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Rankin BD, Rankin S. The MCM2-7 Complex: Roles beyond DNA Unwinding. BIOLOGY 2024; 13:258. [PMID: 38666870 PMCID: PMC11048021 DOI: 10.3390/biology13040258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
The MCM2-7 complex is a hexameric protein complex that serves as a DNA helicase. It unwinds the DNA double helix during DNA replication, thereby providing the single-stranded replication template. In recent years, it has become clear that the MCM2-7 complex has additional functions that extend well beyond its role in DNA replication. Through physical and functional interactions with different pathways, it impacts other nuclear events and activities, including folding of the genome, histone inheritance, chromosome segregation, DNA damage sensing and repair, and gene transcription. Collectively, the diverse roles of the MCM2-7 complex suggest it plays a critical role in maintaining genome integrity by integrating the regulation of DNA replication with other pathways in the nucleus.
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Affiliation(s)
- Brooke D. Rankin
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
- Cell Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Susannah Rankin
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
- Cell Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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2
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Geng Y, Liu C, Xu N, Shi X, Suen MC, Zhou B, Yan B, Wu C, Li H, Song Y, Chen X, Wang Z, Cai Q, Zhu G. The N-terminal region of Cdc6 specifically recognizes human DNA G-quadruplex. Int J Biol Macromol 2024; 260:129487. [PMID: 38237821 DOI: 10.1016/j.ijbiomac.2024.129487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/28/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024]
Abstract
Guanine (G)-rich nucleic acid sequences can form diverse G-quadruplex structures located in functionally significant genome regions, exerting regulatory control over essential biological processes, including DNA replication in vivo. During the initiation of DNA replication, Cdc6 is recruited by the origin recognition complex (ORC) to target specific chromosomal DNA sequences. This study reveals that human Cdc6 interacts with G-quadruplex structure through a distinct region within the N-terminal intrinsically disordered region (IDR), encompassing residues 7-20. The binding region assumes a hook-type conformation, as elucidated by the NMR solution structure in complex with htel21T18. Significantly, mutagenesis and in vivo investigations confirm the highly specific nature of Cdc6's recognition of G-quadruplex. This research enhances our understanding of the fundamental mechanism governing the interaction between G-quadruplex and the N-terminal IDR region of Cdc6, shedding light on the intricate regulation of DNA replication processes.
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Affiliation(s)
- Yanyan Geng
- Clinical Research Institute of the First Affiliated Hospital of Xiamen University, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China; Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Changdong Liu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Naining Xu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xiao Shi
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Monica Ching Suen
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Bo Zhou
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Bing Yan
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Caiming Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hui Li
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yuanjian Song
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xueqin Chen
- Clinical Research Institute of the First Affiliated Hospital of Xiamen University, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Zhanxiang Wang
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Qixu Cai
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, China.
| | - Guang Zhu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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3
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Ogawa M, Moriyama M, Nakamura H, Shibata T, Kuroda K, Sugitani M. Clinical significance of CDT1 mRNA expression in chronic hepatitis C or liver cirrhosis. J Clin Biochem Nutr 2024; 74:169-178. [PMID: 38510682 PMCID: PMC10948353 DOI: 10.3164/jcbn.23-54] [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: 07/09/2023] [Accepted: 08/06/2023] [Indexed: 03/22/2024] Open
Abstract
We have previously reported that chromatin licensing and DNA replication factor 1 (CDT1) is associated with the postoperative recurrence of hepatocellular carcinoma (HCC). Based on this fact, we verified whether CDT1 mRNA expression is also associated with HCC development from chronic hepatitis C (CHC) and liver cirrhosis (LC). There were 142 cases with CHC or LC who underwent liver biopsy. Detection of CDT1 mRNA in liver was performed by RT-qPCR using frozen liver biopsy tissues. We examined the association between the CDT1 mRNA expression and clinical conditions and long-term outcome. We then examined the association between serum cytokine/chemokine levels and CDT1 mRNA expression in 58 cases. The cumulative incidence rates of HCC development in cases with CDT1 mRNA in the low expression group showed significantly lower than those in the high expression group (p = 0.0391). A significant correlation was found between CDT1 mRNA expression and the extent of proliferation of atypical hepatocytes in hematoxylin and eosin-stained sections (p<0.0001). CDT1 mRNA expression has been associated with cytokines involved in tumorigenesis in experimental and human cancers. We found that cases with high CDT1 mRNA expression were at risk for developing HCC, even if they were CHC or LC.
