1
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Wang J, Takyi NA, Hsiao YC, Tang Q, Chen YT, Liu CW, Ma J, Qi R, Bian K, Peng Z, Essigmann JM, Lu K, Wetmore SD, Li D. Stable Interstrand Cross-Links Generated from the Repair of 1, N6-Ethenoadenine in DNA by α-Ketoglutarate/Fe(II)-Dependent Dioxygenase ALKBH2. J Am Chem Soc 2024; 146:10381-10392. [PMID: 38573229 PMCID: PMC11060877 DOI: 10.1021/jacs.3c12890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
DNA cross-links severely challenge replication and transcription in cells, promoting senescence and cell death. In this paper, we report a novel type of DNA interstrand cross-link (ICL) produced as a side product during the attempted repair of 1,N6-ethenoadenine (εA) by human α-ketoglutarate/Fe(II)-dependent enzyme ALKBH2. This stable/nonreversible ICL was characterized by denaturing polyacrylamide gel electrophoresis analysis and quantified by high-resolution LC-MS in well-matched and mismatched DNA duplexes, yielding 5.7% as the highest level for cross-link formation. The binary lesion is proposed to be generated through covalent bond formation between the epoxide intermediate of εA repair and the exocyclic N6-amino group of adenine or the N4-amino group of cytosine residues in the complementary strand under physiological conditions. The cross-links occur in diverse sequence contexts, and molecular dynamics simulations rationalize the context specificity of cross-link formation. In addition, the cross-link generated from attempted εA repair was detected in cells by highly sensitive LC-MS techniques, giving biological relevance to the cross-link adducts. Overall, a combination of biochemical, computational, and mass spectrometric methods was used to discover and characterize this new type of stable cross-link both in vitro and in human cells, thereby uniquely demonstrating the existence of a potentially harmful ICL during DNA repair by human ALKBH2.
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Affiliation(s)
- Jie Wang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Nathania A Takyi
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Yi-Tzai Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jian Ma
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Rui Qi
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Zhiyuan Peng
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - John M Essigmann
- Departments of Biological Engineering, Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
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2
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Vennelakanti V, Jeon M, Kulik HJ. How Do Differences in Electronic Structure Affect the Use of Vanadium Intermediates as Mimics in Nonheme Iron Hydroxylases? Inorg Chem 2024; 63:4997-5011. [PMID: 38428015 DOI: 10.1021/acs.inorgchem.3c04421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
We study active-site models of nonheme iron hydroxylases and their vanadium-based mimics using density functional theory to determine if vanadyl is a faithful structural mimic. We identify crucial structural and energetic differences between ferryl and vanadyl isomers owing to the differences in their ground electronic states, i.e., high spin (HS) for Fe and low spin (LS) for V. For the succinate cofactor bound to the ferryl intermediate, we predict facile interconversion between monodentate and bidentate coordination isomers for ferryl species but difficult rearrangement for vanadyl mimics. We study isomerization of the oxo intermediate between axial and equatorial positions and find the ferryl potential energy surface to be characterized by a large barrier of ca. 10 kcal/mol that is completely absent for the vanadyl mimic. This analysis reveals even starker contrasts between Fe and V in hydroxylases than those observed for this metal substitution in nonheme halogenases. Analysis of the relative bond strengths of coordinating carboxylate ligands for Fe and V reveals that all of the ligands show stronger binding to V than Fe owing to the LS ground state of V in contrast to the HS ground state of Fe, highlighting the limitations of vanadyl mimics of native nonheme iron hydroxylases.
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mugyeom Jeon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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Zhang L, Ding X, Kratka CR, Levine A, Lee JK. Gas Phase Experimental and Computational Studies of AlkB Substrates: Intrinsic Properties and Biological Implications. J Org Chem 2023; 88:13115-13124. [PMID: 37651719 DOI: 10.1021/acs.joc.3c01335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The gas phase acidity and proton affinity of nucleobases that are substrates for the DNA repair enzyme AlkB have been examined using both computational and experimental methods. These thermochemical values have not heretofore been measured and provide experimental data that help benchmark the theoretical results. We also use our gas phase results to lend insight into the AlkB mechanism, particularly in terms of the role AlkB plays in DNA repair, versus its complementary enzyme AlkA.
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Affiliation(s)
- Lanxin Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Xiao Ding
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Catherine R Kratka
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Alec Levine
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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4
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Kastner DW, Nandy A, Mehmood R, Kulik HJ. Mechanistic Insights into Substrate Positioning That Distinguish Non-heme Fe(II)/α-Ketoglutarate-Dependent Halogenases and Hydroxylases. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- David W. Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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5
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Travaglini S, Gurnari C, Antonelli S, Silvestrini G, Noguera NI, Ottone T, Voso MT. The Anti-Leukemia Effect of Ascorbic Acid: From the Pro-Oxidant Potential to the Epigenetic Role in Acute Myeloid Leukemia. Front Cell Dev Biol 2022; 10:930205. [PMID: 35938170 PMCID: PMC9352950 DOI: 10.3389/fcell.2022.930205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Data derived from high-throughput sequencing technologies have allowed a deeper understanding of the molecular landscape of Acute Myeloid Leukemia (AML), paving the way for the development of novel therapeutic options, with a higher efficacy and a lower toxicity than conventional chemotherapy. In the antileukemia drug development scenario, ascorbic acid, a natural compound also known as Vitamin C, has emerged for its potential anti-proliferative and pro-apoptotic activities on leukemic cells. However, the role of ascorbic acid (vitamin C) in the treatment of AML has been debated for decades. Mechanistic insight into its role in many biological processes and, especially, in epigenetic regulation has provided the rationale for the use of this agent as a novel anti-leukemia therapy in AML. Acting as a co-factor for 2-oxoglutarate-dependent dioxygenases (2-OGDDs), ascorbic acid is involved in the epigenetic regulations through the control of TET (ten-eleven translocation) enzymes, epigenetic master regulators with a critical role in aberrant hematopoiesis and leukemogenesis. In line with this discovery, great interest has been emerging for the clinical testing of this drug targeting leukemia epigenome. Besides its role in epigenetics, ascorbic acid is also a pivotal regulator of many physiological processes in human, particularly in the antioxidant cellular response, being able to scavenge reactive oxygen species (ROS) to prevent DNA damage and other effects involved in cancer transformation. Thus, for this wide spectrum of biological activities, ascorbic acid possesses some pharmacologic properties attractive for anti-leukemia therapy. The present review outlines the evidence and mechanism of ascorbic acid in leukemogenesis and its therapeutic potential in AML. With the growing evidence derived from the literature on situations in which the use of ascorbate may be beneficial in vitro and in vivo, we will finally discuss how these insights could be included into the rational design of future clinical trials.
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Affiliation(s)
- S. Travaglini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - C. Gurnari
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, United States
| | - S. Antonelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - G. Silvestrini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - N. I. Noguera
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - T. Ottone
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - M. T. Voso
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
- *Correspondence: M. T. Voso,
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6
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Vennelakanti V, Mehmood R, Kulik HJ. Are Vanadium Intermediates Suitable Mimics in Non-Heme Iron Enzymes? An Electronic Structure Analysis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Zhao W, Li J, Ma Q, Cai J, Li A, Wu W, Lv Y, Cai M. N6-methyladenosine modification participates in neoplastic immunoregulation and tumorigenesis. J Cell Physiol 2022; 237:2729-2739. [PMID: 35342948 DOI: 10.1002/jcp.30730] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 03/05/2022] [Accepted: 03/15/2022] [Indexed: 12/19/2022]
Abstract
This review aims to provide insight into the role of N6-methyladenosine (m6A) modification in neoplastic immunity and subsequent tumorigenesis. m6A modification, which is catalyzed by methyltransferases, demethylases and reader proteins, has emerged as a widespread regulatory mechanism that controls immune-related gene expression and immune reactions during tumorigenesis. Aberrant m6A modification changes the neoplastic immune response in multiple cancers by regulating immune cell infiltration, tumor-promoting inflammation, immunosuppression, immune surveillance, and antitumor immune responses. m6A modification affects immune cell recruitment and cancer-promoting inflammation in hepatocellular carcinoma (HCC) to alter the progression of HCC. m6A modification has been implicated in the infiltration of immune cells and the activation of immune pathways, changing the proliferation and metastasis of gastric cancer. Immune surveillance and the antitumor immune response in breast cancer were enhanced via m6A modification, which inhibited tumor proliferation. m6A modification participates in neoplastic immunoregulation to influence tumor progression.
