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Cottom-Salas W, Becerra A, Lazcano A. RNA or DNA? Revisiting the Chemical Nature of the Cenancestral Genome. J Mol Evol 2024:10.1007/s00239-024-10194-9. [PMID: 39145798 DOI: 10.1007/s00239-024-10194-9] [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: 06/28/2024] [Accepted: 07/31/2024] [Indexed: 08/16/2024]
Abstract
One of the central issues in the understanding of early cellular evolution is the characterisation of the cenancestor. This includes the description of the chemical nature of its genome. The disagreements on this question comprise several proposals, including the possibility that AlkB-mediated methylation repair of alkylated RNA molecules may be interpreted as evidence of a cenancestral RNA genome. We present here an evolutionary analysis of the cupin-like protein superfamily based on tertiary structure-based phylogenies that includes the oxygen-dependent AlkB and its homologs. Our results suggest that the repair of methylated RNA molecules is the outcome of the enzyme substrate ambiguity, and doesn´t necessarily indicates that the last common ancestor was endowed with an RNA genome.
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Affiliation(s)
- Wolfgang Cottom-Salas
- Posgrado en Ciencias Biológicas, UNAM, Cd. Universitaria, 04510, Mexico City, CDMX, Mexico
- Facultad de Ciencias, UNAM, Cd. Universitaria, Apdo.Postal 70-407, 04510, Mexico City, DF, Mexico
- Escuela Nacional Preparatoria, Plantel 8 Miguel E. Schulz, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Arturo Becerra
- Facultad de Ciencias, UNAM, Cd. Universitaria, Apdo.Postal 70-407, 04510, Mexico City, DF, Mexico
| | - Antonio Lazcano
- Facultad de Ciencias, UNAM, Cd. Universitaria, Apdo.Postal 70-407, 04510, Mexico City, DF, Mexico.
- El Colegio Nacional, Donceles 104, Centro Histórico, 06020, Mexico City, CP, Mexico.
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2
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Yang S, Xing J, Liu D, Song Y, Yu H, Xu S, Zuo Y. Review and new insights into the catalytic structural domains of the Fe(ll) and 2-Oxoglutarate families. Int J Biol Macromol 2024; 278:134798. [PMID: 39153678 DOI: 10.1016/j.ijbiomac.2024.134798] [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: 05/06/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
Histone lysine demethylase (KDM), AlkB homolog (ALKBH), and Ten-Eleven Translocation (TET) proteins are members of the 2-Oxoglutarate (2OG) and ferrous iron-dependent oxygenases, each of which harbors a catalytic domain centered on a double-stranded β-helix whose topology restricts the regions directly involved in substrate binding. However, they have different catalytic functions, and the deeply structural biological reasons are not yet clear. In this review, the catalytic domain features of the three protein families are summarized from both sequence and structural perspectives. The construction of the phylogenetic tree and comparison of the structure show ten relatively conserved β-sheets and three key regions with substantial structural differences. We summarize the relationship between three key regions of remarkable differences and the substrate compatibility of the three protein families. This review facilitates research into substrate-selective inhibition and bioengineering by providing new insights into the catalytic domains of KDM, ALKBH, and TET proteins.
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Affiliation(s)
- Siqi Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Jixiang Xing
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Dongyang Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yancheng Song
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Haoyu Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Shuhua Xu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China; State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
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Zhong J, Xu Z, Ding N, Wang Y, Chen W. The biological function of demethylase ALKBH1 and its role in human diseases. Heliyon 2024; 10:e33489. [PMID: 39040364 PMCID: PMC11260981 DOI: 10.1016/j.heliyon.2024.e33489] [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: 02/14/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/24/2024] Open
Abstract
AlkB homolog 1 (ALKBH1) is a member of the AlkB family of dioxygenases that are dependent on Fe(II) and α-ketoglutarate. Mounting evidence demonstrates that ALKBH1 exhibits enzymatic activity against various substrates, including N6-methyladenosine (m6A), N1-methyladenosine (m1A), N3-methylcytidine (m3C), 5-methylcytosine (m5C), N6-methyladenine (N6-mA, 6mA), and H2A, indicating its dual roles in different biological processes and involvement in human diseases. Up to the present, there is ongoing debate regarding ALKBH1's enzymatic activity. In this review, we present a comprehensive summary of recent research on ALKBH1, including its substrate diversity and pathological roles in a wide range of human disorders, the underlying mechanisms of its functions, and its dysregulation. We also explored the potential of ALKBH1 as a prognostic target.
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Affiliation(s)
- Jing Zhong
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310009, China
| | - Zhengyang Xu
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310009, China
| | - Ning Ding
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310009, China
| | - Yanting Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310009, China
| | - Wenwen Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310009, China
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Xie J, Zhang Z. Recent Advances and Therapeutic Implications of 2-Oxoglutarate-Dependent Dioxygenases in Ischemic Stroke. Mol Neurobiol 2024; 61:3949-3975. [PMID: 38041714 DOI: 10.1007/s12035-023-03790-1] [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: 08/04/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023]
Abstract
Ischemic stroke is a common disease with a high disability rate and mortality, which brings heavy pressure on families and medical insurance. Nowadays, the golden treatments for ischemic stroke in the acute phase mainly include endovascular therapy and intravenous thrombolysis. Some drugs are used to alleviate brain injury in patients with ischemic stroke, such as edaravone and 3-n-butylphthalide. However, no effective neuroprotective drug for ischemic stroke has been acknowledged. 2-Oxoglutarate-dependent dioxygenases (2OGDDs) are conserved and common dioxygenases whose activities depend on O2, Fe2+, and 2OG. Most 2OGDDs are expressed in the brain and are essential for the development and functions of the brain. Therefore, 2OGDDs likely play essential roles in ischemic brain injury. In this review, we briefly elucidate the functions of most 2OGDDs, particularly the effects of regulations of 2OGDDs on various cells in different phases after ischemic stroke. It would also provide promising potential therapeutic targets and directions of drug development for protecting the brain against ischemic injury and improving outcomes of ischemic stroke.
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Affiliation(s)
- Jian Xie
- Department of Neurology, Affiliated Zhongda Hospital, Research Institution of Neuropsychiatry, School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Zhijun Zhang
- Department of Neurology, Affiliated Zhongda Hospital, Research Institution of Neuropsychiatry, School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China.
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Department of Mental Health and Public Health, Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China.
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Hasan M, Nishat ZS, Hasan MS, Hossain T, Ghosh A. Identification of m 6A RNA methylation genes in Oryza sativa and expression profiling in response to different developmental and environmental stimuli. Biochem Biophys Rep 2024; 38:101677. [PMID: 38511186 PMCID: PMC10950732 DOI: 10.1016/j.bbrep.2024.101677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Eukaryotic messenger RNAs (mRNAs) transcend their predominant function of protein encoding by incorporating auxiliary components that ultimately contribute to their processing, transportation, translation, and decay. In doing so, additional layers of modifications are incorporated in mRNAs at post-transcriptional stage. Among them, N6-methyladenosine (m6A) is the most frequently found mRNA modification that plays crucial roles in plant development and stress response. In the overall mechanism of m6A methylation, key proteins classified based on their functions such as writers, readers, and erasers dynamically add, read, and subtract methyl groups respectively to deliver relevant functions in response to external stimuli. In this study, we identified 30 m6A regulatory genes (9 writers, 5 erasers, and 16 readers) in rice that encode 53 proteins (13 writers, 7 erasers, and 33 readers) where segmental duplication was found in one writer and four reader gene pairs. Reproductive cells such as sperm, anther and panicle showed high levels of expression for most of the m6A regulatory genes. Notably, writers like OsMTA, OsMTD, and OsMTC showed varied responses in different stress and infection contexts, with initial upregulation in response to early exposure followed by downregulation later. OsALKBH9A, a noteworthy eraser, displayed varied expression in response to different stresses at different time intervals, but upregulation in certain infections. Reader genes like OsECT5, OsCPSF30-L3, and OsECT8 showed continuous upregulation in exertion of all kinds of stress relevant here. Conversely, other reader genes along with OsECT11 and OsCPSF30-L2 were observed to be consistently downregulated. The apparent correlation between the expression patterns of m6A regulatory genes and stress modulation pathways in this study underscores the need for additional research to unravel their intricate regulatory mechanisms that could ultimately contribute to the substantial development of enhanced stress tolerance in rice through mRNA modification.
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Affiliation(s)
| | | | - Md. Soyib Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Tanvir Hossain
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
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Wu Z, Zhou R, Li B, Cao M, Wang W, Li X. Methylation modifications in tRNA and associated disorders: Current research and potential therapeutic targets. Cell Prolif 2024:e13692. [PMID: 38943267 DOI: 10.1111/cpr.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/14/2024] [Accepted: 06/03/2024] [Indexed: 07/01/2024] Open
Abstract
High-throughput sequencing has sparked increased research interest in RNA modifications, particularly tRNA methylation, and its connection to various diseases. However, the precise mechanisms underpinning the development of these diseases remain largely elusive. This review sheds light on the roles of several tRNA methylations (m1A, m3C, m5C, m1G, m2G, m7G, m5U, and Nm) in diverse biological functions, including metabolic processing, stability, protein interactions, and mitochondrial activities. It further outlines diseases linked to aberrant tRNA modifications, related enzymes, and potential underlying mechanisms. Moreover, disruptions in tRNA regulation and abnormalities in tRNA-derived small RNAs (tsRNAs) contribute to disease pathogenesis, highlighting their potential as biomarkers for disease diagnosis. The review also delves into the exploration of drugs development targeting tRNA methylation enzymes, emphasizing the therapeutic prospects of modulating these processes. Continued research is imperative for a comprehensive comprehension and integration of these molecular mechanisms in disease diagnosis and treatment.