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Affiliation(s)
- Masahiro Ogawa
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Mitsuhiko Moriyama
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
- Sashiogi Recuperation Hospital, 1348-1 Hourai, Nishi-ku, Saitama city, Saitama 331-0074, Japan
| | - Hitomi Nakamura
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Toshikatu Shibata
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Kazumichi Kuroda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Masahiko Sugitani
- Department of Pathology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
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4
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Yadav AK, Polasek-Sedlackova H. Quantity and quality of minichromosome maintenance protein complexes couple replication licensing to genome integrity. Commun Biol 2024; 7:167. [PMID: 38336851 PMCID: PMC10858283 DOI: 10.1038/s42003-024-05855-w] [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: 10/05/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Accurate and complete replication of genetic information is a fundamental process of every cell division. The replication licensing is the first essential step that lays the foundation for error-free genome duplication. During licensing, minichromosome maintenance protein complexes, the molecular motors of DNA replication, are loaded to genomic sites called replication origins. The correct quantity and functioning of licensed origins are necessary to prevent genome instability associated with severe diseases, including cancer. Here, we delve into recent discoveries that shed light on the novel functions of licensed origins, the pathways necessary for their proper maintenance, and their implications for cancer therapies.
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Affiliation(s)
- Anoop Kumar Yadav
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Polasek-Sedlackova
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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5
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Taylor B, Tang N, Hao Y, Lee M, Peng S, Bybee R, Hartman L, Garcia-Mansfield K, Sharma R, Pirrotte P, Ma J, Parisian AD, Furnari F, Dhruv HD, Berens ME. Glioblastoma vulnerability to neddylation inhibition is dependent on PTEN status, and dysregulation of the cell cycle and DNA replication. Neurooncol Adv 2024; 6:vdae104. [PMID: 39119276 PMCID: PMC11306933 DOI: 10.1093/noajnl/vdae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
Background Neddylation (NAE) inhibition, affecting posttranslational protein function and turnover, is a promising therapeutic approach to cancer. We report the cytotoxic vulnerability to NAE inhibitors in a subset of glioblastoma (GBM) preclinical models and identify genetic alterations and biological processes underlying differential response. Methods GBM DNA sequencing and transcriptomic data were queried for genes associated with response to NAE inhibition; candidates were validated by molecular techniques. Multi-omics and functional assays revealed processes implicated in NAE inhibition response. Results Transcriptomics and shotgun proteomics depict PTEN signaling, DNA replication, and DNA repair pathways as significant differentiators between sensitive and resistant models. Vulnerability to MLN4924, a NAE inhibitor, is associated with elevated S-phase populations, DNA re-replication, and DNA damage. In a panel of GBM models, loss of WT PTEN is associated with resistance to different NAE inhibitors. A NAE inhibition response gene set could segregate the GBM cell lines that are most resistant to MLN4924. Conclusions Loss of WT PTEN is associated with non-sensitivity to 3 different compounds that inhibit NAE in GBM. A NAE inhibition response gene set largely consisting of DNA replication genes could segregate GBM cell lines most resistant to NAEi and may be the basis for future development of NAE inhibition signatures of vulnerability and clinical trial enrollment within a precision medicine paradigm.
