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Meng F, Sun L, Liu Y, Li X, Tan H, Yuan C, Li X. Theoretical investigation of the reaction mechanism of THP oxidative rearrangement catalysed by BBOX. Phys Chem Chem Phys 2024. [PMID: 39015023 DOI: 10.1039/d4cp01661k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
γ-Butyrobetaine hydroxylase (BBOX) is a non-heme FeII/2OG dependent enzyme that is able to perform two different kinds of catalytic reactions on 3-(2,2,2-trimethylhydrazinium) propionate (THP) to produce distinct catalytic products. Although the structure of BBOX complexed with THP has been resolved, the details of its catalytic mechanism are still elusive. In this study, by employing molecular dynamics (MD) simulations and density functional theory (DFT) calculations, the mechanism of the THP oxidative rearrangement reactions catalysed by BBOX was investigated. Our calculations revealed how the enzyme undergoes a conformational conversion to initiate the catalytic reactions. In the first catalytic step, BBOX performs hydrogen abstraction from the substrate THP as a common non-heme iron enzyme. Due to the structure of the substrate stabilizing the radical species and polarizing the adjacent N-N bond, in the next step, THP takes the pathway for N-N bond homolysis but not regular hydroxyl rebounding. The cleaved ammonium radical could either react with the hydroxyl group on the iron centre of the enzyme or recombine with the other cleaved fragment of the substrate to generate the rearranged product. This study revealed the catalytic mechanism of BBOX, detailing how the enzyme and the substrate regulated the hydroxyl rebound process to generate various products.
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Affiliation(s)
- Fanqi Meng
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Lu Sun
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Yueying Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Xiang Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Chang Yuan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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2
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Wang J, Takyi NA, Hsiao YC, Tang Q, Chen YT, Liu CW, Ma J, Qi R, Bian K, Peng Z, Essigmann JM, Lu K, Wetmore SD, Li D. Stable Interstrand Cross-Links Generated from the Repair of 1, N6-Ethenoadenine in DNA by α-Ketoglutarate/Fe(II)-Dependent Dioxygenase ALKBH2. J Am Chem Soc 2024; 146:10381-10392. [PMID: 38573229 PMCID: PMC11060877 DOI: 10.1021/jacs.3c12890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
DNA cross-links severely challenge replication and transcription in cells, promoting senescence and cell death. In this paper, we report a novel type of DNA interstrand cross-link (ICL) produced as a side product during the attempted repair of 1,N6-ethenoadenine (εA) by human α-ketoglutarate/Fe(II)-dependent enzyme ALKBH2. This stable/nonreversible ICL was characterized by denaturing polyacrylamide gel electrophoresis analysis and quantified by high-resolution LC-MS in well-matched and mismatched DNA duplexes, yielding 5.7% as the highest level for cross-link formation. The binary lesion is proposed to be generated through covalent bond formation between the epoxide intermediate of εA repair and the exocyclic N6-amino group of adenine or the N4-amino group of cytosine residues in the complementary strand under physiological conditions. The cross-links occur in diverse sequence contexts, and molecular dynamics simulations rationalize the context specificity of cross-link formation. In addition, the cross-link generated from attempted εA repair was detected in cells by highly sensitive LC-MS techniques, giving biological relevance to the cross-link adducts. Overall, a combination of biochemical, computational, and mass spectrometric methods was used to discover and characterize this new type of stable cross-link both in vitro and in human cells, thereby uniquely demonstrating the existence of a potentially harmful ICL during DNA repair by human ALKBH2.
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Affiliation(s)
- Jie Wang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Nathania A Takyi
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Yi-Tzai Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jian Ma
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Rui Qi
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Zhiyuan Peng
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - John M Essigmann
- Departments of Biological Engineering, Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
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3
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Kanazhevskaya LY, Gorbunov AA, Lukina MV, Smyshliaev DA, Zhdanova PV, Lomzov AA, Koval VV. The Role of Key Amino Acids of the Human Fe(II)/2OG-Dependent Dioxygenase ALKBH3 in Structural Dynamics and Repair Activity toward Methylated DNA. Int J Mol Sci 2024; 25:1145. [PMID: 38256217 PMCID: PMC10816986 DOI: 10.3390/ijms25021145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Non-heme dioxygenases of the AlkB family hold a unique position among enzymes that repair alkyl lesions in nucleic acids. These enzymes activate the Fe(II) ion and molecular oxygen through the coupled decarboxylation of the 2-oxoglutarate co-substrate to subsequently oxidize the substrate. ALKBH3 is a human homolog of E. coli AlkB, which displays a specific activity toward N1-methyladenine and N3-methylcytosine bases in single-stranded DNA. Due to the lack of a DNA-bound structure of ALKBH3, the basis of its substrate specificity and structure-function relationships requires further exploration. Here we have combined biochemical and biophysical approaches with site-directed mutational analysis to elucidate the role of key amino acids in maintaining the secondary structure and catalytic activity of ALKBH3. Using stopped-flow fluorescence spectroscopy we have shown that conformational dynamics play a crucial role in the catalytic repair process catalyzed by ALKBH3. A transient kinetic mechanism, which comprises the steps of the specific substrate binding, eversion, and anchoring within the DNA-binding cleft, has been described quantitatively by rate and equilibrium constants. Through CD spectroscopy, we demonstrated that replacing side chains of Tyr143, Leu177, and His191 with alanine results in significant alterations in the secondary structure content of ALKBH3 and decreases the stability of mutant proteins. The bulky side chain of Tyr143 is critical for binding the methylated base and stabilizing its flipped-out conformation, while its hydroxyl group is likely involved in facilitating the product release. The removal of the Leu177 and His191 side chains substantially affects the secondary structure content and conformational flexibility, leading to the complete inactivation of the protein. The mutants lacking enzymatic activity exhibit a marked decrease in antiparallel β-strands, offset by an increase in the helical component.
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Affiliation(s)
- Lyubov Yu. Kanazhevskaya
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Alexey A. Gorbunov
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
| | - Maria V. Lukina
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
| | - Denis A. Smyshliaev
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
| | - Polina V. Zhdanova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
| | - Vladimir V. Koval
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
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4
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Shang G, Yang M, Li M, Ma L, Liu Y, Ma J, Chen Y, Wang X, Fan S, Xie M, Wu W, Dai S, Chen Z. Structural Basis of Nucleic Acid Recognition and 6mA Demethylation by Caenorhabditis elegans NMAD-1A. Int J Mol Sci 2024; 25:686. [PMID: 38255759 PMCID: PMC10815869 DOI: 10.3390/ijms25020686] [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: 12/08/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/24/2024] Open
Abstract
N6-methyladenine (6mA) of DNA is an emerging epigenetic mark in the genomes of Chlamydomonas, Caenorhabditis elegans, and mammals recently. Levels of 6mA undergo drastic fluctuation and thus affect fertility during meiosis and early embryogenesis. Here, we showed three complex structures of 6mA demethylase C. elegans NMAD-1A, a canonical isoform of NMAD-1 (F09F7.7). Biochemical results revealed that NMAD-1A prefers 6mA Bubble or Bulge DNAs. Structural studies of NMAD-1A revealed an unexpected "stretch-out" conformation of its Flip2 region, a conserved element that is usually bent over the catalytic center to facilitate substrate base flipping in other DNA demethylases. Moreover, the wide channel between the Flip1 and Flip2 of the NMAD-1A explained the observed preference of NMAD-1A for unpairing substrates, of which the flipped 6mA was primed for catalysis. Structural analysis and mutagenesis studies confirmed that key elements such as carboxy-terminal domain (CTD) and hypothetical zinc finger domain (ZFD) critically contributed to structural integrity, catalytic activity, and nucleosome binding. Collectively, our biochemical and structural studies suggest that NMAD-1A prefers to regulate 6mA in the unpairing regions and is thus possibly associated with dynamic chromosome regulation and meiosis regulation.
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Affiliation(s)
- Guohui Shang
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Meiting Yang
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Min Li
- National Protein Science Facility, Tsinghua University, Beijing 100084, China
| | - Lulu Ma
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yunlong Liu
- School of Life Sciences, Tiangong University, Tianjin 300387, China
| | - Jun Ma
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiyun Chen
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Xue Wang
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shilong Fan
- National Protein Science Facility, Tsinghua University, Beijing 100084, China
| | - Mengjia Xie
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wei Wu
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shaodong Dai
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Zhongzhou Chen
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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5
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Chen Y, Wang W, Zhang W, He M, Li Y, Qu G, Tong J. Emerging roles of biological m 6A proteins in regulating virus infection: A review. Int J Biol Macromol 2023; 253:126934. [PMID: 37722640 DOI: 10.1016/j.ijbiomac.2023.126934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent chemical modifications of intracellular RNA, which recently emerging as a multifaceted effector of viral genomic RNA. As a dynamic process, three groups of biological proteins control the levels of m6A modification in eukaryocyte, designed as m6A writers, erasers, and readers. The m6A writers comprising of methyltransferases complex initiate the modification process. On the contrary, the m6A erasers ALKBH5 or FTO abolish the modification through three-step demethylation: m6A to N6-hydroxymethyl adenosine (hm6A), then hm6A to N6-methyladenosine (f6A), and finally f6A to adenosine. The known m6A readers include the YTH family and the hnRNP family. As m6A modification regulates RNA nuclear exportation, stability, and translation, m6A proteins commonly participate in virus infection by regulating viral genomic RNA synthesis. Moreover, m6A proteins establish molecular linkages between virus genome/viral encode proteins and host cells proteins via their multifunctional roles in cellular RNA metabolism. The m6A writers and erasers directly impact interferon expression and macrophage innate immune responses, facilitating them to act as anti-/pro-viral factors. The m6A readers enable to alter cell metabolism and stress granules (SGs) production to regulate virus-host interactions. Here, the latest progress of m6A proteins in regulating viral infection is reviewed. Demonstrating the roles of m6A proteins will enhance the understanding of epigenetic regulation of virus infection and stimulate the development of novel antiviral strategies.