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Affiliation(s)
- Zhijing Wu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruixin Zhou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Baizao Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingyu Cao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenlong Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Breast Cancer in Hunan Province, Changsha, Hunan, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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7
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Chang R, Tsui KH, Pan LF, Li CJ. Spatial and single-cell analyses uncover links between ALKBH1 and tumor-associated macrophages in gastric cancer. Cancer Cell Int 2024; 24:57. [PMID: 38317214 PMCID: PMC10845659 DOI: 10.1186/s12935-024-03232-5] [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: 11/22/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND AlkB homolog 1, histone H2A dioxygenase (ALKBH1), a crucial enzyme involved in RNA demethylation in humans, plays a significant role in various cellular processes. While its role in tumor progression is well-established, its specific contribution to stomach adenocarcinoma (STAD) remains elusive. This study seeks to explore the clinical and pathological relevance of ALKBH1, its impact on the tumor immune microenvironment, and its potential for precision oncology in STAD. METHODS We adopted a comprehensive multi-omics approach to identify ALKBH1 as an potential diagnostic biomarker for STAD, demonstrating its association with advanced clinical stages and reduced overall survival rates. Our analysis involved the utilization of publicly available datasets from GEO and TCGA. We identified differentially expressed genes in STAD and scrutinized their relationships with immune gene expression, overall survival, tumor stage, gene mutation profiles, and infiltrating immune cells. Moreover, we employed spatial transcriptomics to investigate ALKBH1 expression across distinct regions of STAD. Additionally, we conducted spatial transcriptomic and single-cell RNA-sequencing analyses to elucidate the correlation between ALKBH1 expression and immune cell populations. Our findings were validated through immunohistochemistry and bioinformatics on 60 STAD patient samples. RESULTS Our study unveiled crucial gene regulators in STAD linked with genetic variations, deletions, and the tumor microenvironment. Mutations in these regulators demonstrated a positive association with distinct immune cell populations across six immune datasets, exerting a substantial influence on immune cell infiltration in STAD. Furthermore, we established a connection between elevated ALKBH1 expression and macrophage infiltration in STAD. Pharmacogenomic analysis of gastric cancer cell lines further indicated that ALKBH1 inactivation correlated with heightened sensitivity to specific small-molecule drugs. CONCLUSION In conclusion, our study highlights the potential role of ALKBH1 alterations in the advancement of STAD, shedding light on novel diagnostic and prognostic applications of ALKBH1 in this context. We underscore the significance of ALKBH1 within the tumor immune microenvironment, suggesting its utility as a precision medicine tool and for drug screening in the management of STAD.
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Affiliation(s)
- Renin Chang
- Department of Emergency Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Department of Recreation and Sports Management, Tajen University, Pingtung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Kuan-Hao Tsui
- Department of Obstetrics and Gynaecology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Institute of BioPharmaceutical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
- Department of Obstetrics and Gynaecology, National Yang-Ming University School of Medicine, Taipei, Taiwan
- Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, 114, Taiwan
| | - Li-Fei Pan
- Department of General Affair Office, Kaohsiung Veterans General Hospital, Kaohsiung, 813, Taiwan
| | - Chia-Jung Li
- Department of Obstetrics and Gynaecology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.
- Institute of BioPharmaceutical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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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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Danovski G, Dyankova-Danovska T, Stamatov R, Aleksandrov R, Kanev PB, Stoynov S. CellTool: An Open-Source Software Combining Bio-Image Analysis and Mathematical Modeling for the Study of DNA Repair Dynamics. Int J Mol Sci 2023; 24:16784. [PMID: 38069107 PMCID: PMC10706408 DOI: 10.3390/ijms242316784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Elucidating the dynamics of DNA repair proteins is essential to understanding the mechanisms that preserve genomic stability and prevent carcinogenesis. However, the measurement and modeling of protein dynamics at DNA lesions via currently available image analysis tools is cumbersome. Therefore, we developed CellTool-a stand-alone open-source software with a graphical user interface for the analysis of time-lapse microscopy images. It combines data management, image processing, mathematical modeling, and graphical presentation of data in a single package. Multiple image filters, segmentation, and particle tracking algorithms, combined with direct visualization of the obtained results, make CellTool an ideal application for the comprehensive analysis of DNA repair protein dynamics. This software enables the fitting of obtained kinetic data to predefined or custom mathematical models. Importantly, CellTool provides a platform for easy implementation of custom image analysis packages written in a variety of programing languages. Using CellTool, we demonstrate that the ALKB homolog 2 (ALKBH2) demethylase is excluded from DNA damage sites despite recruitment of its putative interaction partner proliferating cell nuclear antigen (PCNA). Further, CellTool facilitates the straightforward fluorescence recovery after photobleaching (FRAP) analysis of BRCA1 associated RING domain 1 (BARD1) exchange at complex DNA lesions. In summary, the software presented herein enables the time-efficient analysis of a wide range of time-lapse microscopy experiments through a user-friendly interface.
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Affiliation(s)
| | | | | | | | | | - Stoyno Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl. 21, 1113 Sofia, Bulgaria; (T.D.-D.); (R.S.); (R.A.); (P.-B.K.)
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10
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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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11
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Guo C, Liu Z, Zhang H. DNA 6mA demethylase ALKBH1 regulates DDX18 expression to promote proliferation of human head and neck squamous cell carcinoma. Cell Oncol (Dordr) 2023:10.1007/s13402-023-00800-1. [PMID: 36976498 DOI: 10.1007/s13402-023-00800-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2023] [Indexed: 03/29/2023] Open
Abstract
PURPOSE Human head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. Currently, surgical resection plus a combination of chemotherapy and radiotherapy is the standard treatment for HNSCC, and the 5-year survival rate of patients with HNSCC remains very low because of the higher incidence of metastasis with consequent recurrence. Here, we aimed to investigate the potential role of DNA N6-methyladenine (6mA) demethylase ALKBH1 in tumor cell proliferation in HNSCC. METHODS The expression of ALKBH1 in 10 pairs of HNSCC/normal tissues and 3 HNSCC cell lines were measured by qRT‒PCR and western blotting. Colony formation, flow cytometry, patient-derived HNSCC organoid assays were used to assess the role of ALKBH1 in HNSCC cell proliferation in cell lines and human HNSCC patients. MeDIP-seq, RNA sequencing, Dot blotting and western blotting were used to evaluate the regulatory effect of ALKBH1 on the expression of DEAD-box RNA helicase DDX18. A dual-luciferase reporter assay was used to assess the putative effect of DNA 6mA levels on DDX18 transcription. RESULTS ALKBH1 was highly expressed in HNSCC cells and patient tissues. Functional experiments revealed that ALKBH1 knockdown in SCC9, SCC25, and CAL27 cells inhibited their proliferation in vitro. Using patient-derived HNSCC organoid assay, we found that knockdown of ALKBH1 inhibited the proliferation and colony formation of HNSCC patients-derived organoids. Moreover, we found that ALKBH1 can enhance DDX18 expression by erasing DNA 6mA level and regulating its promoter activity. ALKBH1 deficiency blocked tumor cell proliferation by inhibiting DDX18 expression. Exogenous overexpression of DDX18 rescued the cell proliferation arrest caused by ALKBH1 knockdown. CONCLUSION Our data reveal the important role of ALKBH1 in regulating proliferation of HNSCC.
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Affiliation(s)
- Chengli Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China
| | - Zheming Liu
- Cancer Center, Renmin Hospital, Wuhan University, No.185, East Lake Road, Wuhan, Hubei, 430071, China.
| | - Haojian Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China.
- Frontier Science Center for Immunology and Metabolism, Wuhan University, No.185, East Lake Road, Wuhan, Hubei, 430071, China.
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12
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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: 1] [Impact Index Per Article: 1.0] [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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13
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Ruszel KP, Zalewski DP, Stępniewski A, Gałkowski D, Bogucki J, Feldo M, Płachno BJ, Kocki J, Bogucka-Kocka A. Next-Generation Sequencing in the Assessment of the Transcriptomic Landscape of DNA Damage Repair Genes in Abdominal Aortic Aneurysm, Chronic Venous Disease and Lower Extremity Artery Disease. Int J Mol Sci 2022; 24:ijms24010551. [PMID: 36614026 PMCID: PMC9820637 DOI: 10.3390/ijms24010551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Vascular diseases are one of the most common causes of death and morbidity. Lower extremity artery disease (LEAD), abdominal aortic aneurysm (AAA) and chronic venous disease (CVD) belong to this group of conditions and exhibit various presentations and courses; thus, there is an urgent need for revealing new biomarkers for monitoring and potential treatment. Next-generation sequencing of mRNA allows rapid and detailed transcriptome analysis, allowing us to pinpoint the most pronounced differences between the mRNA expression profiles of vascular disease patients. Comparison of expression data of 519 DNA-repair-related genes obtained from mRNA next-generation sequencing revealed significant transcriptomic marks characterizing AAA, CVD and LEAD. Statistical, gene set enrichment analysis (GSEA), gene ontology (GO) and literature analyses were applied and highlighted many DNA repair and accompanying processes, such as cohesin functions, oxidative stress, homologous recombination, ubiquitin turnover, chromatin remodelling and DNA double-strand break repair. Surprisingly, obtained data suggest the contribution of genes engaged in the regulatory function of DNA repair as a key component that could be used to distinguish between analyzed conditions. DNA repair-related genes depicted in the presented study as dysregulated in AAA, CVD and LEAD could be utilized in the design of new biomarkers or therapies associated with these diseases.