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Affiliation(s)
- Brett Taylor
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Nanyun Tang
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Yue Hao
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matthew Lee
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Sen Peng
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Rita Bybee
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Lauren Hartman
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Krystine Garcia-Mansfield
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Ritin Sharma
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Jianhui Ma
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Alison D Parisian
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Frank Furnari
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Harshil D Dhruv
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
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Capece M, Tessari A, Mills J, Vinciguerra GLR, Louke D, Lin C, McElwain BK, Miles WO, Coppola V, Davies AE, Palmieri D, Croce CM. A novel auxin-inducible degron system for rapid, cell cycle-specific targeted proteolysis. Cell Death Differ 2023; 30:2078-2091. [PMID: 37537305 PMCID: PMC10482871 DOI: 10.1038/s41418-023-01191-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 06/02/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
The discrimination of protein biological functions in different phases of the cell cycle is limited by the lack of experimental approaches that do not require pre-treatment with compounds affecting the cell cycle progression. Therefore, potential cycle-specific biological functions of a protein of interest could be biased by the effects of cell treatments. The OsTIR1/auxin-inducible degron (AID) system allows "on demand" selective and reversible protein degradation upon exposure to the phytohormone auxin. In the current format, this technology does not allow to study the effect of acute protein depletion selectively in one phase of the cell cycle, as auxin similarly affects all the treated cells irrespectively of their proliferation status. Therefore, the AID system requires coupling with cell synchronization techniques, which can alter the basal biological status of the studied cell population, as with previously available approaches. Here, we introduce a new AID system to Regulate OsTIR1 Levels based on the Cell Cycle Status (ROLECCS system), which induces proteolysis of both exogenously transfected and endogenous gene-edited targets in specific phases of the cell cycle. We validated the ROLECCS technology by down regulating the protein levels of TP53, one of the most studied tumor suppressor genes, with a widely known role in cell cycle progression. By using our novel tool, we observed that TP53 degradation is associated with increased number of micronuclei, and this phenotype is specifically achieved when TP53 is lost in S/G2/M phases of the cell cycle, but not in G1. Therefore, we propose the use of the ROLECCS system as a new improved way of studying the differential roles that target proteins may have in specific phases of the cell cycle.
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Affiliation(s)
- Marina Capece
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Anna Tessari
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Joseph Mills
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Gian Luca Rampioni Vinciguerra
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Darian Louke
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, 43210, Columbus, OH, USA
| | - Chenyu Lin
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Bryan K McElwain
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Wayne O Miles
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Alexander E Davies
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, 43210, Columbus, OH, USA
| | - Dario Palmieri
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA.
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
- Gene Editing Shared Resource, The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA.
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
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Xun Q, Song Y, Mei M, Ding Y, Ding C. The SMC5/6 complex subunit MMS21 regulates stem cell proliferation in rice. PLANT CELL REPORTS 2023:10.1007/s00299-023-03030-9. [PMID: 37178216 DOI: 10.1007/s00299-023-03030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE SMC5/6 complex subunit OsMMS21 is involved in cell cycle and hormone signaling and required for stem cell proliferation during shoot and root development in rice. The structural maintenance of chromosome (SMC)5/6 complex is required for nucleolar integrity and DNA metabolism. Moreover, METHYL METHANESULFONATE SENSITIVITY GENE 21 (MMS21), a SUMO E3 ligase that is part of the SMC5/6 complex, is essential for the root stem cell niche and cell cycle transition in Arabidopsis. However, its specific role in rice remains unclear. Here, OsSMC5 and OsSMC6 single heterozygous mutants were generated using CRISPR/Cas9 technology to elucidate the function of SMC5/6 subunits, including OsSMC5, OsSMC6, and OsMMS21, in cell proliferation in rice. ossmc5/ + and ossmc6/ + heterozygous single mutants did not yield homozygous mutants in their progeny, indicating that OsSMC5 and OsSMC6 both play necessary roles during embryo formation. Loss of OsMMS21 caused severe defects in both the shoot and roots in rice. Transcriptome analysis showed a significant decrease in the expression of genes involved in auxin signaling in the roots of osmms21 mutants. Moreover, the expression levels of the cycB2-1 and MCM genes, which are involved the cell cycle, were significantly lower in the shoots of the mutants, indicating that OsMMS21 was involved in both hormone signaling pathways and the cell cycle. Overall, these findings indicate that the SUMO E3 ligase OsMMS21 is required for both shoot and root stem cell niches, improving the understanding of the function of the SMC5/6 complex in rice.