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Affiliation(s)
- Yuran Chen
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Wenjing Wang
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Wuchao Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Mei He
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Yuming Li
- School of Public Health, Shandong First Medical University, Shandong Academy of Medical Sciences, Ji'nan 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, Shandong Academy of Medical Sciences, Tai'an 271000, China.
| | - Guosheng Qu
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
| | - Jie Tong
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
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6
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Yu R, Zhang W, Li Y, Tang J, Kim K, Li B. Functional characterisation of Fe (II) and 2OG-dependent dioxygenase TcALKBH4 in the red flour beetle, Tribolium castaneum. INSECT MOLECULAR BIOLOGY 2023; 32:676-688. [PMID: 37462221 DOI: 10.1111/imb.12865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/03/2023] [Indexed: 11/08/2023]
Abstract
Alpha-ketoglutarate-dependent dioxygenase ALKB homologue 4 (ALKBH4) is a member of the Fe (II) and 2-oxoglutarate-dependent ALKB homologue family that plays important roles in epigenetic regulation by alkyl lesions removal in mammals. However, the roles of ALKBH4 in insects are not clear. Here, TcALKBH4 was cloned and functionally characterised in Tribolium castaneum. Temporal expression revealed that TcALKBH4 was highly expressed in early embryos and early pupae. Spatial expression showed that TcALKBH4 was highly expressed in the adult testis, and followed by the ovary. RNA interference targeting TcALKBH4 at different developmental stages in T. castaneum led to apparent phenotypes including the failure of development in larvae, the reduction of food intake and the deficiency of fertility in adult. However, further dot blot analyses showed that TcALKBH4 RNAi does not seem to influence 6 mA levels in vivo. qRT-PCR was used to further explore the underlying molecular mechanisms; the result showed that TcALKBH4 mediates the development of larvae possibly through 20E signalling pathway, and the fertility of female and male adult might be regulated by the expression of vitellogenesis and JH signalling pathway, respectively. Altogether, these findings will provide new insights into the potential function of ALKBH4 in insects.
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Affiliation(s)
- Runnan Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenjing Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yanxiao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jing Tang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - KumChol Kim
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- Department of Life-Science, University of Science, Pyongyang, Democratic People's Republic of Korea
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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7
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Zhang L, Ding X, Kratka CR, Levine A, Lee JK. Gas Phase Experimental and Computational Studies of AlkB Substrates: Intrinsic Properties and Biological Implications. J Org Chem 2023; 88:13115-13124. [PMID: 37651719 DOI: 10.1021/acs.joc.3c01335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The gas phase acidity and proton affinity of nucleobases that are substrates for the DNA repair enzyme AlkB have been examined using both computational and experimental methods. These thermochemical values have not heretofore been measured and provide experimental data that help benchmark the theoretical results. We also use our gas phase results to lend insight into the AlkB mechanism, particularly in terms of the role AlkB plays in DNA repair, versus its complementary enzyme AlkA.
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Affiliation(s)
- Lanxin Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Xiao Ding
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Catherine R Kratka
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Alec Levine
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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8
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Xu Z, Mo Y, Li Z, Ban S, Song H. New small-molecule alcohol synthesis by breaking the space limitation of the "aromatic cage" in Pseudomonas sp. AK1 BBOX. Org Biomol Chem 2023; 21:6397-6404. [PMID: 37497645 DOI: 10.1039/d3ob00830d] [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: 07/28/2023]
Abstract
Fe(II)/2OG-dependent oxygenase γ-butyrobetaine hydroxylase (BBOX) stereoselectively hydroxylates inactive C-H bonds and produces L-carnitine. It has potential applications in the biosynthesis of L-carnitine and the synthesis of other small molecule alcohols. In this paper, we systematically explore the substrate range of Pseudomonas sp. AK1 BBOX (psBBOX), with emphasis on the quaternary ammonium portion of γ-butyrobetaine (γ-BB). The space limitation of the "aromatic cage" in psBBOX in the hydroxylation of large quaternary ammonium analogues was studied, and the role of four aromatic amino acid residues in the substrate binding mode was analyzed. Consequently, the F188A mutant was developed with the ability to hydroxylate cyclic quaternary ammonium analogues and generate new alcohol compounds by breaking the limitation of the "aromatic cage".
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Affiliation(s)
- Zhiqin Xu
- School of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China.
| | - Yaling Mo
- School of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China.
| | - Zhengwen Li
- School of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China.
| | - Shurong Ban
- School of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China.
| | - Heng Song
- College of Chemistry & Molecular Science, Wuhan University, Wuhan, Hubei Province 430072, China.
- Wuhan University Shenzhen Research Institute, Shenzhen, Guangdong Province 518000, China
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9
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Davletgildeeva AT, Tyugashev TE, Zhao M, Kuznetsov NA, Ishchenko AA, Saparbaev M, Kuznetsova AA. Individual Contributions of Amido Acid Residues Tyr122, Ile168, and Asp173 to the Activity and Substrate Specificity of Human DNA Dioxygenase ABH2. Cells 2023; 12:1839. [PMID: 37508504 PMCID: PMC10377887 DOI: 10.3390/cells12141839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Human Fe(II)/α-ketoglutarate-dependent dioxygenase ABH2 plays a crucial role in the direct reversal repair of nonbulky alkyl lesions in DNA nucleobases, e.g., N1-methyladenine (m1A), N3-methylcytosine (m3C), and some etheno derivatives. Moreover, ABH2 is capable of a less efficient oxidation of an epigenetic DNA mark called 5-methylcytosine (m5C), which typically is a specific target of DNA dioxygenases from the TET family. In this study, to elucidate the mechanism of the substrate specificity of ABH2, we investigated the role of several active-site amino acid residues. Functional mapping of the lesion-binding pocket was performed through the analysis of the functions of Tyr122, Ile168, and Asp173 in the damaged base recognition mechanism. Interactions of wild-type ABH2, or its mutants Y122A, I168A, or D173A, with damaged DNA containing the methylated base m1A or m3C or the epigenetic marker m5C were analyzed by molecular dynamics simulations and kinetic assays. Comparative analysis of the enzymes revealed an effect of the substitutions on DNA binding and on catalytic activity. Obtained data clearly demonstrate the effect of the tested amino acid residues on the catalytic activity of the enzymes rather than the DNA-binding ability. Taken together, these data shed light on the molecular and kinetic consequences of the substitution of active-site residues for the mechanism of the substrate recognition.
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Affiliation(s)
- Anastasiia T Davletgildeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Timofey E Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Mingxing Zhao
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander A Ishchenko
- Groupe Mechanisms of DNA Repair and Carcinogenesis, CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, CEDEX, F-94805 Villejuif, France
| | - Murat Saparbaev
- Groupe Mechanisms of DNA Repair and Carcinogenesis, CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, CEDEX, F-94805 Villejuif, France
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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10
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Kietzmann T. Vitamin C: From nutrition to oxygen sensing and epigenetics. Redox Biol 2023; 63:102753. [PMID: 37263060 PMCID: PMC10245123 DOI: 10.1016/j.redox.2023.102753] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
Vitamin C is unbeatable - at least when it comes to sales. Of all the vitamin preparations, those containing vitamin C sell best. This is surprising because vitamin C deficiency is extremely rare. Nevertheless, there is still controversy about whether the additional intake of vitamin C supplements is essential for our health. In this context, the possible additional benefit is in most cases merely reduced to the known effect as an antioxidant. However, new findings in recent years on the mechanisms of oxygen-sensing and epigenetic control underpin the multifaceted role of vitamin C in a biological context and have therefore renewed interest in it. In the present article, therefore, known facts are linked to these new key data. In addition, available clinical data on vitamin C use of cancer therapy are summarized.
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Affiliation(s)
- Thomas Kietzmann
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, P.O. Box 3000, 90014, Oulu, Finland.
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11
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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.
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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
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12
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Chaturvedi SS, Thomas MG, Simahudeen BJSR, White W, Wildey J, Warner C, Schofield CJ, Hu J, Hausinger RP, Karabencheva-Christova TG, Christov CZ. Dioxygen Binding Is Controlled by the Protein Environment in Non-heme Fe II and 2-Oxoglutarate Oxygenases: A Study on Histone Demethylase PHF8 and an Ethylene-Forming Enzyme. Chemistry 2023; 29:e202300138. [PMID: 36701641 PMCID: PMC10305803 DOI: 10.1002/chem.202300138] [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: 01/16/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 01/27/2023]
Abstract
This study investigates dioxygen binding and 2-oxoglutarate (2OG) coordination by two model non-heme FeII /2OG enzymes: a class 7 histone demethylase (PHF8) that catalyzes the hydroxylation of its H3K9me2 histone substrate leading to demethylation reactivity and the ethylene-forming enzyme (EFE), which catalyzes two competing reactions of ethylene generation and substrate l-Arg hydroxylation. Although both enzymes initially bind 2OG by using an off-line 2OG coordination mode, in PHF8, the substrate oxidation requires a transition to an in-line mode, whereas EFE is catalytically productive for ethylene production from 2OG in the off-line mode. We used classical molecular dynamics (MD), quantum mechanics/molecular mechanics (QM/MM) MD and QM/MM metadynamics (QM/MM-MetD) simulations to reveal that it is the dioxygen binding process and, ultimately, the protein environment that control the formation of the in-line FeIII -OO⋅- intermediate in PHF8 and the off-line FeIII -OO⋅- intermediate in EFE.
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Affiliation(s)
| | - Midhun George Thomas
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA
| | | | - Walter White
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA
| | - Jon Wildey
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI 49931, USA
| | - Cait Warner
- Department of Biology, Michigan Technological University, Houghton, MI 49931, USA
| | - Christopher J. Schofield
- The Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Mansfield Road, OX1 3TA, United Kingdom
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P. Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | | | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA
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13
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Li Q, Zhu Q. The role of demethylase AlkB homologs in cancer. Front Oncol 2023; 13:1153463. [PMID: 37007161 PMCID: PMC10060643 DOI: 10.3389/fonc.2023.1153463] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
The AlkB family (ALKBH1-8 and FTO), a member of the Fe (II)- and α-ketoglutarate-dependent dioxygenase superfamily, has shown the ability to catalyze the demethylation of a variety of substrates, including DNA, RNA, and histones. Methylation is one of the natural organisms’ most prevalent forms of epigenetic modifications. Methylation and demethylation processes on genetic material regulate gene transcription and expression. A wide variety of enzymes are involved in these processes. The methylation levels of DNA, RNA, and histones are highly conserved. Stable methylation levels at different stages can coordinate the regulation of gene expression, DNA repair, and DNA replication. Dynamic methylation changes are essential for the abilities of cell growth, differentiation, and division. In some malignancies, the methylation of DNA, RNA, and histones is frequently altered. To date, nine AlkB homologs as demethylases have been identified in numerous cancers’ biological processes. In this review, we summarize the latest advances in the research of the structures, enzymatic activities, and substrates of the AlkB homologs and the role of these nine homologs as demethylases in cancer genesis, progression, metastasis, and invasion. We provide some new directions for the AlkB homologs in cancer research. In addition, the AlkB family is expected to be a new target for tumor diagnosis and treatment.