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Affiliation(s)
- Karol P. Ruszel
- Department of Clinical Genetics, Chair of Medical Genetics, Medical University of Lublin, 11 Radziwiłłowska St., 20-080 Lublin, Poland
- Correspondence: ; Tel.: +48-81-448-6610
| | - Daniel P. Zalewski
- Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland
| | - Andrzej Stępniewski
- Ecotech Complex Analytical and Programme Centre for Advanced Environmentally Friendly Technologies, University of Marie Curie-Skłodowska, 39 Głęboka St., 20-612 Lublin, Poland
| | - Dariusz Gałkowski
- Department of Pathology and Laboratory Medicine, Rutgers-Robert Wood Johnson Medical School, One Robert Wood Johnson Place, New Brunswick, NJ 08903, USA
| | - Jacek Bogucki
- Chair and Department of Organic Chemistry, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland
| | - Marcin Feldo
- Chair and Department of Vascular Surgery and Angiology, Medical University of Lublin, 11 Staszica St., 20-081 Lublin, Poland
| | - Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 9 Gronostajowa St., 30-387 Kraków, Poland
| | - Janusz Kocki
- Department of Clinical Genetics, Chair of Medical Genetics, Medical University of Lublin, 11 Radziwiłłowska St., 20-080 Lublin, Poland
| | - Anna Bogucka-Kocka
- Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland
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14
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Zhao Y, Guo Q, Cao S, Tian Y, Han K, Sun Y, Li J, Yang Q, Ji Q, Sederoff R, Li Y. Genome-wide identification of the AlkB homologs gene family, PagALKBH9B and PagALKBH10B regulated salt stress response in Populus. FRONTIERS IN PLANT SCIENCE 2022; 13:994154. [PMID: 36204058 PMCID: PMC9530910 DOI: 10.3389/fpls.2022.994154] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
The AlkB homologs (ALKBH) gene family regulates N6-methyladenosine (m6A) RNA methylation and is involved in plant growth and the abiotic stress response. Poplar is an important model plant for studying perennial woody plants. Poplars typically have a long juvenile period of 7-10 years, requiring long periods of time for studies of flowering or mature wood properties. Consequently, functional studies of the ALKBH genes in Populus species have been limited. Based on AtALKBHs sequence similarity with Arabidopsis thaliana, 23 PagALKBHs were identified in the genome of the poplar 84K hybrid genotype (P. alba × P. tremula var. glandulosa), and gene structures and conserved domains were confirmed between homologs. The PagALKBH proteins were classified into six groups based on conserved sequence compared with human, Arabidopsis, maize, rice, wheat, tomato, barley, and grape. All homologs of PagALKBHs were tissue-specific; most were highly expressed in leaves. ALKBH9B and ALKBH10B are m6A demethylases and overexpression of their homologs PagALKBH9B and PagALKBH10B reduced m6A RNA methylation in transgenic lines. The number of adventitious roots and the biomass accumulation of transgenic lines decreased compared with WT. Therefore, PagALKBH9B and PagALKBH10B mediate m6A RNA demethylation and play a regulatory role in poplar growth and development. Overexpression of PagALKBH9B and PagALKBH10B can reduce the accumulation of H2O2 and oxidative damage by increasing the activities of SOD, POD, and CAT, and enhancing protection for Chl a/b, thereby increasing the salt tolerance of transgenic lines. However, overexpression lines were more sensitive to drought stress due to reduced proline content. This research revealed comprehensive information about the PagALKBH gene family and their roles in growth and development and responsing to salt stress of poplar.
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Affiliation(s)
- Ye Zhao
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Qi Guo
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Sen Cao
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yanting Tian
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Kunjin Han
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yuhan Sun
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Juan Li
- Natural Resources and Planning Bureau of Yanshan County, Cangzhou, Hebei, China
| | - Qingshan Yang
- Shandong Academy of Forestry, Jinan, Shandong, China
| | - Qingju Ji
- Cangzhou Municipal Forestry Seeding and Cutting Management Center, Cangzhou, China
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Yun Li
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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15
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ALKBH family members as novel biomarkers and prognostic factors in human breast cancer. Aging (Albany NY) 2022; 14:6579-6593. [PMID: 35980268 PMCID: PMC9467415 DOI: 10.18632/aging.204231] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/27/2022] [Indexed: 12/11/2022]
Abstract
Breast cancer is the most common lethal carcinoma worldwide and better targeted therapies are still worthy of exploration, having had some great successes already. Abnormal expression of ALKBH members were found in various cancers, and the roles played by it were the focus of attention. The ALKBH gene family encodes nine homologous enzymes (ALKBH1-8 and FTO) to repair DNA or RNA depending on Fe2+ and α-ketoglutarate (α-KG), which is related to carcinogenesis. In this study, we applied several databases to explore the roles of ALKBHs in breast cancer. We found that ALKBH members were abnormal expression in breast cancer and associated with tumor stage and subclasses. Higher alteration rates of ALKBH family were found in breast cancer. Function enrichment revealed that several cancer-associated signal pathways were related to ALKBH family such as PI3K-Akt signaling pathway and axon guidance. Infiltration of immune cells (Eosinophiles, NK CD56bright cells, mast cells, T helper cells and so on) were strongly related to ALKBHs. Moreover, we further found that there was strong correlation between ALKBH7 and higher age, later T stage, ER/PR positive and post-menopause of breast cancer patients, and patients with higher ALKBH7 expression had shorter overall survival (OS) and post progression survival (PPS). In conclusion, our findings may provide novel insights into ALKBH-targeted therapy for breast cancer patients, and ALKBH7 may be a potential prognostic biomarker.
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16
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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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17
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Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions. Biochem Soc Trans 2022; 50:1179-1190. [PMID: 35521905 PMCID: PMC9246332 DOI: 10.1042/bst20210725] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/14/2022]
Abstract
DNA methylation is an epigenetic modification with a very long evolutionary history. However, DNA methylation evolves surprisingly rapidly across eukaryotes. The genome-wide distribution of methylation diversifies rapidly in different lineages, and DNA methylation is lost altogether surprisingly frequently. The growing availability of genomic and epigenomic sequencing across organisms highlights this diversity but also illuminates potential factors that could explain why both the DNA methylation machinery and its genome-wide distribution evolve so rapidly. Key to this are new discoveries about the fitness costs associated with DNA methylation, and new theories about how the fundamental biochemical mechanisms of DNA methylation introduction and maintenance could explain how new genome-wide patterns of methylation evolve.
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18
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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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19
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DNA Methyltransferases and DNA Damage. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:349-361. [DOI: 10.1007/978-3-031-11454-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Beyond the Double-Strand Breaks: The Role of DNA Repair Proteins in Cancer Stem-Cell Regulation. Cancers (Basel) 2021; 13:cancers13194818. [PMID: 34638302 PMCID: PMC8508278 DOI: 10.3390/cancers13194818] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cancer stem cells (CSCs) are a tumor cell population maintaining tumor growth and promoting tumor relapse if not wholly eradicated during treatment. CSCs are often equipped with molecular mechanisms making them resistant to conventional anti-cancer therapies whose curative potential depends on DNA damage-induced cell death. An elevated expression of some key DNA repair proteins is one of such defense mechanisms. However, new research reveals that the role of critical DNA repair proteins is extending far beyond the DNA repair mechanisms. This review discusses the diverse biological functions of DNA repair proteins in CSC maintenance and the adaptation to replication and oxidative stress, anti-cancer immune response, epigenetic reprogramming, and intracellular signaling mechanisms. It also provides an overview of their potential therapeutic targeting. Abstract Cancer stem cells (CSCs) are pluripotent and highly tumorigenic cells that can re-populate a tumor and cause relapses even after initially successful therapy. As with tissue stem cells, CSCs possess enhanced DNA repair mechanisms. An active DNA damage response alleviates the increased oxidative and replicative stress and leads to therapy resistance. On the other hand, mutations in DNA repair genes cause genomic instability, therefore driving tumor evolution and developing highly aggressive CSC phenotypes. However, the role of DNA repair proteins in CSCs extends beyond the level of DNA damage. In recent years, more and more studies have reported the unexpected role of DNA repair proteins in the regulation of transcription, CSC signaling pathways, intracellular levels of reactive oxygen species (ROS), and epithelial–mesenchymal transition (EMT). Moreover, DNA damage signaling plays an essential role in the immune response towards tumor cells. Due to its high importance for the CSC phenotype and treatment resistance, the DNA damage response is a promising target for individualized therapies. Furthermore, understanding the dependence of CSC on DNA repair pathways can be therapeutically exploited to induce synthetic lethality and sensitize CSCs to anti-cancer therapies. This review discusses the different roles of DNA repair proteins in CSC maintenance and their potential as therapeutic targets.