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Affiliation(s)
- Qian Xun
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ye Song
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Mei
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanfeng Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, 210095, China
| | - Chengqiang Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, China.
- Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, 210095, China.
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Sanada S, Maekawa M, Tate S, Nakaoka H, Fujisawa Y, Sayama K, Higashiyama S. SPOP is essential for DNA replication licensing through maintaining translation of CDT1 and CDC6 in HaCaT cells. Biochem Biophys Res Commun 2023; 651:30-38. [PMID: 36791496 DOI: 10.1016/j.bbrc.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/05/2023]
Abstract
Speckle-type pox virus and zinc finger (POZ) protein (SPOP), a substrate recognition receptor for the cullin-3/RING ubiquitin E3 complex, leads to the ubiquitination of >40 of its target substrates. Since a variety of point mutations in the substrate-binding domain of SPOP have been identified in cancers, including prostate and endometrial cancers, the pathological roles of those cancer-associated SPOP mutants have been extensively elucidated. In this study, we evaluated the cellular functions of wild-type SPOP in non-cancerous human keratinocyte-derived HaCaT cells expressing wild-type SPOP gene. SPOP knockdown using siRNA in HaCaT cells dramatically reduced cell growth and arrested their cell cycles at G1/S phase. The expression of DNA replication licensing factors CDT1 and CDC6 in HaCaT cells drastically decreased on SPOP knockdown as their translation was inhibited. CDT1 and CDC6 downregulation induced p21 expression without p53 activation. Our results suggest that SPOP is essential for DNA replication licensing in non-cancerous keratinocyte HaCaT cells.
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Affiliation(s)
- Sayoko Sanada
- Department of Dermatology, Ehime University Graduate School of Medicine, Toon, Ehime, 791-0295, Japan; Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Ehime, 791-0295, Japan
| | - Masashi Maekawa
- Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Ehime, 791-0295, Japan; Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Toon, Ehime, 791-0295, Japan.
| | - Sota Tate
- Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Ehime, 791-0295, Japan; Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Toon, Ehime, 791-0295, Japan
| | - Hiroki Nakaoka
- Department of Dermatology, Ehime University Graduate School of Medicine, Toon, Ehime, 791-0295, Japan
| | - Yasuhiro Fujisawa
- Department of Dermatology, Ehime University Graduate School of Medicine, Toon, Ehime, 791-0295, Japan
| | - Koji Sayama
- Department of Dermatology, Ehime University Graduate School of Medicine, Toon, Ehime, 791-0295, Japan
| | - Shigeki Higashiyama
- Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Ehime, 791-0295, Japan; Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Toon, Ehime, 791-0295, Japan; Department of Oncogenesis and Tumor Regulation, Osaka International Cancer Institute, Chuo-ku, Osaka, 541-8567, Japan.
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9
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Hu Y, Stillman B. Origins of DNA replication in eukaryotes. Mol Cell 2023; 83:352-372. [PMID: 36640769 PMCID: PMC9898300 DOI: 10.1016/j.molcel.2022.12.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
Errors occurring during DNA replication can result in inaccurate replication, incomplete replication, or re-replication, resulting in genome instability that can lead to diseases such as cancer or disorders such as autism. A great deal of progress has been made toward understanding the entire process of DNA replication in eukaryotes, including the mechanism of initiation and its control. This review focuses on the current understanding of how the origin recognition complex (ORC) contributes to determining the location of replication initiation in the multiple chromosomes within eukaryotic cells, as well as methods for mapping the location and temporal patterning of DNA replication. Origin specification and configuration vary substantially between eukaryotic species and in some cases co-evolved with gene-silencing mechanisms. We discuss the possibility that centromeres and origins of DNA replication were originally derived from a common element and later separated during evolution.
