoMet analogs with extended propargylic chains replacing the sulfonium-bound methyl group can serve as surrogate cofactors for many DNA and RNA MTases enabling covalent deposition of these linear chains to their cognate targets sites in DNA or RNA. Here we describe synthetic procedures for the preparation of two representative examples of AdoMet analogs with a transferable hex-2-ynyl group carrying a terminal azide or amine functionality. Our approach is based on direct chemoselective alkylation of S-adenosyl-L-homocysteine at sulfur with corresponding nosylates under acidic conditions. We also describe synthetic routes to 6-substituted hex-2-yn-1-ols and their conversion to the corresponding nosylates. Using these protocols, synthetic AdoMet analogs can be prepared within 1 to 2 weeks.
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Affiliation(s)
- Viktoras Masevičius
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,Faculty of Chemistry, Vilnius University, Vilnius, Lithuania
| | - Milda Nainytė
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,Faculty of Chemistry, Vilnius University, Vilnius, Lithuania
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27
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Struck AW, Bennett MR, Shepherd SA, Law BJC, Zhuo Y, Wong LS, Micklefield J. An Enzyme Cascade for Selective Modification of Tyrosine Residues in Structurally Diverse Peptides and Proteins. J Am Chem Soc 2016; 138:3038-45. [DOI: 10.1021/jacs.5b10928] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Anna-Winona Struck
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Matthew R. Bennett
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Sarah A. Shepherd
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Brian J. C. Law
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Ying Zhuo
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Lu Shin Wong
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry and Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
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28
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Tomkuvienė M, Kriukienė E, Klimašauskas S. DNA Labeling Using DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:511-535. [PMID: 27826850 PMCID: PMC11032744 DOI: 10.1007/978-3-319-43624-1_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA methyltransferases (MTases) uniquely combine the ability to recognize and covalently modify specific target sequences in DNA using the ubiquitous cofactor S-adenosyl-L-methionine (AdoMet). Although DNA methylation plays important roles in biological signaling, the transferred methyl group is a poor reporter and is highly inert to further biocompatible derivatization. To unlock the biotechnological power of these enzymes, two major types of cofactor AdoMet analogs were developed that permit targeted MTase-directed attachment of larger moieties containing functional or reporter groups onto DNA. One such approach (named sequence-specific methyltransferase-induced labeling, SMILing) uses reactive aziridine or N-mustard mimics of the cofactor AdoMet, which render targeted coupling of a whole cofactor molecule to the target DNA. The second approach (methyltransferase-directed transfer of activated groups, mTAG) uses AdoMet analogs with a sulfonium-bound extended side chain replacing the methyl group, which permits MTase-directed covalent transfer of the activated side chain alone. As the enlarged cofactors are not always compatible with the active sites of native MTases, steric engineering of the active site has been employed to optimize their alkyltransferase activity. In addition to the described cofactor analogs, recently discovered atypical reactions of DNA cytosine-5 MTases involving non-cofactor-like compounds can also be exploited for targeted derivatization and labeling of DNA. Altogether, these approaches offer new powerful tools for sequence-specific covalent DNA labeling, which not only pave the way to developing a variety of useful techniques in DNA research, diagnostics, and nanotechnologies but have already proven practical utility for optical DNA mapping and epigenome studies.
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Affiliation(s)
- Miglė Tomkuvienė
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10222, Lithuania
| | - Edita Kriukienė
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10222, Lithuania
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29
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Rombouts K, Braeckmans K, Remaut K. Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies. Bioconjug Chem 2015; 27:280-97. [PMID: 26670733 DOI: 10.1021/acs.bioconjchem.5b00579] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs.
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Affiliation(s)
- K Rombouts
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Braeckmans
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Remaut
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
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30
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Islam K. Allele-specific chemical genetics: concept, strategies, and applications. ACS Chem Biol 2015; 10:343-63. [PMID: 25436868 DOI: 10.1021/cb500651d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The relationship between DNA and protein sequences is well understood, yet because the members of a protein family/subfamily often carry out the same biochemical reaction, elucidating their individual role in cellular processes presents a challenge. Forward and reverse genetics have traditionally been employed to understand protein functions with considerable success. A fundamentally different approach that has gained widespread application is the use of small organic molecules, known as chemical genetics. However, the slow time-scale of genetics and inherent lack of specificity of small molecules used in chemical genetics have limited the applicability of these methods in deconvoluting the role of individual proteins involved in fast, dynamic biological events. Combining the advantages of both the techniques, the specificity achieved with genetics along with the reversibility and tunability of chemical genetics, has led to the development of a powerful approach to uncover protein functions in complex biological processes. This technique is known as allele-specific chemical genetics and is rapidly becoming an essential toolkit to shed light on proteins and their mechanism of action. The current review attempts to provide a comprehensive description of this approach by discussing the underlying principles, strategies, and successful case studies. Potential future implications of this technology in expanding the frontiers of modern biology are discussed.