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21
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DNA Methylation on N6-Adenine Regulates the Hyphal Development during Dimorphism in the Early-Diverging Fungus Mucor lusitanicus. J Fungi (Basel) 2021; 7:jof7090738. [PMID: 34575776 PMCID: PMC8470550 DOI: 10.3390/jof7090738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 12/14/2022] Open
Abstract
The epigenetic modifications control the pathogenicity of human pathogenic fungi, which have been poorly studied in Mucorales, causative agents of mucormycosis. This order belongs to a group referred to as early-diverging fungi that are characterized by high levels of N6-methyldeoxy adenine (6mA) in their genome with dense 6mA clusters associated with actively expressed genes. AlkB enzymes can act as demethylases of 6mA in DNA, with the most remarkable eukaryotic examples being mammalian ALKBH1 and Caenorhabditis elegans NMAD-1. The Mucor lusitanicus (formerly M. circinelloides f. lusitanicus) genome contains one gene, dmt1, and two genes, dmt2 and dmt3, encoding proteins similar to C. elegans NMAD-1 and ALKBH1, respectively. The function of these three genes was analyzed by the generation of single and double deletion mutants for each gene. Multiple processes were studied in the mutants, but defects were only found in single and double deletion mutants for dmt1. In contrast to the wild-type strain, dmt1 mutants showed an increase in 6mA levels during the dimorphic transition, suggesting that 6mA is associated with dimorphism in M. lusitanicus. Furthermore, the spores of dmt1 mutants challenged with macrophages underwent a reduction in polar growth, suggesting that 6mA also has a role during the spore–macrophage interaction that could be important in the infection process.
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22
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Zhang Y, Wang C. Demethyltransferase AlkBH1 substrate diversity and relationship to human diseases. Mol Biol Rep 2021; 48:4747-4756. [PMID: 34046849 DOI: 10.1007/s11033-021-06421-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/17/2021] [Indexed: 12/22/2022]
Abstract
AlkBH1 is a member of the AlkB superfamily which are kinds of Fe (II) and α-ketoglutarate (α-KG)-dependent dioxygenases. At present, only demethyltransferases FTO and AlkBH5 have relatively clear substrate studies among these members, the types and mechanisms of substrates catalysis of other members are not clear, especially the demethyltransferase AlkBH1. AlkBH1, as a demethylase, has important functions of reversing DNA methylation and repairing DNA damage. And it has become a promising target for the treatment of many cancers, the regulation of neurological and genetic related diseases. Many scholars have made important discoveries in the diversity of AlkBH1 substrates, but there is no comprehensive summary, which affects the design inhibitor target of AlkBH1. Herein, We are absorbed in the latest progress in the study of AlkBH1 substrate diversity and its relationship with human diseases. Besides, we also discuss future research directions and suggest other studies to reveal the specific catalytic effect of AlkBH1 on cancer substrates.
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Affiliation(s)
- Ying Zhang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, China
| | - Caiyan Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, China.
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23
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Jingushi K, Aoki M, Ueda K, Kogaki T, Tanimoto M, Monoe Y, Ando M, Matsumoto T, Minami K, Ueda Y, Kitae K, Hase H, Nagata T, Harada-Takeda A, Yamamoto M, Kawahara K, Tabata K, Furukawa T, Sato M, Tsujikawa K. ALKBH4 promotes tumourigenesis with a poor prognosis in non-small-cell lung cancer. Sci Rep 2021; 11:8677. [PMID: 33883577 PMCID: PMC8060266 DOI: 10.1038/s41598-021-87763-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
The human AlkB homolog family (ALKBH) of proteins play a critical role in some types of cancer. However, the expression and function of the lysine demethylase ALKBH4 in cancer are poorly understood. Here, we examined the expression and function of ALKBH4 in non-small-cell lung cancer (NSCLC) and found that ALKBH4 was highly expressed in NSCLC, as compared to that in adjacent normal lung tissues. ALKBH4 knockdown significantly induced the downregulation of NSCLC cell proliferation via cell cycle arrest at the G1 phase of in vivo tumour growth. ALKBH4 knockdown downregulated E2F transcription factor 1 (E2F1) and its target gene expression in NSCLC cells. ALKBH4 and E2F1 expression was significantly correlated in NSCLC clinical specimens. Moreover, patients with high ALKBH4 expression showed a poor prognosis, suggesting that ALKBH4 plays a pivotal tumour-promoting role in NSCLC.
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Affiliation(s)
- Kentaro Jingushi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Masaya Aoki
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima, 890-8520, Japan
| | - Kazuhiro Ueda
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima, 890-8520, Japan
| | - Takahiro Kogaki
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masaya Tanimoto
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuya Monoe
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masayuki Ando
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takuya Matsumoto
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kentaro Minami
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima, 890-8544, Japan
| | - Yuko Ueda
- 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
| | - Hiroaki Hase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshiyuki Nagata
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima, 890-8520, Japan
| | - Aya Harada-Takeda
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima, 890-8520, Japan
| | - Masatatsu Yamamoto
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima, 890-8544, Japan
| | - Kohichi Kawahara
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima, 890-8544, Japan
| | - Kazuhiro Tabata
- Human Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima City, 890-8544, Japan
| | - Tatsuhiko Furukawa
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima, 890-8544, Japan
| | - Masami Sato
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima, 890-8520, 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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24
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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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25
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Wang Y, Katanski CD, Watkins C, Pan JN, Dai Q, Jiang Z, Pan T. A high-throughput screening method for evolving a demethylase enzyme with improved and new functionalities. Nucleic Acids Res 2021; 49:e30. [PMID: 33337498 PMCID: PMC7968990 DOI: 10.1093/nar/gkaa1213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/26/2023] Open
Abstract
AlkB is a DNA/RNA repair enzyme that removes base alkylations such as N1-methyladenosine (m1A) or N3-methylcytosine (m3C) from DNA and RNA. The AlkB enzyme has been used as a critical tool to facilitate tRNA sequencing and identification of mRNA modifications. As a tool, AlkB mutants with better reactivity and new functionalities are highly desired; however, previous identification of such AlkB mutants was based on the classical approach of targeted mutagenesis. Here, we introduce a high-throughput screening method to evaluate libraries of AlkB variants for demethylation activity on RNA and DNA substrates. This method is based on a fluorogenic RNA aptamer with an internal modified RNA/DNA residue which can block reverse transcription or introduce mutations leading to loss of fluorescence inherent in the cDNA product. Demethylation by an AlkB variant eliminates the blockage or mutation thereby restores the fluorescence signals. We applied our screening method to sites D135 and R210 in the Escherichia coli AlkB protein and identified a variant with improved activity beyond a previously known hyperactive mutant toward N1-methylguanosine (m1G) in RNA. We also applied our method to O6-methylguanosine (O6mG) modified DNA substrates and identified candidate AlkB variants with demethylating activity. Our study provides a high-throughput screening method for in vitro evolution of any demethylase enzyme.
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Affiliation(s)
- Yuru Wang
- Department of Biochemistry and Molecular Biology, USA.,Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | | | - Jessica N Pan
- Department of Biochemistry and Molecular Biology, USA
| | - Qing Dai
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Zhuoxun Jiang
- Department of Biochemistry and Molecular Biology, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, USA
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26
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Doseděl M, Jirkovský E, Macáková K, Krčmová LK, Javorská L, Pourová J, Mercolini L, Remião F, Nováková L, Mladěnka P. Vitamin C-Sources, Physiological Role, Kinetics, Deficiency, Use, Toxicity, and Determination. Nutrients 2021; 13:615. [PMID: 33668681 PMCID: PMC7918462 DOI: 10.3390/nu13020615] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 02/07/2023] Open
Abstract
Vitamin C (L-ascorbic acid) has been known as an antioxidant for most people. However, its physiological role is much larger and encompasses very different processes ranging from facilitation of iron absorption through involvement in hormones and carnitine synthesis for important roles in epigenetic processes. Contrarily, high doses act as a pro-oxidant than an anti-oxidant. This may also be the reason why plasma levels are meticulously regulated on the level of absorption and excretion in the kidney. Interestingly, most cells contain vitamin C in millimolar concentrations, which is much higher than its plasma concentrations, and compared to other vitamins. The role of vitamin C is well demonstrated by miscellaneous symptoms of its absence-scurvy. The only clinically well-documented indication for vitamin C is scurvy. The effects of vitamin C administration on cancer, cardiovascular diseases, and infections are rather minor or even debatable in the general population. Vitamin C is relatively safe, but caution should be given to the administration of high doses, which can cause overt side effects in some susceptible patients (e.g., oxalate renal stones). Lastly, analytical methods for its determination with advantages and pitfalls are also discussed in this review.