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Affiliation(s)
- Yixin Hu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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10
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The proliferation of atypical hepatocytes and CDT1 expression in noncancerous tissue are associated with the postoperative recurrence of hepatocellular carcinoma. Sci Rep 2022; 12:20508. [PMID: 36443564 PMCID: PMC9705552 DOI: 10.1038/s41598-022-25201-6] [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: 08/04/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
Recently, we reported that extent of proliferation of atypical hepatocytes (atypical hepatocytes) was most important histological risk factor for development of hepatocellular carcinoma (HCC) from chronic hepatitis C or liver cirrhosis. Here, we aimed to clarify whether the atypical hepatocytes in noncancerous sections is also involved in postoperative recurrence. Furthermore, we investigated significant genes involved in the atypical hepatocytes. Association between the extent of atypical hepatocytes in noncancerous tissue and postoperative recurrence was validated in 356 patients with HCC. Next, we identified putative signature genes involved in extent of atypical hepatocytes. First, atypical hepatocytes or hepatocytes other than the atypical hepatocyte in noncancerous sections of 4 HCC patients were selectively collected by laser capture microdissection (LCM). Second, the gene expression profiles of the selected hepatocyte populations were compared using Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher SCIENTIFIC, Waltham, MA, USA) analysis. Finally, we validated the mRNA expression of the extracted genes in noncancerous frozen liver tissue from 62 patients with HCC by RT-qPCR to identify the signature genes involved in both the extent of atypical hepatocytes and postoperative recurrence. Furthermore, the extent of atypical hepatocytes and CDT1 expression in noncancerous sections from 8 patients with HCC were also validated by selectively collecting samples using LCM. The extent of atypical hepatocytes was associated with postoperative recurrence. Of the genes that showed significant differences in expression levels between two populations, the expression of the chromatin licensing and DNA replication factor 1 (CDT1) gene was most strongly associated with the extent of atypical hepatocytes and was also associated with postoperative recurrence. Furthermore, CDT1-positive cells that exhibited stronger expression resembled those morphologically considered to be atypical hepatocytes. CDT1 and Ki-67 were colocalized in the nuclei of both hepatocytes and cancer cells. The hepatocytes in noncancerous livers were not uniform in each hepatocyte population, suggesting that the accumulation of genetic abnormalities was variable. We found that the strong degree of atypical hepatocytes and high CDT1 mRNA expression represent a high carcinogenic state of the liver. Thus, we consider the evaluation of degree of these could support the personalized medicine.
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11
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Ferdosi SR, Taylor B, Lee M, Tang N, Peng S, Bybee R, Reid G, Hartman L, Garcia-Mansfield K, Sharma R, Pirrotte P, Ma J, Parisian AD, Furnari F, Dhruv HD, Berens ME. PTEN loss drives resistance to the neddylation inhibitor MLN4924 in glioblastoma and can be overcome with TOP2A inhibitors. Neuro Oncol 2022; 24:1857-1868. [PMID: 35305088 PMCID: PMC9629460 DOI: 10.1093/neuonc/noac067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Neddylation inhibition, affecting posttranslational protein function and turnover, is a promising therapeutic approach to cancer. We report vulnerability to MLN4924 or pevonedistat (a neddylation inhibitor) in a subset of glioblastoma (GBM) preclinical models and identify biomarkers, mechanisms, and signatures of differential response. METHODS GBM sequencing data were queried for genes associated with MLN4924 response status; candidates were validated by molecular techniques. Time-course transcriptomics and proteomics revealed processes implicated in MLN4924 response. RESULTS Vulnerability to MLN4924 is associated with elevated S-phase populations, re-replication, and DNA damage. Transcriptomics and shotgun proteomics depict PTEN signaling, DNA replication, and chromatin instability pathways as significant differentiators between sensitive and resistant models. Loss of PTEN and its nuclear functions is associated with resistance to MLN4924. Time-course proteomics identified elevated TOP2A in resistant models through treatment. TOP2A inhibitors combined with MLN4924 prove synergistic. CONCLUSIONS We show that PTEN status serves as both a novel biomarker for MLN4924 response in GBM and reveals a vulnerability to TOP2A inhibitors in combination with MLN4924.
