1
|
Campbell M, Barton IS, Roop RM, Chien P. Comparison of CcrM-dependent methylation in Caulobacter crescentus and Brucella abortus by nanopore sequencing. J Bacteriol 2024; 206:e0008324. [PMID: 38722176 PMCID: PMC11332171 DOI: 10.1128/jb.00083-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/05/2024] [Indexed: 05/21/2024] Open
Abstract
Bacteria rely on DNA methylation for restriction-modification systems and epigenetic control of gene expression. Here, we use direct detection of methylated bases by nanopore sequencing to monitor global DNA methylation in Alphaproteobacteria, where use of this technique has not yet been reported. One representative of this order, Caulobacter crescentus, relies on DNA methylation to control cell cycle progression, but it is unclear whether other members of this order, such as Brucella abortus, depend on the same systems. We addressed these questions by first measuring CcrM-dependent DNA methylation in Caulobacter and showing excellent correlation between nanopore-based detection and previously published results. We then directly measure the impact of Lon-mediated CcrM degradation on the epigenome, verifying that loss of Lon results in pervasive methylation. We also show that the AlkB demethylase has no global impact on DNA methylation during normal growth. Next, we report on the global DNA methylation in B. abortus for the first time and find that CcrM-dependent methylation is reliant on Lon but impacts the two chromosomes differently. Finally, we explore the impact of the MucR transcription factor, known to compete with CcrM methylation, on the Brucella methylome and share the results with a publicly available visualization package. Our work demonstrates the utility of nanopore-based sequencing for epigenome measurements in Alphaproteobacteria and reveals new features of CcrM-dependent methylation in a zoonotic pathogen.IMPORTANCEDNA methylation plays an important role in bacteria, maintaining genome integrity and regulating gene expression. We used nanopore sequencing to directly measure methylated bases in Caulobacter crescentus and Brucella abortus. In Caulobacter, we showed that stabilization of the CcrM methyltransferase upon loss of the Lon protease results in prolific methylation and discovered that the putative methylase AlkB is unlikely to have a global physiological effect. We measured genome-wide methylation in Brucella for the first time, revealing a similar role for CcrM in cell-cycle methylation but a more complex regulation by the Lon protease than in Caulobacter. Finally, we show how the virulence factor MucR impacts DNA methylation patterns in Brucella.
Collapse
Affiliation(s)
- Maxwell Campbell
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Ian Scott Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, South Carolina, USA
| | - R. Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, South Carolina, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Xiong L, Li F, Guo Y, Zhang J, Xu K, Xiong Z, Tong A, Li L, Yang S. Discovery of a Potent and Cell-Active Inhibitor of DNA 6mA Demethylase ALKBH1. J Am Chem Soc 2024; 146:6992-7006. [PMID: 38437718 DOI: 10.1021/jacs.4c00194] [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: 03/06/2024]
Abstract
N6-Methyladenine (6mA) of DNA has emerged as a novel epigenetic mark in eukaryotes, and several 6mA effector proteins have been identified. However, efforts to selectively inhibit the biological functions of these effector proteins with small molecules are unsuccessful to date. Here we report the first potent and selective small molecule inhibitor (13h) of AlkB homologue 1 (ALKBH1), the only validated 6mA demethylase. 13h showed an IC50 of 0.026 ± 0.013 μM and 1.39 ± 0.13 μM in the fluorescence polarization (FP) and enzyme activity assay, respectively, and a KD of 0.112 ± 0.017 μM in the isothermal titration calorimetry (ITC) assay. The potency of 13h was well explained by the cocrystal structure of the 13h-ALKBH1 complex. Furthermore, 13h displayed excellent selectivity for ALKBH1. In cells, compound 13h and its derivative 16 were able to engage ALKBH1 and modulate the 6mA levels. Collectively, our study identified the first potent, isoform selective, and cell-active ALKBH1 inhibitor, providing a tool compound for exploring the biological functions of ALKBH1 and DNA 6mA.
Collapse
Affiliation(s)
- Liang Xiong
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Feng Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yinping Guo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jian Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ke Xu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zijie Xiong
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Aiping Tong
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengyong Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| |
Collapse
|
4
|
Campbell M, Barton IS, Roop RM, Chien P. Comparison of CcrM-dependent methylation in Caulobacter crescentus and Brucella abortus by nanopore sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.583015. [PMID: 38464217 PMCID: PMC10925313 DOI: 10.1101/2024.03.01.583015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Bacteria rely on DNA methylation for restriction-modification systems and epigenetic control of gene expression. Here, we use direct detection of methylated bases by nanopore sequencing to monitor global DNA methylation in Alphaproteobacteria, where use of this technique has not yet been reported. One representative of this order, Caulobacter crescentus, relies on DNA methylation to control cell cycle progression, but it is unclear whether other members of this order, such as Brucella abortus, depend on the same systems. We addressed these questions by first measuring CcrM-dependent DNA methylation in Caulobacter and show excellent correlation between nanopore-based detection and previously published results. We then directly measure the impact of Lon-mediated CcrM degradation on the epigenome, verifying that loss of Lon results in pervasive methylation. We also show that the AlkB demethylase has no global impact on DNA methylation during normal growth. Next, we report on the global DNA methylation in Brucella abortus for the first time and find that CcrM-dependent methylation is reliant on Lon but impacts the two chromosomes differently. Finally, we explore the impact of the MucR transcription factor, known to compete with CcrM methylation, on the Brucella methylome and share the results with a publicly available visualization package. Our work demonstrates the utility of nanopore-based sequencing for epigenome measurements in Alphaproteobacteria and reveals new features of CcrM-dependent methylation in a zoonotic pathogen.
Collapse
Affiliation(s)
- Maxwell Campbell
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA
| | - Ian Scott Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC
| | - R. Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA
| |
Collapse
|
5
|
Peng Z, Ma J, Christov CZ, Karabencheva-Christova T, Lehnert N, Li D. Kinetic Studies on the 2-Oxoglutarate/Fe(II)-Dependent Nucleic Acid Modifying Enzymes from the AlkB and TET Families. DNA 2023; 3:65-84. [PMID: 38698914 PMCID: PMC11065319 DOI: 10.3390/dna3020005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Nucleic acid methylations are important genetic and epigenetic biomarkers. The formation and removal of these markers is related to either methylation or demethylation. In this review, we focus on the demethylation or oxidative modification that is mediated by the 2-oxoglutarate (2-OG)/Fe(II)-dependent AlkB/TET family enzymes. In the catalytic process, most enzymes oxidize 2-OG to succinate, in the meantime oxidizing methyl to hydroxymethyl, leaving formaldehyde and generating demethylated base. The AlkB enzyme from Escherichia coli has nine human homologs (ALKBH1-8 and FTO) and the TET family includes three members, TET1 to 3. Among them, some enzymes have been carefully studied, but for certain enzymes, few studies have been carried out. This review focuses on the kinetic properties of those 2-OG/Fe(II)-dependent enzymes and their alkyl substrates. We also provide some discussions on the future directions of this field.