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Affiliation(s)
- Martin Doseděl
- Department of Social and Clinical Pharmacy, Faculty of Pharmacy, Charles University, 500 05 Hradec Králové, Czech Republic;
| | - Eduard Jirkovský
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University, 500 05 Hradec Králové, Czech Republic; (E.J.); (J.P.)
| | - Kateřina Macáková
- Department of Pharmacognosy, Faculty of Pharmacy, Charles University, 500 05 Hradec Králové, Czech Republic;
| | - Lenka Kujovská Krčmová
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, 500 05 Hradec Králové, Czech Republic; (L.K.K.); (L.N.)
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, 500 05 Hradec Králové, Czech Republic;
| | - Lenka Javorská
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, 500 05 Hradec Králové, Czech Republic;
| | - Jana Pourová
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University, 500 05 Hradec Králové, Czech Republic; (E.J.); (J.P.)
| | - Laura Mercolini
- Research group of Pharmaco-Toxicological Analysis (PTA Lab), Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum—University of Bologna, 40126 Bologna, Italy;
| | - Fernando Remião
- UCIBIO-REQUIMTE, Laboratory of Toxicology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, 500 05 Hradec Králové, Czech Republic; (L.K.K.); (L.N.)
| | - Přemysl Mladěnka
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University, 500 05 Hradec Králové, Czech Republic; (E.J.); (J.P.)
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27
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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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28
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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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29
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Abstract
Genomic DNA is chemically reactive and therefore susceptible to damage by many exogenous and endogenous sources. Lesions produced from these damaging events can have various mutagenic and genotoxic consequences. This Perspective follows the journey of one particular lesion, 1,N6-ethenoadenine (εA), from its formation to replication and repair, and its role in cancerous tissues and inflammatory diseases. εA is generated by the reaction of adenine (A) with vinyl chloride or lipid peroxidation products. We present the miscoding properties of εA with an emphasis on how bacterial and mammalian cells can process lesions differently, leading to varied mutational spectra. But with information from these assays, we can better understand how the miscoding properties of εA lead to biological consequences and how genomic stability can be maintained via DNA repair mechanisms. We discuss how base excision repair (BER) and direct reversal repair (DRR) can minimize the biological consequences of εA lesions. Kinetic parameters of glycosylases and AlkB family enzymes are described, along with a discussion of the relative contributions of the BER and DRR pathways in the repair of εA. Because eukaryotic DNA is packaged in chromatin, we also discuss the impact of this packaging on BER and DRR, specifically in regards to repair of εA. Studying DNA lesions like εA in this context, from origin to biological implications, can provide crucial information to better understand prevention of mutagenesis and cancer.
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Affiliation(s)
- Katelyn L Rioux
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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30
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Reversal of nucleobase methylation by dioxygenases. Nat Chem Biol 2020; 16:1160-1169. [DOI: 10.1038/s41589-020-00675-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 09/11/2020] [Indexed: 12/12/2022]
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31
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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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32
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Xiao MZ, Liu JM, Xian CL, Chen KY, Liu ZQ, Cheng YY. Therapeutic potential of ALKB homologs for cardiovascular disease. Biomed Pharmacother 2020; 131:110645. [PMID: 32942149 DOI: 10.1016/j.biopha.2020.110645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/05/2020] [Accepted: 08/16/2020] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading causes of human death. Recently, ALKB homologs, including ALKBH1-8 and FTO, have been found to have a variety of biological functions, such as histone demethylation, RNA demethylation, and DNA demethylation. These functions may regulate the physiological and pathological processes of CVDs, including inflammation, oxidative stress, cell apoptosis, and mitochondrial, endothelial, and fat metabolism dysfunction. In the present review, we summarize the biological functions of ALKB homologs and the relationship between the ALKB homologs and CVDs. Importantly, we discuss the roles of ALKB homologs in the regulation of oxidative stress, inflammation, autophagy, and DNA damage in CVDs, as well as the practical applications of ALKB homologs inhibitors or agonists in treating CVDs. In conclusion, the ALKBH family might be a promising target for CVDs therapy.
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Affiliation(s)
- Ming-Zhu Xiao
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jia-Ming Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Cui-Ling Xian
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Keng-Yu Chen
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; The Second Affiliated Hospital of Guangdong Pharmaceutical University, Yunfu, 527300, China
| | - Zhong-Qiu Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China.
| | - Yuan-Yuan Cheng
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China.
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33
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Huong TT, Ngoc LNT, Kang H. Functional Characterization of a Putative RNA Demethylase ALKBH6 in Arabidopsis Growth and Abiotic Stress Responses. Int J Mol Sci 2020; 21:ijms21186707. [PMID: 32933187 PMCID: PMC7555452 DOI: 10.3390/ijms21186707] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022] Open
Abstract
RNA methylation and demethylation, which is mediated by RNA methyltransferases (referred to as “writers”) and demethylases (referred to as “erasers”), respectively, are emerging as a key regulatory process in plant development and stress responses. Although several studies have shown that AlkB homolog (ALKBH) proteins are potential RNA demethylases, the function of most ALKBHs is yet to be determined. The Arabidopsis thaliana genome contains thirteen genes encoding ALKBH proteins, the functions of which are largely unknown. In this study, we characterized the function of a potential eraser protein, ALKBH6 (At4g20350), during seed germination and seedling growth in Arabidopsis under abiotic stresses. The seeds of T-DNA insertion alkbh6 knockdown mutants germinated faster than the wild-type seeds under cold, salt, or abscisic acid (ABA) treatment conditions but not under dehydration stress conditions. Although no differences in seedling and root growth were observed between the alkbh6 mutant and wild-type under normal conditions, the alkbh6 mutant showed a much lower survival rate than the wild-type under salt, drought, or heat stress. Cotyledon greening of the alkbh6 mutants was much higher than that of the wild-type upon ABA application. Moreover, the transcript levels of ABA signaling-related genes, including ABI3 and ABI4, were down-regulated in the alkbh6 mutant compared to wild-type plants. Importantly, the ALKBH6 protein had an ability to bind to both m6A-labeled and m5C-labeled RNAs. Collectively, these results indicate that the potential eraser ALKBH6 plays important roles in seed germination, seedling growth, and survival of Arabidopsis under abiotic stresses.
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Affiliation(s)
- Trinh Thi Huong
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.H.); (L.N.T.N.)
- The Western Highlands Agriculture and Forestry Science Institute, Buon Ma Thuot, DakLak 63000, Vietnam
| | - Le Nguyen Tieu Ngoc
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.H.); (L.N.T.N.)
- Faculty of Forestry Agriculture, Tay Nguyen University, Buon Ma Thuot, DakLak 63000, Vietnam
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.H.); (L.N.T.N.)
- Correspondence: ; Tel.: +82-(62)-530-2181
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34
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Caffrey PJ, Kher R, Bian K, Li D, Delaney S. Comparison of the Base Excision and Direct Reversal Repair Pathways for Correcting 1, N6-Ethenoadenine in Strongly Positioned Nucleosome Core Particles. Chem Res Toxicol 2020; 33:1888-1896. [PMID: 32293880 PMCID: PMC7374743 DOI: 10.1021/acs.chemrestox.0c00089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
1,N6-ethenoadenine (εA) is a
mutagenic lesion and biomarker observed in numerous cancerous tissues.
Two pathways are responsible for its repair: base excision repair
(BER) and direct reversal repair (DRR). Alkyladenine DNA glycosylase
(AAG) is the primary enzyme that excises εA in BER, generating
stable intermediates that are processed by downstream enzymes. For
DRR, the Fe(II)/α-ketoglutarate-dependent ALKBH2 enzyme repairs
εA by direct conversion of εA to A. While the molecular
mechanism of each enzyme is well understood on unpackaged duplex DNA,
less is known about their actions on packaged DNA. The nucleosome
core particle (NCP) forms the minimal packaging unit of DNA in eukaryotic
organisms and is composed of 145–147 base pairs wrapped around
a core of eight histone proteins. In this work, we investigated the
activity of AAG and ALKBH2 on εA lesions globally distributed
at positions throughout a strongly positioned NCP. Overall, we examined
the repair of εA at 23 unique locations in packaged DNA. We
observed a strong correlation between rotational positioning of εA
and AAG activity but not ALKBH2 activity. ALKBH2 was more effective
than AAG at repairing occluded εA lesions, but only AAG was
capable of full repair of any εA in the NCP. However, notable
exceptions to these trends were observed, highlighting the complexity
of the NCP as a substrate for DNA repair. Modeling of binding of the
repair enzymes to NCPs revealed that some of these observations can
be explained by steric interference caused by DNA packaging. Specifically,
interactions between ALKBH2 and the histone proteins obstruct binding
to DNA, which leads to diminished activity. Taken together, these
results support in vivo observations of alkylation
damage profiles and contribute to our understanding of mutational
hotspots.
