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Li F, Wang Y, Zhang J. Kinetic isotope effect study of N-6 methyladenosine chemical demethylation in bicarbonate-activated peroxide system. J Chem Phys 2023; 159:124103. [PMID: 38127372 DOI: 10.1063/5.0169285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/05/2023] [Indexed: 12/23/2023] Open
Abstract
N-6 methyladenosine is the most abundant nucleic acid modification in eukaryotes and plays a crucial role in gene regulation. The AlkB family of alpha-ketoglutarate-dependent dioxygenases is responsible for nucleic acid demethylation. Recent studies have discovered that a chemical demethylation system using hydrogen peroxide and ammonium bicarbonate can effectively demethylate nucleic acids. The addition of ferrous ammonium sulfate boosts the oxidation rate by forming a Fenton reagent with hydrogen peroxide. However, the specific mechanism and key steps of this process remain unclear. In this study, we investigate the influence of ferrous ammonium sulfate concentration on the kinetic isotope effect (KIE) of the chemical demethylation system using LC-MS. As the concentration of ferrous ions increases, the observed KIE decreases from 1.377 ± 0.020 to 1.120 ± 0.016, indicating a combination of the primary isotope effect and inverse α-secondary isotope effect with the ion pairing effect. We propose that the initial hydrogen extraction is the rate-limiting step and observe a tight transition state structure in the formation of the hm6A process through the analysis of KIE trends. The concentration-dependent KIE provides a novel perspective on the mechanism of chemical demethylation and offers a chemical model for enzyme-catalyzed demethylation.
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Affiliation(s)
- Fangya Li
- School of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, People's Republic of China
| | - Ying Wang
- School of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, People's Republic of China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, People's Republic of China
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Braun A, Gee LB, Mara MW, Hill EA, Kroll T, Nordlund D, Sokaras D, Glatzel P, Hedman B, Hodgson KO, Borovik AS, Baker ML, Solomon EI. X-ray Spectroscopic Study of the Electronic Structure of a Trigonal High-Spin Fe(IV)═O Complex Modeling Non-Heme Enzyme Intermediates and Their Reactivity. J Am Chem Soc 2023; 145:18977-18991. [PMID: 37590931 PMCID: PMC10631461 DOI: 10.1021/jacs.3c06181] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Fe K-edge X-ray absorption spectroscopy (XAS) has long been used for the study of high-valent iron intermediates in biological and artificial catalysts. 4p-mixing into the 3d orbitals complicates the pre-edge analysis but when correctly understood via 1s2p resonant inelastic X-ray scattering and Fe L-edge XAS, it enables deeper insight into the geometric structure and correlates with the electronic structure and reactivity. This study shows that in addition to the 4p-mixing into the 3dz2 orbital due to the short iron-oxo bond, the loss of inversion in the equatorial plane leads to 4p mixing into the 3dx2-y2,xy, providing structural insight and allowing the distinction of 6- vs 5-coordinate active sites as shown through application to the Fe(IV)═O intermediate of taurine dioxygenase. Combined with O K-edge XAS, this study gives an unprecedented experimental insight into the electronic structure of Fe(IV)═O active sites and their selectivity for reactivity enabled by the π-pathway involving the 3dxz/yz orbitals. Finally, the large effect of spin polarization is experimentally assigned in the pre-edge (i.e., the α/β splitting) and found to be better modeled by multiplet simulations rather than by commonly used time-dependent density functional theory.
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Affiliation(s)
- Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Leland B Gee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Michael W Mara
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Ethan A Hill
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Dennis Nordlund
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Pieter Glatzel
- ESRF-The European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - A S Borovik
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Michael L Baker
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
- Department of Chemistry, The University of Manchester, Manchester M13 9PL, U.K
- The University of Manchester at Harwell, Diamond Light Source, Harwell Campus, Didcot OX11 0DE, U.K
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
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3
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Li Q, Zhu Q. The role of demethylase AlkB homologs in cancer. Front Oncol 2023; 13:1153463. [PMID: 37007161 PMCID: PMC10060643 DOI: 10.3389/fonc.2023.1153463] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
The AlkB family (ALKBH1-8 and FTO), a member of the Fe (II)- and α-ketoglutarate-dependent dioxygenase superfamily, has shown the ability to catalyze the demethylation of a variety of substrates, including DNA, RNA, and histones. Methylation is one of the natural organisms’ most prevalent forms of epigenetic modifications. Methylation and demethylation processes on genetic material regulate gene transcription and expression. A wide variety of enzymes are involved in these processes. The methylation levels of DNA, RNA, and histones are highly conserved. Stable methylation levels at different stages can coordinate the regulation of gene expression, DNA repair, and DNA replication. Dynamic methylation changes are essential for the abilities of cell growth, differentiation, and division. In some malignancies, the methylation of DNA, RNA, and histones is frequently altered. To date, nine AlkB homologs as demethylases have been identified in numerous cancers’ biological processes. In this review, we summarize the latest advances in the research of the structures, enzymatic activities, and substrates of the AlkB homologs and the role of these nine homologs as demethylases in cancer genesis, progression, metastasis, and invasion. We provide some new directions for the AlkB homologs in cancer research. In addition, the AlkB family is expected to be a new target for tumor diagnosis and treatment.
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Affiliation(s)
- Qiao Li
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Qingsan Zhu
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Qingsan Zhu,
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Perry GS, Das M, Woon ECY. Inhibition of AlkB Nucleic Acid Demethylases: Promising New Epigenetic Targets. J Med Chem 2021; 64:16974-17003. [PMID: 34792334 DOI: 10.1021/acs.jmedchem.1c01694] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The AlkB family of nucleic acid demethylases is currently of intense chemical, biological, and medical interest because of its critical roles in several key cellular processes, including epigenetic gene regulation, RNA metabolism, and DNA repair. Emerging evidence suggests that dysregulation of AlkB demethylases may underlie the pathogenesis of several human diseases, particularly obesity, diabetes, and cancer. Hence there is strong interest in developing selective inhibitors for these enzymes to facilitate their mechanistic and functional studies and to validate their therapeutic potential. Herein we review the remarkable advances made over the past 20 years in AlkB demethylase inhibition research. We discuss the rational design of reported inhibitors, their mode-of-binding, selectivity, cellular activity, and therapeutic opportunities. We further discuss unexplored structural elements of the AlkB subfamilies and propose potential strategies to enable subfamily selectivity. It is hoped that this perspective will inspire novel inhibitor design and advance drug discovery research in this field.
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Affiliation(s)
- Gemma S Perry
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Mohua Das
- Lab of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Esther C Y Woon
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
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Xiang J, Peng M, Pan Y, Luo LJ, Cheng SC, Jin XX, Yiu SM, Man WL, Ko CC, Lau KC, Lau TC. Visible light-induced oxidative N-dealkylation of alkylamines by a luminescent osmium(vi) nitrido complex. Chem Sci 2021; 12:14494-14498. [PMID: 34881000 PMCID: PMC8580045 DOI: 10.1039/d1sc04369b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/08/2021] [Indexed: 01/15/2023] Open
Abstract
N-Dealkylation of amines by metal oxo intermediates (M
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O) is related to drug detoxification and DNA repair in biological systems. In this study, we report the first example of N-dealkylation of various alkylamines by a luminescent osmium(vi) nitrido complex induced by visible light. The visible light-induced N-dealkylation of various alkylamines by a luminescent osmium(vi) nitrido complex has been investigated. We provide definitive evidence that these reactions occur via an ET/PT mechanism.![]()
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Affiliation(s)
- Jing Xiang
- College of Chemistry and Environmental Engineering, Yangtze University Jingzhou 434020 Hubei P. R. China
| | - Min Peng
- College of Chemistry and Environmental Engineering, Yangtze University Jingzhou 434020 Hubei P. R. China
| | - Yi Pan
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong China
| | - Li-Juan Luo
- College of Chemistry and Environmental Engineering, Yangtze University Jingzhou 434020 Hubei P. R. China
| | - Shun-Cheung Cheng
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong China
| | - Xin-Xin Jin
- College of Chemistry and Environmental Engineering, Yangtze University Jingzhou 434020 Hubei P. R. China
| | - Shek-Man Yiu
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong China
| | - Wai-Lun Man
- Department of Chemistry, Hong Kong Baptist University Kowloon Tong Hong Kong 999077 People's Republic of China
| | - Chi-Chiu Ko
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong China
| | - Kai-Chung Lau
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong China
| | - Tai-Chu Lau
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong China
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DNA Demethylation in the Processes of Repair and Epigenetic Regulation Performed by 2-Ketoglutarate-Dependent DNA Dioxygenases. Int J Mol Sci 2021; 22:ijms221910540. [PMID: 34638881 PMCID: PMC8508711 DOI: 10.3390/ijms221910540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/05/2022] Open
Abstract
Site-specific DNA methylation plays an important role in epigenetic regulation of gene expression. Chemical methylation of DNA, including the formation of various methylated nitrogenous bases, leads to the formation of genotoxic modifications that impair DNA functions. Despite the fact that different pathways give rise to methyl groups in DNA, the main pathway for their removal is oxidative demethylation, which is catalyzed by nonheme Fe(II)/α-ketoglutarate–dependent DNA dioxygenases. DNA dioxygenases share a common catalytic mechanism of the oxidation of the alkyl groups on nitrogenous bases in nucleic acids. This review presents generalized data on the catalytic mechanism of action of DNA dioxygenases and on the participation of typical representatives of this superfamily, such as prokaryotic enzyme AlkB and eukaryotic enzymes ALKBH1–8 and TET1–3, in both processes of direct repair of alkylated DNA adducts and in the removal of an epigenetic mark (5-methylcytosine).