Collapse
Affiliation(s)
- Zhiyuan Peng
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Jian Ma
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA
| | | | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| |
Collapse
|
6
|
Fahrer J, Christmann M. DNA Alkylation Damage by Nitrosamines and Relevant DNA Repair Pathways. Int J Mol Sci 2023; 24:ijms24054684. [PMID: 36902118 PMCID: PMC10003415 DOI: 10.3390/ijms24054684] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/17/2023] [Accepted: 02/24/2023] [Indexed: 03/04/2023] Open
Abstract
Nitrosamines occur widespread in food, drinking water, cosmetics, as well as tobacco smoke and can arise endogenously. More recently, nitrosamines have been detected as impurities in various drugs. This is of particular concern as nitrosamines are alkylating agents that are genotoxic and carcinogenic. We first summarize the current knowledge on the different sources and chemical nature of alkylating agents with a focus on relevant nitrosamines. Subsequently, we present the major DNA alkylation adducts induced by nitrosamines upon their metabolic activation by CYP450 monooxygenases. We then describe the DNA repair pathways engaged by the various DNA alkylation adducts, which include base excision repair, direct damage reversal by MGMT and ALKBH, as well as nucleotide excision repair. Their roles in the protection against the genotoxic and carcinogenic effects of nitrosamines are highlighted. Finally, we address DNA translesion synthesis as a DNA damage tolerance mechanism relevant to DNA alkylation adducts.
Collapse
Affiliation(s)
- Jörg Fahrer
- Division of Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Erwin-Schrödinger Strasse 52, D-67663 Kaiserslautern, Germany
- Correspondence: (J.F.); (M.C.); Tel.: +496312052974 (J.F.); Tel: +496131179066 (M.C.)
| | - Markus Christmann
- Department of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany
- Correspondence: (J.F.); (M.C.); Tel.: +496312052974 (J.F.); Tel: +496131179066 (M.C.)
| |
Collapse
|
7
|
Zhu W, Wang H, Li X, Tie W, Huo B, Zhu A, Li L. Amplification, Enrichment, and Sequencing of Mutagenic Methylated DNA Adduct through Specifically Pairing with Unnatural Nucleobases. J Am Chem Soc 2022; 144:20165-20170. [DOI: 10.1021/jacs.2c06110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wuyuan Zhu
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
- State Key Laboratory of Cell Differentiation Regulation and Target Drug, Henan Normal University, Xinxiang 453007, China
| | - Honglei Wang
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xiaohuan Li
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
| | - Wenchao Tie
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
| | - Bianbian Huo
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
| | - Anlian Zhu
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
| | - Lingjun Li
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
- State Key Laboratory of Cell Differentiation Regulation and Target Drug, Henan Normal University, Xinxiang 453007, China
| |
Collapse
|
8
|
Yang Y, Wang Z, Wang J, Dai X, You C. Next-Generation Sequencing-Based Analysis of the Effects of N1- and N6-Methyldeoxyadenosine Adducts on DNA Transcription. Anal Chem 2022; 94:11248-11254. [PMID: 35924299 DOI: 10.1021/acs.analchem.2c01764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA methylation can occur naturally or be induced by various environmental and chemotherapeutic agents. The regioisomeric N1- and N6-methyldeoxyadenosine (1mdA and 6mdA, respectively) represent an important class of methylated DNA adducts. In this study, we developed a shuttle vector- and next-generation sequencing-based assay to quantitatively assess the effects of 1mdA and 6mdA on the accuracy and efficiency of DNA transcription. Our results revealed that 1mdA can induce multiple types of mutant transcripts and strongly inhibit DNA transcription, whereas 6mdA is a nonmutagenic DNA adduct that can exhibit a subtle but significant inhibitory effect on DNA transcription in vitro and in human cells. Moreover, our results demonstrated that the transcription-coupled nucleotide excision repair pathway is dispensable for the removal of 1mdA and 6mdA from the template DNA strand in human cells. These findings provided new important insights into the functional interplay between DNA methylation modifications and transcription in mammalian cells.
Collapse
Affiliation(s)
- Ying Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Ziyu Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Juan Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xiaoxia Dai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Changjun You
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| |
Collapse
|
9
|
Liu H, Zeng T, He C, Rawal VH, Zhou H, Dickinson BC. Development of Mild Chemical Catalysis Conditions for m 1A-to-m 6A Rearrangement on RNA. ACS Chem Biol 2022; 17:1334-1342. [PMID: 35593877 DOI: 10.1021/acschembio.2c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conversion of N1-methyladenosine (m1A) to N6-methyladenosine (m6A) on RNA is an important step for both allowing efficient reverse transcription read-though for sequencing analysis and mapping modifications in the transcriptome. Enzymatic transformation is often used, but the efficiency of the removal can depend on local sequence context. Chemical conversion through the application of the Dimroth rearrangement, in which m1A rearranges into m6A under heat and alkaline conditions, is an alternative, but the required alkaline conditions result in significant RNA degradation by hydrolysis of the phosphodiester backbone. Here, we report novel, mild pH conditions that catalyze m1A-to-m6A arrangement using 4-nitrothiophenol as a catalyst. We demonstrate the efficient rearrangement in mononucleosides, synthetic RNA oligonucleotides, and RNAs isolated from human cell lines, thereby validating a new approach for converting m1A-to-m6A in RNA samples for sequencing analyses.
