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Wu HN, Fujisawa Y, Tozuka Z, Fomenkov A, Nakura Y, Kajiyama SI, Fujiwara S, Yasukawa K, Roberts RJ, Yanagihara I. Identification of an endonuclease and N 6-adenine methyltransferase from Ureaplasma parvum SV3F4 strain. Enzyme Microb Technol 2024; 180:110471. [PMID: 38959818 DOI: 10.1016/j.enzmictec.2024.110471] [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: 12/11/2023] [Revised: 05/12/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024]
Abstract
Here, we report a novel endonuclease and N6-adenine DNA methyltransferase (m6A methyltransferase) in the Ureaplasma parvum SV3F4 strain. Our previous study found that the SV3F4 strain carries 17 unique genes, which are not encoded in the two previously reported U. parvum serovar 3 strain, OMC-P162 and ATCC 700970. Of these 17 unique genes, UP3_c0261 and UP3_c0262, were originally annotated as encoding hypothetical proteins. Comparative genomics analyses more recently indicated they encode a Type II restriction endonuclease and an m6A methyltransferase, respectively. The UP3_c0261 and UP3_c0262 genes were individually expressed and purified in Escherichia coli. The UP3_c0261 recombinant protein showed endonuclease activity on the pT7Blue vector, recognizing and cleaving a GTNAC motif, resulting in a 5 base 5' extension. The UP3_c0261 protein digested a polymerase chain reaction (PCR) product harboring the GTNAC motif. The endonuclease UP3_c0261 was designated as UpaF4I. Treatment of the PCR product with the recombinant protein UP3_c0262 completely blocked the restriction enzyme activity of UpaF4I. Analysis of the treated PCR product harboring a modified nucleotide by UP3_c0262 with HPLC-MS/MS and MS/MS showed that UP3_c0262 was an m6A methyltransferase containing a methylated A residue in both DNA strands of the GTNAC motif. Whole genome methylation analysis of SV3F4 showed that 99.9 % of the GTNAC motif was m6A modified. These results suggest the UP3_c0261 and UP3_c0262 genes may act as a novel Type II restriction-modification system in the Ureaplasma SV3F4 strain.
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Affiliation(s)
- Heng Ning Wu
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Yuya Fujisawa
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan; Division of Biotechnological Science, Graduate School of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa City, Wakayama 649-6493, Japan
| | - Zenzaburo Tozuka
- Center for Supporting Drug Discovery and Life Science Research, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Alexey Fomenkov
- New England Biolabs Inc., 240 County Rd., Ipswich, MA 01938, USA
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Shin-Ichiro Kajiyama
- Division of Biotechnological Science, Graduate School of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa City, Wakayama 649-6493, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, 1 Gakuen-Uegahara, Sanda City, Hyogo 669-1330, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto City 606-8502, Japan
| | | | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan.
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2
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Nakai M, Hase H, Zhao Y, Okawa K, Honda K, Ikuma K, Kitae K, Tsujikawa K. RNA-modifying enzyme Alkbh8 is involved in mouse embryonic development. iScience 2024; 27:110777. [PMID: 39280612 PMCID: PMC11402254 DOI: 10.1016/j.isci.2024.110777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/19/2024] [Accepted: 08/16/2024] [Indexed: 09/18/2024] Open
Abstract
RNAs undergo more than 300 modifications after transcription. Aberrations in RNA modifications can lead to diseases; their involvement in fetal development has been suggested. This study explored the RNA modifications related to fetal development in mice. We quantified changes in RNA modifications present in mouse embryos at each stage: Metaphase II (MII) oocyte; pronucleus; 2-cell; morula; blastocyst; embryonic days (E)10.5, 13.5, 16.5, and 19.5; and newborn (post-natal day [P]0) using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Our results confirm that many RNAs undergo dynamic modifications. In particular, 5-methoxycarbonylmethyluridine (mcm5U) modification was distinctive and increased during the fetal period. In Alkbh8-knockout (KO) mice, the tRNA protein translation efficiency was reduced. Proteome analysis revealed that the factors downregulated in Alkbh8-KO mice were associated with red blood cell and protoporphyrin metabolism. Our results suggest that ALKBH8 facilitates changes in tRNA balance in conjunction with mcm5U, which are essential for normal red blood cell differentiation and embryogenesis in mice.