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Malovic E, Ealy A, Kanthasamy A, Kanthasamy AG. Emerging Roles of N6-Methyladenosine (m6A) Epitranscriptomics in Toxicology. Toxicol Sci 2021; 181:13-22. [PMID: 33616673 PMCID: PMC8599717 DOI: 10.1093/toxsci/kfab021] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Epitranscriptomics, the study of chemically modified RNAs, is a burgeoning field being explored in a variety of scientific disciplines. Of the currently known epitranscriptomic modifications, N6-methyladenosine (m6A) methylation is the most abundant. The m6A modification is predominantly regulated by 3 tiers of protein modulators classified as writers, erasers, and readers. Depending upon cellular needs, these proteins function to deposit, remove, or read the methyl modifications on cognate mRNAs. Many environmental chemicals including heavy metals, pesticides, and other toxic pollutants, are all known to perturb transcription and translation machinery to exert their toxic responses. As such, we herein review how the m6A modification may be affected under different toxicological paradigms. Furthermore, we discuss how toxicants can affect the 3 tiers of regulation directly, and how these effects influence the m6A-modified mRNAs. Lastly, we highlight the disparities between published findings and theories, especially those concerning the m6A reader tier of regulation. In the far-reaching field of toxicology, m6A epitranscriptomics provides another enticing avenue to explore new mechanisms and therapies for a diverse range of environmentally linked disorders and diseases.
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Affiliation(s)
- Emir Malovic
- Department of Biomedical Sciences, Parkinson's Disorder Research Program, Iowa State University, Ames, Iowa 50011
| | - Alyssa Ealy
- Department of Biomedical Sciences, Parkinson's Disorder Research Program, Iowa State University, Ames, Iowa 50011
| | - Arthi Kanthasamy
- Department of Biomedical Sciences, Parkinson's Disorder Research Program, Iowa State University, Ames, Iowa 50011
| | - Anumantha G Kanthasamy
- Department of Biomedical Sciences, Parkinson's Disorder Research Program, Iowa State University, Ames, Iowa 50011
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9
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Zhang Y, Wang C. Demethyltransferase AlkBH1 substrate diversity and relationship to human diseases. Mol Biol Rep 2021; 48:4747-4756. [PMID: 34046849 DOI: 10.1007/s11033-021-06421-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/17/2021] [Indexed: 12/22/2022]
Abstract
AlkBH1 is a member of the AlkB superfamily which are kinds of Fe (II) and α-ketoglutarate (α-KG)-dependent dioxygenases. At present, only demethyltransferases FTO and AlkBH5 have relatively clear substrate studies among these members, the types and mechanisms of substrates catalysis of other members are not clear, especially the demethyltransferase AlkBH1. AlkBH1, as a demethylase, has important functions of reversing DNA methylation and repairing DNA damage. And it has become a promising target for the treatment of many cancers, the regulation of neurological and genetic related diseases. Many scholars have made important discoveries in the diversity of AlkBH1 substrates, but there is no comprehensive summary, which affects the design inhibitor target of AlkBH1. Herein, We are absorbed in the latest progress in the study of AlkBH1 substrate diversity and its relationship with human diseases. Besides, we also discuss future research directions and suggest other studies to reveal the specific catalytic effect of AlkBH1 on cancer substrates.
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Affiliation(s)
- Ying Zhang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, China
| | - Caiyan Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, China.
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10
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Wang Y, Katanski CD, Watkins C, Pan JN, Dai Q, Jiang Z, Pan T. A high-throughput screening method for evolving a demethylase enzyme with improved and new functionalities. Nucleic Acids Res 2021; 49:e30. [PMID: 33337498 PMCID: PMC7968990 DOI: 10.1093/nar/gkaa1213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/26/2023] Open
Abstract
AlkB is a DNA/RNA repair enzyme that removes base alkylations such as N1-methyladenosine (m1A) or N3-methylcytosine (m3C) from DNA and RNA. The AlkB enzyme has been used as a critical tool to facilitate tRNA sequencing and identification of mRNA modifications. As a tool, AlkB mutants with better reactivity and new functionalities are highly desired; however, previous identification of such AlkB mutants was based on the classical approach of targeted mutagenesis. Here, we introduce a high-throughput screening method to evaluate libraries of AlkB variants for demethylation activity on RNA and DNA substrates. This method is based on a fluorogenic RNA aptamer with an internal modified RNA/DNA residue which can block reverse transcription or introduce mutations leading to loss of fluorescence inherent in the cDNA product. Demethylation by an AlkB variant eliminates the blockage or mutation thereby restores the fluorescence signals. We applied our screening method to sites D135 and R210 in the Escherichia coli AlkB protein and identified a variant with improved activity beyond a previously known hyperactive mutant toward N1-methylguanosine (m1G) in RNA. We also applied our method to O6-methylguanosine (O6mG) modified DNA substrates and identified candidate AlkB variants with demethylating activity. Our study provides a high-throughput screening method for in vitro evolution of any demethylase enzyme.
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Affiliation(s)
- Yuru Wang
- Department of Biochemistry and Molecular Biology, USA.,Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | | | - Jessica N Pan
- Department of Biochemistry and Molecular Biology, USA
| | - Qing Dai
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Zhuoxun Jiang
- Department of Biochemistry and Molecular Biology, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, USA
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11
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Nigam R, Raveendra Babu K, Ghosh T, Kumari B, Das P, Anindya R, Ahmed Khan F. Synthesis of 2-Chloro-3-amino indenone derivatives and their evaluation as inhibitors of DNA dealkylation repair. Chem Biol Drug Des 2021; 97:1170-1184. [PMID: 33764683 DOI: 10.1111/cbdd.13839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/30/2021] [Accepted: 03/07/2021] [Indexed: 12/24/2022]
Abstract
DNA alkylation damage, emanating from the exposure to environmental alkylating agents or produced by certain endogenous metabolic processes, affects cell viability and genomic stability. Fe(II)/2-oxoglutarate-dependent dioxygenase enzymes, such as Escherichia coli AlkB, are involved in protecting DNA from alkylation damage. Inspired by the natural product indenone derivatives reported to inhibit this class of enzymes, and a set of 2-chloro-3-amino indenone derivatives was synthesized and screened for their inhibitory properties against AlkB. The synthesis of 2-chloro-3-amino indenone derivatives was achieved from 2,3-dichloro indenones through addition-elimination method using alkyl/aryl amines under catalyst-free conditions. Using an in vitro reconstituted DNA repair assay, we have identified a 2-chloro-3-amino indenone compound 3o to be an inhibitor of AlkB. We have determined the binding affinity, mode of interaction, and kinetic parameters of inhibition of 3o and tested its ability to sensitize cells to methyl methanesulfonate that mainly produce DNA alkylation damage. This study established the potential of indenone-derived compounds as inhibitors of Fe(II)/2-oxoglutarate-dependent dioxygenase AlkB.