Collapse
Affiliation(s)
- Huachun Liu
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Tony Zeng
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Viresh H. Rawal
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Huiqing Zhou
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
10
|
Sun J, Antczak NM, Gahlon HL, Sturla SJ. Molecular beacons with oxidized bases report on substrate specificity of DNA oxoguanine glycosylases. Chem Sci 2022; 13:4295-4302. [PMID: 35509469 PMCID: PMC9007065 DOI: 10.1039/d1sc05648d] [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: 10/13/2021] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
DNA glycosylase enzymes recognize and remove structurally distinct modified forms of DNA bases, thereby repairing genomic DNA from chemically induced damage or erasing epigenetic marks. However, these enzymes are often promiscuous, and advanced tools are needed to evaluate and engineer their substrate specificity. Thus, in the present study, we developed a new strategy to rapidly profile the substrate specificity of 8-oxoguanine glycosylases, which cleave biologically relevant oxidized forms of guanine. We monitored the enzymatic excision of fluorophore-labeled oligonucleotides containing synthetic modifications 8-oxoG and FapyG, or G. Using this molecular beacon approach, we identified several hOGG1 mutants with higher specificity for FapyG than 8-oxoG. This approach and the newly synthesized probes will be useful for the characterization of glycosylase substrate specificity and damage excision mechanisms, as well as for evaluating engineered enzymes with altered reactivities.
Collapse
Affiliation(s)
- Jingjing Sun
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
- Department of Biological Engineering, Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Nicole M Antczak
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
- Department of Chemistry, Skidmore College 815 North Broadway Saratoga Springs NY 12866 USA
| | - Hailey L Gahlon
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
| |
Collapse
|
11
|
Chen J, Chen J, Wang S, Bao X, Li S, Wei B, Zhang H, Wang H. Amycolachromones A–F, Isolated from a Streptomycin-Resistant Strain of the Deep-Sea Marine Actinomycete Amycolatopsis sp. WP1. Mar Drugs 2022; 20:md20030162. [PMID: 35323461 PMCID: PMC8949813 DOI: 10.3390/md20030162] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023] Open
Abstract
In this study, a detailed chemical investigation of a streptomycin-resistant strain of the deep-sea marine, actinomycete Amycolatopsis sp. WP1, yielded six novel amycolachromones A–F (1–6), together with five known analogues (7–11). Amycolachromones A–B (1–2) possessed unique dimer skeletons. The structures and relative configurations of compounds 1–11 were elucidated by extensive spectroscopic data analyses combined with X-ray crystal diffraction analysis. Plausible biogenetic pathways of amycolachromones A–F were also proposed.
Collapse
Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (J.C.); (S.W.); (X.B.); (S.L.); (B.W.); (H.Z.)
| | - Jun Chen
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an 237499, China;
| | - Siqi Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (J.C.); (S.W.); (X.B.); (S.L.); (B.W.); (H.Z.)
| | - Xiaoze Bao
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (J.C.); (S.W.); (X.B.); (S.L.); (B.W.); (H.Z.)
| | - Songwei Li
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (J.C.); (S.W.); (X.B.); (S.L.); (B.W.); (H.Z.)
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (J.C.); (S.W.); (X.B.); (S.L.); (B.W.); (H.Z.)
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (J.C.); (S.W.); (X.B.); (S.L.); (B.W.); (H.Z.)
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (J.C.); (S.W.); (X.B.); (S.L.); (B.W.); (H.Z.)
- Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou 310014, China
- Correspondence: ; Tel.: +86-0571-8832-0622
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Qi R, Bian K, Chen F, Tang Q, Zhou X, Li D. Sequence Dependent Repair of 1, N6-Ethenoadenine by DNA Repair Enzymes ALKBH2, ALKBH3, and AlkB. Molecules 2021; 26:molecules26175285. [PMID: 34500720 PMCID: PMC8434105 DOI: 10.3390/molecules26175285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/17/2021] [Accepted: 08/25/2021] [Indexed: 11/16/2022] Open
Abstract
Mutation patterns of DNA adducts, such as mutational spectra and signatures, are useful tools for diagnostic and prognostic purposes. Mutational spectra of carcinogens derive from three sources: adduct formation, replication bypass, and repair. Here, we consider the repair aspect of 1,N6-ethenoadenine (εA) by the 2-oxoglutarate/Fe(II)-dependent AlkB family enzymes. Specifically, we investigated εA repair across 16 possible sequence contexts (5'/3' flanking base to εA varied as G/A/T/C). The results revealed that repair efficiency is altered according to sequence, enzyme, and strand context (ss- versus ds-DNA). The methods can be used to study other aspects of mutational spectra or other pathways of repair.
Collapse
|
14
|
Huang R, Zhou PK. DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy. Signal Transduct Target Ther 2021; 6:254. [PMID: 34238917 PMCID: PMC8266832 DOI: 10.1038/s41392-021-00648-7] [Citation(s) in RCA: 262] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/28/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Genomic instability is the hallmark of various cancers with the increasing accumulation of DNA damage. The application of radiotherapy and chemotherapy in cancer treatment is typically based on this property of cancers. However, the adverse effects including normal tissues injury are also accompanied by the radiotherapy and chemotherapy. Targeted cancer therapy has the potential to suppress cancer cells' DNA damage response through tailoring therapy to cancer patients lacking specific DNA damage response functions. Obviously, understanding the broader role of DNA damage repair in cancers has became a basic and attractive strategy for targeted cancer therapy, in particular, raising novel hypothesis or theory in this field on the basis of previous scientists' findings would be important for future promising druggable emerging targets. In this review, we first illustrate the timeline steps for the understanding the roles of DNA damage repair in the promotion of cancer and cancer therapy developed, then we summarize the mechanisms regarding DNA damage repair associated with targeted cancer therapy, highlighting the specific proteins behind targeting DNA damage repair that initiate functioning abnormally duo to extrinsic harm by environmental DNA damage factors, also, the DNA damage baseline drift leads to the harmful intrinsic targeted cancer therapy. In addition, clinical therapeutic drugs for DNA damage and repair including therapeutic effects, as well as the strategy and scheme of relative clinical trials were intensive discussed. Based on this background, we suggest two hypotheses, namely "environmental gear selection" to describe DNA damage repair pathway evolution, and "DNA damage baseline drift", which may play a magnified role in mediating repair during cancer treatment. This two new hypothesis would shed new light on targeted cancer therapy, provide a much better or more comprehensive holistic view and also promote the development of new research direction and new overcoming strategies for patients.