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Affiliation(s)
- Kabirul Islam
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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31
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Hanz GM, Jung B, Giesbertz A, Juhasz M, Weinhold E. Sequence-specific labeling of nucleic acids and proteins with methyltransferases and cofactor analogues. J Vis Exp 2014:e52014. [PMID: 25490674 DOI: 10.3791/52014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
S-Adenosyl-l-methionine (AdoMet or SAM)-dependent methyltransferases (MTase) catalyze the transfer of the activated methyl group from AdoMet to specific positions in DNA, RNA, proteins and small biomolecules. This natural methylation reaction can be expanded to a wide variety of alkylation reactions using synthetic cofactor analogues. Replacement of the reactive sulfonium center of AdoMet with an aziridine ring leads to cofactors which can be coupled with DNA by various DNA MTases. These aziridine cofactors can be equipped with reporter groups at different positions of the adenine moiety and used for Sequence-specific Methyltransferase-Induced Labeling of DNA (SMILing DNA). As a typical example we give a protocol for biotinylation of pBR322 plasmid DNA at the 5'-ATCGAT-3' sequence with the DNA MTase M.BseCI and the aziridine cofactor 6BAz in one step. Extension of the activated methyl group with unsaturated alkyl groups results in another class of AdoMet analogues which are used for methyltransferase-directed Transfer of Activated Groups (mTAG). Since the extended side chains are activated by the sulfonium center and the unsaturated bond, these cofactors are called double-activated AdoMet analogues. These analogues not only function as cofactors for DNA MTases, like the aziridine cofactors, but also for RNA, protein and small molecule MTases. They are typically used for enzymatic modification of MTase substrates with unique functional groups which are labeled with reporter groups in a second chemical step. This is exemplified in a protocol for fluorescence labeling of histone H3 protein. A small propargyl group is transferred from the cofactor analogue SeAdoYn to the protein by the histone H3 lysine 4 (H3K4) MTase Set7/9 followed by click labeling of the alkynylated histone H3 with TAMRA azide. MTase-mediated labeling with cofactor analogues is an enabling technology for many exciting applications including identification and functional study of MTase substrates as well as DNA genotyping and methylation detection.
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Affiliation(s)
- Gisela Maria Hanz
- Institute of Organic Chemistry, Department of Chemistry, RWTH Aachen University
| | - Britta Jung
- Institute of Organic Chemistry, Department of Chemistry, RWTH Aachen University
| | - Anna Giesbertz
- Institute of Organic Chemistry, Department of Chemistry, RWTH Aachen University
| | - Matyas Juhasz
- Institute of Organic Chemistry, Department of Chemistry, RWTH Aachen University
| | - Elmar Weinhold
- Institute of Organic Chemistry, Department of Chemistry, RWTH Aachen University;
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32
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Plotnikova A, Osipenko A, Masevičius V, Vilkaitis G, Klimašauskas S. Selective Covalent Labeling of miRNA and siRNA Duplexes Using HEN1 Methyltransferase. J Am Chem Soc 2014; 136:13550-3. [DOI: 10.1021/ja507390s] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | - Aleksandr Osipenko
- Institute
of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Viktoras Masevičius
- Institute
of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
- Faculty
of Chemistry, Vilnius University, Vilnius LT-03225, Lithuania
| | - Giedrius Vilkaitis
- Institute
of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
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33
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Metadynamics simulation study on the conformational transformation of HhaI methyltransferase: an induced-fit base-flipping hypothesis. BIOMED RESEARCH INTERNATIONAL 2014; 2014:304563. [PMID: 25045662 PMCID: PMC4090504 DOI: 10.1155/2014/304563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/12/2014] [Indexed: 12/02/2022]
Abstract
DNA methyltransferases play crucial roles in establishing and maintenance of DNA methylation, which is an important epigenetic mark. Flipping the target cytosine out of the DNA helical stack and into the active site of protein provides DNA methyltransferases with an opportunity to access and modify the genetic information hidden in DNA. To investigate the conversion process of base flipping in the HhaI methyltransferase (M.HhaI), we performed different molecular simulation approaches on M.HhaI-DNA-S-adenosylhomocysteine ternary complex. The results demonstrate that the nonspecific binding of DNA to M.HhaI is initially induced by electrostatic interactions. Differences in chemical environment between the major and minor grooves determine the orientation of DNA. Gln237 at the target recognition loop recognizes the GCGC base pair from the major groove side by hydrogen bonds. In addition, catalytic loop motion is a key factor during this process. Our study indicates that base flipping is likely to be an “induced-fit” process. This study provides a solid foundation for future studies on the discovery and development of mechanism-based DNA methyltransferases regulators.