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Affiliation(s)
- Wanzhen Zhao
- Department of Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jianjun Li
- Department of Urological Surgical, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Qiang Ma
- First People's Hospital of Shaoyang, Shaoyang, Hunan, China
| | - Jijie Cai
- Class 8, Grade 2019, The First Clinical College, Changsha Medical College, Changsha, Hunan, China
| | - Aixin Li
- Department of Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Weijun Wu
- Department of Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yuncheng Lv
- Guangxi Key Laboratory of Diabetic Systems Medicine, Faculty of Basic Medical Sciences, Guilin Medical University, Guilin, Guangxi, China
| | - Manbo Cai
- Department of Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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8
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Aralov AV, Gubina N, Cabrero C, Tsvetkov VB, Turaev AV, Fedeles BI, Croy RG, Isaakova EA, Melnik D, Dukova S, Ryazantsev DY, Khrulev AA, Varizhuk AM, González C, Zatsepin TS, Essigmann JM. 7,8-Dihydro-8-oxo-1,N6-ethenoadenine: an exclusively Hoogsteen-paired thymine mimic in DNA that induces A→T transversions in Escherichia coli. Nucleic Acids Res 2022; 50:3056-3069. [PMID: 35234900 PMCID: PMC8989528 DOI: 10.1093/nar/gkac148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/09/2022] [Accepted: 02/25/2022] [Indexed: 12/15/2022] Open
Abstract
This work investigated the structural and biological properties of DNA containing 7,8-dihydro-8-oxo-1,N6-ethenoadenine (oxo-ϵA), a non-natural synthetic base that combines structural features of two naturally occurring DNA lesions (7,8-dihydro-8-oxoadenine and 1,N6-ethenoadenine). UV-, CD-, NMR spectroscopies and molecular modeling of DNA duplexes revealed that oxo-ϵA adopts the non-canonical syn conformation (χ = 65º) and fits very well among surrounding residues without inducing major distortions in local helical architecture. The adduct remarkably mimics the natural base thymine. When considered as an adenine-derived DNA lesion, oxo-ϵA was >99% mutagenic in living cells, causing predominantly A→T transversion mutations in Escherichia coli. The adduct in a single-stranded vector was not repaired by base excision repair enzymes (MutM and MutY glycosylases) or the AlkB dioxygenase and did not detectably affect the efficacy of DNA replication in vivo. When the biological and structural data are viewed together, it is likely that the nearly exclusive syn conformation and thymine mimicry of oxo-ϵA defines the selectivity of base pairing in vitro and in vivo, resulting in lesion pairing with A during replication. The base pairing properties of oxo-ϵA, its strong fluorescence and its invisibility to enzymatic repair systems in vivo are features that are sought in novel DNA-based probes and modulators of gene expression.
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Affiliation(s)
- Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Nina Gubina
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Institute of Theoretical and Experimental Biophysics RAS, Pushchino 142290, Russia
| | - Cristina Cabrero
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid 28006, Spain
| | - Vladimir B Tsvetkov
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia.,World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow 119146, Russia
| | - Anton V Turaev
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia
| | - Bogdan I Fedeles
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert G Croy
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ekaterina A Isaakova
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia
| | - Denis Melnik
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Svetlana Dukova
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Dmitriy Y Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Alexei A Khrulev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Carlos González
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid 28006, Spain
| | - Timofei S Zatsepin
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia.,Chemistry Department, Lomonosov Moscow State University, Moscow 119992, Russia
| | - John M Essigmann
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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9
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Song X, Liu J, Wang B. Emergence of Function from Nonheme Diiron Oxygenases: A Quantum Mechanical/Molecular Mechanical Study of Oxygen Activation and Organophosphonate Catabolism Mechanisms by PhnZ. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xitong Song
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Jia Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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10
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Schmidl D, Jonasson NSW, Menke A, Schneider S, Daumann L. Spectroscopic and in vitro investigations of Fe2+/α-Ketoglutarate-dependent enzymes involved in nucleic acid repair and modification. Chembiochem 2022; 23:e202100605. [PMID: 35040547 PMCID: PMC9401043 DOI: 10.1002/cbic.202100605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/14/2022] [Indexed: 11/08/2022]
Abstract
The activation of molecular oxygen for the highly selective functionalization and repair of DNA and RNA nucleobases is achieved by α-ketoglutarate (α-KG)/iron-dependent dioxygenases. Enzymes of special interest are the human homologs AlkBH of Escherichia coli EcAlkB and ten-eleven translocation (TET) enzymes. These enzymes are involved in demethylation or dealkylation of DNA and RNA, although additional physiological functions are continuously being revealed. Given their importance, studying enzyme-substrate interactions, turnover and kinetic parameters is pivotal for the understanding of the mode of action of these enzymes. Diverse analytical methods, including X-ray crystallography, UV/Vis absorption, electron paramagnetic resonance (EPR), circular dichroism (CD) and NMR spectroscopy have been employed to study the changes in the active site and the overall enzyme structure upon substrate, cofactor and inhibitor addition. Several methods are now available to assess activity of these enzymes. By discussing limitations and possibilities of these techniques for EcAlkB, AlkBH and TET we aim to give a comprehensive synopsis from a bioinorganic point of view, addressing researchers from different disciplines working in the highly interdisciplinary and rapidly evolving field of epigenetic processes and DNA/RNA repair and modification.
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Affiliation(s)
- David Schmidl
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Niko S W Jonasson
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Annika Menke
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Sabine Schneider
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Lena Daumann
- Ludwig-Maximilians-Universität München, Department of Chemistry, Butenandtstr. 5-13, 81377, München, GERMANY
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11
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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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12
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Berger MB, Walker AR, Vázquez-Montelongo EA, Cisneros GA. Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families. Phys Chem Chem Phys 2021; 23:22227-22240. [PMID: 34586107 PMCID: PMC8516722 DOI: 10.1039/d1cp03800a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA alkylation is used as the key epigenetic mark in eukaryotes, however, most alkylation in DNA can result in deleterious effects. Therefore, this process needs to be tightly regulated. The enzymes of the AlkB and Ten-Eleven Translocation (TET) families are members of the Fe and alpha-ketoglutarate-dependent superfamily of enzymes that are tasked with dealkylating DNA and RNA in cells. Members of these families span all species and are an integral part of transcriptional regulation. While both families catalyze oxidative dealkylation of various bases, each has specific preference for alkylated base type as well as distinct catalytic mechanisms. This perspective aims to provide an overview of computational work carried out to investigate several members of these enzyme families including AlkB, ALKB Homolog 2, ALKB Homolog 3 and Ten-Eleven Translocate 2. Insights into structural details, mutagenesis studies, reaction path analysis, electronic structure features in the active site, and substrate preferences are presented and discussed.
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Affiliation(s)
- Madison B Berger
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
| | - Alice R Walker
- Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
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13
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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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Ramanan R, Waheed SO, Schofield CJ, Christov CZ. What Is the Catalytic Mechanism of Enzymatic Histone N-Methyl Arginine Demethylation and Can It Be Influenced by an External Electric Field? Chemistry 2021; 27:11827-11836. [PMID: 33989435 DOI: 10.1002/chem.202101174] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Indexed: 11/11/2022]
Abstract
Arginine methylation is an important mechanism of epigenetic regulation. Some Fe(II) and 2-oxoglutarate dependent Jumonji-C (JmjC) Nϵ-methyl lysine histone demethylases also have N-methyl arginine demethylase activity. We report combined molecular dynamic (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) studies on the mechanism of N-methyl arginine demethylation by human KDM4E and compare the results with those reported for N-methyl lysine demethylation by KDM4A. At the KDM4E active site, Glu191, Asn291, and Ser197 form a conserved scaffold that restricts substrate dynamics; substrate binding is also mediated by an out of active site hydrogen-bond between the substrate Ser1 and Tyr178. The calculations imply that in either C-H or N-H potential bond cleaving pathways for hydrogen atom transfer (HAT) during N-methyl arginine demethylation, electron transfer occurs via a σ-channel; the transition state for the N-H pathway is ∼10 kcal/mol higher than for the C-H pathway due to the higher bond dissociation energy of the N-H bond. The results of applying external electric fields (EEFs) reveal EEFs with positive field strengths parallel to the Fe=O bond have a significant barrier-lowering effect on the C-H pathway, by contrast, such EEFs inhibit the N-H activation rate. The overall results imply that KDM4 catalyzed N-methyl arginine demethylation and N-methyl lysine demethylation occur via similar C-H abstraction and rebound mechanisms leading to methyl group hydroxylation, though there are differences in the interactions leading to productive binding of intermediates.