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Affiliation(s)
- Qiao Li
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Qingsan Zhu
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Qingsan Zhu,
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14
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Wu Y, Zhang S, Chen C, Pang J. Dysregulation and implications of N6-methyladenosine modification in renal cell carcinoma. Curr Urol 2023; 17:45-51. [PMID: 37692138 PMCID: PMC10487297 DOI: 10.1097/cu9.0000000000000135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/24/2022] [Indexed: 12/24/2022] Open
Abstract
Increasing evidence indicates that N6-methyladenosine (m6A) methylation modification serves important functions in biological metabolism. Dysregulation of m6A regulators is related to the progression of different malignancies, including renal cell carcinoma (RCC). Recent studies have reported preliminary findings on the influence of m6A regulator dysregulation on RCC tumorigenesis and development. However, no comprehensive review that integrates and analyzes the roles of m6A modification in RCC has been published to date. In this review, we focus on the dysregulation of m6A regulators as it relates to RCC tumorigenesis and development, as well as possible applications of m6A modification in RCC diagnosis and therapeutics.
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Affiliation(s)
| | | | | | - Jun Pang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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15
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Maghsoud Y, Vázquez-Montelongo EA, Yang X, Liu C, Jing Z, Lee J, Harger M, Smith AK, Espinoza M, Guo HF, Kurie JM, Dalby KN, Ren P, Cisneros GA. Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. J Chem Inf Model 2023; 63:986-1001. [PMID: 36779232 PMCID: PMC10233724 DOI: 10.1021/acs.jcim.2c01448] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The catalytic function of lysyl hydroxylase-2 (LH2), a member of the Fe(II)/αKG-dependent oxygenase superfamily, is to catalyze the hydroxylation of lysine to hydroxylysine in collagen, resulting in stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs). Reports show that high amounts of LH2 lead to the accumulation of HLCCs, causing fibrosis and specific types of cancer metastasis. Some members of the Fe(II)/αKG-dependent family have also been reported to have intramolecular O2 tunnels, which aid in transporting one of the required cosubstrates into the active site. While LH2 can be a promising target to combat these diseases, efficacious inhibitors are still lacking. We have used computational simulations to investigate a series of 44 small molecules as lead compounds for LH2 inhibition. Tunneling analyses indicate the existence of several intramolecular tunnels. The lengths of the calculated O2-transporting tunnels in holoenzymes are relatively longer than those in the apoenzyme, suggesting that the ligands may affect the enzyme's structure and possibly block (at least partially) the tunnels. The sequence alignment analysis between LH enzymes from different organisms shows that all of the amino acid residues with the highest occurrence rate in the oxygen tunnels are conserved. Our results suggest that the enolate form of diketone compounds establishes stronger interactions with the Fe(II) in the active site. Branching the enolate compounds with functional groups such as phenyl and pyridinyl enhances the interaction with various residues around the active site. Our results provide information about possible leads for further LH2 inhibition design and development.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Erik Antonio Vázquez-Montelongo
- Department of Physical Medicine and Rehabilitation, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Xudong Yang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Juhoon Lee
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Matthew Harger
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ally K Smith
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Miguel Espinoza
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Hou-Fu Guo
- Department of Molecular and Cellular Biochemistry, College of Medicine, The University of Kentucky, Lexington, Kentucky 40536, United States
| | - Jonathan M Kurie
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77005, United States
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
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16
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Conformational Dynamics of Human ALKBH2 Dioxygenase in the Course of DNA Repair as Revealed by Stopped-Flow Fluorescence Spectroscopy. Molecules 2022; 27:molecules27154960. [PMID: 35956910 PMCID: PMC9370705 DOI: 10.3390/molecules27154960] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
Elucidation of physicochemical mechanisms of enzymatic processes is one of the main tasks of modern biology. High efficiency and selectivity of enzymatic catalysis are mostly ensured by conformational dynamics of enzymes and substrates. Here, we applied a stopped-flow kinetic analysis based on fluorescent spectroscopy to investigate mechanisms of conformational transformations during the removal of alkylated bases from DNA by ALKBH2, a human homolog of Escherichia coli AlkB dioxygenase. This enzyme protects genomic DNA against various alkyl lesions through a sophisticated catalytic mechanism supported by a cofactor (Fe(II)), a cosubstrate (2-oxoglutarate), and O2. We present here a comparative study of conformational dynamics in complexes of the ALKBH2 protein with double-stranded DNA substrates containing N1-methyladenine, N3-methylcytosine, or 1,N6-ethenoadenine. By means of fluorescent labels of different types, simultaneous detection of conformational transitions in the protein globule and DNA substrate molecule was performed. Fitting of the kinetic curves by a nonlinear-regression method yielded a molecular mechanism and rate constants of its individual steps. The results shed light on overall conformational dynamics of ALKBH2 and damaged DNA during the catalytic cycle.
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17
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Li RN, Chen SL. Mechanism for the Halogenation and Azidation of Lysine Catalyzed by Non-heme Iron BesD Enzyme. Chem Asian J 2022; 17:e202200438. [PMID: 35763338 DOI: 10.1002/asia.202200438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/23/2022] [Indexed: 11/09/2022]
Abstract
Selective halogenation is important in synthetic chemistry. BesD, a new member of the non-heme Fe(II)/α-ketoglutarate (αKG)-dependent halogenase family, can activate the sp3 C-H bond and halogenate lysine, in particular without a carrier protein. Using the density functional calculations, a chlorination mechanism in BesD has been proposed, mainly including the formation of Cl-Fe(IV)=O through the αKG decarboxylation, the isomerization of Cl-Fe(IV)=O, the substrate hydrogen abstraction by Fe(IV)=O, and the rebound of chloro to the substrate carbon radical. The hydrogen abstraction is rate-limiting. The isomerization of Cl-Fe(IV)=O is essential for the hydrogen abstraction and the chiral selectivity. The BesD-catalyzed bromination and azidation of lysine adopt the same mechanism as the chlorination. The hardly-changed overall barriers indicate that the introduced ligands (X) do not affect the reaction rate significantly, implying that the X-introduced reactions catalyzed by BesD may be extended to other X anions.
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Affiliation(s)
- Rui-Ning Li
- Beijing Institute of Technology, School of Chemistry and Chemical Engineering, 100081, Beijing, CHINA
| | - Shi-Lu Chen
- Beijing Institute of Technology, School of Chemistry and Chemical Engineering, 5th, ZhongGuanCun South Street, 100081, Beijing, CHINA
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18
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Tan T, Li Y, Tang B, Chen Y, Chen X, Xie Q, Hu Z, Chen G. Knockout of SlALKBH2 weakens the DNA damage repair ability of tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111266. [PMID: 35487670 DOI: 10.1016/j.plantsci.2022.111266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/01/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
During the growth and evolution of plants, genomic DNA is subject to constant assault from endogenous and environmental DNA damage compounds, which will result in mutagenic or genotoxic covalent adducts. Whether for prokaryotes, eukaryotes or even viruses, maintaining genome integrity is critical for the continuation of life. Escherichia coli and mammals have evolved the AlkB family of Fe(II)/alpha-ketoglutarate-dependent dioxygenases that repair DNA alkylation damage. We identified a functional homologue with EsAlkB and HsALKBH2 in tomatoes, and named it SlALKBH2. In our study, the SlALKBH2 knockout mutant showed hypersensitivity to the DNA mutagen MMS and displayed more severe growth abnormalities than wild-type plants under mutagen treatment, such as slow growth, leaf deformation and early senescence. Additionally, genes with high transcriptional activity, such as rDNA, have increased methylation under MMS treatment. In conclusion, this study shows that the tomato SlALKBH2 gene may play an important role in ensuring the integrity of the genome.
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Affiliation(s)
- Tingting Tan
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Yangyang Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Boyan Tang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Yating Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Xinru Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
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19
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Kaur S, Tam NY, McDonough MA, Schofield CJ, Aik W. Mechanisms of substrate recognition and N6-methyladenosine demethylation revealed by crystal structures of ALKBH5-RNA complexes. Nucleic Acids Res 2022; 50:4148-4160. [PMID: 35333330 PMCID: PMC9023255 DOI: 10.1093/nar/gkac195] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 01/12/2023] Open
Abstract
AlkB homologue 5 (ALKBH5) is a ferrous iron and 2-oxoglutarate dependent oxygenase that demethylates RNA N6-methyladenosine (m6A), a post-transcriptional RNA modification with an emerging set of regulatory roles. Along with the fat mass and obesity-associated protein (FTO), ALKBH5 is one of only two identified human m6A RNA oxidizing enzymes and is a potential target for cancer treatment. Unlike FTO, ALKBH5 efficiently catalyzes fragmentation of its proposed nascent hemiaminal intermediate to give formaldehyde and a demethylated nucleoside. A detailed analysis of the molecular mechanisms used by ALKBH5 for substrate recognition and m6A demethylation is lacking. We report three crystal structures of ALKBH5 in complex with an m6A-ssRNA 8-mer substrate and supporting biochemical analyses. Strikingly, the single-stranded RNA substrate binds to the active site of ALKBH5 in a 5'-3' orientation that is opposite to single-stranded or double-stranded DNA substrates observed for other AlkB subfamily members, including single-stranded DNA bound to FTO. The combined structural and biochemical results provide insight into the preference of ALKBH5 for substrates containing a (A/G)m6AC consensus sequence motif. The results support a mechanism involving formation of an m6A hemiaminal intermediate, followed by efficient ALKBH5 catalyzed demethylation, enabled by a proton shuttle network involving Lys132 and Tyr139.