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34
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Chaikind B, Ostermeier M. Directed evolution of improved zinc finger methyltransferases. PLoS One 2014; 9:e96931. [PMID: 24810747 PMCID: PMC4014571 DOI: 10.1371/journal.pone.0096931] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/14/2014] [Indexed: 01/09/2023] Open
Abstract
The ability to target DNA methylation toward a single, user-designated CpG site in vivo may have wide applicability for basic biological and biomedical research. A tool for targeting methylation toward single sites could be used to study the effects of individual methylation events on transcription, protein recruitment to DNA, and the dynamics of such epigenetic alterations. Although various tools for directing methylation to promoters exist, none offers the ability to localize methylation solely to a single CpG site. In our ongoing research to create such a tool, we have pursued a strategy employing artificially bifurcated DNA methyltransferases; each methyltransferase fragment is fused to zinc finger proteins with affinity for sequences flanking a targeted CpG site for methylation. We sought to improve the targeting of these enzymes by reducing the methyltransferase activity at non-targeted sites while maintaining high levels of activity at a targeted site. Here we demonstrate an in vitro directed evolution selection strategy to improve methyltransferase specificity and use it to optimize an engineered zinc finger methyltransferase derived from M.SssI. The unusual restriction enzyme McrBC is a key component of this strategy and is used to select against methyltransferases that methylate multiple sites on a plasmid. This strategy allowed us to quickly identify mutants with high levels of methylation at the target site (up to ∼80%) and nearly unobservable levels of methylation at a off-target sites (<1%), as assessed in E. coli. We also demonstrate that replacing the zinc finger domains with new zinc fingers redirects the methylation to a new target CpG site flanked by the corresponding zinc finger binding sequences.
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Affiliation(s)
- Brian Chaikind
- Chemistry-Biology Interface Graduate Program, 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
- * E-mail:
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35
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Liutkevičiu̅tė Z, Kriukienė E, Ličytė J, Rudytė M, Urbanavičiu̅tė G, Klimašauskas S. Direct Decarboxylation of 5-Carboxylcytosine by DNA C5- Methyltransferases. J Am Chem Soc 2014; 136:5884-7. [DOI: 10.1021/ja5019223] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zita Liutkevičiu̅tė
- Department of Biological
DNA Modification, Institute of Biotechnology, Vilnius University, 02241 Vilnius, Lithuania
| | - Edita Kriukienė
- Department of Biological
DNA Modification, Institute of Biotechnology, Vilnius University, 02241 Vilnius, Lithuania
| | - Janina Ličytė
- Department of Biological
DNA Modification, Institute of Biotechnology, Vilnius University, 02241 Vilnius, Lithuania
| | - Milda Rudytė
- Department of Biological
DNA Modification, Institute of Biotechnology, Vilnius University, 02241 Vilnius, Lithuania
| | - Giedrė Urbanavičiu̅tė
- Department of Biological
DNA Modification, Institute of Biotechnology, Vilnius University, 02241 Vilnius, Lithuania
| | - Saulius Klimašauskas
- Department of Biological
DNA Modification, Institute of Biotechnology, Vilnius University, 02241 Vilnius, Lithuania
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36
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Kriukienė E, Labrie V, Khare T, Urbanavičiūtė G, Lapinaitė A, Koncevičius K, Li D, Wang T, Pai S, Ptak C, Gordevičius J, Wang SC, Petronis A, Klimašauskas S. DNA unmethylome profiling by covalent capture of CpG sites. Nat Commun 2014; 4:2190. [PMID: 23877302 DOI: 10.1038/ncomms3190] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/26/2013] [Indexed: 11/09/2022] Open
Abstract
Dynamic patterns of cytosine-5 methylation and successive hydroxylation are part of epigenetic regulation in eukaryotes, including humans, which contributes to normal phenotypic variation and disease risk. Here we present an approach for the mapping of unmodified regions of the genome, which we call the unmethylome. Our technique is based on DNA methyltransferase-directed transfer of activated groups and covalent biotin tagging of unmodified CpG sites followed by affinity enrichment and interrogation on tiling microarrays or next generation sequencing. Control experiments and pilot studies of human genomic DNA from cultured cells and tissues demonstrate that, along with providing a unique cross-section through the chemical landscape of the epigenome, the methyltransferase-directed transfer of activated groups-based approach offers high precision and robustness as compared with existing affinity-based techniques.
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Affiliation(s)
- Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
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37
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Vranken C, Deen J, Dirix L, Stakenborg T, Dehaen W, Leen V, Hofkens J, Neely RK. Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry. Nucleic Acids Res 2014; 42:e50. [PMID: 24452797 PMCID: PMC3985630 DOI: 10.1093/nar/gkt1406] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).