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Affiliation(s)
- Rajeev Ramanan
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA.,Present address: Department of Chemistry, National Institute of Technology, Rourkela, Odisha, 769001, India
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Christopher J Schofield
- The Department of Chemistry and the Ineos Oxford Institute for, Antimicrobial Research, The Chemistry Research Laboratory, University of Oxford, Mansfield Road, OX1 5JJ, Oxford, UK
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
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Liu J, Wu P, Yan S, Li Y, Cao Z, Wang B. Spin-Regulated Inner-Sphere Electron Transfer Enables Efficient O—O Bond Activation in Nonheme Diiron Monooxygenase MIOX. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jia Liu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Peng Wu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Shengheng Yan
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuanyuan Li
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Zexing Cao
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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Marcinkowski M, Pilžys T, Garbicz D, Piwowarski J, Mielecki D, Nowaczyk G, Taube M, Gielnik M, Kozak M, Winiewska-Szajewska M, Szołajska E, Dębski J, Maciejewska AM, Przygońska K, Ferenc K, Grzesiuk E, Poznański J. Effect of Posttranslational Modifications on the Structure and Activity of FTO Demethylase. Int J Mol Sci 2021; 22:ijms22094512. [PMID: 33925955 PMCID: PMC8123419 DOI: 10.3390/ijms22094512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 12/13/2022] Open
Abstract
The FTO protein is involved in a wide range of physiological processes, including adipogenesis and osteogenesis. This two-domain protein belongs to the AlkB family of 2-oxoglutarate (2-OG)- and Fe(II)-dependent dioxygenases, displaying N6-methyladenosine (N6-meA) demethylase activity. The aim of the study was to characterize the relationships between the structure and activity of FTO. The effect of cofactors (Fe2+/Mn2+ and 2-OG), Ca2+ that do not bind at the catalytic site, and protein concentration on FTO properties expressed in either E. coli (ECFTO) or baculovirus (BESFTO) system were determined using biophysical methods (DSF, MST, SAXS) and biochemical techniques (size-exclusion chromatography, enzymatic assay). We found that BESFTO carries three phosphoserines (S184, S256, S260), while there were no such modifications in ECFTO. The S256D mutation mimicking the S256 phosphorylation moderately decreased FTO catalytic activity. In the presence of Ca2+, a slight stabilization of the FTO structure was observed, accompanied by a decrease in catalytic activity. Size exclusion chromatography and MST data confirmed the ability of FTO from both expression systems to form homodimers. The MST-determined dissociation constant of the FTO homodimer was consistent with their in vivo formation in human cells. Finally, a low-resolution structure of the FTO homodimer was built based on SAXS data.
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Affiliation(s)
- Michał Marcinkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
| | - Tomaš Pilžys
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
| | - Damian Garbicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
| | - Jan Piwowarski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
| | - Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
| | - Grzegorz Nowaczyk
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland;
| | - Michał Taube
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614 Poznan, Poland; (M.T.); (M.G.); (M.K.)
| | - Maciej Gielnik
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614 Poznan, Poland; (M.T.); (M.G.); (M.K.)
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614 Poznan, Poland; (M.T.); (M.G.); (M.K.)
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Czerwone Maki 98, 30-392 Kraków, Poland
| | - Maria Winiewska-Szajewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
| | - Ewa Szołajska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
| | - Janusz Dębski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
| | - Agnieszka M. Maciejewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
| | - Kaja Przygońska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
| | - Karolina Ferenc
- Veterinary Research Centre, Department of Large Animal Diseases and Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 100, 02-797 Warsaw, Poland;
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
- Correspondence: (E.G.); (J.P.)
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (M.M.); (T.P.); (D.G.); (J.P.); (D.M.); (M.W.-S.); (E.S.); (J.D.); (A.M.M.); (K.P.)
- Correspondence: (E.G.); (J.P.)
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17
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Zhao S, Devega R, Francois A, Kidane D. Human ALKBH6 Is Required for Maintenance of Genomic Stability and Promoting Cell Survival During Exposure of Alkylating Agents in Pancreatic Cancer. Front Genet 2021; 12:635808. [PMID: 33897761 PMCID: PMC8058185 DOI: 10.3389/fgene.2021.635808] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/08/2021] [Indexed: 12/21/2022] Open
Abstract
Alpha-ketoglutarate-dependent dioxygenase (ALKBH) is a DNA repair gene involved in the repair of alkylating DNA damage. There are nine types of ALKBH (ALKBH1-8 and FTO) identified in humans. In particular, certain types of ALKBH enzymes are dioxygenases that directly reverse DNA methylation damage via transfer of a methyl group from the DNA adduct onto α-ketoglutarate and release of metabolic products including succinate and formaldehyde. Here, we tested whether ALKBH6 plays a significant role in preventing alkylating DNA damage and decreasing genomic instability in pancreatic cancer cells. Using an E. coli strain deficient with ALKB, we found that ALKBH6 complements ALKB deficiency and increases resistance after alkylating agent treatment. In particular, the loss of ALKBH6 in human pancreatic cancer cells increases alkylating agent-induced DNA damage and significantly decreases cell survival. Furthermore, in silico analysis from The Cancer Genome Atlas (TCGA) database suggests that overexpression of ALKBH6 provides better survival outcomes in patients with pancreatic cancer. Overall, our data suggest that ALKBH6 is required to maintain the integrity of the genome and promote cell survival of pancreatic cancer cells.
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Affiliation(s)
- Shengyuan Zhao
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
| | - Rodan Devega
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
| | - Aaliyah Francois
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
| | - Dawit Kidane
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
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18
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de Polo A, Labbé DP. Diet-Dependent Metabolic Regulation of DNA Double-Strand Break Repair in Cancer: More Choices on the Menu. Cancer Prev Res (Phila) 2021; 14:403-414. [PMID: 33509805 DOI: 10.1158/1940-6207.capr-20-0470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/27/2020] [Accepted: 01/21/2021] [Indexed: 11/16/2022]
Abstract
Despite several epidemiologic and preclinical studies supporting the role of diet in cancer progression, the complexity of the diet-cancer link makes it challenging to deconvolute the underlying mechanisms, which remain scantly elucidated. This review focuses on genomic instability as one of the cancer hallmarks affected by diet-dependent metabolic alterations. We discuss how altered dietary intake of metabolites of the one-carbon metabolism, including methionine, folate, and vitamins B and C, can impact the methylation processes and thereby tumorigenesis. We present the concept that the protumorigenic effect of certain diets, such as the Western diet, is in part due to a diet-induced erosion of the DNA repair capacity caused by altered epigenetic and epitranscriptomic landscapes, while the protective effect of other dietary patterns, such as the Mediterranean diet, can be partly explained by their ability to sustain a proficient DNA repair. In particular, considering that diet-dependent alterations of the one-carbon metabolism can impact the rate of methylation processes, changes in dietary patterns can affect the activity of writers and erasers of histone and RNA methyl marks and consequently impair their role in ensuring a proficient DNA damage repair.
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Affiliation(s)
- Anna de Polo
- Division of Urology, Department of Surgery, McGill University and Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - David P Labbé
- Division of Urology, Department of Surgery, McGill University and Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada.
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19
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Oxidative demethylase ALKBH5 repairs DNA alkylation damage and protects against alkylation-induced toxicity. Biochem Biophys Res Commun 2020; 534:114-120. [PMID: 33321288 DOI: 10.1016/j.bbrc.2020.12.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/05/2020] [Indexed: 11/22/2022]
Abstract
DNA integrity is challenged by both exogenous and endogenous alkylating agents. DNA repair proteins such as Escherichia coli AlkB family of enzymes can repair 1-methyladenine and 3-methylcytosine adducts by oxidative demethylation. Human AlkB homologue 5 (ALKBH5) is RNA N6-methyladenine demethylase and not known to be involved in DNA repair. Herein we show that ALKBH5 also has weak DNA repair activity and it can demethylate DNA 3-methylcytosine. The mutation of the amino acid residues involved in demethylation also abolishes the DNA repair activity of ALKBH5. Overexpression of ALKBH5 decreases the 3-methylcytosine level in genomic DNA and reduces the cytotoxic effects of the DNA damaging alkylating agent methyl methanesulfonate. Thus, demethylation by ALKBH5 might play a supporting role in maintaining genome integrity.
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20
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Latifi R, Minnick JL, Quesne MG, de Visser SP, Tahsini L. Computational studies of DNA base repair mechanisms by nonheme iron dioxygenases: selective epoxidation and hydroxylation pathways. Dalton Trans 2020; 49:4266-4276. [PMID: 32141456 DOI: 10.1039/d0dt00007h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
DNA base repair mechanisms of alkylated DNA bases is an important reaction in chemical biology and particularly in the human body. It is typically catalyzed by an α-ketoglutarate-dependent nonheme iron dioxygenase named the AlkB repair enzyme. In this work we report a detailed computational study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases. In particular, we investigate the aliphatic hydroxylation and C[double bond, length as m-dash]C epoxidation mechanisms of alkylated DNA bases by a high-valent iron(iv)-oxo intermediate. Our computational studies use quantum mechanics/molecular mechanics methods on full enzymatic structures as well as cluster models on active site systems. The work shows that the iron(iv)-oxo species is rapidly formed after dioxygen binding to an iron(ii) center and passes a bicyclic ring structure as intermediate. Subsequent cluster models explore the mechanism of substrate hydroxylation and epoxidation of alkylated DNA bases. The work shows low energy barriers for substrate activation and consequently energetically feasible pathways are predicted. Overall, the work shows that a high-valent iron(iv)-oxo species can efficiently dealkylate alkylated DNA bases and return them into their original form.