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Affiliation(s)
- Simranjeet Kaur
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Nok Yin Tam
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Michael A McDonough
- The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Wei Shen Aik
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
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20
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Zuidhof HR, Calkhoven CF. Oncogenic and tumor-suppressive functions of the RNA demethylase FTO. Cancer Res 2022; 82:2201-2212. [PMID: 35303057 DOI: 10.1158/0008-5472.can-21-3710] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/04/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022]
Abstract
The epitranscriptome represents the more than 140 types of chemically varying and reversable RNA modifications affecting RNA fate. Among these, the most relevant for this review are the mRNA-modifications N6-methyladenosine (m6A) and N6,2'-O-dimethyladenosine (m6Am). Epitranscriptomic mRNA biology involves RNA methyltransferases (so called "writers"), RNA demethylases ("erasers"), and RNA-binding proteins ("readers") that interact with methylation sites to determine the functional outcome of the modification. In this review, we discuss the role of a specific RNA demethylase encoded by the fat mass and obesity associated gene (FTO) in cancer. FTO initially became known as the strongest genetic link for human obesity. Only in 2010, 16 years after its discovery, was its enzymatic function as a demethylase clarified, and only recently has its role in the development of cancer been revealed. FTO functions are challenging to study and interpret because of its genome-wide effects on transcript turnover and translation. We review the discovery of FTO and its enzymatic function, the tumor-promoting and suppressive roles of FTO in selected cancer types, and its potential as a therapeutic target.
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21
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Qu J, Yan H, Hou Y, Cao W, Liu Y, Zhang E, He J, Cai Z. RNA demethylase ALKBH5 in cancer: from mechanisms to therapeutic potential. J Hematol Oncol 2022; 15:8. [PMID: 35063010 PMCID: PMC8780705 DOI: 10.1186/s13045-022-01224-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/03/2022] [Indexed: 12/16/2022] Open
Abstract
RNA demethylase ALKBH5 takes part in the modulation of N6-methyladenosine (m6A) modification and controls various cell processes. ALKBH5-mediated m6A demethylation regulates gene expression by affecting multiple events in RNA metabolism, e.g., pre-mRNA processing, mRNA decay and translation. Mounting evidence shows that ALKBH5 plays critical roles in a variety of human malignancies, mostly via post-transcriptional regulation of oncogenes or tumor suppressors in an m6A-dependent manner. Meanwhile, increasing non-coding RNAs are recognized as functional targets of ALKBH5 in cancers. Here we reviewed up-to-date findings about the pathological roles of ALKBH5 in cancer, the molecular mechanisms by which it exerts its functions, as well as the underlying mechanism of its dysregulation. We also discussed the therapeutic implications of targeting ALKBH5 in cancer and potential ALKBH5-targeting strategies.
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Affiliation(s)
- Jianwei Qu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haimeng Yan
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yifan Hou
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wen Cao
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yang Liu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Enfan Zhang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingsong He
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Cai
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
- Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.
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22
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Schmidl D, Jonasson NSW, Menke A, Schneider S, Daumann L. Spectroscopic and in vitro investigations of Fe2+/α-Ketoglutarate-dependent enzymes involved in nucleic acid repair and modification. Chembiochem 2022; 23:e202100605. [PMID: 35040547 PMCID: PMC9401043 DOI: 10.1002/cbic.202100605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/14/2022] [Indexed: 11/08/2022]
Abstract
The activation of molecular oxygen for the highly selective functionalization and repair of DNA and RNA nucleobases is achieved by α-ketoglutarate (α-KG)/iron-dependent dioxygenases. Enzymes of special interest are the human homologs AlkBH of Escherichia coli EcAlkB and ten-eleven translocation (TET) enzymes. These enzymes are involved in demethylation or dealkylation of DNA and RNA, although additional physiological functions are continuously being revealed. Given their importance, studying enzyme-substrate interactions, turnover and kinetic parameters is pivotal for the understanding of the mode of action of these enzymes. Diverse analytical methods, including X-ray crystallography, UV/Vis absorption, electron paramagnetic resonance (EPR), circular dichroism (CD) and NMR spectroscopy have been employed to study the changes in the active site and the overall enzyme structure upon substrate, cofactor and inhibitor addition. Several methods are now available to assess activity of these enzymes. By discussing limitations and possibilities of these techniques for EcAlkB, AlkBH and TET we aim to give a comprehensive synopsis from a bioinorganic point of view, addressing researchers from different disciplines working in the highly interdisciplinary and rapidly evolving field of epigenetic processes and DNA/RNA repair and modification.
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Affiliation(s)
- David Schmidl
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Niko S W Jonasson
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Annika Menke
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Sabine Schneider
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Lena Daumann
- Ludwig-Maximilians-Universität München, Department of Chemistry, Butenandtstr. 5-13, 81377, München, GERMANY
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23
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Pasin F, Daròs JA, Tzanetakis IE. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6534904. [PMID: 35195244 PMCID: PMC9249622 DOI: 10.1093/femsre/fuac011] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Potyviridae, the largest family of known RNA viruses (realm Riboviria), belongs to the picorna-like supergroup and has important agricultural and ecological impacts. Potyvirid genomes are translated into polyproteins, which are in turn hydrolyzed to release mature products. Recent sequencing efforts revealed an unprecedented number of potyvirids with a rich variability in gene content and genomic layouts. Here, we review the heterogeneity of non-core modules that expand the structural and functional diversity of the potyvirid proteomes. We provide a family-wide classification of P1 proteinases into the functional Types A and B, and discuss pretty interesting sweet potato potyviral ORF (PISPO), putative zinc fingers, and alkylation B (AlkB)—non-core modules found within P1 cistrons. The atypical inosine triphosphate pyrophosphatase (ITPase/HAM1), as well as the pseudo tobacco mosaic virus-like coat protein (TMV-like CP) are discussed alongside homologs of unrelated virus taxa. Family-wide abundance of the multitasking helper component proteinase (HC-pro) is revised. Functional connections between non-core modules are highlighted to support host niche adaptation and immune evasion as main drivers of the Potyviridae evolutionary radiation. Potential biotechnological and synthetic biology applications of potyvirid leader proteinases and non-core modules are finally explored.
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Affiliation(s)
- Fabio Pasin
- Corresponding author: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIC-UPV), UPV Building 8E, Ingeniero Fausto Elio, 46011 Valencia, Spain. E-mail:
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIC-UPV), 46011 Valencia, Spain
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, 72701 Fayetteville, AR, USA
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Vincent MS, Uphoff S. Cellular heterogeneity in DNA alkylation repair increases population genetic plasticity. Nucleic Acids Res 2021; 49:12320-12331. [PMID: 34850170 PMCID: PMC8643705 DOI: 10.1093/nar/gkab1143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022] Open
Abstract
DNA repair mechanisms fulfil a dual role, as they are essential for cell survival and genome maintenance. Here, we studied how cells regulate the interplay between DNA repair and mutation. We focused on the adaptive response that increases the resistance of Escherichia coli cells to DNA alkylation damage. Combination of single-molecule imaging and microfluidic-based single-cell microscopy showed that noise in the gene activation timing of the master regulator Ada is accurately propagated to generate a distinct subpopulation of cells in which all proteins of the adaptive response are essentially absent. Whereas genetic deletion of these proteins causes extreme sensitivity to alkylation stress, a temporary lack of expression is tolerated and increases genetic plasticity of the whole population. We demonstrated this by monitoring the dynamics of nascent DNA mismatches during alkylation stress as well as the frequency of fixed mutations that are generated by the distinct subpopulations of the adaptive response. We propose that stochastic modulation of DNA repair capacity by the adaptive response creates a viable hypermutable subpopulation of cells that acts as a source of genetic diversity in a clonal population.
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Affiliation(s)
- Maxence S Vincent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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25
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Perry GS, Das M, Woon ECY. Inhibition of AlkB Nucleic Acid Demethylases: Promising New Epigenetic Targets. J Med Chem 2021; 64:16974-17003. [PMID: 34792334 DOI: 10.1021/acs.jmedchem.1c01694] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The AlkB family of nucleic acid demethylases is currently of intense chemical, biological, and medical interest because of its critical roles in several key cellular processes, including epigenetic gene regulation, RNA metabolism, and DNA repair. Emerging evidence suggests that dysregulation of AlkB demethylases may underlie the pathogenesis of several human diseases, particularly obesity, diabetes, and cancer. Hence there is strong interest in developing selective inhibitors for these enzymes to facilitate their mechanistic and functional studies and to validate their therapeutic potential. Herein we review the remarkable advances made over the past 20 years in AlkB demethylase inhibition research. We discuss the rational design of reported inhibitors, their mode-of-binding, selectivity, cellular activity, and therapeutic opportunities. We further discuss unexplored structural elements of the AlkB subfamilies and propose potential strategies to enable subfamily selectivity. It is hoped that this perspective will inspire novel inhibitor design and advance drug discovery research in this field.
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Affiliation(s)
- Gemma S Perry
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Mohua Das
- Lab of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Esther C Y Woon
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
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26
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Berger MB, Walker AR, Vázquez-Montelongo EA, Cisneros GA. Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families. Phys Chem Chem Phys 2021; 23:22227-22240. [PMID: 34586107 PMCID: PMC8516722 DOI: 10.1039/d1cp03800a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA alkylation is used as the key epigenetic mark in eukaryotes, however, most alkylation in DNA can result in deleterious effects. Therefore, this process needs to be tightly regulated. The enzymes of the AlkB and Ten-Eleven Translocation (TET) families are members of the Fe and alpha-ketoglutarate-dependent superfamily of enzymes that are tasked with dealkylating DNA and RNA in cells. Members of these families span all species and are an integral part of transcriptional regulation. While both families catalyze oxidative dealkylation of various bases, each has specific preference for alkylated base type as well as distinct catalytic mechanisms. This perspective aims to provide an overview of computational work carried out to investigate several members of these enzyme families including AlkB, ALKB Homolog 2, ALKB Homolog 3 and Ten-Eleven Translocate 2. Insights into structural details, mutagenesis studies, reaction path analysis, electronic structure features in the active site, and substrate preferences are presented and discussed.
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Affiliation(s)
- Madison B Berger
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
| | - Alice R Walker
- Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
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27
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Zhou LL, Xu H, Huang Y, Yang CG. Targeting the RNA demethylase FTO for cancer therapy. RSC Chem Biol 2021; 2:1352-1369. [PMID: 34704042 PMCID: PMC8496078 DOI: 10.1039/d1cb00075f] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/26/2021] [Indexed: 01/02/2023] Open
Abstract
N 6-Methyladenosine (m6A) is the most prevalent internal modification on mRNA and represents a new layer of gene expression in eukaryotes. The field of m6A-encoded epitranscriptomics was rejuvenated with the discovery of fat mass and obesity-associated protein (FTO) as the first m6A demethylase responsible for RNA modification in cells. Increasing evidence has revealed that FTO is significantly involved in physiological processes, and its dysregulation is implicated in various human diseases. Considering this functional significance, developing small-molecule modulators of the FTO protein represents a novel direction for biology research. However, such modulators remain in the early stages of development. Here, our review mainly focuses on the progress of FTO inhibitor development to date. We summarize screening methods used to identify FTO modulators, techniques used to assess the biological effects of these modulators, strategies used to achieve selective inhibition of FTO rather than its homologues, and the results of investigations of FTO modulator modes of action and anticancer efficacy. Thus, this review aims to facilitate novel chemical entity discovery, probe FTO biology, and promote the validation of FTO as a clinical drug target for cancer treatment.