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Affiliation(s)
- Manami Nakai
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1- 6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroaki Hase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1- 6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yutong Zhao
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1- 6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Katsuya Okawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1- 6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kohei Honda
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1- 6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kaori Ikuma
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1- 6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kaori Kitae
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1- 6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1- 6 Yamadaoka, Suita, Osaka 565-0871, Japan
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3
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Ammann G, Berg M, Dalwigk JF, Kaiser SM. Pitfalls in RNA Modification Quantification Using Nucleoside Mass Spectrometry. Acc Chem Res 2023; 56:3121-3131. [PMID: 37944919 PMCID: PMC10666278 DOI: 10.1021/acs.accounts.3c00402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
In recent years, there has been a high interest in researching RNA modifications, as they are involved in many cellular processes and in human diseases. A substantial set of enzymes within the cell, called RNA writers, place RNA modifications selectively and site-specifically. Another set of enzymes, called readers, recognize these modifications which guide the fate of the modified RNA. Although RNA is a transient molecule and RNA modification could be removed by RNA degradation, a subclass of enzymes, called RNA erasers, remove RNA modifications selectively and site-specifically to alter the characteristics of the RNA. The detection of RNA modifications can be done by various methods including second and next generation sequencing but also mass spectrometry. An approach capable of both qualitative and quantitative RNA modification analysis is liquid chromatography coupled to mass spectrometry of enzymatic hydrolysates of RNA into nucleosides. However, for successful detection and quantification, various factors must be considered to avoid biased identification and inaccurate quantification. In this Account, we identify three classes of errors that may distort the analysis. These classes comprise (I) errors related to chemical instabilities, (II) errors revolving around enzymatic hydrolysis to nucleosides, and (III) errors arising from issues with chromatographic separation and/or subsequent mass spectrometric analysis.A prominent example for class 1 is Dimroth rearrangement of m1A to m6A, but class 1 also comprises hydrolytic reactions and reactions with buffer components. Here, we also present the conversion of m3C to m3U under mild alkaline conditions and propose a practical solution to overcome these instabilities. Class 2 errors-such as contaminations in hydrolysis reagents or nuclease specificities-have led to erroneous discoveries of nucleosides in the past and possess the potential for misquantification of nucleosides. Impurities in the samples may also lead to class 3 errors: For instance, issues with chromatographic separation may arise from residual organic solvents, and salt adducts may hamper mass spectrometric quantification. This Account aims to highlight various errors connected to mass spectrometry analysis of nucleosides and presents solutions for how to overcome or circumnavigate those issues. Therefore, the authors anticipate that many scientists, but especially those who plan on doing nucleoside mass spectrometry, will benefit from the collection of data presented in this Account as a raised awareness, toward the variety of potential pitfalls, may further enhance the quality of data.
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Affiliation(s)
- Gregor Ammann
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Maximilian Berg
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Jan Felix Dalwigk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Stefanie M. Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
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Kogaki T, Hase H, Tanimoto M, Tashiro A, Kitae K, Ueda Y, Jingushi K, Tsujikawa K. ALKBH4 is a novel enzyme that promotes translation through modified uridine regulation. J Biol Chem 2023; 299:105093. [PMID: 37507018 PMCID: PMC10465949 DOI: 10.1016/j.jbc.2023.105093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Epitranscriptomics studies the mechanisms of acquired RNA modifications. The epitranscriptome is dynamically regulated by specific enzymatic reactions, and the proper execution of these enzymatic RNA modifications regulates a variety of physiological RNA functions. However, the lack of experimental tools, such as antibodies for RNA modification, limits the development of epitranscriptomic research. Furthermore, the regulatory enzymes of many RNA modifications have not yet been identified. Herein, we aimed to identify new molecular mechanisms involved in RNA modification by focusing on the AlkB homolog (ALKBH) family molecules, a family of RNA demethylases. We demonstrated that ALKBH4 interacts with small RNA, regulating the formation and metabolism of the (R)-5-carboxyhydroxymethyl uridine methyl ester. We also found that the reaction of ALKBH4 with small RNA enhances protein translation efficiency in an in vitro assay system. These findings indicate that ALKBH4 is involved in the regulation of uridine modification and expand on the role of tRNA-mediated translation control through ALKBH4.