Collapse
Affiliation(s)
- Ruixue Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China.
| |
Collapse
|
15
|
Warren JM, Sloan DB. Hopeful monsters: unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense-antisense pairs. NAR Genom Bioinform 2021; 3:lqaa111. [PMID: 33575653 PMCID: PMC7803006 DOI: 10.1093/nargab/lqaa111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
Although tRNA structure is one of the most conserved and recognizable shapes in molecular biology, aberrant tRNAs are frequently found in the mitochondrial genomes of metazoans. The extremely degenerate structures of several mitochondrial tRNAs (mt-tRNAs) have led to doubts about their expression and function. Mites from the arachnid superorder Acariformes are predicted to have some of the shortest mt-tRNAs, with a complete loss of cloverleaf-like shape. While performing mitochondrial isolations and recently developed tRNA-seq methods in plant tissue, we inadvertently sequenced the mt-tRNAs from a common plant pest, the acariform mite Tetranychus urticae, to a high enough coverage to detect all previously annotated T. urticae tRNA regions. The results not only confirm expression, CCA-tailing and post-transcriptional base modification of these highly divergent tRNAs, but also revealed paired sense and antisense expression of multiple T. urticae mt-tRNAs. Mirrored expression of mt-tRNA genes has been hypothesized but not previously demonstrated to be common in any system. We discuss the functional roles that these divergent tRNAs could have as both decoding molecules in translation and processing signals in transcript maturation pathways, as well as how sense–antisense pairs add another dimension to the bizarre tRNA biology of mitochondrial genomes.
Collapse
Affiliation(s)
- Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO, 80521 USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80521 USA
| |
Collapse
|
16
|
Warren JM, Salinas-Giegé T, Hummel G, Coots NL, Svendsen JM, Brown KC, Drouard L, Sloan DB. Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification. RNA Biol 2021; 18:64-78. [PMID: 32715941 PMCID: PMC7834048 DOI: 10.1080/15476286.2020.1792089] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in Arabidopsis thaliana, which exhibited many anciently conserved similarities with humans but also positions that appear to be 'hot spots' for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.
Collapse
Affiliation(s)
- Jessica M. Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Thalia Salinas-Giegé
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Guillaume Hummel
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Nicole L. Coots
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Kristen C. Brown
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Laurence Drouard
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
17
|
Ke B, Ye K, Cheng S. ALKBH2 inhibition alleviates malignancy in colorectal cancer by regulating BMI1-mediated activation of NF-κB pathway. World J Surg Oncol 2020; 18:328. [PMID: 33302959 PMCID: PMC7731553 DOI: 10.1186/s12957-020-02106-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/02/2020] [Indexed: 01/23/2023] Open
Abstract
Background The alkB homolog 2, alpha-ketoglutarate-dependent dioxygenase (ALKBH2) gene is involved in DNA repair and is expressed in different types of malignancies. However, the role of ALKBH2 in colorectal carcinoma (CRC) remains unclear. This study aimed to explore the potential mechanism of ALKBH2 and its function in CRC. Methods The expression levels of ALKBH2 in CRC tissues and cells were determined by qRT-PCR. Following that, the role of ALKBH2 in cell proliferation, invasion, and epithelial-mesenchymal transition (EMT) in CRC cells (Caco-2 and LOVO) were assessed by Cell Counting Kit-8 (CCK-8), transwell assays, and Western blotting, respectively. The effect of ALKBH2 on B cell-specific Moloney murine leukemia virus integration site 1 (BMI1) and downstream NF-κB pathway was determined by Western blotting and luciferase reporter assay. Results The expression of ALKBH2 was significantly upregulated both in CRC tissues and cells. Further experiments demonstrated that reduction of ALKBH2 suppressed Caco-2 and LOVO cell proliferation and invasion. Moreover, ALKBH2 knockdown also suppressed EMT, which increased E-cadherin expression and reduced N-cadherin expression. Besides, ALKBH2 silencing inhibited BMI1 expression and reduced nuclear accumulation of the NF-κB p65 protein, as well as the luciferase activity of NF-κB p65. Upregulation of BMI1 reversed the effect of ALKBH2 knockdown on the proliferation and invasion in CRC cells. Conclusions Our findings suggest that suppression of ALKBH2 alleviates malignancy in CRC by regulating BMI1-mediated activation of NF-κB pathway. ALKBH2 may serve as a potential treatment target for human CRC.
Collapse
Affiliation(s)
- Bingxin Ke
- Department of Colorectal Surgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79, Qingchun Road, Xiacheng District, Hangzhou City, 310003, Zhejiang Province, China.
| | - Kejun Ye
- Department of Colorectal Surgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79, Qingchun Road, Xiacheng District, Hangzhou City, 310003, Zhejiang Province, China
| | - Shaobing Cheng
- Department of Colorectal Surgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79, Qingchun Road, Xiacheng District, Hangzhou City, 310003, Zhejiang Province, China
| |
Collapse
|
18
|
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.
Collapse
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.
| |
Collapse
|
19
|
Xiao MZ, Liu JM, Xian CL, Chen KY, Liu ZQ, Cheng YY. Therapeutic potential of ALKB homologs for cardiovascular disease. Biomed Pharmacother 2020; 131:110645. [PMID: 32942149 DOI: 10.1016/j.biopha.2020.110645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/05/2020] [Accepted: 08/16/2020] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading causes of human death. Recently, ALKB homologs, including ALKBH1-8 and FTO, have been found to have a variety of biological functions, such as histone demethylation, RNA demethylation, and DNA demethylation. These functions may regulate the physiological and pathological processes of CVDs, including inflammation, oxidative stress, cell apoptosis, and mitochondrial, endothelial, and fat metabolism dysfunction. In the present review, we summarize the biological functions of ALKB homologs and the relationship between the ALKB homologs and CVDs. Importantly, we discuss the roles of ALKB homologs in the regulation of oxidative stress, inflammation, autophagy, and DNA damage in CVDs, as well as the practical applications of ALKB homologs inhibitors or agonists in treating CVDs. In conclusion, the ALKBH family might be a promising target for CVDs therapy.