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Affiliation(s)
- Lin-Lin Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of the Chinese Academy of Sciences Beijing 100049 China
| | - Hongjiao Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of the Chinese Academy of Sciences Beijing 100049 China
| | - Yue Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of the Chinese Academy of Sciences Beijing 100049 China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
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28
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DNA Demethylation in the Processes of Repair and Epigenetic Regulation Performed by 2-Ketoglutarate-Dependent DNA Dioxygenases. Int J Mol Sci 2021; 22:ijms221910540. [PMID: 34638881 PMCID: PMC8508711 DOI: 10.3390/ijms221910540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/05/2022] Open
Abstract
Site-specific DNA methylation plays an important role in epigenetic regulation of gene expression. Chemical methylation of DNA, including the formation of various methylated nitrogenous bases, leads to the formation of genotoxic modifications that impair DNA functions. Despite the fact that different pathways give rise to methyl groups in DNA, the main pathway for their removal is oxidative demethylation, which is catalyzed by nonheme Fe(II)/α-ketoglutarate–dependent DNA dioxygenases. DNA dioxygenases share a common catalytic mechanism of the oxidation of the alkyl groups on nitrogenous bases in nucleic acids. This review presents generalized data on the catalytic mechanism of action of DNA dioxygenases and on the participation of typical representatives of this superfamily, such as prokaryotic enzyme AlkB and eukaryotic enzymes ALKBH1–8 and TET1–3, in both processes of direct repair of alkylated DNA adducts and in the removal of an epigenetic mark (5-methylcytosine).
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29
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Purslow JA, Nguyen TT, Khatiwada B, Singh A, Venditti V. N 6-methyladenosine binding induces a metal-centered rearrangement that activates the human RNA demethylase Alkbh5. SCIENCE ADVANCES 2021; 7:7/34/eabi8215. [PMID: 34407931 PMCID: PMC8373141 DOI: 10.1126/sciadv.abi8215] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/29/2021] [Indexed: 05/13/2023]
Abstract
Alkbh5 catalyzes demethylation of the N 6-methyladenosine (m6A), an epigenetic mark that controls several physiological processes including carcinogenesis and stem cell differentiation. The activity of Alkbh5 comprises two coupled reactions. The first reaction involves decarboxylation of α-ketoglutarate (αKG) and formation of a Fe4+═O species. This oxyferryl intermediate oxidizes the m6A to reestablish the canonical base. Despite coupling between the two reactions being required for the correct Alkbh5 functioning, the mechanisms linking dioxygen activation to m6A binding are not fully understood. Here, we use solution NMR to investigate the structure and dynamics of apo and holo Alkbh5. We show that binding of m6A to Alkbh5 induces a metal-centered rearrangement of αKG that increases the exposed area of the metal, making it available for binding O2 Our study reveals the molecular mechanisms underlying activation of Alkbh5, therefore opening new perspectives for the design of novel strategies to control gene expression and cancer progression.
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Affiliation(s)
| | - Trang T Nguyen
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | | | - Aayushi Singh
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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30
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Zhao S, Devega R, Francois A, Kidane D. Human ALKBH6 Is Required for Maintenance of Genomic Stability and Promoting Cell Survival During Exposure of Alkylating Agents in Pancreatic Cancer. Front Genet 2021; 12:635808. [PMID: 33897761 PMCID: PMC8058185 DOI: 10.3389/fgene.2021.635808] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/08/2021] [Indexed: 12/21/2022] Open
Abstract
Alpha-ketoglutarate-dependent dioxygenase (ALKBH) is a DNA repair gene involved in the repair of alkylating DNA damage. There are nine types of ALKBH (ALKBH1-8 and FTO) identified in humans. In particular, certain types of ALKBH enzymes are dioxygenases that directly reverse DNA methylation damage via transfer of a methyl group from the DNA adduct onto α-ketoglutarate and release of metabolic products including succinate and formaldehyde. Here, we tested whether ALKBH6 plays a significant role in preventing alkylating DNA damage and decreasing genomic instability in pancreatic cancer cells. Using an E. coli strain deficient with ALKB, we found that ALKBH6 complements ALKB deficiency and increases resistance after alkylating agent treatment. In particular, the loss of ALKBH6 in human pancreatic cancer cells increases alkylating agent-induced DNA damage and significantly decreases cell survival. Furthermore, in silico analysis from The Cancer Genome Atlas (TCGA) database suggests that overexpression of ALKBH6 provides better survival outcomes in patients with pancreatic cancer. Overall, our data suggest that ALKBH6 is required to maintain the integrity of the genome and promote cell survival of pancreatic cancer cells.
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Affiliation(s)
- Shengyuan Zhao
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
| | - Rodan Devega
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
| | - Aaliyah Francois
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
| | - Dawit Kidane
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
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31
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Li Q, He W, Wan G. Methyladenosine Modification in RNAs: Classification and Roles in Gastrointestinal Cancers. Front Oncol 2021; 10:586789. [PMID: 33598423 PMCID: PMC7883673 DOI: 10.3389/fonc.2020.586789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Cellular ribonucleic acids (RNAs), including messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs), harbor more than 150 forms of chemical modifications, among which methylation modifications are dynamically regulated and play significant roles in RNA metabolism. Recently, dysregulation of RNA methylation modifications is found to be linked to various physiological bioprocesses and many human diseases. Gastric cancer (GC) and colorectal cancer (CRC) are two main gastrointestinal-related cancers (GIC) and the most leading causes of cancer-related death worldwide. In-depth understanding of molecular mechanisms on GIC can provide important insights in developing novel treatment strategies for GICs. In this review, we focus on the multitude of epigenetic changes of RNA methlyadenosine modifications in gene expression, and their roles in GIC tumorigenesis, progression, and drug resistance, and aim to provide the potential therapeutic regimens for GICs.
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Affiliation(s)
- Qinghai Li
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Weiling He
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Guohui Wan
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
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32
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Xu B, Liu D, Wang Z, Tian R, Zuo Y. Multi-substrate selectivity based on key loops and non-homologous domains: new insight into ALKBH family. Cell Mol Life Sci 2021; 78:129-141. [PMID: 32642789 PMCID: PMC11072825 DOI: 10.1007/s00018-020-03594-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/24/2020] [Accepted: 07/03/2020] [Indexed: 12/16/2022]
Abstract
AlkB homologs (ALKBH) are a family of specific demethylases that depend on Fe2+ and α-ketoglutarate to catalyze demethylation on different substrates, including ssDNA, dsDNA, mRNA, tRNA, and proteins. Previous studies have made great progress in determining the sequence, structure, and molecular mechanism of the ALKBH family. Here, we first review the multi-substrate selectivity of the ALKBH demethylase family from the perspective of sequence and structural evolution. The construction of the phylogenetic tree and the comparison of key loops and non-homologous domains indicate that the paralogs with close evolutionary relationship have similar domain compositions. The structures show that the lack and variations of four key loops change the shape of clefts to cause the differences in substrate affinity, and non-homologous domains may be related to the compatibility of multiple substrates. We anticipate that the new insights into selectivity determinants of the ALKBH family are useful for understanding the demethylation mechanisms.
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Affiliation(s)
- Baofang Xu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Dongyang Liu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zerong Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ruixia Tian
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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Oxidative demethylase ALKBH5 repairs DNA alkylation damage and protects against alkylation-induced toxicity. Biochem Biophys Res Commun 2020; 534:114-120. [PMID: 33321288 DOI: 10.1016/j.bbrc.2020.12.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/05/2020] [Indexed: 11/22/2022]
Abstract
DNA integrity is challenged by both exogenous and endogenous alkylating agents. DNA repair proteins such as Escherichia coli AlkB family of enzymes can repair 1-methyladenine and 3-methylcytosine adducts by oxidative demethylation. Human AlkB homologue 5 (ALKBH5) is RNA N6-methyladenine demethylase and not known to be involved in DNA repair. Herein we show that ALKBH5 also has weak DNA repair activity and it can demethylate DNA 3-methylcytosine. The mutation of the amino acid residues involved in demethylation also abolishes the DNA repair activity of ALKBH5. Overexpression of ALKBH5 decreases the 3-methylcytosine level in genomic DNA and reduces the cytotoxic effects of the DNA damaging alkylating agent methyl methanesulfonate. Thus, demethylation by ALKBH5 might play a supporting role in maintaining genome integrity.
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34
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Latifi R, Minnick JL, Quesne MG, de Visser SP, Tahsini L. Computational studies of DNA base repair mechanisms by nonheme iron dioxygenases: selective epoxidation and hydroxylation pathways. Dalton Trans 2020; 49:4266-4276. [PMID: 32141456 DOI: 10.1039/d0dt00007h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
DNA base repair mechanisms of alkylated DNA bases is an important reaction in chemical biology and particularly in the human body. It is typically catalyzed by an α-ketoglutarate-dependent nonheme iron dioxygenase named the AlkB repair enzyme. In this work we report a detailed computational study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases. In particular, we investigate the aliphatic hydroxylation and C[double bond, length as m-dash]C epoxidation mechanisms of alkylated DNA bases by a high-valent iron(iv)-oxo intermediate. Our computational studies use quantum mechanics/molecular mechanics methods on full enzymatic structures as well as cluster models on active site systems. The work shows that the iron(iv)-oxo species is rapidly formed after dioxygen binding to an iron(ii) center and passes a bicyclic ring structure as intermediate. Subsequent cluster models explore the mechanism of substrate hydroxylation and epoxidation of alkylated DNA bases. The work shows low energy barriers for substrate activation and consequently energetically feasible pathways are predicted. Overall, the work shows that a high-valent iron(iv)-oxo species can efficiently dealkylate alkylated DNA bases and return them into their original form.