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Affiliation(s)
- Takahiro Kogaki
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Hiroaki Hase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
| | - Masaya Tanimoto
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Atyuya Tashiro
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Kaori Kitae
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Yuko Ueda
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Kentaro Jingushi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
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Miyake K, Costa Cruz PH, Nagatomo I, Kato Y, Motooka D, Satoh S, Adachi Y, Takeda Y, Kawahara Y, Kumanogoh A. A cancer-associated METTL14 mutation induces aberrant m6A modification, affecting tumor growth. Cell Rep 2023; 42:112688. [PMID: 37355987 DOI: 10.1016/j.celrep.2023.112688] [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: 01/26/2022] [Revised: 04/25/2023] [Accepted: 06/08/2023] [Indexed: 06/27/2023] Open
Abstract
The methyltransferase-like 3 (METTL3)-/METTL14-containing complex predominantly catalyzes N6-methyladenosine (m6A) modification, which affects mRNA stability. Although the METTL14 R298P mutation is found in multiple cancer types, its biological effects are not completely understood. Here, we show that the heterozygous R298P mutation promotes cancer cell proliferation, whereas the homozygous mutation reduces proliferation. Methylated RNA immunoprecipitation sequencing analysis indicates that the R298P mutation reduces m6A modification at canonical motifs. Furthermore, this mutation induces m6A modification at aberrant motifs, which is evident only in cell lines harboring the homozygous mutation. The aberrant recognition of m6A modification sites alters the methylation efficiency at surrounding canonical motifs. One example is c-MET mRNA, which is highly methylated at canonical motifs close to the aberrantly methylated sites. Consequently, c-MET mRNA is severely destabilized, reducing c-Myc expression and suppressing cell proliferation. These data suggest that the METTL14 R298P mutation affects target recognition for m6A modification, perturbing gene expression patterns and cell growth.
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Affiliation(s)
- Kotaro Miyake
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Pedro Henrique Costa Cruz
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Izumi Nagatomo
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuki Kato
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shingo Satoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuichi Adachi
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; Department of Immunopathology, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan.
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6
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Dodson TA, Nieuwoudt S, Morse CN, Pierre V, Liu C, Senyo SE, Prestwich EG. Ribonucleosides from tRNA in hyperglycemic mammalian cells and diabetic murine cardiac models. Life Sci 2023; 318:121462. [PMID: 36736767 PMCID: PMC9992345 DOI: 10.1016/j.lfs.2023.121462] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023]
Abstract
AIMS Cardiomyopathy is a diabetic comorbidity with few molecular targets. To address this, we evaluated transfer RNA (tRNA) modifications in the diabetic heart because tRNA modifications have been implicated in diabetic etiologies. MAIN METHODS tRNA was isolated from aorta, apex, and atrial tissue of healthy and diabetic murine hearts and related hyperglycemic cell models. tRNA modifications and canonical ribonucleosides were quantified by liquid-chromatography tandem mass spectrometry (LC-MS/MS) using stable isotope dilution. Correlations between ribonucleosides and diabetic comorbidity pathology were assessed using statistical analyses. KEY FINDINGS Total tRNA ribonucleoside levels were analyzed from cell types and healthy and diabetic murine heart tissue. Each heart structure had characteristic ribonucleoside profiles and quantities. Several ribonucleosides were observed as significantly different in hyperglycemic cells and diabetic tissues. In hyperglycemic models, ribonucleosides N4-acetylcytidine (ac4C), 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), 5-methylcytidine (m5C), and N1-methylguanosine (m1G) were anomalous. Specific tRNA modifications known to be on murine tRNAIni(CAU) were higher in diabetic heart tissue which suggests that tRNA modifications could be regulating translation in diabetes. SIGNIFICANCE We identified tRNA ribonucleosides and tRNA species associated with hyperglycemia and diabetic etiology.