Collapse
Affiliation(s)
- Ming-Zhu Xiao
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jia-Ming Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Cui-Ling Xian
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Keng-Yu Chen
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; The Second Affiliated Hospital of Guangdong Pharmaceutical University, Yunfu, 527300, China
| | - Zhong-Qiu Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China.
| | - Yuan-Yuan Cheng
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China.
| |
Collapse
|
20
|
Xu Y, Manghrani A, Liu B, Shi H, Pham U, Liu A, Al-Hashimi HM. Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage. J Biol Chem 2020; 295:15933-15947. [PMID: 32913127 DOI: 10.1074/jbc.ra120.014530] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/24/2020] [Indexed: 11/06/2022] Open
Abstract
As the Watson-Crick faces of nucleobases are protected in dsDNA, it is commonly assumed that deleterious alkylation damage to the Watson-Crick faces of nucleobases predominantly occurs when DNA becomes single-stranded during replication and transcription. However, damage to the Watson-Crick faces of nucleobases has been reported in dsDNA in vitro through mechanisms that are not understood. In addition, the extent of protection from methylation damage conferred by dsDNA relative to ssDNA has not been quantified. Watson-Crick base pairs in dsDNA exist in dynamic equilibrium with Hoogsteen base pairs that expose the Watson-Crick faces of purine nucleobases to solvent. Whether this can influence the damage susceptibility of dsDNA remains unknown. Using dot-blot and primer extension assays, we measured the susceptibility of adenine-N1 to methylation by dimethyl sulfate (DMS) when in an A-T Watson-Crick versus Hoogsteen conformation. Relative to unpaired adenines in a bulge, Watson-Crick A-T base pairs in dsDNA only conferred ∼130-fold protection against adenine-N1 methylation, and this protection was reduced to ∼40-fold for A(syn)-T Hoogsteen base pairs embedded in a DNA-drug complex. Our results indicate that Watson-Crick faces of nucleobases are accessible to alkylating agents in canonical dsDNA and that Hoogsteen base pairs increase this accessibility. Given the higher abundance of dsDNA relative to ssDNA, these results suggest that dsDNA could be a substantial source of cytotoxic damage. The work establishes DMS probing as a method for characterizing A(syn)-T Hoogsteen base pairs in vitro and also lays the foundation for a sequencing approach to map A(syn)-T Hoogsteen and unpaired adenines genome-wide in vivo.
Collapse
Affiliation(s)
- Yu Xu
- Department of Chemistry, Duke University, Durham, North Carolina, USA
| | - Akanksha Manghrani
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina, USA
| | - Uyen Pham
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
| | - Amy Liu
- Department of Chemistry, Duke University, Durham, North Carolina, USA
| | - Hashim M Al-Hashimi
- Department of Chemistry, Duke University, Durham, North Carolina, USA; Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA.
| |
Collapse
|
21
|
Mrugała B, Miłaczewska A, Porebski PJ, Niedzialkowska E, Guzik M, Minor W, Borowski T. A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates. FEBS J 2020; 288:1366-1386. [PMID: 32592631 DOI: 10.1111/febs.15462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/09/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Kanamycin A is an aminoglycoside antibiotic isolated from Streptomyces kanamyceticus and used against a wide spectrum of bacteria, including Mycobacterium tuberculosis. Biosynthesis of kanamycin involves an oxidative deamination step catalyzed by kanamycin B dioxygenase (KanJ), thereby the C2' position of kanamycin B is transformed into a keto group upon release of ammonia. Here, we present for the first time, structural models of KanJ with several ligands, which along with the results of ITC binding assays and HPLC activity tests explain substrate specificity of the enzyme. The large size of the binding pocket suggests that KanJ can accept a broad range of substrates, which was confirmed by activity tests. Specificity of the enzyme with respect to its substrate is determined by the hydrogen bond interactions between the methylamino group of the antibiotic and highly conserved Asp134 and Cys150 as well as between hydroxyl groups of the substrate and Asn120 and Gln80. Upon antibiotic binding, the C terminus loop is significantly rearranged and Gln80 and Asn120, which are directly involved in substrate recognition, change their conformations. Based on reaction energy profiles obtained by density functional theory (DFT) simulations, we propose a mechanism of ketone formation involving the reactive FeIV = O and proceeding either via OH rebound, which yields a hemiaminal intermediate or by abstraction of two hydrogen atoms, which leads to an imine species. At acidic pH, the latter involves a lower barrier than the OH rebound, whereas at basic pH, the barrier leading to an imine vanishes completely. DATABASES: Structural data are available in PDB database under the accession numbers: 6S0R, 6S0T, 6S0U, 6S0W, 6S0V, 6S0S. Diffraction images are available at the Integrated Resource for Reproducibility in Macromolecular Crystallography at http://proteindiffraction.org under DOIs: 10.18430/m36s0t, 10.18430/m36s0u, 10.18430/m36s0r, 10.18430/m36s0s, 10.18430/m36s0v, 10.18430/m36s0w. A data set collection of computational results is available in the Mendeley Data database under DOI: 10.17632/sbyzssjmp3.1 and in the ioChem-BD database under DOI: 10.19061/iochem-bd-4-18.
Collapse
Affiliation(s)
- Beata Mrugała
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Anna Miłaczewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Przemyslaw Jerzy Porebski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Ewa Niedzialkowska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Maciej Guzik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| |
Collapse
|
22
|
Baldwin MR, Admiraal SJ, O'Brien PJ. Transient kinetic analysis of oxidative dealkylation by the direct reversal DNA repair enzyme AlkB. J Biol Chem 2020; 295:7317-7326. [PMID: 32284330 PMCID: PMC7247310 DOI: 10.1074/jbc.ra120.013517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/10/2020] [Indexed: 11/06/2022] Open
Abstract
AlkB is a bacterial Fe(II)- and 2-oxoglutarate-dependent dioxygenase that repairs a wide range of alkylated nucleobases in DNA and RNA as part of the adaptive response to exogenous nucleic acid-alkylating agents. Although there has been longstanding interest in the structure and specificity of Escherichia coli AlkB and its homologs, difficulties in assaying their repair activities have limited our understanding of their substrate specificities and kinetic mechanisms. Here, we used quantitative kinetic approaches to determine the transient kinetics of recognition and repair of alkylated DNA by AlkB. These experiments revealed that AlkB is a much faster alkylation repair enzyme than previously reported and that it is significantly faster than DNA repair glycosylases that recognize and excise some of the same base lesions. We observed that whereas 1,N6-ethenoadenine can be repaired by AlkB with similar efficiencies in both single- and double-stranded DNA, 1-methyladenine is preferentially repaired in single-stranded DNA. Our results lay the groundwork for future studies of AlkB and its human homologs ALKBH2 and ALKBH3.