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Affiliation(s)
- Shayesteh R Ferdosi
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Brett Taylor
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Matthew Lee
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Nanyun Tang
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Sen Peng
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Rita Bybee
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - George Reid
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Lauren Hartman
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Krystine Garcia-Mansfield
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Ritin Sharma
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Jianhui Ma
- Ludwig Cancer Research, San Diego Branch, La Jolla, CA 92093, USA
| | | | - Frank Furnari
- Ludwig Cancer Research, San Diego Branch, La Jolla, CA 92093, USA
- Department of Pathology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Harshil D Dhruv
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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12
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Gaglia G, Kabraji S, Rammos D, Dai Y, Verma A, Wang S, Mills CE, Chung M, Bergholz JS, Coy S, Lin JR, Jeselsohn R, Metzger O, Winer EP, Dillon DA, Zhao JJ, Sorger PK, Santagata S. Temporal and spatial topography of cell proliferation in cancer. Nat Cell Biol 2022; 24:316-326. [PMID: 35292783 PMCID: PMC8959396 DOI: 10.1038/s41556-022-00860-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/31/2022] [Indexed: 02/06/2023]
Abstract
Proliferation is a fundamental trait of cancer cells, but its properties and spatial organization in tumours are poorly characterized. Here we use highly multiplexed tissue imaging to perform single-cell quantification of cell cycle regulators and then develop robust, multivariate, proliferation metrics. Across diverse cancers, proliferative architecture is organized at two spatial scales: large domains, and smaller niches enriched for specific immune lineages. Some tumour cells express cell cycle regulators in the (canonical) patterns expected of freely growing cells, a phenomenon we refer to as 'cell cycle coherence'. By contrast, the cell cycles of other tumour cell populations are skewed towards specific phases or exhibit non-canonical (incoherent) marker combinations. Coherence varies across space, with changes in oncogene activity and therapeutic intervention, and is associated with aggressive tumour behaviour. Thus, multivariate measures from high-plex tissue images capture clinically significant features of cancer proliferation, a fundamental step in enabling more precise use of anti-cancer therapies.
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Affiliation(s)
- Giorgio Gaglia
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sheheryar Kabraji
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Danae Rammos
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yang Dai
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana Verma
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shu Wang
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Mirra Chung
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Johann S Bergholz
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Shannon Coy
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Otto Metzger
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Eric P Winer
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jean J Zhao
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA.
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13
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CRL4Cdt2 Ubiquitin Ligase, A Genome Caretaker Controlled by Cdt2 Binding to PCNA and DNA. Genes (Basel) 2022; 13:genes13020266. [PMID: 35205311 PMCID: PMC8871960 DOI: 10.3390/genes13020266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/22/2022] Open
Abstract
The ubiquitin ligase CRL4Cdt2 plays a vital role in preserving genomic integrity by regulating essential proteins during S phase and after DNA damage. Deregulation of CRL4Cdt2 during the cell cycle can cause DNA re-replication, which correlates with malignant transformation and tumor growth. CRL4Cdt2 regulates a broad spectrum of cell cycle substrates for ubiquitination and proteolysis, including Cdc10-dependent transcript 1 or Chromatin licensing and DNA replication factor 1 (Cdt1), histone H4K20 mono-methyltransferase (Set8) and cyclin-dependent kinase inhibitor 1 (p21), which regulate DNA replication. However, the mechanism it operates via its substrate receptor, Cdc10-dependent transcript 2 (Cdt2), is not fully understood. This review describes the essential features of the N-terminal and C-terminal parts of Cdt2 that regulate CRL4 ubiquitination activity, including the substrate recognition domain, intrinsically disordered region (IDR), phosphorylation sites, the PCNA-interacting protein-box (PIP) box motif and the DNA binding domain. Drugs targeting these specific domains of Cdt2 could have potential for the treatment of cancer.