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Affiliation(s)
- Charlotte Vranken
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium, Life Science Technologies, Imec, Kapeldreef 75, 3001 Heverlee, Belgium and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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38
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Wang R, Luo M. A journey toward Bioorthogonal Profiling of Protein Methylation inside living cells. Curr Opin Chem Biol 2013; 17:729-37. [PMID: 24035694 DOI: 10.1016/j.cbpa.2013.08.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/13/2013] [Accepted: 08/15/2013] [Indexed: 12/21/2022]
Abstract
Human protein methyltransferases (PMTs) play essential roles through methylating histone and nonhistone targets. It is very challenging to profile global methylation (or methylome) in the context of relevant cellular settings. Unlike other posttranslational modifications such as lysine acetylation or Ser/Thr/Tyr/His phosphorylation, methylation of lysine or arginine does not significantly alter its physical properties (e.g. charge and size) and therefore may not be probed readily by conventional biological tools such antibodies. It is also not trivial to assign unambiguously dynamic methylation events to specific PMTs given their potential redundancy. This review focuses on the decade-long progress in developing complementary chemical tools to elucidate targets of designated PMTs. One of such efforts was to develop the Bioorthogonal Profiling of Protein Methylation (BPPM) technology in vitro and inside living cells.
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Affiliation(s)
- Rui Wang
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, United States; Program of Pharmacology, Weill Graduate School of Medical Science, Cornell University, New York, NY 10021, United States
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39
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Zeng YP, Hu J, Long Y, Zhang CY. Sensitive detection of DNA methyltransferase using hairpin probe-based primer generation rolling circle amplification-induced chemiluminescence. Anal Chem 2013; 85:6143-50. [PMID: 23692336 DOI: 10.1021/ac4011292] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
DNA methyltransferases (MTases) catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to the 5-positon of cytosine in CpG islands, eventually inducing the DNA methylation in both prokaryotes and eukaryotes. Despite the development of various methods for the MTase assay, most of them are laborious and costly with poor sensitivity. Herein, we develop a highly sensitive chemiluminescence method for the MTase assay using hairpin probe-based primer generation rolling circle amplification (PG-RCA). In the presence of DNA adenine methylation (Dam) MTase, the methylation-responsive sequence of hairpin probe is methylated and cleaved by the methylation-sensitive restriction endonuclease Dpn I. The cleaved hairpin probe then functions as a signal primer to initiate PG-RCA reaction by hybridizing with the circular DNA template, producing a large number of horseradish peroxidase-mimicking DNAzyme chains, which can catalyze the oxidation of luminal by H2O2 in the presence of hemin to yield distinct chemiluminescence signal. While in the absence of Dam MTase, neither methylation/cleavage nor PG-RCA reaction can be initiated and no chemiluminescence signal is observed. The proposed method exhibits a wide dynamic range from 0.025 to 400 U/mL and an extremely low detection limit of 1.29 × 10(-4) U/mL, which is superior to most conventional approaches for the MTase assay. This method can be used for the screening of antimicrobial drugs and has a great potential to be further applied in early clinical diagnosis.
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Affiliation(s)
- Ya-ping Zeng
- Single-Molecule Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Guangdong 518055, China
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40
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Lukinavičius G, Tomkuvienė M, Masevičius V, Klimašauskas S. Enhanced chemical stability of adomet analogues for improved methyltransferase-directed labeling of DNA. ACS Chem Biol 2013; 8:1134-9. [PMID: 23557731 DOI: 10.1021/cb300669x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Methyltransferases catalyze specific transfers of methyl groups from the ubiquitous cofactor S-adenosyl-l-methionine (AdoMet) to various nucleophilic positions in biopolymers like DNA, RNA, and proteins. We had previously described synthesis and application of AdoMet analogues carrying sulfonium-bound 4-substituted but-2-ynyl side chains for transfer by methyltransferases. Although useful in certain applications, these cofactor analogues exhibited short lifetimes in physiological buffers. Examination of the reaction kinetics and products showed that their fast inactivation followed a different pathway than observed for AdoMet and rather involved a pH-dependent addition of a water molecule to the side chain. This side reaction was eradicated by synthesis of a series of cofactor analogues in which the separation between an electronegative group and the triple bond was increased from one to three carbon units. The designed hex-2-ynyl moiety-based cofactor analogues with terminal amino, azide, or alkyne groups showed a markedly improved enzymatic transalkylation activity and proved well suitable for methyltransferase-directed sequence-specific labeling of DNA in vitro and in bacterial cell lysates.
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Affiliation(s)
| | - Miglė Tomkuvienė
- Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Viktoras Masevičius
- Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
- Faculty of Chemistry, Vilnius University, LT-03225 Vilnius, Lithuania
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