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Affiliation(s)
- Richa Nigam
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Kaki Raveendra Babu
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Topi Ghosh
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Bhavini Kumari
- Department of Chemistry, Indian Institute of Technology Patna, Patna, India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna, Patna, India
| | - Roy Anindya
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Faiz Ahmed Khan
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy, India
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Srnec M, Iyer SR, Dassama LMK, Park K, Wong SD, Sutherlin KD, Yoda Y, Kobayashi Y, Kurokuzu M, Saito M, Seto M, Krebs C, Bollinger JM, Solomon EI. Nuclear Resonance Vibrational Spectroscopic Definition of the Facial Triad Fe IV═O Intermediate in Taurine Dioxygenase: Evaluation of Structural Contributions to Hydrogen Atom Abstraction. J Am Chem Soc 2020; 142:18886-18896. [PMID: 33103886 DOI: 10.1021/jacs.0c08903] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The α-ketoglutarate (αKG)-dependent oxygenases catalyze a diverse range of chemical reactions using a common high-spin FeIV═O intermediate that, in most reactions, abstract a hydrogen atom from the substrate. Previously, the FeIV═O intermediate in the αKG-dependent halogenase SyrB2 was characterized by nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations, which demonstrated that it has a trigonal-pyramidal geometry with the scissile C-H bond of the substrate calculated to be perpendicular to the Fe-O bond. Here, we have used NRVS and DFT calculations to show that the FeIV═O complex in taurine dioxygenase (TauD), the αKG-dependent hydroxylase in which this intermediate was first characterized, also has a trigonal bipyramidal geometry but with an aspartate residue replacing the equatorial halide of the SyrB2 intermediate. Computational analysis of hydrogen atom abstraction by square pyramidal, trigonal bipyramidal, and six-coordinate FeIV═O complexes in two different substrate orientations (one more along [σ channel] and another more perpendicular [π channel] to the Fe-O bond) reveals similar activation barriers. Thus, both substrate approaches to all three geometries are competent in hydrogen atom abstraction. The equivalence in reactivity between the two substrate orientations arises from compensation of the promotion energy (electronic excitation within the d manifold) required to access the π channel by the significantly larger oxyl character present in the pπ orbital oriented toward the substrate, which leads to an earlier transition state along the C-H coordinate.
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Affiliation(s)
- Martin Srnec
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States.,J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, Prague 8 182 23, Czech Republic
| | - Shyam R Iyer
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
| | - Laura M K Dassama
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kiyoung Park
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
| | - Shaun D Wong
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
| | - Kyle D Sutherlin
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | | | | | - Makina Saito
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
| | - Makoto Seto
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
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Van Deuren V, Plessers S, Robben J. Structural determinants of nucleobase modification recognition in the AlkB family of dioxygenases. DNA Repair (Amst) 2020; 96:102995. [PMID: 33069898 DOI: 10.1016/j.dnarep.2020.102995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 01/29/2023]
Abstract
Iron-dependent dioxygenases of the AlkB protein family found in most organisms throughout the tree of life play a major role in oxidative dealkylation processes. Many of these enzymes have attracted the attention of researchers across different fields and have been subjected to thorough biochemical characterization because of their link to human health and disease. For example, several mammalian AlkB homologues are involved in the direct reversal of alkylation damage in DNA, while others have been shown to play a regulatory role in epigenetic or epitranscriptomic nucleic acid methylation or in post-translational modifications such as acetylation of actin filaments. These studies show that that divergence in amino acid sequence and structure leads to different characteristics and substrate specificities. In this review, we aim to summarize current insights in the structural features involved in the substrate selection of AlkB homologues, with focus on nucleic acid interactions.
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Affiliation(s)
- V Van Deuren
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001, Heverlee, Belgium
| | - S Plessers
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001, Heverlee, Belgium
| | - J Robben
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001, Heverlee, Belgium.
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Warren JM, Sloan DB. Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria. Mitochondrion 2020; 52:144-156. [PMID: 32184120 DOI: 10.1016/j.mito.2020.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 01/31/2023]
Abstract
Transfer RNAs (tRNAs) remain one of the very few classes of genes still encoded in the mitochondrial genome. These key components of the protein translation system must interact with a large enzymatic network of nuclear-encoded gene products to maintain mitochondrial function. Plants have an evolutionarily dynamic mitochondrial tRNA population, including ongoing tRNA gene loss and replacement by both horizontal gene transfer from diverse sources and import of nuclear-expressed tRNAs from the cytosol. Thus, plant mitochondria represent an excellent model for understanding how anciently divergent genes can act as "interchangeable parts" during the evolution of complex molecular systems. In particular, understanding the integration of the mitochondrial translation system with elements of the corresponding machinery used in cytosolic protein synthesis is a key area for eukaryotic cellular evolution. Here, we review the increasingly detailed phylogenetic data about the evolutionary history of mitochondrial tRNA gene loss, transfer, and functional replacement that has created extreme variation in mitochondrial tRNA populations across plant species. We describe emerging tRNA-seq methods with promise for refining our understanding of the expression and subcellular localization of tRNAs. Finally, we summarize current evidence and identify open questions related to coevolutionary changes in nuclear-encoded enzymes that have accompanied turnover in mitochondrial tRNA populations.
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Affiliation(s)
- Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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15
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Evaluation of a concerted vs. sequential oxygen activation mechanism in α-ketoglutarate-dependent nonheme ferrous enzymes. Proc Natl Acad Sci U S A 2020; 117:5152-5159. [PMID: 32094179 DOI: 10.1073/pnas.1922484117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Determining the requirements for efficient oxygen (O2) activation is key to understanding how enzymes maintain efficacy and mitigate unproductive, often detrimental reactivity. For the α-ketoglutarate (αKG)-dependent nonheme iron enzymes, both a concerted mechanism (both cofactor and substrate binding prior to reaction with O2) and a sequential mechanism (cofactor binding and reaction with O2 precede substrate binding) have been proposed. Deacetoxycephalosporin C synthase (DAOCS) is an αKG-dependent nonheme iron enzyme for which both of these mechanisms have been invoked to generate an intermediate that catalyzes oxidative ring expansion of penicillin substrates in cephalosporin biosynthesis. Spectroscopy shows that, in contrast to other αKG-dependent enzymes (which are six coordinate when only αKG is bound to the FeII), αKG binding to FeII-DAOCS results in ∼45% five-coordinate sites that selectively react with O2 relative to the remaining six-coordinate sites. However, this reaction produces an FeIII species that does not catalyze productive ring expansion. Alternatively, simultaneous αKG and substrate binding to FeII-DAOCS produces five-coordinate sites that rapidly react with O2 to form an FeIV=O intermediate that then reacts with substrate to produce cephalosporin product. These results demonstrate that the concerted mechanism is operative in DAOCS and by extension, other nonheme iron enzymes.
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16
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Muenter MM, Aiken A, Akanji JO, Baig S, Bellou S, Carlson A, Conway C, Cowell CM, DeLateur NA, Hester A, Joshi C, Kramer C, Leifer BS, Nash E, Qi MH, Travers M, Wong KC, Hu M, Gou N, Giese RW, Gu AZ, Beuning PJ. The response of Escherichia coli to the alkylating agents chloroacetaldehyde and styrene oxide. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2019; 840:1-10. [PMID: 30857727 DOI: 10.1016/j.mrgentox.2019.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
Abstract
DNA damage is ubiquitous and can arise from endogenous or exogenous sources. DNA-damaging alkylating agents are present in environmental toxicants as well as in cancer chemotherapy drugs and are a constant threat, which can lead to mutations or cell death. All organisms have multiple DNA repair and DNA damage tolerance pathways to resist the potentially negative effects of exposure to alkylating agents. In bacteria, many of the genes in these pathways are regulated as part of the SOS reponse or the adaptive response. In this work, we probed the cellular responses to the alkylating agents chloroacetaldehyde (CAA), which is a metabolite of 1,2-dichloroethane used to produce polyvinyl chloride, and styrene oxide (SO), a major metabolite of styrene used in the production of polystyrene and other polymers. Vinyl chloride and styrene are produced on an industrial scale of billions of kilograms annually and thus have a high potential for environmental exposure. To identify stress response genes in E. coli that are responsible for tolerance to the reactive metabolites CAA and SO, we used libraries of transcriptional reporters and gene deletion strains. In response to both alkylating agents, genes associated with several different stress pathways were upregulated, including protein, membrane, and oxidative stress, as well as DNA damage. E. coli strains lacking genes involved in base excision repair and nucleotide excision repair were sensitive to SO, whereas strains lacking recA and the SOS gene ybfE were sensitive to both alkylating agents tested. This work indicates the varied systems involved in cellular responses to alkylating agents, and highlights the specific DNA repair genes involved in the responses.
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Affiliation(s)
- Mark M Muenter
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Ariel Aiken
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Jadesola O Akanji
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Samir Baig
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Sirine Bellou
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Alyssa Carlson
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Charles Conway
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Courtney M Cowell
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Nicholas A DeLateur
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Alexis Hester
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Christopher Joshi
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Caitlin Kramer
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Becky S Leifer
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Emma Nash
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Macee H Qi
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Meghan Travers
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Kelly C Wong
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Man Hu
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, 02115 USA
| | - Na Gou
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, 02115 USA; School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Roger W Giese
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, 02115 USA
| | - April Z Gu
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, 02115 USA; School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Penny J Beuning
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA.