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Affiliation(s)
- Reza Latifi
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
| | - Jennifer L Minnick
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
| | - Matthew G Quesne
- Cardiff University, School of Chemistry, Main Building, Park Place, Cardiff, CF10 3AT, UK. and Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon, OX110FA, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, 131 Princess Street, Manchester M1 7DN, UK.
| | - Laleh Tahsini
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
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Abstract
Genomic DNA is chemically reactive and therefore susceptible to damage by many exogenous and endogenous sources. Lesions produced from these damaging events can have various mutagenic and genotoxic consequences. This Perspective follows the journey of one particular lesion, 1,N6-ethenoadenine (εA), from its formation to replication and repair, and its role in cancerous tissues and inflammatory diseases. εA is generated by the reaction of adenine (A) with vinyl chloride or lipid peroxidation products. We present the miscoding properties of εA with an emphasis on how bacterial and mammalian cells can process lesions differently, leading to varied mutational spectra. But with information from these assays, we can better understand how the miscoding properties of εA lead to biological consequences and how genomic stability can be maintained via DNA repair mechanisms. We discuss how base excision repair (BER) and direct reversal repair (DRR) can minimize the biological consequences of εA lesions. Kinetic parameters of glycosylases and AlkB family enzymes are described, along with a discussion of the relative contributions of the BER and DRR pathways in the repair of εA. Because eukaryotic DNA is packaged in chromatin, we also discuss the impact of this packaging on BER and DRR, specifically in regards to repair of εA. Studying DNA lesions like εA in this context, from origin to biological implications, can provide crucial information to better understand prevention of mutagenesis and cancer.
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Affiliation(s)
- Katelyn L Rioux
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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22
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Reversal of nucleobase methylation by dioxygenases. Nat Chem Biol 2020; 16:1160-1169. [DOI: 10.1038/s41589-020-00675-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 09/11/2020] [Indexed: 12/12/2022]
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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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Antioxidants as an Epidermal Stem Cell Activator. Antioxidants (Basel) 2020; 9:antiox9100958. [PMID: 33036398 PMCID: PMC7600937 DOI: 10.3390/antiox9100958] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 01/18/2023] Open
Abstract
Antioxidants may modulate the microenvironment of epidermal stem cells by reducing the production of reactive oxygen species or by regulating the expression of extracellular matrix protein. The extracellular membrane is an important component of the stem cell niche, and microRNAs regulate extracellular membrane-mediated basal keratinocyte proliferation. In this narrative review, we will discuss several antioxidants such as ascorbic acid, plant extracts, peptides and hyaluronic acid, and their effect on the epidermal stem cell niche and the proliferative potential of interfollicular epidermal stem cells in 3D skin equivalent models.
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25
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Lenz SAP, Li D, Wetmore SD. Insights into the Direct Oxidative Repair of Etheno Lesions: MD and QM/MM Study on the Substrate Scope of ALKBH2 and AlkB. DNA Repair (Amst) 2020; 96:102944. [PMID: 33161373 DOI: 10.1016/j.dnarep.2020.102944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 01/09/2023]
Abstract
E. coli AlkB and human ALKBH2 belong to the AlkB family enzymes, which contain several α-ketoglutarate (α-KG)/Fe(II)-dependent dioxygenases that repair alkylated DNA. Specifically, the AlkB enzymes catalyze decarboxylation of α-KG to generate a high-valent Fe(IV)-oxo species that oxidizes alkyl groups on DNA adducts. AlkB and ALKBH2 have been reported to differentially repair select etheno adducts, with preferences for 1,N6-ethenoadenine (1,N6-εA) and 3,N4-ethenocytosine (3,N4-εC) over 1,N2-ethenoguanine (1,N2-εG). However, N2,3-ethenoguanine (N2,3-εG), the most common etheno adduct, is not repaired by the AlkB enzymes. Unfortunately, a structural understanding of the differential activity of E. coli AlkB and human ALKBH2 is lacking due to challenges acquiring atomistic details for a range of substrates using experiments. This study uses both molecular dynamics (MD) simulations and ONIOM(QM:MM) calculations to determine how the active site changes upon binding each etheno adduct and characterizes the corresponding catalytic impacts. Our data reveal that the preferred etheno substrates (1,N6-εA and 3,N4-εC) form favorable interactions with catalytic residues that situate the lesion near the Fe(IV)-oxo species and permit efficient oxidation. In contrast, although the damage remains correctly aligned with respect to the Fe(IV)-oxo moiety, repair of 1,N2-εG is mitigated by increased solvation of the active site and a larger distance between Fe(IV)-oxo and the aberrant carbons. Binding of non-substrate N2,3-εG in the active site disrupts key DNA-enzyme interactions, and positions the aberrant carbon atoms even further from the Fe(IV)-oxo species, leading to prohibitively high barriers for oxidative catalysis. Overall, our calculations provide the first structural insight required to rationalize the experimentally-reported substrate specificities of AlkB and ALKBH2 and thereby highlight the roles of several active site residues in the repair of etheno adducts that directly correlates with available experimental data. These proposed catalytic strategies can likely be generalized to other α-KG/Fe(II)-dependent dioxygenases that play similar critical biological roles, including epigenetic and post-translational regulation.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, 02881, USA
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
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The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase. Nat Commun 2020; 11:4437. [PMID: 32895378 PMCID: PMC7477556 DOI: 10.1038/s41467-020-18290-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/14/2020] [Indexed: 02/05/2023] Open
Abstract
Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein-DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA helix and facilitates their extrusion for repair. DNA glycosylases are lesion-specific enzymes that recognize specific nucleobase damages and catalyze their excision through cleavage of the glycosidic bond. Here, the authors present the crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase bound to undamaged DNA and to DNA containing an intrahelical oxoG lesion and further analyse these structures with molecular dynamics simulations, which allows them to characterise the base-extrusion pathways.
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27
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Rabe P, Beale JH, Butryn A, Aller P, Dirr A, Lang PA, Axford DN, Carr SB, Leissing TM, McDonough MA, Davy B, Ebrahim A, Orlans J, Storm SLS, Orville AM, Schofield CJ, Owen RL. Anaerobic fixed-target serial crystallography. IUCRJ 2020; 7:901-912. [PMID: 32939282 PMCID: PMC7467159 DOI: 10.1107/s2052252520010374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/27/2020] [Indexed: 05/04/2023]
Abstract
Cryogenic X-ray diffraction is a powerful tool for crystallographic studies on enzymes including oxygenases and oxidases. Amongst the benefits that cryo-conditions (usually employing a nitro-gen cryo-stream at 100 K) enable, is data collection of di-oxy-gen-sensitive samples. Although not strictly anaerobic, at low temperatures the vitreous ice conditions severely restrict O2 diffusion into and/or through the protein crystal. Cryo-conditions limit chemical reactivity, including reactions that require significant conformational changes. By contrast, data collection at room temperature imposes fewer restrictions on diffusion and reactivity; room-temperature serial methods are thus becoming common at synchrotrons and XFELs. However, maintaining an anaerobic environment for di-oxy-gen-dependent enzymes has not been explored for serial room-temperature data collection at synchrotron light sources. This work describes a methodology that employs an adaptation of the 'sheet-on-sheet' sample mount, which is suitable for the low-dose room-temperature data collection of anaerobic samples at synchrotron light sources. The method is characterized by easy sample preparation in an anaerobic glovebox, gentle handling of crystals, low sample consumption and preservation of a localized anaerobic environment over the timescale of the experiment (<5 min). The utility of the method is highlighted by studies with three X-ray-radiation-sensitive Fe(II)-containing model enzymes: the 2-oxoglutarate-dependent l-arginine hy-droxy-lase VioC and the DNA repair enzyme AlkB, as well as the oxidase isopenicillin N synthase (IPNS), which is involved in the biosynthesis of all penicillin and cephalosporin antibiotics.