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Affiliation(s)
- Paul J Caffrey
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Raadhika Kher
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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35
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Tudek A, Czerwińska J, Kosicki K, Zdżalik-Bielecka D, Shahmoradi Ghahe S, Bażlekowa-Karaban M, Borsuk EM, Speina E. DNA damage, repair and the improvement of cancer therapy - A tribute to the life and research of Barbara Tudek. Mutat Res 2020; 852:503160. [PMID: 32265045 DOI: 10.1016/j.mrgentox.2020.503160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 10/25/2022]
Abstract
Professor Barbara Tudek received the Frits Sobels Award in 2019 from the European Environmental Mutagenesis and Genomics Society (EEMGS). This article presents her outstanding character and most important lines of research. The focus of her studies covered alkylative and oxidative damage to DNA bases, in particular mutagenic and carcinogenic properties of purines with an open imidazole ring and 8-oxo-7,8-dihydroguanine (8-oxoGua). They also included analysis of mutagenic properties and pathways for the repair of DNA adducts of lipid peroxidation (LPO) products arising in large quantities during inflammation. Professor Tudek did all of this in the hope of deciphering the mechanisms of DNA damage removal, in particular by the base excision repair (BER) pathway. Some lines of research aimed at discovering factors that can modulate the activity of DNA damage repair in hope to enhance existing anti-cancer therapies. The group's ongoing research aims at deciphering the resistance mechanisms of cancer cell lines acquired following prolonged exposure to photodynamic therapy (PDT) and the possibility of re-sensitizing cells to PDT in order to increase the application of this minimally invasive therapeutic method.
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Affiliation(s)
- Agnieszka Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Jolanta Czerwińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Konrad Kosicki
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Daria Zdżalik-Bielecka
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Somayeh Shahmoradi Ghahe
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Milena Bażlekowa-Karaban
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland; UMR 8200 C.N.R.S., Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Ewelina M Borsuk
- Laboratory of Structural Biology, International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Elżbieta Speina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
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36
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Drosophila Alpha-ketoglutarate-dependent dioxygenase AlkB is involved in repair from neuronal disorders induced by ultraviolet damage. Neuroreport 2019; 30:1039-1047. [PMID: 31503204 DOI: 10.1097/wnr.0000000000001323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AlkB family proteins are enzymes that repair alkylated DNA and RNA by oxidative demethylation. Nine homologs have been identified and characterized in mammals. ALKBH1 is conserved among metazoans including Drosophila. Although the ALKBH1 mouse homolog, Alkbh1 functions in neurogenesis, it currently remains unclear whether ALKBH1 plays a role in neuronal disorders induced by ultraviolet-induced DNA damage. We herein demonstrated that the Drosophila ALKBH1 homolog, AlkB contributed to recovery from neuronal disorders induced by ultraviolet damage. The knockdown of AlkB resulted in not only learning defects but also altered crawling behavior in Drosophila larvae after ultraviolet irradiation. A molecular analysis revealed that AlkB contributed to the repair of ultraviolet-induced DNA damage in the central nervous system of larvae. Therefore, we propose that ALKBH1 plays a role in the repair of ultraviolet-induced DNA damage in central nervous system. Ultraviolet-induced DNA damage is involved in the pathogenesis of xeroderma pigmentosum, and has recently been implicated in Parkinson's disease. The present results will contribute to our understanding of neuronal diseases induced by ultraviolet-induced DNA damage.
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Pilžys T, Marcinkowski M, Kukwa W, Garbicz D, Dylewska M, Ferenc K, Mieczkowski A, Kukwa A, Migacz E, Wołosz D, Mielecki D, Klungland A, Piwowarski J, Poznański J, Grzesiuk E. ALKBH overexpression in head and neck cancer: potential target for novel anticancer therapy. Sci Rep 2019; 9:13249. [PMID: 31519943 PMCID: PMC6744417 DOI: 10.1038/s41598-019-49550-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/27/2019] [Indexed: 01/12/2023] Open
Abstract
The nine identified human homologues of E. coli AlkB 2-oxoglutarate (2OG) and Fe(II)-dependent dioxygenase, ALKBH1-8 and FTO, display different substrate specificities and diverse biological functions. Here we discovered the combined overexpression of members of the ALKBH family in head and neck squamous cell carcinomas (HNSCC). We found direct correlation of ALKBH3 and FTO expression with primary HNSCC tumor size. We observed unidentified thus far cytoplasmic localization of ALKBH2 and 5 in HNSCC, suggesting abnormal role(s) of ALKBH proteins in cancer. Further, high expression of ALKBHs was observed not only in HNSCC, but also in several cancerous cell lines and silencing ALKBH expression in HeLa cancer cells resulted in dramatically decreased survival. Considering the discovered impact of high expression of ALKBH proteins on HNSCC development, we screened for ALKBH blockers among newly synthetized anthraquinone derivatives and demonstrated their potential to support standard anticancer therapy.
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Affiliation(s)
- Tomaš Pilžys
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Marcinkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Wojciech Kukwa
- Department of Otolaryngology, Medical University of Warsaw, Warsaw, Poland
| | - Damian Garbicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Małgorzata Dylewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Ferenc
- Veterinary Research Centre and Center for Biomedical Research, Department of Large Animal Diseases with the Clinic, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland
| | - Adam Mieczkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Andrzej Kukwa
- Department of Otolaryngology, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Migacz
- Department of Otolaryngology, Medical University of Warsaw, Warsaw, Poland
| | - Dominika Wołosz
- Department of Pathology, Medical University of Warsaw, Warsaw, Poland
| | - Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jan Piwowarski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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38
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Jaroy EG, Acosta-Jimenez L, Hotta R, Goldstein AM, Emblem R, Klungland A, Ougland R. "Too much guts and not enough brains": (epi)genetic mechanisms and future therapies of Hirschsprung disease - a review. Clin Epigenetics 2019; 11:135. [PMID: 31519213 PMCID: PMC6743154 DOI: 10.1186/s13148-019-0718-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022] Open
Abstract
Hirschsprung disease is a neurocristopathy, characterized by aganglionosis in the distal bowel. It is caused by failure of the enteric nervous system progenitors to migrate, proliferate, and differentiate in the gut. Development of an enteric nervous system is a tightly regulated process. Both the neural crest cells and the surrounding environment are regulated by different genes, signaling pathways, and morphogens. For this process to be successful, the timing of gene expression is crucial. Hence, alterations in expression of genes specific for the enteric nervous system may contribute to the pathogenesis of Hirschsprung’s disease. Several epigenetic mechanisms contribute to regulate gene expression, such as modifications of DNA and RNA, histone modifications, and microRNAs. Here, we review the current knowledge of epigenetic and epitranscriptomic regulation in the development of the enteric nervous system and its potential significance for the pathogenesis of Hirschsprung’s disease. We also discuss possible future therapies and how targeting epigenetic and epitranscriptomic mechanisms may open new avenues for novel treatment.
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Affiliation(s)
- Emilie G Jaroy
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027, Oslo, Norway.,Department of Pediatric Surgery, Oslo University Hospital, Rikshospitalet, 0424, Oslo, Norway.,Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317, Oslo, Norway
| | - Lourdes Acosta-Jimenez
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027, Oslo, Norway.,Department of Pediatric Surgery, Oslo University Hospital, Rikshospitalet, 0424, Oslo, Norway.,Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317, Oslo, Norway
| | - Ryo Hotta
- Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Allan M Goldstein
- Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ragnhild Emblem
- Department of Pediatric Surgery, Oslo University Hospital, Rikshospitalet, 0424, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
| | - Arne Klungland
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027, Oslo, Norway.,Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317, Oslo, Norway
| | - Rune Ougland
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027, Oslo, Norway. .,Department of Surgery, Baerum Hospital, Vestre Viken Hospital Trust, 3004, Drammen, Norway.
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39
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Jiang Z, You Q, Zhang X. Medicinal chemistry of metal chelating fragments in metalloenzyme active sites: A perspective. Eur J Med Chem 2019; 165:172-197. [PMID: 30684796 DOI: 10.1016/j.ejmech.2019.01.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/22/2018] [Accepted: 01/08/2019] [Indexed: 12/25/2022]
Abstract
Numerous metal-containing enzymes (metalloenzymes) have been considered as drug targets related to diseases such as cancers, diabetes, anemia, AIDS, malaria, bacterial infection, fibrosis, and neurodegenerative diseases. Inhibitors of the metalloenzymes have been developed independently, most of which are mimics of substrates of the corresponding enzymes. However, little attention has been paid to the interactions between inhibitors and active site metal ions. This review is focused on different metal binding fragments and their chelating properties in the metal-containing active binding pockets of metalloenzymes. We have enumerated over one hundred of inhibitors targeting various metalloenzymes and identified over ten kinds of fragments with different binding patterns. Furthermore, we have investigated the inhibitors that are undergoing clinical evaluation in order to help looking for more potential scaffolds bearing metal binding fragments. This review will provide deep insights for the rational design of novel inhibitors targeting the metal-containing binding sites of specific proteins.
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Affiliation(s)
- Zhensheng Jiang
- Sate Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Sate Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xiaojin Zhang
- Sate Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing, 211198, China.