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Affiliation(s)
- Reza Latifi
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
| | - Jennifer L Minnick
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
| | - Matthew G Quesne
- Cardiff University, School of Chemistry, Main Building, Park Place, Cardiff, CF10 3AT, UK. and Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon, OX110FA, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, 131 Princess Street, Manchester M1 7DN, UK.
| | - Laleh Tahsini
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
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35
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Van Deuren V, Plessers S, Robben J. Structural determinants of nucleobase modification recognition in the AlkB family of dioxygenases. DNA Repair (Amst) 2020; 96:102995. [PMID: 33069898 DOI: 10.1016/j.dnarep.2020.102995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 01/29/2023]
Abstract
Iron-dependent dioxygenases of the AlkB protein family found in most organisms throughout the tree of life play a major role in oxidative dealkylation processes. Many of these enzymes have attracted the attention of researchers across different fields and have been subjected to thorough biochemical characterization because of their link to human health and disease. For example, several mammalian AlkB homologues are involved in the direct reversal of alkylation damage in DNA, while others have been shown to play a regulatory role in epigenetic or epitranscriptomic nucleic acid methylation or in post-translational modifications such as acetylation of actin filaments. These studies show that that divergence in amino acid sequence and structure leads to different characteristics and substrate specificities. In this review, we aim to summarize current insights in the structural features involved in the substrate selection of AlkB homologues, with focus on nucleic acid interactions.
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Affiliation(s)
- V Van Deuren
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001, Heverlee, Belgium
| | - S Plessers
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001, Heverlee, Belgium
| | - J Robben
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001, Heverlee, Belgium.
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Carpentier P, Leprêtre C, Basset C, Douki T, Torelli S, Duarte V, Hamdane D, Fontecave M, Atta M. Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction. Nucleic Acids Res 2020; 48:9918-9930. [PMID: 32785618 PMCID: PMC7515727 DOI: 10.1093/nar/gkaa667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 11/30/2022] Open
Abstract
MiaE (2-methylthio-N6-isopentenyl-adenosine37-tRNA monooxygenase) is a unique non-heme diiron enzyme that catalyzes the O2-dependent post-transcriptional allylic hydroxylation of a hypermodified nucleotide 2-methylthio-N6-isopentenyl-adenosine (ms2i6A37) at position 37 of selected tRNA molecules to produce 2-methylthio-N6-4-hydroxyisopentenyl-adenosine (ms2io6A37). Here, we report the in vivo activity, biochemical, spectroscopic characterization and X-ray crystal structure of MiaE from Pseudomonas putida. The investigation demonstrates that the putative pp-2188 gene encodes a MiaE enzyme. The structure shows that Pp-MiaE consists of a catalytic diiron(III) domain with a four alpha-helix bundle fold. A docking model of Pp-MiaE in complex with tRNA, combined with site directed mutagenesis and in vivo activity shed light on the importance of an additional linker region for substrate tRNA recognition. Finally, krypton-pressurized Pp-MiaE experiments, revealed the presence of defined O2 site along a conserved hydrophobic tunnel leading to the diiron active center.
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Affiliation(s)
- Philippe Carpentier
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Chloé Leprêtre
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Christian Basset
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Thierry Douki
- Univ. Grenoble Alpes, CEA, CNRS, SyMMES, F-38000, 17 avenue des martyrs Grenoble, France
| | - Stéphane Torelli
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Victor Duarte
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, UMR CNRS 8229, Collège de France-CNRS-Sorbonne Université, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR CNRS 8229, Collège de France-CNRS-Sorbonne Université, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Mohamed Atta
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
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Lenz SAP, Li D, Wetmore SD. Insights into the Direct Oxidative Repair of Etheno Lesions: MD and QM/MM Study on the Substrate Scope of ALKBH2 and AlkB. DNA Repair (Amst) 2020; 96:102944. [PMID: 33161373 DOI: 10.1016/j.dnarep.2020.102944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 01/09/2023]
Abstract
E. coli AlkB and human ALKBH2 belong to the AlkB family enzymes, which contain several α-ketoglutarate (α-KG)/Fe(II)-dependent dioxygenases that repair alkylated DNA. Specifically, the AlkB enzymes catalyze decarboxylation of α-KG to generate a high-valent Fe(IV)-oxo species that oxidizes alkyl groups on DNA adducts. AlkB and ALKBH2 have been reported to differentially repair select etheno adducts, with preferences for 1,N6-ethenoadenine (1,N6-εA) and 3,N4-ethenocytosine (3,N4-εC) over 1,N2-ethenoguanine (1,N2-εG). However, N2,3-ethenoguanine (N2,3-εG), the most common etheno adduct, is not repaired by the AlkB enzymes. Unfortunately, a structural understanding of the differential activity of E. coli AlkB and human ALKBH2 is lacking due to challenges acquiring atomistic details for a range of substrates using experiments. This study uses both molecular dynamics (MD) simulations and ONIOM(QM:MM) calculations to determine how the active site changes upon binding each etheno adduct and characterizes the corresponding catalytic impacts. Our data reveal that the preferred etheno substrates (1,N6-εA and 3,N4-εC) form favorable interactions with catalytic residues that situate the lesion near the Fe(IV)-oxo species and permit efficient oxidation. In contrast, although the damage remains correctly aligned with respect to the Fe(IV)-oxo moiety, repair of 1,N2-εG is mitigated by increased solvation of the active site and a larger distance between Fe(IV)-oxo and the aberrant carbons. Binding of non-substrate N2,3-εG in the active site disrupts key DNA-enzyme interactions, and positions the aberrant carbon atoms even further from the Fe(IV)-oxo species, leading to prohibitively high barriers for oxidative catalysis. Overall, our calculations provide the first structural insight required to rationalize the experimentally-reported substrate specificities of AlkB and ALKBH2 and thereby highlight the roles of several active site residues in the repair of etheno adducts that directly correlates with available experimental data. These proposed catalytic strategies can likely be generalized to other α-KG/Fe(II)-dependent dioxygenases that play similar critical biological roles, including epigenetic and post-translational regulation.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, 02881, USA
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
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Rabe P, Beale JH, Butryn A, Aller P, Dirr A, Lang PA, Axford DN, Carr SB, Leissing TM, McDonough MA, Davy B, Ebrahim A, Orlans J, Storm SLS, Orville AM, Schofield CJ, Owen RL. Anaerobic fixed-target serial crystallography. IUCRJ 2020; 7:901-912. [PMID: 32939282 PMCID: PMC7467159 DOI: 10.1107/s2052252520010374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/27/2020] [Indexed: 05/04/2023]
Abstract
Cryogenic X-ray diffraction is a powerful tool for crystallographic studies on enzymes including oxygenases and oxidases. Amongst the benefits that cryo-conditions (usually employing a nitro-gen cryo-stream at 100 K) enable, is data collection of di-oxy-gen-sensitive samples. Although not strictly anaerobic, at low temperatures the vitreous ice conditions severely restrict O2 diffusion into and/or through the protein crystal. Cryo-conditions limit chemical reactivity, including reactions that require significant conformational changes. By contrast, data collection at room temperature imposes fewer restrictions on diffusion and reactivity; room-temperature serial methods are thus becoming common at synchrotrons and XFELs. However, maintaining an anaerobic environment for di-oxy-gen-dependent enzymes has not been explored for serial room-temperature data collection at synchrotron light sources. This work describes a methodology that employs an adaptation of the 'sheet-on-sheet' sample mount, which is suitable for the low-dose room-temperature data collection of anaerobic samples at synchrotron light sources. The method is characterized by easy sample preparation in an anaerobic glovebox, gentle handling of crystals, low sample consumption and preservation of a localized anaerobic environment over the timescale of the experiment (<5 min). The utility of the method is highlighted by studies with three X-ray-radiation-sensitive Fe(II)-containing model enzymes: the 2-oxoglutarate-dependent l-arginine hy-droxy-lase VioC and the DNA repair enzyme AlkB, as well as the oxidase isopenicillin N synthase (IPNS), which is involved in the biosynthesis of all penicillin and cephalosporin antibiotics.
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Affiliation(s)
- Patrick Rabe
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Agata Butryn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Anna Dirr
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Pauline A. Lang
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Danny N. Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Stephen B. Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot Oxfordshire OX11 0FA, United Kingdom
| | - Thomas M. Leissing
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A. McDonough
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Bradley Davy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Ali Ebrahim
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Julien Orlans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- UMR0203, Biologie Fonctionnelle, Insectes et Interactions, Institut National des Sciences Appliquées de Lyon, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, University of Lyon, Villeurbanne F-69621, France
| | - Selina L. S. Storm
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
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Mammalian ALKBH1 serves as an N 6-mA demethylase of unpairing DNA. Cell Res 2020; 30:197-210. [PMID: 32051560 PMCID: PMC7054317 DOI: 10.1038/s41422-019-0237-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/30/2019] [Indexed: 01/07/2023] Open
Abstract
N6-methyladenine (N6-mA) of DNA is an emerging epigenetic mark in mammalian genome. Levels of N6-mA undergo drastic fluctuation during early embryogenesis, indicative of active regulation. Here we show that the 2-oxoglutarate-dependent oxygenase ALKBH1 functions as a nuclear eraser of N6-mA in unpairing regions (e.g., SIDD, Stress-Induced DNA Double Helix Destabilization regions) of mammalian genomes. Enzymatic profiling studies revealed that ALKBH1 prefers bubbled or bulged DNAs as substrate, instead of single-stranded (ss-) or double-stranded (ds-) DNAs. Structural studies of ALKBH1 revealed an unexpected "stretch-out" conformation of its "Flip1" motif, a conserved element that usually bends over catalytic center to facilitate substrate base flipping in other DNA demethylases. Thus, lack of a bending "Flip1" explains the observed preference of ALKBH1 for unpairing substrates, in which the flipped N6-mA is primed for catalysis. Co-crystal structural studies of ALKBH1 bound to a 21-mer bulged DNA explained the need of both flanking duplexes and a flipped base for recognition and catalysis. Key elements (e.g., an ALKBH1-specific α1 helix) as well as residues contributing to structural integrity and catalytic activity were validated by structure-based mutagenesis studies. Furthermore, ssDNA-seq and DIP-seq analyses revealed significant co-occurrence of base unpairing regions with N6-mA in mouse genome. Collectively, our biochemical, structural and genomic studies suggest that ALKBH1 is an important DNA demethylase that regulates genome N6-mA turnover of unpairing regions associated with dynamic chromosome regulation.