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Affiliation(s)
- Patrick Rabe
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Agata Butryn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Anna Dirr
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Pauline A. Lang
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Danny N. Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Stephen B. Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot Oxfordshire OX11 0FA, United Kingdom
| | - Thomas M. Leissing
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A. McDonough
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Bradley Davy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Ali Ebrahim
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Julien Orlans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- UMR0203, Biologie Fonctionnelle, Insectes et Interactions, Institut National des Sciences Appliquées de Lyon, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, University of Lyon, Villeurbanne F-69621, France
| | - Selina L. S. Storm
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
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28
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Kansara S, Pandey V, Lobie PE, Sethi G, Garg M, Pandey AK. Mechanistic Involvement of Long Non-Coding RNAs in Oncotherapeutics Resistance in Triple-Negative Breast Cancer. Cells 2020; 9:cells9061511. [PMID: 32575858 PMCID: PMC7349003 DOI: 10.3390/cells9061511] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most lethal forms of breast cancer (BC), with a significant disease burden worldwide. Chemoresistance and lack of targeted therapeutics are major hindrances to effective treatments in the clinic and are crucial causes of a worse prognosis and high rate of relapse/recurrence in patients diagnosed with TNBC. In the last decade, long non-coding RNAs (lncRNAs) have been found to perform a pivotal role in most cellular functions. The aberrant functional expression of lncRNAs plays an ever-increasing role in the progression of diverse malignancies, including TNBC. Therefore, lncRNAs have been recently studied as predictors and modifiers of chemoresistance. Our review discusses the potential involvement of lncRNAs in drug-resistant mechanisms commonly found in TNBC and highlights various therapeutic strategies to target lncRNAs in this malignancy.
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Affiliation(s)
- Samarth Kansara
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India;
| | - Vijay Pandey
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518005, China; (V.P.); (P.E.L.)
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Peter E. Lobie
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518005, China; (V.P.); (P.E.L.)
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- Correspondence: (G.S.); (A.K.P.)
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Sector-125, Noida 201313, India;
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India;
- Correspondence: (G.S.); (A.K.P.)
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29
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Waheed S, Ramanan R, Chaturvedi SS, Lehnert N, Schofield CJ, Christov CZ, Karabencheva-Christova TG. Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair. ACS CENTRAL SCIENCE 2020; 6:795-814. [PMID: 32490196 PMCID: PMC7256942 DOI: 10.1021/acscentsci.0c00312] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Indexed: 05/08/2023]
Abstract
AlkB and its human homologue AlkBH2 are Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases that repair alkylated DNA bases occurring as a consequence of reactions with mutagenic agents. We used molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) methods to investigate how structural dynamics influences the selectivity and mechanisms of the AlkB- and AlkBH2-catalyzed demethylation of 3-methylcytosine (m3C) in single (ssDNA) and double (dsDNA) stranded DNA. Dynamics studies reveal the importance of the flexibility in both the protein and DNA components in determining the preferences of AlkB for ssDNA and of AlkBH2 for dsDNA. Correlated motions, including of a hydrophobic β-hairpin, are involved in substrate binding in AlkBH2-dsDNA. The calculations reveal that 2OG rearrangement prior to binding of dioxygen to the active site Fe is preferred over a ferryl rearrangement to form a catalytically productive Fe(IV)=O intermediate. Hydrogen atom transfer proceeds via a σ-channel in AlkBH2-dsDNA and AlkB-dsDNA; in AlkB-ssDNA, there is a competition between σ- and π-channels, implying that the nature of the complexed DNA has potential to alter molecular orbital interactions during the substrate oxidation. Our results reveal the importance of the overall protein-DNA complex in determining selectivity and how the nature of the substrate impacts the mechanism.
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Affiliation(s)
- Sodiq
O. Waheed
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Rajeev Ramanan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Shobhit S. Chaturvedi
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Nicolai Lehnert
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Christopher J. Schofield
- The
Chemistry Research Laboratory, The Department of Chemistry, Mansfield
Road, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christo Z. Christov
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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30
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Hong JY, Davaa G, Yoo H, Hong K, Hyun JK. Ascorbic Acid Promotes Functional Restoration after Spinal Cord Injury Partly by Epigenetic Modulation. Cells 2020; 9:cells9051310. [PMID: 32466098 PMCID: PMC7290865 DOI: 10.3390/cells9051310] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/09/2020] [Accepted: 05/22/2020] [Indexed: 02/07/2023] Open
Abstract
Axonal regeneration after spinal cord injury (SCI) is difficult to achieve, and no fundamental treatment can be applied in clinical settings. DNA methylation has been suggested to play a role in regeneration capacity and neuronal growth after SCI by controlling the expression of regeneration-associated genes (RAGs). The aim of this study was to examine changes in neuronal DNA methylation status after SCI and to determine whether modulation of DNA methylation with ascorbic acid can enhance neuronal regeneration or functional restoration after SCI. Changes in epigenetic marks (5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC)); the expression of Ten-eleven translocation (Tet) family genes; and the expression of genes related to inflammation, regeneration, and degeneration in the brain motor cortex were determined following SCI. The 5hmC level within the brain was increased after SCI, especially in the acute and subacute stages, and the mRNA levels of Tet gene family members (Tet1, Tet2, and Tet3) were also increased. Administration of ascorbic acid (100 mg/kg) to SCI rats enhanced 5hmC levels; increased the expression of the Tet1, Tet2, and Tet3 genes within the brain motor cortex; promoted axonal sprouting within the lesion cavity of the spinal cord; and enhanced recovery of locomotor function until 12 weeks. In conclusion, we found that epigenetic status in the brain motor cortex is changed after SCI and that epigenetic modulation using ascorbic acid may contribute to functional recovery after SCI.
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Affiliation(s)
- Jin Young Hong
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea; (J.Y.H.); (G.D.)
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea
| | - Ganchimeg Davaa
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea; (J.Y.H.); (G.D.)
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea
| | - Hyunjin Yoo
- Department of Stem Cell & Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea;
| | - Kwonho Hong
- Department of Stem Cell & Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea;
- Correspondence: (K.H.); (J.K.H.); Tel.: +82-10-3678-7189 (K.H.); +81-10-2293-3415 (J.K.H.)
| | - Jung Keun Hyun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea; (J.Y.H.); (G.D.)
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea
- Department of Rehabilitation Medicine, College of Medicine, Dankook University, Cheonan 31116, Korea
- UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan 31116, Korea
- Wiregene, Co., Ltd., Cheonan 31116, Korea
- Correspondence: (K.H.); (J.K.H.); Tel.: +82-10-3678-7189 (K.H.); +81-10-2293-3415 (J.K.H.)
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31
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Mammalian ALKBH1 serves as an N 6-mA demethylase of unpairing DNA. Cell Res 2020; 30:197-210. [PMID: 32051560 PMCID: PMC7054317 DOI: 10.1038/s41422-019-0237-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/30/2019] [Indexed: 01/07/2023] Open
Abstract
N6-methyladenine (N6-mA) of DNA is an emerging epigenetic mark in mammalian genome. Levels of N6-mA undergo drastic fluctuation during early embryogenesis, indicative of active regulation. Here we show that the 2-oxoglutarate-dependent oxygenase ALKBH1 functions as a nuclear eraser of N6-mA in unpairing regions (e.g., SIDD, Stress-Induced DNA Double Helix Destabilization regions) of mammalian genomes. Enzymatic profiling studies revealed that ALKBH1 prefers bubbled or bulged DNAs as substrate, instead of single-stranded (ss-) or double-stranded (ds-) DNAs. Structural studies of ALKBH1 revealed an unexpected "stretch-out" conformation of its "Flip1" motif, a conserved element that usually bends over catalytic center to facilitate substrate base flipping in other DNA demethylases. Thus, lack of a bending "Flip1" explains the observed preference of ALKBH1 for unpairing substrates, in which the flipped N6-mA is primed for catalysis. Co-crystal structural studies of ALKBH1 bound to a 21-mer bulged DNA explained the need of both flanking duplexes and a flipped base for recognition and catalysis. Key elements (e.g., an ALKBH1-specific α1 helix) as well as residues contributing to structural integrity and catalytic activity were validated by structure-based mutagenesis studies. Furthermore, ssDNA-seq and DIP-seq analyses revealed significant co-occurrence of base unpairing regions with N6-mA in mouse genome. Collectively, our biochemical, structural and genomic studies suggest that ALKBH1 is an important DNA demethylase that regulates genome N6-mA turnover of unpairing regions associated with dynamic chromosome regulation.