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40
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Hu J, Manduzio S, Kang H. Epitranscriptomic RNA Methylation in Plant Development and Abiotic Stress Responses. FRONTIERS IN PLANT SCIENCE 2019; 10:500. [PMID: 31110512 PMCID: PMC6499213 DOI: 10.3389/fpls.2019.00500] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 04/01/2019] [Indexed: 05/19/2023]
Abstract
Recent advances in methylated RNA immunoprecipitation followed by sequencing and mass spectrometry have revealed widespread chemical modifications on mRNAs. Methylation of RNA bases such as N 6-methyladenosine (m6A) and 5-methylcytidine (m5C) is the most prevalent mRNA modifications found in eukaryotes. In recent years, cellular factors introducing, interpreting, and deleting specific methylation marks on mRNAs, designated as "writers (methyltransferase)," "readers (RNA-binding protein)," and "erasers (demethylase)," respectively, have been identified in plants and animals. An emerging body of evidence shows that methylation on mRNAs affects diverse aspects of RNA metabolism, including stability, splicing, nucleus-to-cytoplasm export, alternative polyadenylation, and translation. Although our understanding for roles of writers, readers, and erasers in plants is far behind that for their animal counterparts, accumulating reports clearly demonstrate that these factors are essential for plant growth and abiotic stress responses. This review emphasizes the crucial roles of epitranscriptomic modifications of RNAs in new layer of gene expression regulation during the growth and response of plants to abiotic stresses.
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41
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Evolutionary analysis indicates that DNA alkylation damage is a byproduct of cytosine DNA methyltransferase activity. Nat Genet 2018; 50:452-459. [PMID: 29459678 PMCID: PMC5865749 DOI: 10.1038/s41588-018-0061-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/16/2018] [Indexed: 01/31/2023]
Abstract
Methylation at the 5 position of cytosine in DNA (5meC) is a key epigenetic mark in eukaryotes. Once introduced, 5meC can be maintained through DNA replication by the activity of 'maintenance' DNA methyltransferases (DNMTs). Despite their ancient origin, DNA methylation pathways differ widely across animals, such that 5meC is either confined to transcribed genes or lost altogether in several lineages. We used comparative epigenomics to investigate the evolution of DNA methylation. Although the model nematode Caenorhabditis elegans lacks DNA methylation, more basal nematodes retain cytosine DNA methylation, which is targeted to repeat loci. We found that DNA methylation coevolved with the DNA alkylation repair enzyme ALKB2 across eukaryotes. In addition, we found that DNMTs introduced the toxic lesion 3-methylcytosine into DNA both in vitro and in vivo. Alkylation damage is therefore intrinsically associated with DNMT activity, and this may promote the loss of DNA methylation in many species.
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42
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Silva J, Aivio S, Knobel PA, Bailey LJ, Casali A, Vinaixa M, Garcia-Cao I, Coyaud É, Jourdain AA, Pérez-Ferreros P, Rojas AM, Antolin-Fontes A, Samino-Gené S, Raught B, González-Reyes A, Ribas de Pouplana L, Doherty AJ, Yanes O, Stracker TH. EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Nat Cell Biol 2018; 20:162-174. [PMID: 29335528 DOI: 10.1038/s41556-017-0016-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 11/27/2017] [Indexed: 02/08/2023]
Abstract
Mitochondria are subcellular organelles that are critical for meeting the bioenergetic and biosynthetic needs of the cell. Mitochondrial function relies on genes and RNA species encoded both in the nucleus and mitochondria, and on their coordinated translation, import and respiratory complex assembly. Here, we characterize EXD2 (exonuclease 3'-5' domain-containing 2), a nuclear-encoded gene, and show that it is targeted to the mitochondria and prevents the aberrant association of messenger RNAs with the mitochondrial ribosome. Loss of EXD2 results in defective mitochondrial translation, impaired respiration, reduced ATP production, increased reactive oxygen species and widespread metabolic abnormalities. Depletion of the Drosophila melanogaster EXD2 orthologue (CG6744) causes developmental delays and premature female germline stem cell attrition, reduced fecundity and a dramatic extension of lifespan that is reversed with an antioxidant diet. Our results define a conserved role for EXD2 in mitochondrial translation that influences development and ageing.
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Affiliation(s)
- Joana Silva
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Suvi Aivio
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Philip A Knobel
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department for Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Laura J Bailey
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Andreu Casali
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Maria Vinaixa
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Isabel Garcia-Cao
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexis A Jourdain
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pablo Pérez-Ferreros
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,EMBL Australia, University of New South Wales, Lowy Cancer Research Center, Single Molecule Science Node, Sydney and Arc Center of Excellence in Advance Molecular Imaging, Sydney, New South Wales, Australia
| | - Ana M Rojas
- Computational Biology and Bioinformatics Group, Institute of Biomedicine of Seville (IBIS/CSIC/US/JA), Campus Hospital Universitario Virgen del Rocio, Seville, Spain
| | - Albert Antolin-Fontes
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sara Samino-Gené
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Acaimo González-Reyes
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/JA, Seville, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Oscar Yanes
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
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43
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Sun Q, Liu X, Gong B, Wu D, Meng A, Jia S. Alkbh4 and Atrn Act Maternally to Regulate Zebrafish Epiboly. Int J Biol Sci 2017; 13:1051-1066. [PMID: 28924386 PMCID: PMC5599910 DOI: 10.7150/ijbs.19203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 07/11/2017] [Indexed: 01/04/2023] Open
Abstract
During embryonic gastrulation, coordinated cell movements occur to bring cells to their correct position. Among them, epiboly produces the first distinct morphological changes, which is essential for the early development of zebrafish. Despite its fundamental importance, little is known to understand the underlying molecular mechanisms. By generating maternal mutant lines with CRISPR/Cas9 technology and using morpholino knockdown strategy, we showed that maternal Alkbh4 depletion leads to severe epiboly defects in zebrafish. Immunofluorescence assays revealed that Alkbh4 promotes zebrafish embryonic epiboly through regulating actomyosin contractile ring formation, which is composed of Actin and non-muscular myosin II (NMII). To further investigate this process, yeast two hybridization assay was performed and Atrn was identified as a binding partner of Alkbh4. Combining with the functional results of Alkbh4, we found that maternal Atrn plays a similar role in zebrafish embryonic morphogenesis by regulating actomyosin formation. On the molecular level, our data revealed that Atrn prefers to interact with the active form of Alkbh4 and functions together with it to regulate the demethylation of Actin, the actomyosin formation, and subsequently the embryonic epiboly.
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Affiliation(s)
- Qingrui Sun
- State Key Laboratory of Membrane biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xingfeng Liu
- State Key Laboratory of Membrane biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Bo Gong
- State Key Laboratory of Membrane biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Di Wu
- State Key Laboratory of Membrane biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- State Key Laboratory of Membrane biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shunji Jia
- State Key Laboratory of Membrane biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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44
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Jordan JJ, Chhim S, Margulies CM, Allocca M, Bronson RT, Klungland A, Samson LD, Fu D. ALKBH7 drives a tissue and sex-specific necrotic cell death response following alkylation-induced damage. Cell Death Dis 2017; 8:e2947. [PMID: 28726787 PMCID: PMC5550884 DOI: 10.1038/cddis.2017.343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/14/2017] [Indexed: 12/12/2022]
Abstract
Regulated necrosis has emerged as a major cell death mechanism in response to different forms of physiological and pharmacological stress. The AlkB homolog 7 (ALKBH7) protein is required for regulated cellular necrosis in response to chemotherapeutic alkylating agents but its role within a whole organism is unknown. Here, we show that ALKBH7 modulates alkylation-induced cellular death through a tissue and sex-specific mechanism. At the whole-animal level, we find that ALKBH7 deficiency confers increased resistance to MMS-induced toxicity in male but not female mice. Moreover, ALKBH7-deficient mice exhibit protection against alkylation-mediated cytotoxicity in retinal photoreceptor and cerebellar granule cells, two cell types that undergo necrotic death through the initiation of the base excision repair pathway and hyperactivation of the PARP1/ARTD1 enzyme. Notably, the protection against alkylation-induced cerebellar degeneration is specific to ALKBH7-deficient male but not female mice. Our results uncover an in vivo role for ALKBH7 in mediating a sexually dimorphic tissue response to alkylation damage that could influence individual responses to chemotherapies based upon alkylating agents.