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17
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Thapar R, Bacolla A, Oyeniran C, Brickner JR, Chinnam NB, Mosammaparast N, Tainer JA. RNA Modifications: Reversal Mechanisms and Cancer. Biochemistry 2018; 58:312-329. [PMID: 30346748 DOI: 10.1021/acs.biochem.8b00949] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An emerging molecular understanding of RNA alkylation and its removal is transforming our knowledge of RNA biology and its interplay with cancer chemotherapy responses. DNA modifications are known to perform critical functions depending on the genome template, including gene expression, DNA replication timing, and DNA damage protection, yet current results suggest that the chemical diversity of DNA modifications pales in comparison to those on RNA. More than 150 RNA modifications have been identified to date, and their complete functional implications are still being unveiled. These include intrinsic roles such as proper processing and RNA maturation; emerging evidence has furthermore uncovered RNA modification "readers", seemingly analogous to those identified for histone modifications. These modification recognition factors may regulate mRNA stability, localization, and interaction with translation machinery, affecting gene expression. Not surprisingly, tumors differentially modulate factors involved in expressing these marks, contributing to both tumorigenesis and responses to alkylating chemotherapy. Here we describe the current understanding of RNA modifications and their removal, with a focus primarily on methylation and alkylation as functionally relevant changes to the transcriptome. Intriguingly, some of the same RNA modifications elicited by physiological processes are also produced by alkylating agents, thus blurring the lines between what is a physiological mark and a damage-induced modification. Furthermore, we find that a high level of gene expression of enzymes with RNA dealkylation activity is a sensitive readout for poor survival in four different cancer types, underscoring the likely importance of examining RNA dealkylation mechanisms to cancer biology and for cancer treatment and prognosis.
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Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Clement Oyeniran
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Joshua R Brickner
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Naga Babu Chinnam
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - John A Tainer
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
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18
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Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David SS, Rokas A, Eichman BF. Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. EMBO J 2018; 37:63-74. [PMID: 29054852 PMCID: PMC5753038 DOI: 10.15252/embj.201797833] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/11/2017] [Accepted: 09/22/2017] [Indexed: 01/07/2023] Open
Abstract
DNA glycosylases preserve genome integrity and define the specificity of the base excision repair pathway for discreet, detrimental modifications, and thus, the mechanisms by which glycosylases locate DNA damage are of particular interest. Bacterial AlkC and AlkD are specific for cationic alkylated nucleobases and have a distinctive HEAT-like repeat (HLR) fold. AlkD uses a unique non-base-flipping mechanism that enables excision of bulky lesions more commonly associated with nucleotide excision repair. In contrast, AlkC has a much narrower specificity for small lesions, principally N3-methyladenine (3mA). Here, we describe how AlkC selects for and excises 3mA using a non-base-flipping strategy distinct from that of AlkD. A crystal structure resembling a catalytic intermediate complex shows how AlkC uses unique HLR and immunoglobulin-like domains to induce a sharp kink in the DNA, exposing the damaged nucleobase to active site residues that project into the DNA This active site can accommodate and excise N3-methylcytosine (3mC) and N1-methyladenine (1mA), which are also repaired by AlkB-catalyzed oxidative demethylation, providing a potential alternative mechanism for repair of these lesions in bacteria.
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Affiliation(s)
- Rongxin Shi
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Kori T Lay
- Department of Chemistry, University of California, Davis, CA, USA
| | - Philip K Yuen
- Department of Chemistry, University of California, Davis, CA, USA
| | - Sheila S David
- Department of Chemistry, University of California, Davis, CA, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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19
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Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-ι. Sci Rep 2017; 7:43904. [PMID: 28272441 PMCID: PMC5341039 DOI: 10.1038/srep43904] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/31/2017] [Indexed: 12/17/2022] Open
Abstract
N1-methyl-deoxyadenosine (1-MeA) is formed by methylation of deoxyadenosine at the N1 atom. 1-MeA presents a block to replicative DNA polymerases due to its inability to participate in Watson-Crick (W-C) base pairing. Here we determine how human DNA polymerase-ι (Polι) promotes error-free replication across 1-MeA. Steady state kinetic analyses indicate that Polι is ~100 fold more efficient in incorporating the correct nucleotide T versus the incorrect nucleotide C opposite 1-MeA. To understand the basis of this selectivity, we determined ternary structures of Polι bound to template 1-MeA and incoming dTTP or dCTP. In both structures, template 1-MeA rotates to the syn conformation but pairs differently with dTTP versus dCTP. Thus, whereas dTTP partakes in stable Hoogsteen base pairing with 1-MeA, dCTP fails to gain a "foothold" and is largely disordered. Together, our kinetic and structural studies show how Polι maintains discrimination between correct and incorrect incoming nucleotide opposite 1-MeA in preserving genome integrity.
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20
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Zhu Y, Ksibe AZ, Schäfer H, Blindauer CA, Bugg TDH, Chen Y. O2-independent demethylation of trimethylamineN-oxide by Tdm ofMethylocella silvestris. FEBS J 2016; 283:3979-3993. [DOI: 10.1111/febs.13902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/09/2016] [Accepted: 09/15/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Yijun Zhu
- School of Life Sciences; University of Warwick; Coventry UK
| | - Amira Z. Ksibe
- Department of Chemistry; University of Warwick; Coventry UK
| | | | | | | | - Yin Chen
- School of Life Sciences; University of Warwick; Coventry UK
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21
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Longbotham JE, Levy C, Johannissen LO, Tarhonskaya H, Jiang S, Loenarz C, Flashman E, Hay S, Schofield CJ, Scrutton NS. Structure and Mechanism of a Viral Collagen Prolyl Hydroxylase. Biochemistry 2015; 54:6093-105. [PMID: 26368022 PMCID: PMC4613865 DOI: 10.1021/acs.biochem.5b00789] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
Fe(II)- and 2-oxoglutarate (2-OG)-dependent dioxygenases comprise
a large and diverse enzyme superfamily the members of which have multiple
physiological roles. Despite this diversity, these enzymes share a
common chemical mechanism and a core structural fold, a double-stranded
β-helix (DSBH), as well as conserved active site residues. The
prolyl hydroxylases are members of this large superfamily. Prolyl
hydroxylases are involved in collagen biosynthesis and oxygen sensing
in mammalian cells. Structural–mechanistic studies with prolyl
hydroxylases have broader implications for understanding mechanisms
in the Fe(II)- and 2-OG-dependent dioxygenase superfamily. Here, we
describe crystal structures of an N-terminally truncated viral collagen
prolyl hydroxylase (vCPH). The crystal structure shows that vCPH contains
the conserved DSBH motif and iron binding active site residues of
2-OG oxygenases. Molecular dynamics simulations are used to delineate
structural changes in vCPH upon binding its substrate. Kinetic investigations
are used to report on reaction cycle intermediates and compare them
to the closest homologues of vCPH. The study highlights the utility
of vCPH as a model enzyme for broader mechanistic analysis of Fe(II)-
and 2-OG-dependent dioxygenases, including those of biomedical interest.
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Affiliation(s)
- James E Longbotham
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Colin Levy
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Linus O Johannissen
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Hanna Tarhonskaya
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Shuo Jiang
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christoph Loenarz
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Emily Flashman
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sam Hay
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Nigel S Scrutton
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester , Manchester M1 7DN, United Kingdom
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22
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Lu X, Zhao BS, He C. TET family proteins: oxidation activity, interacting molecules, and functions in diseases. Chem Rev 2015; 115:2225-39. [PMID: 25675246 DOI: 10.1021/cr500470n] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xingyu Lu
- †Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.,‡Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Boxuan Simen Zhao
- †Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.,‡Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Chuan He
- †Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.,‡Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
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23
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Barbieri A, De Gennaro M, Di Stefano S, Lanzalunga O, Lapi A, Mazzonna M, Olivo G, Ticconi B. Isotope effect profiles in the N-demethylation of N,N-dimethylanilines: a key to determine the pKa of nonheme Fe(iii)–OH complexes. Chem Commun (Camb) 2015; 51:5032-5. [DOI: 10.1039/c5cc00411j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
pKa of [(N4Py)FeIII–OH]2+ is obtained from the kinetic isotope effect profiles in the N-demethylation of N,N-dimethylanilines promoted by [(N4Py)FeIVO]2+.