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32
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Liu ZQ. Bridging free radical chemistry with drug discovery: A promising way for finding novel drugs efficiently. Eur J Med Chem 2019; 189:112020. [PMID: 32006794 DOI: 10.1016/j.ejmech.2019.112020] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/06/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023]
Abstract
Many diseases have been regarded to correlate with the in vivo oxidative damages, which are caused by overproduced free radicals from metabolic process or reactive oxygen species (ROS). This background motivates chemists to explore free radical reactions and to design a number of antioxidants, but whether free radical chemistry can be applied to accelerate the efficacy of the drug discovery is still underrepresented. Herein, in light of recent findings as well as kinetics on free radical reaction, the discipline of free radical chemistry is introduced to be a novel tool for finding potential drugs from antioxidant libraries accumulated during the study on free radical chemistry. These antioxidants provide with such abundant types of structural skeleton that might be employed to inhibit oxidations in different biological microenvironments. Although the in vitro characterization on the antioxidative property exerts a potential role of an antioxidant as a prodrug, the in vivo investigation on the property for quenching free radicals will make a final decision for the antioxidant whether it is worthy to be further explored pharmacologically. Therefore, it is reasonable to expect that bridging free radical chemistry with the pharmacological research will provide with a succinct way for finding novel drugs efficiently.
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Affiliation(s)
- Zai-Qun Liu
- Department of Organic Chemistry, College of Chemistry, Jilin University, No.2519 Jiefang Road, Changchun, 130021, People's Republic of China.
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33
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Li H, Zhu W, Liu Y. Mechanism of Uncoupled Carbocyclization and Epimerization Catalyzed by Two Non-Heme Iron/α-Ketoglutarate Dependent Enzymes. J Chem Inf Model 2019; 59:5086-5098. [PMID: 31790238 DOI: 10.1021/acs.jcim.9b00837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The non-heme iron/α-ketoglutarate dependent enzymes SnoK and SnoN from Streptomyces nogalater are involved in the biosynthesis of anthracycline nogalamycin. Although they have similar active sites, SnoK is responsible for carbocyclization whereas SnoN solely catalyzes the hydroxyl epimerization. Herein, we performed docking, molecular simulations, and a series of combined quantum mechanics and molecular mechanics (QM/MM) calculations to illuminate the mechanisms of two enzymes. The catalytic reactions of two enzymes occur on the quintet state surface. For SnoK, the whole reaction includes two separated hydrogen-abstraction steps and one radical addition, and the latter step is calculated to be rate limiting with an energy barrier of 21.7 kcal/mol. Residue D106 is confirmed to participate in the construction of the hydrogen bond network, which plays a crucial role in positioning the bulky substrate in a specific orientation. Moreover, it is found that SnoN is only responsible for the hydrogen abstraction of the intermediate, and no residue was suggested to be suitable for donating a hydrogen atom to the substrate radical, which further confirms the suggestion based on experiments that either a cellular reductant or another enzyme protein could donate a hydrogen atom to the substrate. Our docking results coincide with the previous structural study that the different roles of two enzymes are achieved by minor changes in the alignment of the substrates in front of the reactive ferryl-oxo species. This work highlights the reaction mechanisms catalyzed by SnoK and SnoN, which is helpful for engineering the enzymes for the biosynthesis of anthracycline nogalamycin.
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Affiliation(s)
- Hong Li
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , China
| | - Wenyou Zhu
- College of Chemistry and Chemical Engineering , Xuzhou Institute of Technology , Xuzhou , Jiangsu 221111 , China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , China
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34
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Bian K, Lenz SAP, Tang Q, Chen F, Qi R, Jost M, Drennan CL, Essigmann JM, Wetmore SD, Li D. DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro. Nucleic Acids Res 2019; 47:5522-5529. [PMID: 31114894 PMCID: PMC6582317 DOI: 10.1093/nar/gkz395] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 01/08/2023] Open
Abstract
5-Methylcytosine (5mC) in DNA CpG islands is an important epigenetic biomarker for mammalian gene regulation. It is oxidized to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) by the ten-eleven translocation (TET) family enzymes, which are α-ketoglutarate (α-KG)/Fe(II)-dependent dioxygenases. In this work, we demonstrate that the epigenetic marker 5mC is modified to 5hmC, 5fC, and 5caC in vitro by another class of α-KG/Fe(II)-dependent proteins—the DNA repair enzymes in the AlkB family, which include ALKBH2, ALKBH3 in huamn and AlkB in Escherichia coli. Theoretical calculations indicate that these enzymes may bind 5mC in the syn-conformation, placing the methyl group comparable to 3-methylcytosine, the prototypic substrate of AlkB. This is the first demonstration of the AlkB proteins to oxidize a methyl group attached to carbon, instead of nitrogen, on a DNA base. These observations suggest a broader role in epigenetics for these DNA repair proteins.
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Affiliation(s)
- Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Fangyi Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Rui Qi
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John M Essigmann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
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35
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Xue J, Lu J, Lai W. Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation versusl-Arg hydroxylation. Phys Chem Chem Phys 2019; 21:9957-9968. [PMID: 31041955 DOI: 10.1039/c9cp00794f] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ethylene-forming enzyme (EFE) is a unique member of the Fe(ii)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases. It converts 2OG into ethylene plus three CO2 molecules (ethylene-forming reaction) and also catalyzes the C5 hydroxylation of l-arginine coupled to the oxidative decarboxylation of 2OG (l-Arg hydroxylation reaction). To uncover the mechanisms of the dual transformations by EFE, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out. Based on the results, a branched mechanism was proposed. An FeII-peroxysuccinate complex with a dissociated CO2 generated through the nucleophilic attack of the superoxo moiety of the Fe-O2 species on the keto carbon of 2OG is the key common intermediate in both reactions. A competition between the subsequent CO2 insertion (a key step in the ethylene-forming pathway) and the O-O bond cleavage (leading to the formation of succinate) governs the product selectivity. The calculated reaction barriers suggested that the CO2 insertion is favored over the O-O bond cleavage. This is consistent with the product preference observed in experiments. By comparison with the results of AsqJ (an Fe/2OG oxygenase that leads to substrate oxidation exclusively), the protein environment was found to be crucial for the selectivity. Further calculations demonstrated that the local electric field of the protein environment in EFE promotes ethylene formation by acting as a charge template, exemplifying the importance of the electrostatic interaction in enzyme catalysis. These findings offer mechanistic insights into the EFE catalysis and provide important clues for better understanding the unique ethylene-forming capability of EFE compared with other Fe/2OG oxygenases.
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Affiliation(s)
- Junqin Xue
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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36
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Moore C, Meng B. Prediction of the molecular boundary and functionality of novel viral AlkB domains using homology modelling and principal component analysis. J Gen Virol 2019; 100:691-703. [PMID: 30835193 DOI: 10.1099/jgv.0.001237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Alkylation B (AlkB) proteins are ubiquitous among diverse cellular organisms, where they act to reverse the damage in DNA and RNA due to methylation, such as 1-methyladenine and 3-methylcytosine. This process is found in virtually all forms of life, with the notable exception of archaea and yeast. This protein family is so significant to all forms of life that it was recently discovered that an AlkB domain is encoded as part of the replicase (poly)protein in a small subset of single-stranded, positive-sense RNA viruses, mainly belonging to the families Alphaflexiviridae, Betaflexiviridae and Closteroviridae. Interestingly, these AlkB-containing viruses are mostly important pathogens of woody perennials such as fruit crops, and are responsible for significant economic losses. As a newly identified protein domain in RNA viruses, the origin and molecular boundary of the viral AlkB domain, as well as its function in viral replication, virus-host interactions and infection are unknown. This is due to the limited sequence conservation of viral AlkB domains, especially at the N-terminal region corresponding to the nucleotide recognition lid. Here we apply several independent analytical approaches (homology modelling, principal component analysis and the Shannon diversity index) for the first time, to better understand this viral domain. We conclude that a functional AlkB domain in these viruses comprises approximately 150-170 amino acids. Although the exact function of the viral AlkB domain remains unknown, we hypothesize that it counteracts a host defence mechanism that is unique in these perennial plants and was acquired to enhance the long-term survival of these RNA viruses that infect perennial plants. Interestingly, a majority of these viruses have a tissue tropism for the phloem. Furthermore, we identified several additional amino acid residues that are uniquely conserved among viral AlkBs. This work helps to provide a foundation for further investigation of the function of viral AlkBs and critical residues involved in AlkB function.
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Affiliation(s)
- Clayton Moore
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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Walport LJ, Schofield CJ. Adventures in Defining Roles of Oxygenases in the Regulation of Protein Biosynthesis. CHEM REC 2018; 18:1760-1781. [PMID: 30151867 DOI: 10.1002/tcr.201800056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022]
Abstract
The 2-oxoglutarate (2OG) dependent oxygenases were first identified as having roles in the post-translational modification of procollagen in animals. Subsequently in plants and microbes, they were shown to have roles in the biosynthesis of many secondary metabolites, including signalling molecules and the penicillin/cephalosporin antibiotics. Crystallographic studies of microbial 2OG oxygenases and related enzymes, coupled to DNA sequence analyses, led to the prediction that 2OG oxygenases are widely distributed in aerobic biology. This personal account begins with examples of the roles of 2OG oxygenases in antibiotic biosynthesis, and then describes efforts to assign functions to other predicted 2OG oxygenases. In humans, 2OG oxygenases have been found to have roles in small molecule metabolism, as well as in the epigenetic regulation of protein and nucleic acid biosynthesis and function. The roles and functions of human 2OG oxygenases are compared, focussing on discussion of their substrate and product selectivities. The account aims to emphasize how scoping the substrate selectivity of, sometimes promiscuous, enzymes can provide insights into their functions and so enable therapeutic work.