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Affiliation(s)
- Jennifer J Jordan
- Department of Biological Engineering, Biology, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sophea Chhim
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Carrie M Margulies
- Department of Biological Engineering, Biology, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mariacarmela Allocca
- Department of Biological Engineering, Biology, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Arne Klungland
- Department of Molecular Microbiology A3.3021, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Leona D Samson
- Department of Biological Engineering, Biology, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dragony Fu
- Department of Biology, University of Rochester, Rochester, NY, USA
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45
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Stefansson OA, Hermanowicz S, van der Horst J, Hilmarsdottir H, Staszczak Z, Jonasson JG, Tryggvadottir L, Gudjonsson T, Sigurdsson S. CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer. BMC Cancer 2017; 17:469. [PMID: 28679371 PMCID: PMC5498885 DOI: 10.1186/s12885-017-3453-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 06/26/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND DNA repair of alkylation damage is defective in various cancers. This occurs through somatically acquired inactivation of the MGMT gene in various cancer types, including breast cancers. In addition to MGMT, the two E. coli AlkB homologs ALKBH2 and ALKBH3 have also been linked to direct reversal of alkylation damage. However, it is currently unknown whether ALKBH2 or ALKBH3 are found inactivated in cancer. METHODS Methylome datasets (GSE52865, GSE20713, GSE69914), available through Omnibus, were used to determine whether ALKBH2 or ALKBH3 are found inactivated by CpG promoter methylation. TCGA dataset enabled us to then assess the impact of CpG promoter methylation on mRNA expression for both ALKBH2 and ALKBH3. DNA methylation analysis for the ALKBH3 promoter region was carried out by pyrosequencing (PyroMark Q24) in 265 primary breast tumours and 30 proximal normal breast tissue samples along with 8 breast-derived cell lines. ALKBH3 mRNA and protein expression were analysed in cell lines using RT-PCR and Western blotting, respectively. DNA alkylation damage assay was carried out in cell lines based on immunofluorescence and confocal imaging. Data on clinical parameters and survival outcomes in patients were obtained and assessed in relation to ALKBH3 promoter methylation. RESULTS The ALKBH3 gene, but not ALKBH2, undergoes CpG promoter methylation and transcriptional silencing in breast cancer. We developed a quantitative alkylation DNA damage assay based on immunofluorescence and confocal imaging revealing higher levels of alkylation damage in association with epigenetic inactivation of the ALKBH3 gene (P = 0.029). In our cohort of 265 primary breast cancer, we found 72 cases showing aberrantly high CpG promoter methylation over the ALKBH3 promoter (27%; 72 out of 265). We further show that increasingly higher degree of ALKBH3 promoter methylation is associated with reduced breast-cancer specific survival times in patients. In this analysis, ALKBH3 promoter methylation at >20% CpG methylation was found to be statistically significantly associated with reduced survival (HR = 2.3; P = 0.012). By thresholding at the clinically relevant CpG methylation level (>20%), we find the incidence of ALKBH3 promoter methylation to be 5% (13 out of 265). CONCLUSIONS ALKBH3 is a novel addition to the catalogue of DNA repair genes found inactivated in breast cancer. Our results underscore a link between defective alkylation repair and breast cancer which, additionally, is found in association with poor disease outcome.
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Affiliation(s)
- Olafur Andri Stefansson
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Stefan Hermanowicz
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Department of Biochemistry and Molecular Biology, Biomedical Center, Vatnsmyrarvegur 16 (5th floor), 101 Reykjavik, Iceland
| | - Jasper van der Horst
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Holmfridur Hilmarsdottir
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Zuzanna Staszczak
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Jon Gunnlaugur Jonasson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Icelandic Cancer Registry, Skogarhlid 8, Reykjavik, Iceland
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
| | - Laufey Tryggvadottir
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Icelandic Cancer Registry, Skogarhlid 8, Reykjavik, Iceland
| | - Thorkell Gudjonsson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Department of Biochemistry and Molecular Biology, Biomedical Center, Vatnsmyrarvegur 16 (5th floor), 101 Reykjavik, Iceland
| | - Stefan Sigurdsson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Department of Biochemistry and Molecular Biology, Biomedical Center, Vatnsmyrarvegur 16 (5th floor), 101 Reykjavik, Iceland
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46
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Chen F, Bian K, Tang Q, Fedeles BI, Singh V, Humulock ZT, Essigmann JM, Li D. Oncometabolites d- and l-2-Hydroxyglutarate Inhibit the AlkB Family DNA Repair Enzymes under Physiological Conditions. Chem Res Toxicol 2017; 30:1102-1110. [PMID: 28269980 DOI: 10.1021/acs.chemrestox.7b00009] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Cancer-associated mutations often lead to perturbed cellular energy metabolism and accumulation of potentially harmful oncometabolites. One example is the chiral molecule 2-hydroxyglutarate (2HG); its two stereoisomers (d- and l-2HG) have been found at abnormally high concentrations in tumors featuring anomalous metabolic pathways. 2HG has been demonstrated to competitively inhibit several α-ketoglutarate (αKG)- and non-heme iron-dependent dioxygenases, including some of the AlkB family DNA repair enzymes, such as ALKBH2 and ALKBH3. However, previous studies have only provided the IC50 values of d-2HG on the enzymes, and the results have not been correlated to physiologically relevant concentrations of 2HG and αKG in cancer cells. In this work, we performed detailed kinetic analyses of DNA repair reactions catalyzed by ALKBH2, ALKBH3, and the bacterial AlkB in the presence of d- and l-2HG in both double- and single-stranded DNA contexts. We determined the kinetic parameters of inhibition, including kcat, KM, and Ki. We also correlated the relative concentrations of 2HG and αKG previously measured in tumor cells with the inhibitory effect of 2HG on the AlkB family enzymes. Both d- and l-2HG significantly inhibited the human DNA repair enzymes ALKBH2 and ALKBH3 at pathologically relevant concentrations (73-88% for d-2HG and 31-58% for l-2HG inhibition). This work provides a new perspective that the elevation of the d- or l-2HG concentration in cancer cells may contribute to an increased mutation rate by inhibiting the DNA repair performed by the AlkB family enzymes and thus exacerbate the genesis and progression of tumors.
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Affiliation(s)
- Fangyi Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Bogdan I Fedeles
- Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Vipender Singh
- Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Zachary T Humulock
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - John M Essigmann
- Department of Biological Engineering, Department of Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
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47
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Haag S, Sloan KE, Ranjan N, Warda AS, Kretschmer J, Blessing C, Hübner B, Seikowski J, Dennerlein S, Rehling P, Rodnina MV, Höbartner C, Bohnsack MT. NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation. EMBO J 2016; 35:2104-2119. [PMID: 27497299 PMCID: PMC5048346 DOI: 10.15252/embj.201694885] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/20/2016] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial gene expression uses a non‐universal genetic code in mammals. Besides reading the conventional AUG codon, mitochondrial (mt‐)tRNAMet mediates incorporation of methionine on AUA and AUU codons during translation initiation and on AUA codons during elongation. We show that the RNA methyltransferase NSUN3 localises to mitochondria and interacts with mt‐tRNAMet to methylate cytosine 34 (C34) at the wobble position. NSUN3 specifically recognises the anticodon stem loop (ASL) of the tRNA, explaining why a mutation that compromises ASL basepairing leads to disease. We further identify ALKBH1/ABH1 as the dioxygenase responsible for oxidising m5C34 of mt‐tRNAMet to generate an f5C34 modification. In vitro codon recognition studies with mitochondrial translation factors reveal preferential utilisation of m5C34 mt‐tRNAMet in initiation. Depletion of either NSUN3 or ABH1 strongly affects mitochondrial translation in human cells, implying that modifications generated by both enzymes are necessary for mt‐tRNAMet function. Together, our data reveal how modifications in mt‐tRNAMet are generated by the sequential action of NSUN3 and ABH1, allowing the single mitochondrial tRNAMet to recognise the different codons encoding methionine.
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Affiliation(s)
- Sara Haag
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Katherine E Sloan
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Namit Ranjan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ahmed S Warda
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Jens Kretschmer
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Charlotte Blessing
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Benedikt Hübner
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Jan Seikowski
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sven Dennerlein
- Institute for Cellular Biochemistry, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Peter Rehling
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany Institute for Cellular Biochemistry, University Medical Center Göttingen Georg-August-University, Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany
| | - Markus T Bohnsack
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, Göttingen, Germany
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48
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Simms CL, Zaher HS. Quality control of chemically damaged RNA. Cell Mol Life Sci 2016; 73:3639-53. [PMID: 27155660 DOI: 10.1007/s00018-016-2261-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 04/15/2016] [Accepted: 04/29/2016] [Indexed: 01/10/2023]
Abstract
The "central dogma" of molecular biology describes how information contained in DNA is transformed into RNA and finally into proteins. In order for proteins to maintain their functionality in both the parent cell and subsequent generations, it is essential that the information encoded in DNA and RNA remains unaltered. DNA and RNA are constantly exposed to damaging agents, which can modify nucleic acids and change the information they encode. While much is known about how cells respond to damaged DNA, the importance of protecting RNA has only become appreciated over the past decade. Modification of the nucleobase through oxidation and alkylation has long been known to affect its base-pairing properties during DNA replication. Similarly, recent studies have begun to highlight some of the unwanted consequences of chemical damage on mRNA decoding during translation. Oxidation and alkylation of mRNA appear to have drastic effects on the speed and fidelity of protein synthesis. As some mRNAs can persist for days in certain tissues, it is not surprising that it has recently emerged that mRNA-surveillance and RNA-repair pathways have evolved to clear or correct damaged mRNA.
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Affiliation(s)
- Carrie L Simms
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO, 63130, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO, 63130, USA.
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Vohhodina J, Harkin DP, Savage KI. Dual roles of DNA repair enzymes in RNA biology/post-transcriptional control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:604-19. [PMID: 27126972 DOI: 10.1002/wrna.1353] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 12/12/2022]
Abstract
Despite consistent research into the molecular principles of the DNA damage repair pathway for almost two decades, it has only recently been found that RNA metabolism is very tightly related to this pathway, and the two ancient biochemical mechanisms act in alliance to maintain cellular genomic integrity. The close links between these pathways are well exemplified by examining the base excision repair pathway, which is now well known for dual roles of many of its members in DNA repair and RNA surveillance, including APE1, SMUG1, and PARP1. With additional links between these pathways steadily emerging, this review aims to provide a summary of the emerging roles for DNA repair proteins in the post-transcriptional regulation of RNAs. WIREs RNA 2016, 7:604-619. doi: 10.1002/wrna.1353 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jekaterina Vohhodina
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - D Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Kienan I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
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