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Affiliation(s)
- Alessia Barbieri
- Dipartimento di Chimica
- Sapienza Università di Roma and Istituto CNR di Metodologie Chimiche (IMC-CNR)
- Sezione Meccanismi di Reazione
- c/o Dipartimento di Chimica
- Sapienza Università di Roma
| | - Martina De Gennaro
- Dipartimento di Chimica
- Sapienza Università di Roma and Istituto CNR di Metodologie Chimiche (IMC-CNR)
- Sezione Meccanismi di Reazione
- c/o Dipartimento di Chimica
- Sapienza Università di Roma
| | - Stefano Di Stefano
- Dipartimento di Chimica
- Sapienza Università di Roma and Istituto CNR di Metodologie Chimiche (IMC-CNR)
- Sezione Meccanismi di Reazione
- c/o Dipartimento di Chimica
- Sapienza Università di Roma
| | - Osvaldo Lanzalunga
- Dipartimento di Chimica
- Sapienza Università di Roma and Istituto CNR di Metodologie Chimiche (IMC-CNR)
- Sezione Meccanismi di Reazione
- c/o Dipartimento di Chimica
- Sapienza Università di Roma
| | - Andrea Lapi
- Dipartimento di Chimica
- Sapienza Università di Roma and Istituto CNR di Metodologie Chimiche (IMC-CNR)
- Sezione Meccanismi di Reazione
- c/o Dipartimento di Chimica
- Sapienza Università di Roma
| | - Marco Mazzonna
- Dipartimento di Chimica
- Sapienza Università di Roma and Istituto CNR di Metodologie Chimiche (IMC-CNR)
- Sezione Meccanismi di Reazione
- c/o Dipartimento di Chimica
- Sapienza Università di Roma
| | - Giorgio Olivo
- Dipartimento di Chimica
- Sapienza Università di Roma and Istituto CNR di Metodologie Chimiche (IMC-CNR)
- Sezione Meccanismi di Reazione
- c/o Dipartimento di Chimica
- Sapienza Università di Roma
| | - Barbara Ticconi
- Dipartimento di Chimica
- Sapienza Università di Roma and Istituto CNR di Metodologie Chimiche (IMC-CNR)
- Sezione Meccanismi di Reazione
- c/o Dipartimento di Chimica
- Sapienza Università di Roma
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24
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Fang D, Cisneros GA. Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations. J Chem Theory Comput 2014; 10:5136-5148. [PMID: 25400523 PMCID: PMC4230374 DOI: 10.1021/ct500572t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Indexed: 12/14/2022]
Abstract
AlkB is the title enzyme of a family of DNA dealkylases that catalyze the direct oxidative dealkylation of nucleobases. The conventional mechanism for the dealkylation of N1-methyl adenine (1-meA) catalyzed by AlkB after the formation of FeIV-oxo is comprised by a reorientation of the oxo moiety, hydrogen abstraction, OH rebound from the Fe atom to the methyl adduct, and the dissociation of the resulting methoxide to obtain the repaired adenine base and formaldehyde. An alternative pathway with hydroxide as a ligand bound to the iron atom is proposed and investigated by QM/MM simulations. The results show OH- has a small impact on the barriers for the hydrogen abstraction and OH rebound steps. The effects of the enzyme and the OH- ligand on the hydrogen abstraction by the FeIV-oxo moiety are discussed in detail. The new OH rebound step is coupled with a proton transfer to the OH- ligand and results in a novel zwitterion intermediate. This zwitterion structure can also be characterized as Fe-O-C complex and facilitates the formation of formaldehyde. In contrast, for the pathway with H2O bound to iron, the hydroxyl product of the OH rebound step first needs to unbind from the metal center before transferring a proton to Glu136 or other residue/substrate. The consistency between our theoretical results and experimental findings is discussed. This study provides new insights into the oxidative repair mechanism of DNA repair by nonheme FeII and α-ketoglutarate (α-KG) dependent dioxygenases and a possible explanation for the substrate preference of AlkB.
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Affiliation(s)
- Dong Fang
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - G. Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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25
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Silvestrov P, Müller TA, Clark KN, Hausinger RP, Cisneros GA. Homology modeling, molecular dynamics, and site-directed mutagenesis study of AlkB human homolog 1 (ALKBH1). J Mol Graph Model 2014; 54:123-30. [PMID: 25459764 DOI: 10.1016/j.jmgm.2014.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 10/16/2014] [Accepted: 10/21/2014] [Indexed: 02/03/2023]
Abstract
The ability to repair DNA is important for the conservation of genetic information of living organisms. Cells have a number of ways to restore damaged DNA, such as direct DNA repair, base excision repair, and nucleotide excision repair. One of the proteins that can perform direct repair of DNA bases is Escherichia coli AlkB. In humans, there are 9 identified AlkB homologs, including AlkB homolog 1 (ALKBH1). Many of these proteins catalyze the direct oxidative dealkylation of DNA and RNA bases and, as such, have an important role in repairing DNA from damage induced by alkylating agents. In addition to the dealkylase activity, ALKBH1 can also function as an apyrimidinic/apurinic lyase and was proposed to have a distinct lyase active site. To our knowledge, no crystal structure or complete homology model of ALKBH1 protein is available. In this study, we have used homology modeling to predict the structure of ALKBH1 based on AlkB and Duffy-binding-like domain crystal structures as templates. Molecular dynamics simulations were subsequently performed on the predicted structure of ALKBH1. The positions of two disulfide bonds or a zinc-finger motif and a disulfide bond were predicted and the importance of these features was tested by mutagenesis. Possible locations for the lyase active site are proposed based on the analysis of our predicted structures and previous experimental results.
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Affiliation(s)
- Pavel Silvestrov
- Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
| | - Tina A Müller
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States
| | - Kristen N Clark
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States
| | - Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States
| | - G Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, MI 48202, United States.
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26
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Lu L, Zhu C, Xia B, Yi C. Oxidative Demethylation of DNA and RNA Mediated by Non-Heme Iron-Dependent Dioxygenases. Chem Asian J 2014; 9:2018-29. [DOI: 10.1002/asia.201402148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 11/10/2022]
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27
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Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Ye Fu
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Chuan He
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
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Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
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Quesne MG, Latifi R, Gonzalez-Ovalle LE, Kumar D, de Visser SP. Quantum mechanics/molecular mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair enzymes. Chemistry 2014; 20:435-46. [PMID: 24339041 PMCID: PMC3994944 DOI: 10.1002/chem.201303282] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Indexed: 01/09/2023]
Abstract
AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N(1) -methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)-oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ- and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.
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Affiliation(s)
- Matthew G Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK)
| | - Reza Latifi
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK)
- Department of Chemistry, Tufts UniversityMedford MA, 02155 (USA)
| | - Luis E Gonzalez-Ovalle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK)
| | - Devesh Kumar
- Department of Applied Physics, School of Physical Sciences, Babasaheb, Bhimrao Ambedkar UniversityVidya Vihar, Rae Bareilly Road, Lucknow 226-025 (India)
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK)
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30
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Solvent effects on oxygen atom transfer reaction between manganese(V)-oxo corrole and alkene. CHINESE CHEM LETT 2013. [DOI: 10.1016/j.cclet.2013.03.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Fujii T, Shimada K, Anai S, Fujimoto K, Konishi N. ALKBH2, a novel AlkB homologue, contributes to human bladder cancer progression by regulating MUC1 expression. Cancer Sci 2013; 104:321-7. [PMID: 23279696 DOI: 10.1111/cas.12089] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 12/09/2012] [Accepted: 12/16/2012] [Indexed: 12/12/2022] Open
Abstract
The ALKBH family of proteins are highly expressed in various types of human cancer where they are involved in tumor growth and progression. However, multiple isoforms of ALKBH exist and the effect of individual isoforms on the development of urinary bladder cancer is unknown, particularly the molecular mechanisms involved in the progression from a noninvasive to invasive phenotype. We examined the role and function of ALKBH2 in human bladder cancer development in vitro and provide the first report that suppression of ALKBH2 in a human urothelial carcinoma cell line, KU7, reduces the expression of the transmembrane mucin protein, MUC1, and induces G1 cell cycle arrest. Moreover, reduction of ALKBH2 suppressed epithelial to mesenchymal transition (EMT) via increasing E-cadherin and decreasing vimentin expression. Transfection of MUC1 siRNA inhibited cell proliferation and EMT to the same extent as ALKBH2 gene silencing in vitro. ALKBH2 knockdown significantly suppressed MUC1 expression and tumor volume of bladder cancers in vivo as assessed in an orthotopic mouse model using ALKBH2 shRNA transfected KU7 cells. Immunohistochemical examination showed high expression levels of ALKBH2 in human urothelial carcinoma samples, especially in high-grade, superficially and deeply invasive carcinomas (pT(1) and >pT(2)), and in carcinoma in situ but not in normal urothelium. This study demonstrates that ALKBH2 is an upstream molecule of the oncoprotein, MUC1, and regulates cell cycle and EMT, resulting in progression of urothelial carcinomas.