Collapse
Affiliation(s)
- Michael R Baldwin
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Suzanne J Admiraal
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Patrick J O'Brien
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600.
| |
Collapse
|
23
|
Caffrey PJ, Kher R, Bian K, Li D, Delaney S. Comparison of the Base Excision and Direct Reversal Repair Pathways for Correcting 1, N6-Ethenoadenine in Strongly Positioned Nucleosome Core Particles. Chem Res Toxicol 2020; 33:1888-1896. [PMID: 32293880 PMCID: PMC7374743 DOI: 10.1021/acs.chemrestox.0c00089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
1,N6-ethenoadenine (εA) is a
mutagenic lesion and biomarker observed in numerous cancerous tissues.
Two pathways are responsible for its repair: base excision repair
(BER) and direct reversal repair (DRR). Alkyladenine DNA glycosylase
(AAG) is the primary enzyme that excises εA in BER, generating
stable intermediates that are processed by downstream enzymes. For
DRR, the Fe(II)/α-ketoglutarate-dependent ALKBH2 enzyme repairs
εA by direct conversion of εA to A. While the molecular
mechanism of each enzyme is well understood on unpackaged duplex DNA,
less is known about their actions on packaged DNA. The nucleosome
core particle (NCP) forms the minimal packaging unit of DNA in eukaryotic
organisms and is composed of 145–147 base pairs wrapped around
a core of eight histone proteins. In this work, we investigated the
activity of AAG and ALKBH2 on εA lesions globally distributed
at positions throughout a strongly positioned NCP. Overall, we examined
the repair of εA at 23 unique locations in packaged DNA. We
observed a strong correlation between rotational positioning of εA
and AAG activity but not ALKBH2 activity. ALKBH2 was more effective
than AAG at repairing occluded εA lesions, but only AAG was
capable of full repair of any εA in the NCP. However, notable
exceptions to these trends were observed, highlighting the complexity
of the NCP as a substrate for DNA repair. Modeling of binding of the
repair enzymes to NCPs revealed that some of these observations can
be explained by steric interference caused by DNA packaging. Specifically,
interactions between ALKBH2 and the histone proteins obstruct binding
to DNA, which leads to diminished activity. Taken together, these
results support in vivo observations of alkylation
damage profiles and contribute to our understanding of mutational
hotspots.
Collapse
Affiliation(s)
- Paul J Caffrey
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Raadhika Kher
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Chen F, Tang Q, Ma H, Bian K, Seeram NP, Li D. Hydrolyzable Tannins Are Iron Chelators That Inhibit DNA Repair Enzyme ALKBH2. Chem Res Toxicol 2019; 32:1082-1086. [PMID: 31088072 DOI: 10.1021/acs.chemrestox.8b00398] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hydrolyzable tannins are a class of polyphenolic compounds commonly found in natural products. In this work, we studied the in vitro inhibitory mechanism of six molecules in this class on ALKBH2, an Fe(II)/α-ketoglutarate-dependent DNA repair enzyme in the AlkB family. We determined the IC50 values of these compounds on the repair of 3-methylcytosine and 1-methyladenine, the prototypical substrates of ALKBH2. A structure-activity relationship was also observed between the strength of inhibition and the number of galloyl moieties in a molecule. In addition, we found that the inhibition by this class of polyphenolic compounds on ALKBH2 is through an iron-chelating mechanism.
Collapse
Affiliation(s)
- Fangyi Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy , University of Rhode Island , Kingston , Rhode Island 02881 , United States
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy , University of Rhode Island , Kingston , Rhode Island 02881 , United States
| | - Hang Ma
- 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
| | - Navindra P Seeram
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy , University of Rhode Island , Kingston , Rhode Island 02881 , United States
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy , University of Rhode Island , Kingston , Rhode Island 02881 , United States
| |
Collapse
|
26
|
Krais AM, Kliem C, Arlt VM, Schmeiser HH. Determination of genomic N3-methylthymidine in human cancer cells treated with nitrosamines using capillary electrophoresis with laser-induced fluorescence. Electrophoresis 2019; 40:1535-1539. [PMID: 30767246 DOI: 10.1002/elps.201800495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/14/2019] [Accepted: 02/03/2019] [Indexed: 11/09/2022]
Abstract
Methylating substances alter DNA by forming N3-methylthymidine (N3mT), a mutagenic base modification. To develop a sensitive analytical method for the detection of N3mT in DNA based on capillary electrophoresis with laser-induced fluorescence detection (CE-LIF), we synthesized the N3mT-3'-phosphate as a chemical standard. The limit of detection was 1.9 amol of N3mT, which corresponds to one molecule of N3mT per 1000 normal nucleotides or 0.1%. With this method, we demonstrated that the carcinogenic nitrosamine N'-nitrosonornicotine (NNN) induced N3mT in the human lung cancer cell line A549. Treatment with NNN also caused an elevated degree of 5-hydroxymethylcytidine (5hmdC) in DNA, while the methylation degree (i.e. 5-methylcytidine; 5mdC) stayed constant. According to our data, NNN could, via yet unknown mechanisms, play a role in the formation of N3mT as well as 5hmdC. In this study we have developed a new sensitive analytical method using CE-LIF for the simultaneous detection of the three DNA modifications, 5mdC, 5hmdC and N3mT.
Collapse
Affiliation(s)
- Annette M Krais
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Occupational and Environmental Medicine, Institute of Laboratory Medicine, Lund University, Lund, Sweden
| | - Christian Kliem
- Technology Transfer Office, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker M Arlt
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, UK.,NIHR Health Protection Research Unit in Health Impact of Environmental Hazards at King's College London in partnership with Public Health England, London and Imperial College London, London, UK
| | - Heinz H Schmeiser
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
27
|
Wilson DL, Beharry AA, Srivastava A, O'Connor TR, Kool ET. Fluorescence Probes for ALKBH2 Allow the Measurement of DNA Alkylation Repair and Drug Resistance Responses. Angew Chem Int Ed Engl 2018; 57:12896-12900. [PMID: 30098084 PMCID: PMC6478024 DOI: 10.1002/anie.201807593] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 01/18/2023]
Abstract
The DNA repair enzyme ALKBH2 is implicated in both tumorigenesis as well as resistance to chemotherapy in certain cancers. It is currently under study as a potential diagnostic marker and has been proposed as a therapeutic target. To date, however, there exist no direct methods for measuring the repair activity of ALKBH2 in vitro or in biological samples. Herein, we report a highly specific, fluorogenic probe design based on an oligonucleotide scaffold that reports directly on ALKBH2 activity both in vitro and in cell lysates. Importantly, the probe enables the monitoring of cellular regulation of ALKBH2 activity in response to treatment with the chemotherapy drug temozolomide through a simple fluorescence assay, which has only previously been observed through indirect means such as qPCR and western blots. Furthermore, the probe provides a viable high-throughput assay for drug discovery.