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Affiliation(s)
- Taylor A Dodson
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, United States
| | - Stephan Nieuwoudt
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Chase N Morse
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, United States
| | - Valinteshley Pierre
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Chao Liu
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Samuel E Senyo
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Erin G Prestwich
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, United States.
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7
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Prokhorova DV, Vokhtantsev IP, Tolstova PO, Zhuravlev ES, Kulishova LM, Zharkov DO, Stepanov GA. Natural Nucleoside Modifications in Guide RNAs Can Modulate the Activity of the CRISPR-Cas9 System In Vitro. CRISPR J 2022; 5:799-812. [PMID: 36350691 DOI: 10.1089/crispr.2022.0069] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
At the present time, the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system has been widely adopted as an efficient genomic editing tool. However, there are some actual problems such as the off-target effects, cytotoxicity, and immunogenicity. The incorporation of modifications into guide RNAs permits enhancing both the efficiency and the specificity of the CRISPR-Cas9 system. In this study, we demonstrate that the inclusion of N6-methyladenosine, 5-methylcytidine, and pseudouridine in trans-activating RNA (tracrRNA) or in single guide RNA (sgRNA) enables efficient gene editing in vitro. We found that the complexes of modified guide RNAs with Cas9 protein promoted cleavage of the target short/long duplexes and plasmid substrates. In addition, the modified monomers in guide RNAs allow increasing the specificity of CRISPR-Cas9 system in vitro and promote diminishing both the immunostimulating and the cytotoxic effects of sgRNAs.
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Affiliation(s)
- Daria V Prokhorova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Ivan P Vokhtantsev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Polina O Tolstova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgenii S Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lilia M Kulishova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Grigory A Stepanov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Takahashi H, Hase H, Yoshida T, Tashiro J, Hirade Y, Kitae K, Tsujikawa K. Discovery of two novel ALKBH5 selective inhibitors that exhibit uncompetitive or competitive type and suppress the growth activity of glioblastoma multiforme. Chem Biol Drug Des 2022; 100:1-12. [PMID: 35384315 DOI: 10.1111/cbdd.14051] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/20/2022] [Accepted: 03/26/2022] [Indexed: 12/12/2022]
Abstract
A group of RNA methylation enzymes is currently of interest as a new target for cancer therapy. Alpha-ketoglutarate-dependent dioxygenase B (AlkB) homolog 5 (ALKBH5) is an N6 -methyladenosine (m6 A) demethylation enzyme, and by high-throughput screening from pure small molecule compounds, we identified two novel inhibitors, Ena15 and Ena21, against it. Each compound showed either uncompetitive or competitive inhibition for 2-oxoglutarate (2OG). In addition, Ena21 had little inhibitory activity for fat mass and obesity-associated protein (FTO), which is another N6 -methyladenosine demethylation enzyme, while Ena15 enhanced the demethylase activity of FTO. The predicted binding poses of both compounds with the crystal structure of ALKBH5 (PDB ID: 4NRO) were comparable with these observations pertaining to the interaction of the 2OG catalytic site in this enzyme kinetics. Furthermore, either knockdown of ALKBH5 or inhibition with Ena15 or Ena21 inhibited cell proliferation of glioblastoma multiforme-derived cell lines, decreased cell population in the synthesis phase of the cell cycle, increased m6 A RNA level, and stabilized FOXM1 mRNA. Based on these results, Ena15 and Ena21 were found to be potential candidates that might help in further research into the biological function of ALKBH5.
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Affiliation(s)
- Hikaru Takahashi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Hiroaki Hase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Takuya Yoshida
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Junki Tashiro
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Yoshihiro Hirade
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Kaori Kitae
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
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