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Affiliation(s)
- Tomomi Fujii
- Department of Pathology, Nara Medical University School of Medicine, Nara, Japan
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Kopylovich MN, Mac Leod TC, Haukka M, Amanullayeva GI, Mahmudov KT, Pombeiro AJ. Aquasoluble iron(III)-arylhydrazone-β-diketone complexes: Structure and catalytic activity for the peroxidative oxidation of C5–C8 cycloalkanes. J Inorg Biochem 2012; 115:72-7. [DOI: 10.1016/j.jinorgbio.2012.05.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 05/21/2012] [Accepted: 05/21/2012] [Indexed: 10/28/2022]
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Karkhanis V, Wang L, Tae S, Hu YJ, Imbalzano AN, Sif S. Protein arginine methyltransferase 7 regulates cellular response to DNA damage by methylating promoter histones H2A and H4 of the polymerase δ catalytic subunit gene, POLD1. J Biol Chem 2012; 287:29801-14. [PMID: 22761421 DOI: 10.1074/jbc.m112.378281] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Covalent modification of histones by protein arginine methyltransferases (PRMTs) impacts genome organization and gene expression. In this report, we show that PRMT7 interacts with the BRG1-based hSWI/SNF chromatin remodeling complex and specifically methylates histone H2A Arg-3 (H2AR3) and histone H4 Arg-3 (H4R3). To elucidate the biological function of PRMT7, we knocked down its expression in NIH 3T3 cells and analyzed global gene expression. Our findings show that PRMT7 negatively regulates expression of genes involved in DNA repair, including ALKBH5, APEX2, POLD1, and POLD2. Chromatin immunoprecipitation (ChIP) revealed that PRMT7 and dimethylated H2AR3 and H4R3 are enriched at target DNA repair genes in parental cells, whereas PRMT7 knockdown caused a significant decrease in PRMT7 recruitment and H2AR3/H4R3 methylation. Decreased PRMT7 expression also resulted in derepression of target DNA repair genes and enhanced cell resistance to DNA-damaging agents. Furthermore, we show that BRG1 co-localizes with PRMT7 on target promoters and that expression of a catalytically inactive form of BRG1 results in derepression of PRMT7 target DNA repair genes. Remarkably, reducing expression of individual PRMT7 target DNA repair genes showed that only the catalytic subunit of DNA polymerase, POLD1, was able to resensitize PRMT7 knock-down cells to DNA-damaging agents. These results provide evidence for the important role played by PRMT7 in epigenetic regulation of DNA repair genes and cellular response to DNA damage.
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Affiliation(s)
- Vrajesh Karkhanis
- Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, OH 43210, USA
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Prá D, Franke SIR, Henriques JAP, Fenech M. Iron and genome stability: an update. Mutat Res 2012; 733:92-9. [PMID: 22349350 DOI: 10.1016/j.mrfmmm.2012.02.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 02/02/2012] [Accepted: 02/05/2012] [Indexed: 01/07/2023]
Abstract
Iron is an essential micronutrient which is required in a relatively narrow range for maintaining metabolic homeostasis and genome stability. Iron participates in oxygen transport and mitochondrial respiration as well as in antioxidant and nucleic acid metabolism. Iron deficiency impairs these biological pathways, leading to oxidative stress and possibly carcinogenesis. Iron overload has been linked to genome instability as well as to cancer risk increase, as seen in hereditary hemochromatosis. Iron is an extremely reactive transition metal that can interact with hydrogen peroxide to generate hydroxyl radicals that form the 8-hydroxy-guanine adduct, cause point mutations as well as DNA single and double strand breaks. Iron overload also induces DNA hypermethylation and can reduce telomere length. The current Recommended Dietary Allowances (RDA) for iron, according with Institute of Medicine Dietary Reference Intake (DRI), is based in the concept of preventing anemia, and ranges from 7mg/day to 18mg/day depending on life stage and gender. Pregnant women need 27mg/day. The maximum safety level for iron intake, the Upper Level (UL), is 40-45mg/day, based on the prevention of gastrointestinal distress associated to high iron intakes. Preliminary evidence indicates that 20mg/day iron, an intake slightly higher than the RDA, may reduce the risk of gastrointestinal cancer in the elderly as well as increasing genome stability in lymphocytes of children and adolescents. Current dietary recommendations do not consider the concept of genome stability which is of concern because damage to the genome has been linked to the origin and progression of many diseases and is the most fundamental pathology. Given the importance of iron for homeostasis and its potential influence over genome stability and cancer it is recommended to conduct further studies that conclusively define these relationships.
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Affiliation(s)
- Daniel Prá
- PPG em Promoção da Saúde, Universidade de Santa Cruz do Sul (UNISC), Santa Cruz do Sul, RS, Brazil. daniel
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35
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Nay SL, Lee DH, Bates SE, O'Connor TR. Alkbh2 protects against lethality and mutation in primary mouse embryonic fibroblasts. DNA Repair (Amst) 2012; 11:502-10. [PMID: 22429847 DOI: 10.1016/j.dnarep.2012.02.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/14/2012] [Accepted: 02/23/2012] [Indexed: 12/11/2022]
Abstract
Alkylating agents modify DNA and RNA forming adducts that disrupt replication and transcription, trigger cell cycle checkpoints and/or initiate apoptosis. If left unrepaired, some of the damage can be cytotoxic and/or mutagenic. In Escherichia coli, the alkylation repair protein B (AlkB) provides one form of resistance to alkylating agents by eliminating mainly 1-methyladenine and 3-methylcytosine, thereby increasing survival and preventing mutation. To examine the biological role of the mammalian AlkB homologs Alkbh2 and Alkbh3, which both have similar enzymatic activities to that of AlkB, we evaluated the survival and mutagenesis of primary Big Blue mouse embryonic fibroblasts (MEFs) that had targeted deletions in the Alkbh2 or Alkbh3 genes. Both Alkbh2- and Alkbh3-deficient MEFs were ∼2-fold more sensitive to methyl methanesulfonate (MMS) induced cytotoxicity compared to the wild type control cells. Spontaneous mutant frequencies were similar for the wild type, Alkbh2-/- and Alkbh3-/- MEFs (average--1.3×10(-5)). However, despite the similar survival of the two mutant MEFs after MMS treatment, only the Alkbh2-deficient MEFs showed a statistically significant increase in mutant frequency compared to wild type MEFs after MMS treatment. Therefore, although both Alkbh2 and Alkbh3 can protect against MMS-induced cell death, only Alkbh2 shows statistically significant protection of MEF DNA against mutations following treatment with this exogenous methylating agent.
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Affiliation(s)
- Stephanie L Nay
- Biology Division, Beckman Research Institute, Irell and Manella Graduate School of Biological Sciences, City of Hope National Medical Center, 1450 East Duarte Road, Duarte, CA 91010, United States
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Manso JA, Camacho IFC, Calle E, Casado J. Alkylating potential of α,β-unsaturated compounds. Org Biomol Chem 2011; 9:6226-33. [PMID: 21773622 DOI: 10.1039/c1ob05298e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alkylation reactions of the nucleoside guanosine (Guo) by the α,β-unsaturated compounds (α,β-UC) acrylonitrile (AN), acrylamide (AM), acrylic acid (AA) and acrolein (AC), which can act as alkylating agents of DNA, were investigated kinetically. The following conclusions were drawn: i) The Guo alkylation mechanism by AC is different from those brought about the other α,β-UC; ii) for the first three, the following sequence of alkylating potential was found: AN > AM > AA; iii) A correlation between the chemical reactivity (alkylation rate constants) of AN, AM, and AA and their capacity to form adducts with biomarkers was found. iv) Guo alkylation reactions for AN and AM occur through Michael addition mechanisms, reversible in the first case, and irreversible in the second. The equilibrium constant for the formation of the Guo-AN adduct is K(eq) (37 °C) = 5 × 10(-4); v) The low energy barrier (≈10 kJ mol(-1)) to reverse the Guo alkylation by AN reflects the easy reversibility of this reaction and its possible correction by repair mechanisms; vi) No reaction was observed for AN, AM, and AA at pH < 8.0. In contrast, Guo alkylation by AC was observed under cellular pH conditions. The reaction rate constants for the formation of the α-OH-Guo adduct (the most genotoxic isomer), is 1.5-fold faster than that of γ-OH-Guo. vii) a correlation between the chemical reactivity of α,β-UC (alkylation rate constants) and mutagenicity was found.
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Affiliation(s)
- José A Manso
- Departamento de Química Física, Universidad de Salamanca, Salamanca, Spain
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37
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Gao W, Li L, Xu P, Fang J, Xiao S, Chen S. Frequent down-regulation of hABH2 in gastric cancer and its involvement in growth of cancer cells. J Gastroenterol Hepatol 2011; 26:577-84. [PMID: 21155885 DOI: 10.1111/j.1440-1746.2010.06531.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND AND AIM Methyl or 1, N(6) -ethenoadenine base lesions are frequent and highly-mutagenic or -carcinogenic events in mammalian DNA. Human AlkB homologue-2 (hABH2), a homologue of the Escherichia coli AlkB protein, has been found to be the principal dioxygenase for the repair of these lesions. Mounting evidence indicates that impaired DNA repair contributes to gastric cancer induction and progression. Whether hABH2 is involved in this malignancy is unknown. The present study was aimed to investigate the expression profile of hABH2 in gastric cancer and the effect of hABH2 on cancer cell growth. METHODS The expression of hABH2 in 35 pair-matched gastric neoplastic and adjacent non-neoplastic tissues, and in five gastric cancer cell lines, was examined by real-time polymerase chain reaction (PCR), immunohistochemistry, or Western blot. The cell growth was determined using cell-counting kit-8 assay. The apoptosis or cell-cycle analysis was determined using flow cytometry. RESULTS The hABH2 expression was downregulated in 68% (24/35) of primary gastric cancers, as determined by real-time PCR; the hABH2 expression was also substantially decreased in gastric cancer cell lines. Immunohistochemical or Western blot analysis further confirmed the downregulation of hABH2 expression in gastric cancers. The overexpression of hABH2 significantly inhibited the proliferation of gastric cancer cells, and induced G(1) arrest of the cell cycle, while hABH2 knockdown promoted cell growth and cell-cycle progression of gastric cancer cells. CONCLUSIONS These results suggest that hABH2 is downregulated in a subset of gastric cancers, and might be involved in the molecular mechanism of gastric cancer through inhibiting the proliferation of gastric cancer cells.