Collapse
Affiliation(s)
- David L Wilson
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Andrew A Beharry
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ON, L5L 1C6, Canada
| | - Avinash Srivastava
- Department of Cancer Biology, Beckman Research Institute, Duarte, CA, 91010, USA
| | - Timothy R O'Connor
- Department of Cancer Biology, Beckman Research Institute, Duarte, CA, 91010, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| |
Collapse
|
28
|
Wilson DL, Beharry AA, Srivastava A, O'Connor TR, Kool ET. Fluorescence Probes for ALKBH2 Allow the Measurement of DNA Alkylation Repair and Drug Resistance Responses. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- David L. Wilson
- Department of Chemistry; Stanford University; Stanford CA 94305 USA
| | - Andrew A. Beharry
- Department of Chemical and Physical Sciences; University of Toronto; Mississauga ON L5L 1C6 Canada
| | - Avinash Srivastava
- Department of Cancer Biology; Beckman Research Institute; Duarte CA 91010 USA
| | - Timothy R. O'Connor
- Department of Cancer Biology; Beckman Research Institute; Duarte CA 91010 USA
| | - Eric T. Kool
- Department of Chemistry; Stanford University; Stanford CA 94305 USA
| |
Collapse
|
29
|
Abstract
DNA repair is now understood to play a key role in a variety of disease states, most notably cancer. Tools for studying DNA have typically relied on traditional biochemical methods which are often laborious and indirect. Efforts to study the biology and therapeutic relevance of DNA repair pathways can be limited by such methods. Recently, specific fluorescent probes have been developed to aid in the study of DNA repair. Fluorescent probes offer the advantage of being able to directly assay for DNA repair activity in a simple, mix-and-measure format. This review will summarize the distinct classes of probe designs and their potential utility in varied research and preclinical settings.
Collapse
Affiliation(s)
- David L. Wilson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
30
|
Felske LR, Lenz SAP, Wetmore SD. Quantum Chemical Studies of the Structure and Stability of N-Methylated DNA Nucleobase Dimers: Insights into the Mutagenic Base Pairing of Damaged DNA. J Phys Chem A 2017; 122:410-419. [PMID: 29189004 DOI: 10.1021/acs.jpca.7b10485] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA is constantly under attack from exogenous and endogenous sources that modify the chemical structure of the nucleobases. A common type of nucleobase damage is N-methylation, which can result in mutagenesis. Nevertheless, these lesions are often repaired by the DNA repair enzyme AlkB, albeit at varying rates. Herein we use density functional theory (B3LYP-D3(BJ)/6-311++G(2df,2p)//B3LYP/6-31G(d,p)) to comprehensively examine the structural and energetic properties of base pairs between seven nucleobase lesions resulting from N-methylation on the Watson-Crick (WC) binding face and each canonical nucleobase. By characterizing 105 stable nucleobase dimers, we provide fundamental details regarding the preferred lesion base pairings. Specifically, we reveal that the flexibility of the methylamino group resulting from methylation of an exocyclic amino substituent allows the 2MeG, 4MeC, and 6MeA lesions to maintain a preference for canonical WC base pairing, which correlates with the experimentally reported lack of mutagenicity for these damage products. In contrast, calculated distortions in key structural parameters and altered binding energies for base pairs involving adducts formed upon methylation of a ring nitrogen (namely, 1MeG, 3MeT, 1MeA, and 3MeC) help rationalize the associated mutagenicity and repair efficiencies. Most importantly, our work provides molecular-level information about the interactions between N-methylated and canonical nucleobases that is critical for future large-scale modeling of damaged DNA and enzyme-DNA complexes that strive to further uncover the mutagenicity and repair propensities of these detrimental lesions.
Collapse
Affiliation(s)
- Lindey R Felske
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
| | - Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
| |
Collapse
|
31
|
Metabolomics reveals novel blood plasma biomarkers associated to the BRCA1-mutated phenotype of human breast cancer. Sci Rep 2017; 7:17831. [PMID: 29259228 PMCID: PMC5736621 DOI: 10.1038/s41598-017-17897-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/01/2017] [Indexed: 01/09/2023] Open
Abstract
Hereditary breast and ovarian cancer syndrome (HBOC) is partly due to the presence of mutations in the BRCA genes. Triple-negative (TN) breast cancer (BC) shares histological characteristics with germline BRCA1 mutation-associated tumours. We have investigated the metabolic profiles of human breast cancer (BC) cell lines carrying BRCA1 pathogenic mutations by non-targeted liquid chromatography coupled to mass spectrometry technology. Based on our in vitro results, we performed a targeted metabolomic analysis of plasma samples from TN HBOC patients taking into account their BRCA1 genotype. BRCA1 promoter hypermethylation and the BRCAness phenotype of BC cell lines were also studied. The purpose of this study was to determine the metabolic signature of HBOC syndrome and TNBC patients and to evaluate the potential contribution of the metabolites identified to the genetic diagnosis of breast cancer. The present results show the existence of a differential metabolic signature for BC cells based on the BRCA1 functionality. None of the studied BC cell lines presented hypermethylation of the BRCA1 promoter region. We provide evidence of the existence of free methylated nucleotides capable of distinguishing plasma samples from HBOC patients as BRCA1-mutated and BRCA1 non-mutated, suggesting that they might be considered as BRCA1-like biomarkers for TNBC and HBOC syndrome.