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Affiliation(s)
- Louise J Walport
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
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Dunham NP, Mitchell AJ, Del Río Pantoja JM, Krebs C, Bollinger JM, Boal AK. α-Amine Desaturation of d-Arginine by the Iron(II)- and 2-(Oxo)glutarate-Dependent l-Arginine 3-Hydroxylase, VioC. Biochemistry 2018; 57:6479-6488. [PMID: 30403469 DOI: 10.1021/acs.biochem.8b00901] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
When challenged with substrate analogues, iron(II)- and 2-(oxo)glutarate-dependent (Fe/2OG) oxygenases can promote transformations different from those they enact upon their native substrates. We show here that the Fe/2OG enzyme, VioC, which is natively an l-arginine 3-hydroxylase, catalyzes an efficient oxidative deamination of its substrate enantiomer, d-Arg. The reactant complex with d-Arg retains all interactions between enzyme and substrate functional groups, but the required structural adjustments and opposite configuration of C2 position this carbon more optimally than C3 to donate hydrogen (H•) to the ferryl intermediate. The simplest possible mechanism, C2 hydroxylation followed by elimination of ammonia, is inconsistent with the demonstrated solvent origin of the ketone oxygen in the product. Rather, the reaction proceeds via a hydrolytically labile C2-iminium intermediate, demonstrated by its reductive trapping in solution with NaB2H4 to produce racemic [2H]Arg. Of two alternative pathways to the iminium species, C2 hydroxylation followed by dehydration versus direct desaturation, the latter possibility appears to be more likely, because the former mechanism would be expected to result in detectable incorporation of 18O from 18O2. The direct desaturation of a C-N bond implied by this analysis is analogous to that recently posited for the reaction of the l-Arg 4,5-desaturase, NapI, thus lending credence to the prior mechanistic proposal. Such a pathway could also potentially be operant in a subset of reactions catalyzed by Fe/2OG N-demethylases, which have instead been purported to enact C-N bond cleavage by methyl hydroxylation and elimination of formaldehyde.
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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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40
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Cimmino L, Neel BG, Aifantis I. Vitamin C in Stem Cell Reprogramming and Cancer. Trends Cell Biol 2018; 28:698-708. [PMID: 29724526 PMCID: PMC6102081 DOI: 10.1016/j.tcb.2018.04.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/04/2023]
Abstract
Vitamin C is an essential dietary requirement for humans. In addition to its known role as an antioxidant, vitamin C is a cofactor for Fe2+- and α-ketoglutarate-dependent dioxygenases (Fe2+/α-KGDDs) which comprise a large number of diverse enzymes, including collagen prolyl hydroxylases and epigenetic regulators of histone and DNA methylation. Vitamin C can modulate embryonic stem cell (ESC) function, enhance reprogramming of fibroblasts to induced pluripotent stem cells (iPSCs), and hinder the aberrant self-renewal of hematopoietic stem cells (HSCs) through its ability to enhance the activity of either Jumonji C (JmjC) domain-containing histone demethylases or ten-eleven translocation (TET) DNA hydroxylases. Given that epigenetic dysregulation is a known driver of malignancy, vitamin C may play a novel role as an epigenetic anticancer agent.
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Affiliation(s)
- Luisa Cimmino
- Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA.,Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA.,To Whom Correspondence Should Be Addressed: Luisa Cimmino, Ph.D. or Iannis Aifantis, Ph.D. Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine 521 First Avenue, Smilow 1303 New York, NY 10016 or
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA.,Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA.,To Whom Correspondence Should Be Addressed: Luisa Cimmino, Ph.D. or Iannis Aifantis, Ph.D. Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine 521 First Avenue, Smilow 1303 New York, NY 10016 or
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41
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Mohan M, Pandya V, Anindya R. Escherichia coli AlkB and single-stranded DNA binding protein SSB interaction explored by Molecular Dynamics Simulation. J Mol Graph Model 2018; 84:29-35. [DOI: 10.1016/j.jmgm.2018.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/30/2018] [Accepted: 05/16/2018] [Indexed: 12/15/2022]
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Wang R, Leung PYM, Huang F, Tang Q, Kaneko T, Huang M, Li Z, Li SSC, Wang Y, Xia J. Reverse Binding Mode of Phosphotyrosine Peptides with SH2 Protein. Biochemistry 2018; 57:5257-5269. [PMID: 30091902 DOI: 10.1021/acs.biochem.8b00677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Discerning the different interaction states during dynamic protein-ligand binding is difficult. Here we apply site-specific cysteine-α-chloroacetyl cross-linking to scrutinize the binding between the Src homology 2 (SH2) domain and phosphotyrosine (pY) peptides, a highly dynamic interaction that is a key to cellular signal transduction. From a model SH2 protein to a set of representative SH2 domains, we showed here that a proximity-induced cysteine-α-chloroacetyl reaction cross-linked two spatially adjacent chemical groups as a result of the binding interaction, and reciprocally, the information about the interaction states can be deduced from the cross-linked products. To our surprise, we found SH2 domains can adopt a reverse binding mode with "single-pronged", "two-pronged", and "half" pY peptides. This finding was further supported by a set of 500 ns molecular dynamics simulations. This serendipitous finding defies the canonical theory of SH2 binding, suggests a possible answer about the source of the versatility of SH2 signaling, and sets a model for other protein binding interactions.
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Affiliation(s)
- Rui Wang
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | | | | | | | - Tomonori Kaneko
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | - Mei Huang
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | - Zigang Li
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China
| | - Shawn S C Li
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
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43
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Huyet J, Ozeir M, Burgevin MC, Pinson B, Chesney F, Remy JM, Siddiqi AR, Lupoli R, Pinon G, Saint-Marc C, Gibert JF, Morales R, Ceballos-Picot I, Barouki R, Daignan-Fornier B, Olivier-Bandini A, Augé F, Nioche P. Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase. Cell Chem Biol 2018; 25:666-676.e4. [PMID: 29576532 DOI: 10.1016/j.chembiol.2018.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 01/05/2018] [Accepted: 02/22/2018] [Indexed: 10/17/2022]
Abstract
Phosphoribosyltransferases catalyze the displacement of a PRPP α-1'-pyrophosphate to a nitrogen-containing nucleobase. How they control the balance of substrates/products binding and activities is poorly understood. Here, we investigated the human adenine phosphoribosyltransferase (hAPRT) that produces AMP in the purine salvage pathway. We show that a single oxygen atom from the Tyr105 side chain is responsible for selecting the active conformation of the 12 amino acid long catalytic loop. Using in vitro, cellular, and in crystallo approaches, we demonstrated that Tyr105 is key for the fine-tuning of the kinetic activity efficiencies of the forward and reverse reactions. Together, our results reveal an evolutionary pressure on the strictly conserved Tyr105 and on the dynamic motion of the flexible loop in phosphoribosyltransferases that is essential for purine biosynthesis in cells. These data also provide the framework for designing novel adenine derivatives that could modulate, through hAPRT, diseases-involved cellular pathways.
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Affiliation(s)
- Jessica Huyet
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France
| | - Mohammad Ozeir
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France
| | | | - Benoît Pinson
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | - Françoise Chesney
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Jean-Marc Remy
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Roland Lupoli
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France
| | - Gregory Pinon
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France
| | - Christelle Saint-Marc
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | | | - Renaud Morales
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Irène Ceballos-Picot
- Laboratoire de Biochimie Métabolomique et Protéomique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Paris Descartes, Paris 75015, France
| | - Robert Barouki
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Laboratoire de Biochimie Métabolomique et Protéomique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Paris Descartes, Paris 75015, France
| | - Bertrand Daignan-Fornier
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | | | - Franck Augé
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France.
| | - Pierre Nioche
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France.