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Affiliation(s)
- Wei Gao
- Department of Gastroenterology, Renji Hospital, Shanghai Institute of Digestive Disease, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Down-regulation of ALKBH2 increases cisplatin sensitivity in H1299 lung cancer cells. Acta Pharmacol Sin 2011; 32:393-8. [PMID: 21278781 DOI: 10.1038/aps.2010.216] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIM To elucidate the combined effect of alkylated DNA repair protein alkB homolog 2 (ALKBH2)-targeting gene therapy and cisplatin (cDDP) chemotherapy on the non-small cell lung cancer (NSCLC) H1299 cell line. METHODS ALKBH2 was down-regulated in H1299 cells by lentivirus-mediated RNA interference (RNAi). Changes in ALKBH2 expression were determined using real-time RT-PCR and Western blotting. Cell viability was evaluated using MTT assay. DNA synthesis in proliferating cells was determined using BrdU incorporation assay. Cell apoptosis was determined using flow cytometry. RESULTS Lentivirus-mediated ALKBH2 silencing alone did not induce apoptosis or attenuate the growth potential of H1299 cells within five days post-infection. Combined treatment modalities with lentivirus-mediated ALKBH2 down-regulation and cDDP (333 μmol/L) were significantly more potent in inhibiting cell growth and inducing apoptosis than mono-chemotherapy. CONCLUSION Combined treatment modalities of ALKBH2 knockdown and cDDP chemotherapy have the potential to improve the efficacy in the treatment of NSCLC.
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Iron intake, red cell indicators of iron status, and DNA damage in young subjects. Nutrition 2011; 27:293-7. [DOI: 10.1016/j.nut.2010.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 01/30/2010] [Accepted: 02/03/2010] [Indexed: 01/02/2023]
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40
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Kato M, Araiso Y, Noma A, Nagao A, Suzuki T, Ishitani R, Nureki O. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Nucleic Acids Res 2010; 39:1576-85. [PMID: 20972222 PMCID: PMC3045595 DOI: 10.1093/nar/gkq919] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Wybutosine (yW) is a hypermodified nucleoside found in position 37 of tRNA(Phe), and is essential for correct phenylalanine codon translation. yW derivatives widely exist in eukaryotes and archaea, and their chemical structures have many species-specific variations. Among them, its hydroxylated derivative, hydroxywybutosine (OHyW), is found in eukaryotes including human, but the modification mechanism remains unknown. Recently, we identified a novel Jumonji C (JmjC)-domain-containing protein, TYW5 (tRNA yW-synthesizing enzyme 5), which forms the OHyW nucleoside by carbon hydroxylation, using Fe(II) ion and 2-oxoglutarate (2-OG) as cofactors. In this work, we present the crystal structures of human TYW5 (hTYW5) in the free and complex forms with 2-OG and Ni(II) ion at 2.5 and 2.8 Å resolutions, respectively. The structure revealed that the catalytic domain consists of a β-jellyroll fold, a hallmark of the JmjC domains and other Fe(II)/2-OG oxygenases. hTYW5 forms a homodimer through C-terminal helix bundle formation, thereby presenting a large, positively charged patch involved in tRNA binding. A comparison with the structures of other JmjC-domain-containing proteins suggested a mechanism for substrate nucleotide recognition. Functional analyses of structure-based mutants revealed the essential Arg residues participating in tRNA recognition by TYW5. These findings extend the repertoire of the tRNA modification enzyme into the Fe(II)/2-OG oxygenase superfamily.
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Affiliation(s)
- Megumi Kato
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501 and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuhei Araiso
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501 and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akiko Noma
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501 and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Asuteka Nagao
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501 and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501 and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ryuichiro Ishitani
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501 and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- *To whom correspondence should be addressed. Tel: +81 3 5841 4392; Fax: +81 3 5841 8057;
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501 and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- *To whom correspondence should be addressed. Tel: +81 3 5841 4392; Fax: +81 3 5841 8057;
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Maciejewska AM, Ruszel KP, Nieminuszczy J, Lewicka J, Sokołowska B, Grzesiuk E, Kuśmierek JT. Chloroacetaldehyde-induced mutagenesis in Escherichia coli: the role of AlkB protein in repair of 3,N(4)-ethenocytosine and 3,N(4)-alpha-hydroxyethanocytosine. Mutat Res 2010; 684:24-34. [PMID: 19941873 DOI: 10.1016/j.mrfmmm.2009.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 11/06/2009] [Accepted: 11/18/2009] [Indexed: 05/28/2023]
Abstract
Etheno (epsilon) adducts are formed in reaction of DNA bases with various environmental carcinogens and endogenously created products of lipid peroxidation. Chloroacetaldehyde (CAA), a metabolite of carcinogen vinyl chloride, is routinely used to generate epsilon-adducts. We studied the role of AlkB, along with AlkA and Mug proteins, all engaged in repair of epsilon-adducts, in CAA-induced mutagenesis. The test system used involved pIF102 and pIF104 plasmids bearing the lactose operon of CC102 or CC104 origin (Cupples and Miller (1989) [17]) which allowed to monitor Lac(+) revertants, the latter arose by GC-->AT or GC-->TA substitutions, respectively, as a result of modification of guanine and cytosine. The plasmids were CAA-damaged in vitro and replicated in Escherichia coli of various genetic backgrounds. To modify the levels of AlkA and AlkB proteins, mutagenesis was studied in E. coli cells induced or not in adaptive response. Formation of varepsilonC proceeds via a relatively stable intermediate, 3,N(4)-alpha-hydroxyethanocytosine (HEC), which allowed to compare repair of both adducts. The results indicate that all three genes, alkA, alkB and microg, are engaged in alleviation of CAA-induced mutagenesis. The frequency of mutation was higher in AlkA-, AlkB- and Mug-deficient strains in comparison to alkA(+), alkB(+), and microg(+) controls. Considering the levels of CAA-induced Lac(+) revertants in strains harboring the pIF plasmids and induced or not in adaptive response, we conclude that AlkB protein is engaged in the repair of epsilonC and HEC in vivo. Using the modified TTCTT 5-mers as substrates, we confirmed in vitro that AlkB protein repairs epsilonC and HEC although far less efficiently than the reference adduct 3-methylcytosine. The pH optimum for repair of HEC and epsilonC is significantly different from that for 3-methylcytosine. We propose that the protonated form of adduct interact in active site of AlkB protein.
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Affiliation(s)
- Agnieszka M Maciejewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, 5A Pawińskiego Str, Poland
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Cisneros GA. DFT study of a model system for the dealkylation step catalyzed by AlkB. Interdiscip Sci 2010; 2:70-7. [PMID: 20640798 DOI: 10.1007/s12539-010-0092-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 11/18/2009] [Accepted: 11/25/2009] [Indexed: 11/25/2022]
Abstract
E. coli AlkB is a DNA repair enzyme that catalyzes the de-methylation of DNA by means of a non-heme iron and alpha-keto glutarate as a co-factor. The proposed reaction mechanism can be separated in four stages. The first stage involves the binding of the co-factor and molecular oxygen to the Fe in the active site. This is followed by the formation of a ferryl intermediate in a high-spin state, along with CO(2) and succinate. Subsequently, the O atom on the Fe center is reoriented. The last stage comprises the oxidative de-methylation of the base to produce the native DNA base and formaldehyde. This stage also includes the rate limiting step in the reaction. Here, the last stage of the proposed reaction mechanism of AlkB has been studied for a model of the active site with DFT methods. Minimum structures have been calculated for all intermediates along the path in triplet and quintet spin states. Our results point to the quintet states as more stable, in agreement with previously reported calculations. Potential energy barriers have been obtained for all the steps along this last stage in the quintet state. In the first step the oxygen bound to the Fe center of the ferryl intermediate abstracts a hydrogen atom from the methyl moiety. This first step corresponds to the rate limiting step in the reaction. The calculated barrier for this step is 26.7 kcal/mol. The subsequent steps are highly exoergic. This energetic picture is in qualitative agreement with previously reported results. The calculated energy difference between the ferryl intermediate and the final product is -75.7 kcal/mol for a model with succinate in the active site and -49.3 kcal/mol for a model where the succinate is replaced by water. Our calculated mechanism is slightly different than the previously reported one. These results suggest the possibility of more than one mechanism. This is currently under investigation by ab initio QM/MM methods.