Collapse
|
32
|
Tang Q, Cai A, Bian K, Chen F, Delaney JC, Adusumalli S, Bach AC, Akhlaghi F, Cho BP, Li D. Characterization of Byproducts from Chemical Syntheses of Oligonucleotides Containing 1-Methyladenine and 3-Methylcytosine. ACS OMEGA 2017; 2:8205-8212. [PMID: 29214236 PMCID: PMC5709782 DOI: 10.1021/acsomega.7b01482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/01/2017] [Indexed: 06/07/2023]
Abstract
Oligonucleotides serve as important tools for biological, chemical, and medical research. The preparation of oligonucleotides through automated solid-phase synthesis is well-established. However, identification of byproducts generated from DNA synthesis, especially from oligonucleotides containing site-specific modifications, is sometimes challenging. Typical high-performance liquid chromatography (HPLC), mass spectrometry (MS), and gel electrophoresis methods alone are not sufficient for characterizing unexpected byproducts, especially for those having identical or very similar molecular weight (MW) to the products. We used a rigorous quality control procedure to characterize byproducts generated during oligonucleotide syntheses: (1) purify oligonucleotides by different HPLC systems; (2) determine exact MW by high-resolution MS; (3) locate modification position by MS/MS or exonuclease digestion with matrix-assisted laser desorption ionization-time of flight analysis; and (4) conduct, where applicable, enzymatic assays. We applied these steps to characterize byproducts in the syntheses of oligonucleotides containing biologically important methyl DNA adducts 1-methyladenine (m1A) and 3-methylcytosine (m3C). In m1A synthesis, we differentiated a regioisomeric byproduct 6-methyladenine, which possesses a MW identical to uncharged m1A. As for m3C, we identified a deamination byproduct 3-methyluracil, which is only 1 Da greater than uncharged m3C in the ∼4900 Da context. The detection of these byproducts would be very challenging if the abovementioned procedure was not adopted.
Collapse
Affiliation(s)
- Qi Tang
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Ang Cai
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Ke Bian
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Fangyi Chen
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - James C. Delaney
- Visterra
Inc., One Kendall Square, Cambridge, Massachusetts 02139, United States
| | - Sravani Adusumalli
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Alvin C. Bach
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Fatemeh Akhlaghi
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Bongsup P. Cho
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Deyu Li
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| |
Collapse
|
33
|
Bian K, Chen F, Humulock ZT, Tang Q, Li D. Copper Inhibits the AlkB Family DNA Repair Enzymes under Wilson's Disease Condition. Chem Res Toxicol 2017; 30:1794-1796. [PMID: 28926697 DOI: 10.1021/acs.chemrestox.7b00230] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Disturbed metabolism of copper ions can cause diseases such as Wilson's disease (WD). In this work, we investigated the inhibitory effect of Cu(II) ion in vitro on the AlkB family DNA repair enzymes, which are members of the Fe(II)/alpha-ketoglutarate-dependent dioxygenase and include human ALKBH2, ALKBH3, and E. coli AlkB proteins. None of the three proteins was significantly inhibited under normal cellular copper concentrations. However, under WD related condition, we observed that the activities of all three enzymes were strongly suppressed (from 95.2 to 100.0%). We also noted the repair efficiency under ds-DNA condition was less susceptible than ss-DNA to the inhibition.
Collapse
Affiliation(s)
- Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Fangyi Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Zachary T Humulock
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| |
Collapse
|
34
|
Chen F, Bian K, Tang Q, Fedeles BI, Singh V, Humulock ZT, Essigmann JM, Li D. Oncometabolites d- and l-2-Hydroxyglutarate Inhibit the AlkB Family DNA Repair Enzymes under Physiological Conditions. Chem Res Toxicol 2017; 30:1102-1110. [PMID: 28269980 DOI: 10.1021/acs.chemrestox.7b00009] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Cancer-associated mutations often lead to perturbed cellular energy metabolism and accumulation of potentially harmful oncometabolites. One example is the chiral molecule 2-hydroxyglutarate (2HG); its two stereoisomers (d- and l-2HG) have been found at abnormally high concentrations in tumors featuring anomalous metabolic pathways. 2HG has been demonstrated to competitively inhibit several α-ketoglutarate (αKG)- and non-heme iron-dependent dioxygenases, including some of the AlkB family DNA repair enzymes, such as ALKBH2 and ALKBH3. However, previous studies have only provided the IC50 values of d-2HG on the enzymes, and the results have not been correlated to physiologically relevant concentrations of 2HG and αKG in cancer cells. In this work, we performed detailed kinetic analyses of DNA repair reactions catalyzed by ALKBH2, ALKBH3, and the bacterial AlkB in the presence of d- and l-2HG in both double- and single-stranded DNA contexts. We determined the kinetic parameters of inhibition, including kcat, KM, and Ki. We also correlated the relative concentrations of 2HG and αKG previously measured in tumor cells with the inhibitory effect of 2HG on the AlkB family enzymes. Both d- and l-2HG significantly inhibited the human DNA repair enzymes ALKBH2 and ALKBH3 at pathologically relevant concentrations (73-88% for d-2HG and 31-58% for l-2HG inhibition). This work provides a new perspective that the elevation of the d- or l-2HG concentration in cancer cells may contribute to an increased mutation rate by inhibiting the DNA repair performed by the AlkB family enzymes and thus exacerbate the genesis and progression of tumors.
Collapse
Affiliation(s)
- Fangyi Chen
- 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
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Bogdan I Fedeles
- Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Vipender Singh
- Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Zachary T Humulock
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - John M Essigmann
- Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| |
Collapse
|
35
|
Zhou H, Kimsey IJ, Nikolova EN, Sathyamoorthy B, Grazioli G, McSally J, Bai T, Wunderlich CH, Kreutz C, Andricioaei I, Al-Hashimi HM. m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nat Struct Mol Biol 2016; 23:803-10. [PMID: 27478929 PMCID: PMC5016226 DOI: 10.1038/nsmb.3270] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/05/2016] [Indexed: 12/13/2022]
Abstract
The B-DNA double helix can dynamically accommodate G-C and A-T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G-C(+) (in which + indicates protonation) and A-U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result,N(1)-methyladenosine and N(1)-methylguanosine, which occur in DNA as a form of alkylation damage and in RNA as post-transcriptional modifications, have dramatically different consequences. Whereas they create G-C(+) and A-T Hoogsteen base pairs in duplex DNA, thereby maintaining the structural integrity of the double helix, they block base-pairing and induce local duplex melting in RNA. These observations provide a mechanism for disrupting RNA structure through post-transcriptional modifications. The different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help cells meet the opposing requirements of maintaining genome stability, on the one hand, and of dynamically modulating the structure of the epitranscriptome, on the other.
Collapse
Affiliation(s)
- Huiqing Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | - Isaac J. Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | - Evgenia N. Nikolova
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California USA
| | | | - Gianmarc Grazioli
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - James McSally
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - Tianyu Bai
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | | | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck Austria
| | - Ioan Andricioaei
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
- Department of Chemistry, Duke University, Durham, North Carolina USA
| |
Collapse
|