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Chaturvedi S, Ramanan R, Lehnert N, Schofield CJ, Karabencheva-Christova TG, Christov CZ. Catalysis by the Non-Heme Iron(II) Histone Demethylase PHF8 Involves Iron Center Rearrangement and Conformational Modulation of Substrate Orientation. ACS Catal 2020; 10:1195-1209. [PMID: 31976154 PMCID: PMC6970271 DOI: 10.1021/acscatal.9b04907] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/10/2019] [Indexed: 02/07/2023]
Abstract
PHF8 (KDM7B) is a human non-heme 2-oxoglutarate (2OG) JmjC domain oxygenase that catalyzes the demethylation of the di/mono-Nε-methylated K9 residue of histone H3. Altered PHF8 activity is linked to genetic diseases and cancer; thus, it is an interesting target for epigenetic modulation. We describe the use of combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations to explore the mechanism of PHF8, including dioxygen activation, 2OG binding modes, and substrate demethylation steps. A PHF8 crystal structure manifests the 2OG C-1 carboxylate bound to iron in a nonproductive orientation, i.e., trans to His247. A ferryl-oxo intermediate formed by activating dioxygen bound to the vacant site in this complex would be nonproductive, i.e., "off-line" with respect to reaction with Nε-methylated K9. We show rearrangement of the "off-line" ferryl-oxo intermediate to a productive "in-line" geometry via a solvent exchange reaction (called "ferryl-flip") is energetically unfavorable. The calculations imply that movement of the 2OG C-1 carboxylate prior to dioxygen binding at a five-coordination stage in catalysis proceeds with a low barrier, suggesting that two possible 2OG C-1 carboxylate geometries can coexist at room temperature. We explored alternative mechanisms for hydrogen atom transfer and show that second sphere interactions orient the Nε-methylated lysine in a conformation where hydrogen abstraction from a methyl C-H bond is energetically more favorable than hydrogen abstraction from the N-H bond of the protonated Nε-methyl group. Using multiple HAT reaction path calculations, we demonstrate the crucial role of conformational flexibility in effective hydrogen transfer. Subsequent hydroxylation occurs through a rebound mechanism, which is energetically preferred compared to desaturation, due to second sphere interactions. The overall mechanistic insights reveal the crucial role of iron-center rearrangement, second sphere interactions, and conformational flexibility in PHF8 catalysis and provide knowledge useful for the design of mechanism-based PHF8 inhibitors.
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Affiliation(s)
- Shobhit
S. Chaturvedi
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Rajeev Ramanan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Nicolai Lehnert
- Department
of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | - Christo Z. Christov
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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41
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Kanazhevskaya LY, Smyshlyaev DA, Alekseeva IV, Fedorova OS. Conformational Dynamics of Dioxygenase AlkB and DNA in the Course of Catalytically Active Enzyme–Substrate Complex Formation. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019060190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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42
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Li H, Zhu W, Liu Y. Mechanism of Uncoupled Carbocyclization and Epimerization Catalyzed by Two Non-Heme Iron/α-Ketoglutarate Dependent Enzymes. J Chem Inf Model 2019; 59:5086-5098. [PMID: 31790238 DOI: 10.1021/acs.jcim.9b00837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The non-heme iron/α-ketoglutarate dependent enzymes SnoK and SnoN from Streptomyces nogalater are involved in the biosynthesis of anthracycline nogalamycin. Although they have similar active sites, SnoK is responsible for carbocyclization whereas SnoN solely catalyzes the hydroxyl epimerization. Herein, we performed docking, molecular simulations, and a series of combined quantum mechanics and molecular mechanics (QM/MM) calculations to illuminate the mechanisms of two enzymes. The catalytic reactions of two enzymes occur on the quintet state surface. For SnoK, the whole reaction includes two separated hydrogen-abstraction steps and one radical addition, and the latter step is calculated to be rate limiting with an energy barrier of 21.7 kcal/mol. Residue D106 is confirmed to participate in the construction of the hydrogen bond network, which plays a crucial role in positioning the bulky substrate in a specific orientation. Moreover, it is found that SnoN is only responsible for the hydrogen abstraction of the intermediate, and no residue was suggested to be suitable for donating a hydrogen atom to the substrate radical, which further confirms the suggestion based on experiments that either a cellular reductant or another enzyme protein could donate a hydrogen atom to the substrate. Our docking results coincide with the previous structural study that the different roles of two enzymes are achieved by minor changes in the alignment of the substrates in front of the reactive ferryl-oxo species. This work highlights the reaction mechanisms catalyzed by SnoK and SnoN, which is helpful for engineering the enzymes for the biosynthesis of anthracycline nogalamycin.
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Affiliation(s)
- Hong Li
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , China
| | - Wenyou Zhu
- College of Chemistry and Chemical Engineering , Xuzhou Institute of Technology , Xuzhou , Jiangsu 221111 , China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , China
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43
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Kanazhevskaya LY, Alekseeva IV, Fedorova OS. A Single-Turnover Kinetic Study of DNA Demethylation Catalyzed by Fe(II)/α-Ketoglutarate-Dependent Dioxygenase AlkB. Molecules 2019; 24:molecules24244576. [PMID: 31847292 PMCID: PMC6943663 DOI: 10.3390/molecules24244576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/26/2019] [Accepted: 12/11/2019] [Indexed: 01/31/2023] Open
Abstract
AlkB is a Fe(II)/α-ketoglutarate-dependent dioxygenase that repairs some alkylated bases of DNA and RNA in Escherichia coli. In the course of catalysis, oxidation of a co-substrate (α-ketoglutarate, αKG) leads to the formation of a highly reactive ‘oxyferryl’ enzyme-bound intermediate, Fe(IV) = O, ensuring hydroxylation of the alkyl nucleobase adducts. Previous studies have revealed that AlkB is a flexible protein and can adopt different conformations during interactions with cofactors and DNA. To assess the conformational dynamics of the enzyme in complex with single- or double-stranded DNA in real-time mode, we employed the stopped-flow fluorescence method. N1-Methyladenine (m1A) introduced into a sequence of 15-mer oligonucleotides was chosen as the specific damage. Single-turnover kinetics were monitored by means of intrinsic fluorescence of the protein’s Trp residues, fluorescent base analogue 2-aminopurine (2aPu), and a dye–quencher pair (FAM/BHQ1). For all the fluorescent labels, the fluorescent traces showed several phases of consistent conformational changes, which were assigned to specific steps of the enzymatic process. These data offer an overall picture of the structural dynamics of AlkB and DNA during their interaction.
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Affiliation(s)
| | | | - Olga S. Fedorova
- Correspondence: (L.Y.K.); (O.S.F.); Tel.: +7-(383)-3635175 (O.S.F.)
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44
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Bian K, Lenz SAP, Tang Q, Chen F, Qi R, Jost M, Drennan CL, Essigmann JM, Wetmore SD, Li D. DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro. Nucleic Acids Res 2019; 47:5522-5529. [PMID: 31114894 PMCID: PMC6582317 DOI: 10.1093/nar/gkz395] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 01/08/2023] Open
Abstract
5-Methylcytosine (5mC) in DNA CpG islands is an important epigenetic biomarker for mammalian gene regulation. It is oxidized to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) by the ten-eleven translocation (TET) family enzymes, which are α-ketoglutarate (α-KG)/Fe(II)-dependent dioxygenases. In this work, we demonstrate that the epigenetic marker 5mC is modified to 5hmC, 5fC, and 5caC in vitro by another class of α-KG/Fe(II)-dependent proteins—the DNA repair enzymes in the AlkB family, which include ALKBH2, ALKBH3 in huamn and AlkB in Escherichia coli. Theoretical calculations indicate that these enzymes may bind 5mC in the syn-conformation, placing the methyl group comparable to 3-methylcytosine, the prototypic substrate of AlkB. This is the first demonstration of the AlkB proteins to oxidize a methyl group attached to carbon, instead of nitrogen, on a DNA base. These observations suggest a broader role in epigenetics for these DNA repair proteins.
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Affiliation(s)
- Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Fangyi Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Rui Qi
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John M Essigmann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
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Wang SY, Mao H, Shibuya H, Uzawa S, O’Brown ZK, Wesenberg S, Shin N, Saito TT, Gao J, Meyer BJ, Colaiácovo MP, Greer EL. The demethylase NMAD-1 regulates DNA replication and repair in the Caenorhabditis elegans germline. PLoS Genet 2019; 15:e1008252. [PMID: 31283754 PMCID: PMC6638966 DOI: 10.1371/journal.pgen.1008252] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/18/2019] [Accepted: 06/18/2019] [Indexed: 01/03/2023] Open
Abstract
The biological roles of nucleic acid methylation, other than at the C5-position of cytosines in CpG dinucleotides, are still not well understood. Here, we report genetic evidence for a critical role for the putative DNA demethylase NMAD-1 in regulating meiosis in C. elegans. nmad-1 mutants have reduced fertility. They show defects in prophase I of meiosis, which leads to reduced embryo production and an increased incidence of males due to defective chromosomal segregation. In nmad-1 mutant worms, nuclear staging beginning at the leptotene and zygotene stages is disorganized, the cohesin complex is mislocalized at the diplotene and diakinesis stages, and chromosomes are improperly condensed, fused, or lost by the end of diakinesis. RNA sequencing of the nmad-1 germline revealed reduced induction of DNA replication and DNA damage response genes during meiosis, which was coupled with delayed DNA replication, impaired DNA repair and increased apoptosis of maturing oocytes. To begin to understand how NMAD-1 regulates DNA replication and repair, we used immunoprecipitation and mass spectrometry to identify NMAD-1 binding proteins. NMAD-1 binds to multiple proteins that regulate DNA repair and replication, including topoisomerase TOP-2 and co-localizes with TOP-2 on chromatin. Moreover, the majority of TOP-2 binding to chromatin depends on NMAD-1. These results suggest that NMAD-1 functions at DNA replication sites to regulate DNA replication and repair during meiosis. Errors in meiosis are the leading cause of miscarriages, as well as developmental and intellectual disabilities. We have identified that NMAD-1, an enzyme which removes methyl moieties from nucleic acids, is essential for appropriate DNA damage response, DNA replication and meiosis in the nematode C. elegans. We have cytologically and genetically characterized the defects which occur due to deletion of NMAD-1 in the C. elegans germline. Additionally, we have begun to determine molecularly how NMAD-1 can regulate DNA replication, by demonstrating that NMAD-1 binds to components of the DNA replication machinery and is required for their appropriate localization to DNA. Characterizing how epigenetic modifications and the corresponding enzymes that add or remove epigenetic modifications can control the fundamental process of meiosis will have broad implications for understanding and eventually correcting errors in meiosis that disrupt normal development.