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Affiliation(s)
- G Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
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Pitié M, Pratviel G. Activation of DNA Carbon−Hydrogen Bonds by Metal Complexes. Chem Rev 2010; 110:1018-59. [DOI: 10.1021/cr900247m] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Marguerite Pitié
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
| | - Geneviève Pratviel
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
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Prá D, Rech Franke SI, Pegas Henriques JA, Fenech M. A possible link between iron deficiency and gastrointestinal carcinogenesis. Nutr Cancer 2009; 61:415-26. [PMID: 19838913 DOI: 10.1080/01635580902803701] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is definitive evidence that iron overload induces oxidative stress and DNA damage, which can enhance carcinogenic risk. However, other evidence suggests that iron deficiency and anemia also increase oxidative stress and DNA damage, which might increase carcinogenesis risk, especially in the gastrointestinal (GI) tract. The aim of this review is to provide essential background information for the accurate interpretation of future research on iron deficiency and increased GI cancer risk. Based on clinical, epidemiological, and experimental evidence, we discuss how iron deficiency might contribute to increased cancer risk through the impairment of several iron-dependent metabolic functions that are related to genome protection and maintenance (e.g., immune responses against cancer-initiated cells, metabolism of toxic compounds, and redox regulation of DNA biosynthesis and repair). Some epidemiological studies have indicated increased risk of GI tumors among individuals with low iron intake or low somatic iron stores, and in vivo data from rodent cancer models indicates the early progression of GI tumors during iron deficiency. Given the preliminary but consistent evidence relating iron deficiency to cancer risk and the fact that iron deficiency affects about one third of the world's population, further studies are needed to define the extent to which iron deficiency might increase GI cancer risk.
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Affiliation(s)
- Daniel Prá
- Universidade Católica de Pelotas, Pelotas, RS, Brasil.
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Yang CG, Garcia K, He C. Damage detection and base flipping in direct DNA alkylation repair. Chembiochem 2009; 10:417-23. [PMID: 19145606 DOI: 10.1002/cbic.200800580] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
THE FOREIGN LESION: The mechanistic questions for DNA base damage detection by repair proteins are discussed in this Minireview. Repair proteins could either probe and locate a weakened base pair that results from base damage, or passively capture an extrahelical base lesion in the first step of damage searching on double-stranded DNA. How some repair proteins, such as AGT (see figure), locate base lesions in DNA is still not fully understood.To remove a few damaged bases efficiently from the context of the entire genome, the DNA base repair proteins rely on remarkably specific detection mechanisms to locate base lesions. This efficient molecular recognition event inside cells has been extensively studied with various structural and biochemical tools. These studies suggest that DNA base damage can be located by repair proteins by using two mechanisms: a repair protein can probe and detect a weakened base pair that results from mutagenic or cytotoxic base damage; alternatively, a protein can passively capture and stabilize an extrahelical base lesion. Our chemical and structural studies on the direct DNA repair proteins hAGT, C-Ada and ABH2 suggest that these proteins search for weakened base pairs in their first step of damage searching. We have also discovered a very unique base-flipping mechanism used by the DNA repair protein AlkB. This protein distorts DNA and favors single stranded DNA (ssDNA) substrates over double-stranded (dsDNA) ones. Potentially, it locates base lesions in dsDNA by imposing a constraint that targets less rigid regions of the duplex DNA. The exact mechanism of how AlkB and related proteins search for damage in ssDNA and dsDNA still awaits further studies.
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Affiliation(s)
- Cai-Guang Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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46
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Jia G, Yang CG, Yang S, Jian X, Yi C, Zhou Z, He C. Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO. FEBS Lett 2008; 582:3313-9. [PMID: 18775698 DOI: 10.1016/j.febslet.2008.08.019] [Citation(s) in RCA: 323] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 08/24/2008] [Accepted: 08/25/2008] [Indexed: 11/26/2022]
Abstract
The human obesity susceptibility gene, FTO, encodes a protein that is homologous to the DNA repair AlkB protein. The AlkB family proteins utilize iron(II), alpha-ketoglutarate (alpha-KG) and dioxygen to perform oxidative repair of alkylated nucleobases in DNA and RNA. We demonstrate here the oxidative demethylation of 3-methylthymine (3-meT) in single-stranded DNA (ssDNA) and 3-methyluracil (3-meU) in single-stranded RNA (ssRNA) by recombinant human FTO protein in vitro. Both human and mouse FTO proteins preferentially repair 3-meT in ssDNA over other base lesions tested. They showed negligible activities against 3-meT in double-stranded DNA (dsDNA). In addition, these two proteins can catalyze the demethylation of 3-meU in ssRNA with a slightly higher efficiency over that of 3-meT in ssDNA, suggesting that methylated RNAs are the preferred substrates for FTO.
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Affiliation(s)
- Guifang Jia
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
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47
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Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature 2008; 452:961-5. [PMID: 18432238 DOI: 10.1038/nature06889] [Citation(s) in RCA: 197] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Accepted: 03/05/2008] [Indexed: 11/10/2022]
Abstract
Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.
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Affiliation(s)
- Cai-Guang Yang
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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Transcription increases methylmethane sulfonate-induced mutations in alkB strains of Escherichia coli. DNA Repair (Amst) 2008; 7:1289-97. [PMID: 18515192 DOI: 10.1016/j.dnarep.2008.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 04/14/2008] [Accepted: 04/15/2008] [Indexed: 11/17/2022]
Abstract
Methylmethane sulfonate (MMS) produces DNA base lesions, including 3-methylcytosine (m3C), more effectively in single-stranded DNA. The repair of m3C in Escherichia coli is mediated by AlkB through oxidative demethylation and in the absence of repair, m3C leads to base-substitution mutations. We describe here results of experiments that were designed to investigate whether transcription of a gene in E. coli affects the process of mutagenesis by MMS and the roles played by AlkB and lesion bypass polymerase PolV. Using a genetic reversion assay, we have confirmed that MMS mutagenesis is suppressed by AlkB, but is enhanced by PolV. High transcription of the target gene enhances reversion frequency in an orientation-dependent manner. When the cytosines that are the likely targets of MMS were in the non-template strand (NTS), transcription increased the MMS-induced reversion frequency several fold. This increase was dependent on the presence of PolV. In contrast, when the same cytosines were present in the template strand, transcription had little effect on reversion frequency induced by MMS. These data suggest that MMS creates 3-methylcytosine adducts in the NTS and are consistent with an idea proposed previously that transcription makes the NTS transiently single-stranded and more accessible to chemicals. We propose that this is the underlying cause of its increased sensitivity to MMS and suggest that transcriptionally active DNA may be a preferred target for the action of alkylating agents that prefer single-stranded DNA.
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Bruijnincx PCA, van Koten G, Klein Gebbink RJM. Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies. Chem Soc Rev 2008; 37:2716-44. [DOI: 10.1039/b707179p] [Citation(s) in RCA: 412] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Abstract
Abstract
In animals, cellular and physiological responses to oxygen level variations are regulated via the post-translational modification of the heterodimeric hypoxia-inducible transcription factor (HIF). Hydroxylation of the HIF-α subunit at either of two conserved prolyl residues enables binding to the von Hippel-Lindau protein (pVHL) elongin C/B complex (VCB) which targets HIF-α for degradation via the ubiquitin proteasome pathway. Hydroxylation of an asparaginyl residue in the C-terminal transcriptional activation domain of HIF-α reduces its interaction with the transcriptional coactivator p300. Thus, post-translational hydroxylation is used both to "make" (HIF-VCB) and "break" (HIF-p300) protein-protein interactions in the hypoxic response. The requirement for oxygen of the HIF prolyl and asparaginyl hydroxylases in catalysis links changes in oxygen concentration and transcription of the gene array that enables cells to adapt to hypoxia. All four identified human HIF hydroxylases are members of the Fe(II) and 2-oxoglutarate (2OG)-dependent family of oxygenases. Inhibition of HIF hydroxylases mimics the hypoxic response resulting in the upregulation of erythropoietin (EPO), vascular endothelial growth factor (VEGF), and other proteins of biomedicinal importance. We briefly review biochemical analyses on the HIF hydroxylases and discuss how their structural and mechanistic characteristics may make them suited to their oxygen-sensing role.
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