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44
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Wilkins SE, Islam MS, Gannon JM, Markolovic S, Hopkinson RJ, Ge W, Schofield CJ, Chowdhury R. JMJD5 is a human arginyl C-3 hydroxylase. Nat Commun 2018; 9:1180. [PMID: 29563586 PMCID: PMC5862942 DOI: 10.1038/s41467-018-03410-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 02/12/2018] [Indexed: 12/21/2022] Open
Abstract
Oxygenase-catalysed post-translational modifications of basic protein residues, including lysyl hydroxylations and Nε-methyl lysyl demethylations, have important cellular roles. Jumonji-C (JmjC) domain-containing protein 5 (JMJD5), which genetic studies reveal is essential in animal development, is reported as a histone Nε-methyl lysine demethylase (KDM). Here we report how extensive screening with peptides based on JMJD5 interacting proteins led to the finding that JMJD5 catalyses stereoselective C-3 hydroxylation of arginine residues in sequences from human regulator of chromosome condensation domain-containing protein 1 (RCCD1) and ribosomal protein S6 (RPS6). High-resolution crystallographic analyses reveal overall fold, active site and substrate binding/product release features supporting the assignment of JMJD5 as an arginine hydroxylase rather than a KDM. The results will be useful in the development of selective oxygenase inhibitors for the treatment of cancer and genetic diseases.
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Affiliation(s)
- Sarah E Wilkins
- The Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Md Saiful Islam
- The Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Joan M Gannon
- The Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Suzana Markolovic
- The Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Richard J Hopkinson
- The Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
- Leicester Institute of Structural and Chemical Biology and Department of Chemistry, University of Leicester, Lancaster Road, Leicester, LE1 7RH, UK
| | - Wei Ge
- The Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | | | - Rasheduzzaman Chowdhury
- The Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
- Stanford University School of Medicine, Department of Molecular and Cellular Physiology, Clark Center, Stanford, CA, 94305-5345, USA.
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45
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Song X, Lu J, Lai W. Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations. Phys Chem Chem Phys 2018; 19:20188-20197. [PMID: 28726913 DOI: 10.1039/c7cp02687k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the mechanism of dioxygen activation, oxygen atom exchange and substrate epoxidation processes by AsqJ, an FeII/α-ketoglutarate-dependent dioxygenase (α-KGD) using a 2-His-1-Asp facial triad. Our results demonstrated that the whole reaction proceeds through a quintet surface. The dioxygen activation by AsqJ leads to a quintet penta-coordinated FeIV-oxo species, which has a square pyramidal geometry with the oxo group trans to His134. This penta-coordinated FeIV-oxo species is not the reactive one in the substrate epoxidation reaction since its oxo group is pointing away from the target C[double bond, length as m-dash]C bond. Instead, it can undergo the oxo group isomerization followed by water binding or the water binding followed by oxygen atom exchange to form the reactive hexa-coordinated FeIV-oxo species with the oxo group trans to His211. The calculated parameters of Mössbauer spectra for this hexa-coordinated FeIV-oxo intermediate are in excellent agreement with the experimental values, suggesting that it is most likely the experimentally trapped species. The calculated energetics indicated that the rate-limiting step is the substrate C[double bond, length as m-dash]C bond activation. This work improves our understanding of the dioxygen activation by α-KGD and provides important structural information about the reactive FeIV-oxo species.
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Affiliation(s)
- Xudan Song
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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46
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Jayanth N, Ogirala N, Yadav A, Puranik M. Structural basis for substrate discrimination by E. colirepair enzyme, AlkB. RSC Adv 2018; 8:1281-1291. [PMID: 35540905 PMCID: PMC9076979 DOI: 10.1039/c7ra11333a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 11/14/2017] [Indexed: 11/21/2022] Open
Abstract
Positive charge on methylated nucleotides is a prime criterion for substrate recognition byE. coliAlkB.
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Affiliation(s)
- Namrata Jayanth
- National Centre for Biological Sciences
- Tata Institute of Fundamental Research
- GKVK Campus
- Bangalore 560065
- India
| | - Nirmala Ogirala
- National Centre for Biological Sciences
- Tata Institute of Fundamental Research
- GKVK Campus
- Bangalore 560065
- India
| | - Anil Yadav
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
| | - Mrinalini Puranik
- National Centre for Biological Sciences
- Tata Institute of Fundamental Research
- GKVK Campus
- Bangalore 560065
- India
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47
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Martinie RJ, Pollock CJ, Matthews ML, Bollinger JM, Krebs C, Silakov A. Vanadyl as a Stable Structural Mimic of Reactive Ferryl Intermediates in Mononuclear Nonheme-Iron Enzymes. Inorg Chem 2017; 56:13382-13389. [PMID: 28960972 DOI: 10.1021/acs.inorgchem.7b02113] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The iron(II)- and 2-(oxo)glutarate-dependent (Fe/2OG) oxygenases catalyze an array of challenging transformations via a common iron(IV)-oxo (ferryl) intermediate, which in most cases abstracts hydrogen (H•) from an aliphatic carbon of the substrate. Although it has been shown that the relative disposition of the Fe-O and C-H bonds can control the rate of H• abstraction and fate of the resultant substrate radical, there remains a paucity of structural information on the actual ferryl states, owing to their high reactivity. We demonstrate here that the stable vanadyl ion [(VIV-oxo)2+] binds along with 2OG or its decarboxylation product, succinate, in the active site of two different Fe/2OG enzymes to faithfully mimic their transient ferryl states. Both ferryl and vanadyl complexes of the Fe/2OG halogenase, SyrB2, remain stably bound to its carrier protein substrate (l-aminoacyl-S-SyrB1), whereas the corresponding complexes harboring transition metals (Fe, Mn) in lower oxidation states dissociate. In the well-studied taurine:2OG dioxygenase (TauD), the disposition of the substrate C-H bond relative to the vanadyl ion defined by pulse electron paramagnetic resonance methods is consistent with the crystal structure of the reactant complex and computational models of the ferryl state. Vanadyl substitution may thus afford access to structural details of the key ferryl intermediates in this important enzyme class.
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Affiliation(s)
| | | | - Megan L Matthews
- Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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48
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Chaim IA, Gardner A, Wu J, Iyama T, Wilson DM, Samson LD. A novel role for transcription-coupled nucleotide excision repair for the in vivo repair of 3,N4-ethenocytosine. Nucleic Acids Res 2017; 45:3242-3252. [PMID: 28115629 PMCID: PMC5389632 DOI: 10.1093/nar/gkx015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/20/2017] [Indexed: 12/13/2022] Open
Abstract
Etheno (ε) DNA base adducts are highly mutagenic lesions produced endogenously via reactions with lipid peroxidation (LPO) products. Cancer-promoting conditions, such as inflammation, can induce persistent oxidative stress and increased LPO, resulting in the accumulation of ε-adducts in different tissues. Using a recently described fluorescence multiplexed host cell reactivation assay, we show that a plasmid reporter bearing a site-specific 3,N4-ethenocytosine (εC) causes transcriptional blockage. Notably, this blockage is exacerbated in Cockayne Syndrome and xeroderma pigmentosum patient-derived lymphoblastoid and fibroblast cells. Parallel RNA-Seq expression analysis of the plasmid reporter identifies novel transcriptional mutagenesis properties of εC. Our studies reveal that beyond the known pathways, such as base excision repair, the process of transcription-coupled nucleotide excision repair plays a role in the removal of εC from the genome, and thus in the protection of cells and tissues from collateral damage induced by inflammatory responses.
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Affiliation(s)
- Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alycia Gardner
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jie Wu
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility in the Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Teruaki Iyama
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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49
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Ignatov A, Bondarenko K, Makarova A. Non-bulky Lesions in Human DNA: the Ways of Formation, Repair, and Replication. Acta Naturae 2017; 9:12-26. [PMID: 29104772 PMCID: PMC5662270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 11/06/2022] Open
Abstract
DNA damage is a major cause of replication interruption, mutations, and cell death. DNA damage is removed by several types of repair processes. The involvement of specialized DNA polymerases in replication provides an important mechanism that helps tolerate persistent DNA damage. Specialized DNA polymerases incorporate nucleotides opposite lesions with high efficiency but demonstrate low accuracy of DNA synthesis. In this review, we summarize the types and mechanisms of formation and repair of non-bulky DNA lesions, and we provide an overview of the role of specialized DNA polymerases in translesion DNA synthesis.
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Affiliation(s)
- A.V. Ignatov
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
- Department of Molecular Biology, Faculty of Biology, Moscow State University, Leninskie Gory 1, bldg. 12, Moscow, 119991, Russia
| | - K.A. Bondarenko
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
| | - A.V. Makarova
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
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Qiao QA, Li Q, Liu C, Sun X, Cai H, Sun L, Wang H. A Theoretical Study on the Mechanism of Decarboxylations for Hydroxymandelate Synthase. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Qing-An Qiao
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Qiuxian Li
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Changchun Liu
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Xiao Sun
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Honglan Cai
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Lixiang Sun
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Huayang Wang
- School of Physics and Optoelectronic Engineering; Ludong University; Yantai 264025 China
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