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Affiliation(s)
- Simon Yuan Wang
- Division of Newborn Medicine, Children’s Hospital Boston, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston Massachusetts, United States of America
| | - Hui Mao
- Division of Newborn Medicine, Children’s Hospital Boston, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston Massachusetts, United States of America
| | - Hiroki Shibuya
- Division of Newborn Medicine, Children’s Hospital Boston, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston Massachusetts, United States of America
| | - Satoru Uzawa
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Zach Klapholz O’Brown
- Division of Newborn Medicine, Children’s Hospital Boston, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston Massachusetts, United States of America
| | - Sage Wesenberg
- Division of Newborn Medicine, Children’s Hospital Boston, Boston, Massachusetts, United States of America
| | - Nara Shin
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Takamune T. Saito
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jinmin Gao
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Barbara J. Meyer
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Monica P. Colaiácovo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Eric Lieberman Greer
- Division of Newborn Medicine, Children’s Hospital Boston, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston Massachusetts, United States of America
- * E-mail:
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46
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Xue J, Lu J, Lai W. Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation versusl-Arg hydroxylation. Phys Chem Chem Phys 2019; 21:9957-9968. [PMID: 31041955 DOI: 10.1039/c9cp00794f] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ethylene-forming enzyme (EFE) is a unique member of the Fe(ii)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases. It converts 2OG into ethylene plus three CO2 molecules (ethylene-forming reaction) and also catalyzes the C5 hydroxylation of l-arginine coupled to the oxidative decarboxylation of 2OG (l-Arg hydroxylation reaction). To uncover the mechanisms of the dual transformations by EFE, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out. Based on the results, a branched mechanism was proposed. An FeII-peroxysuccinate complex with a dissociated CO2 generated through the nucleophilic attack of the superoxo moiety of the Fe-O2 species on the keto carbon of 2OG is the key common intermediate in both reactions. A competition between the subsequent CO2 insertion (a key step in the ethylene-forming pathway) and the O-O bond cleavage (leading to the formation of succinate) governs the product selectivity. The calculated reaction barriers suggested that the CO2 insertion is favored over the O-O bond cleavage. This is consistent with the product preference observed in experiments. By comparison with the results of AsqJ (an Fe/2OG oxygenase that leads to substrate oxidation exclusively), the protein environment was found to be crucial for the selectivity. Further calculations demonstrated that the local electric field of the protein environment in EFE promotes ethylene formation by acting as a charge template, exemplifying the importance of the electrostatic interaction in enzyme catalysis. These findings offer mechanistic insights into the EFE catalysis and provide important clues for better understanding the unique ethylene-forming capability of EFE compared with other Fe/2OG oxygenases.
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Affiliation(s)
- Junqin Xue
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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47
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Moore C, Meng B. Prediction of the molecular boundary and functionality of novel viral AlkB domains using homology modelling and principal component analysis. J Gen Virol 2019; 100:691-703. [PMID: 30835193 DOI: 10.1099/jgv.0.001237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Alkylation B (AlkB) proteins are ubiquitous among diverse cellular organisms, where they act to reverse the damage in DNA and RNA due to methylation, such as 1-methyladenine and 3-methylcytosine. This process is found in virtually all forms of life, with the notable exception of archaea and yeast. This protein family is so significant to all forms of life that it was recently discovered that an AlkB domain is encoded as part of the replicase (poly)protein in a small subset of single-stranded, positive-sense RNA viruses, mainly belonging to the families Alphaflexiviridae, Betaflexiviridae and Closteroviridae. Interestingly, these AlkB-containing viruses are mostly important pathogens of woody perennials such as fruit crops, and are responsible for significant economic losses. As a newly identified protein domain in RNA viruses, the origin and molecular boundary of the viral AlkB domain, as well as its function in viral replication, virus-host interactions and infection are unknown. This is due to the limited sequence conservation of viral AlkB domains, especially at the N-terminal region corresponding to the nucleotide recognition lid. Here we apply several independent analytical approaches (homology modelling, principal component analysis and the Shannon diversity index) for the first time, to better understand this viral domain. We conclude that a functional AlkB domain in these viruses comprises approximately 150-170 amino acids. Although the exact function of the viral AlkB domain remains unknown, we hypothesize that it counteracts a host defence mechanism that is unique in these perennial plants and was acquired to enhance the long-term survival of these RNA viruses that infect perennial plants. Interestingly, a majority of these viruses have a tissue tropism for the phloem. Furthermore, we identified several additional amino acid residues that are uniquely conserved among viral AlkBs. This work helps to provide a foundation for further investigation of the function of viral AlkBs and critical residues involved in AlkB function.
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Affiliation(s)
- Clayton Moore
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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Thapar R, Bacolla A, Oyeniran C, Brickner JR, Chinnam NB, Mosammaparast N, Tainer JA. RNA Modifications: Reversal Mechanisms and Cancer. Biochemistry 2018; 58:312-329. [PMID: 30346748 DOI: 10.1021/acs.biochem.8b00949] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An emerging molecular understanding of RNA alkylation and its removal is transforming our knowledge of RNA biology and its interplay with cancer chemotherapy responses. DNA modifications are known to perform critical functions depending on the genome template, including gene expression, DNA replication timing, and DNA damage protection, yet current results suggest that the chemical diversity of DNA modifications pales in comparison to those on RNA. More than 150 RNA modifications have been identified to date, and their complete functional implications are still being unveiled. These include intrinsic roles such as proper processing and RNA maturation; emerging evidence has furthermore uncovered RNA modification "readers", seemingly analogous to those identified for histone modifications. These modification recognition factors may regulate mRNA stability, localization, and interaction with translation machinery, affecting gene expression. Not surprisingly, tumors differentially modulate factors involved in expressing these marks, contributing to both tumorigenesis and responses to alkylating chemotherapy. Here we describe the current understanding of RNA modifications and their removal, with a focus primarily on methylation and alkylation as functionally relevant changes to the transcriptome. Intriguingly, some of the same RNA modifications elicited by physiological processes are also produced by alkylating agents, thus blurring the lines between what is a physiological mark and a damage-induced modification. Furthermore, we find that a high level of gene expression of enzymes with RNA dealkylation activity is a sensitive readout for poor survival in four different cancer types, underscoring the likely importance of examining RNA dealkylation mechanisms to cancer biology and for cancer treatment and prognosis.
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Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Clement Oyeniran
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Joshua R Brickner
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Naga Babu Chinnam
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - John A Tainer
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
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Purslow JA, Nguyen TT, Egner TK, Dotas RR, Khatiwada B, Venditti V. Active Site Breathing of Human Alkbh5 Revealed by Solution NMR and Accelerated Molecular Dynamics. Biophys J 2018; 115:1895-1905. [PMID: 30352661 DOI: 10.1016/j.bpj.2018.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 02/06/2023] Open
Abstract
AlkB homolog 5 (Alkbh5) is one of nine members of the AlkB family, which are nonheme Fe2+/α-ketoglutarate-dependent dioxygenases that catalyze the oxidative demethylation of modified nucleotides and amino acids. Alkbh5 is highly selective for the N6-methyladenosine modification, an epigenetic mark that has spawned significant biological and pharmacological interest because of its involvement in important physiological processes, such as carcinogenesis and stem cell differentiation. Herein, we investigate the structure and dynamics of human Alkbh5 in solution. By using 15N and 13Cmethyl relaxation dispersion and 15N-R1 and R1ρ NMR experiments, we show that the active site of apo Alkbh5 experiences conformational dynamics on multiple timescales. Consistent with this observation, backbone amide residual dipolar couplings measured for Alkbh5 in phage pf1 are inconsistent with the static crystal structure of the enzyme. We developed a simple approach that combines residual dipolar coupling data and accelerated molecular dynamics simulations to calculate a conformational ensemble of Alkbh5 that is fully consistent with the experimental NMR data. Our structural model reveals that Alkbh5 is more disordered in solution than what is observed in the crystal state and undergoes breathing motions that expand the active site and allow access to α-ketoglutarate. Disordered-to-ordered conformational changes induced by sequential substrate/cofactor binding events have been often invoked to interpret biochemical data on the activity and specificity of AlkB proteins. The structural ensemble reported in this work provides the first atomic-resolution model of an AlkB protein in its disordered conformational state to our knowledge.
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Affiliation(s)
- Jeffrey A Purslow
- Department of Chemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa
| | - Trang T Nguyen
- Department of Chemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa
| | - Timothy K Egner
- Department of Chemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa
| | - Rochelle R Dotas
- Department of Chemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa
| | - Balabhadra Khatiwada
- Department of Chemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa
| | - Vincenzo Venditti
- Department of Chemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa; Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa.
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Wei J, Liu F, Lu Z, Fei Q, Ai Y, He PC, Shi H, Cui X, Su R, Klungland A, Jia G, Chen J, He C. Differential m 6A, m 6A m, and m 1A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm. Mol Cell 2018; 71:973-985.e5. [PMID: 30197295 PMCID: PMC6151148 DOI: 10.1016/j.molcel.2018.08.011] [Citation(s) in RCA: 508] [Impact Index Per Article: 84.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 06/03/2018] [Accepted: 08/02/2018] [Indexed: 10/28/2022]
Abstract
FTO, the first RNA demethylase discovered, mediates the demethylation of internal N6-methyladenosine (m6A) and N6, 2-O-dimethyladenosine (m6Am) at the +1 position from the 5' cap in mRNA. Here we demonstrate that the cellular distribution of FTO is distinct among different cell lines, affecting the access of FTO to different RNA substrates. We find that FTO binds multiple RNA species, including mRNA, snRNA, and tRNA, and can demethylate internal m6A and cap m6Am in mRNA, internal m6A in U6 RNA, internal and cap m6Am in snRNAs, and N1-methyladenosine (m1A) in tRNA. FTO-mediated demethylation has a greater effect on the transcript levels of mRNAs possessing internal m6A than the ones with cap m6Am in the tested cells. We also show that FTO can directly repress translation by catalyzing m1A tRNA demethylation. Collectively, FTO-mediated RNA demethylation occurs to m6A and m6Am in mRNA and snRNA as well as m1A in tRNA.
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Affiliation(s)
- Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Fange Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Zhike Lu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Hangzhou 310064, China
| | - Qili Fei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Yuxi Ai
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - P Cody He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Hailing Shi
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Xiaolong Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Arne Klungland
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway Institute of Basic Medical Sciences, University of Oslo, PO Box 1018 Blindern, 0315 Oslo, Norway
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA.
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