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14
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Depletion of NK6 Homeobox 3 (NKX6.3) causes gastric carcinogenesis through copy number alterations by inducing impairment of DNA replication and repair regulation. Oncogenesis 2021; 10:85. [PMID: 34893582 PMCID: PMC8664813 DOI: 10.1038/s41389-021-00365-4] [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: 06/15/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 11/21/2022] Open
Abstract
Genomic stability maintenance requires correct DNA replication, chromosome segregation, and DNA repair, while defects of these processes result in tumor development or cell death. Although abnormalities in DNA replication and repair regulation are proposed as underlying causes for genomic instability, the detailed mechanism remains unclear. Here, we investigated whether NKX6.3 plays a role in the maintenance of genomic stability in gastric epithelial cells. NKX6.3 functioned as a transcription factor for CDT1 and RPA1, and its depletion increased replication fork rate, and fork asymmetry. Notably, we showed that abnormal DNA replication by the depletion of NKX6.3 caused DNA damage and induced homologous recombination inhibition. Depletion of NKX6.3 also caused copy number alterations of various genes in the vast chromosomal region. Hence, our findings underscore NKX6.3 might be a crucial factor of DNA replication and repair regulation from genomic instability in gastric epithelial cells.
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15
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Wu K, Hopkins BD, Sanchez R, DeVita RJ, Pan ZQ. Targeting Cullin-RING E3 Ubiquitin Ligase 4 by Small Molecule Modulators. JOURNAL OF CELLULAR SIGNALING 2021; 2:195-205. [PMID: 34604860 PMCID: PMC8486283 DOI: 10.33696/signaling.2.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cullin-RING E3 ubiquitin ligase 4 (CRL4) plays an essential role in cell cycle progression. Recent efforts using high throughput screening and follow up hit-to-lead studies have led to identification of small molecules 33-11 and KH-4-43 that inhibit E3 CRL4's core ligase complex and exhibit anticancer potential. This review provides: 1) an updated perspective of E3 CRL4, including structural organization, major substrate targets and role in cancer; 2) a discussion of the challenges and strategies for finding the CRL inhibitor; and 3) a summary of the properties of the identified CRL4 inhibitors as well as a perspective on their potential utility to probe CRL4 biology and act as therapeutic agents.
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Affiliation(s)
- Kenneth Wu
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029-6574, USA
| | - Benjamin D Hopkins
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029-6574, USA.,Genetics and Genomics, The Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029-6574, USA
| | - Roberto Sanchez
- Department of Pharmacological Sciences, The Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029-6574, USA.,Drug Discovery Institute, The Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029-6574, USA
| | - Robert J DeVita
- Department of Pharmacological Sciences, The Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029-6574, USA.,Drug Discovery Institute, The Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029-6574, USA
| | - Zhen-Qiang Pan
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029-6574, USA
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16
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SPOP mutation induces replication over-firing by impairing Geminin ubiquitination and triggers replication catastrophe upon ATR inhibition. Nat Commun 2021; 12:5779. [PMID: 34599168 PMCID: PMC8486843 DOI: 10.1038/s41467-021-26049-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 09/09/2021] [Indexed: 12/28/2022] Open
Abstract
Geminin and its binding partner Cdt1 are essential for the regulation of DNA replication. Here we show that the CULLIN3 E3 ubiquitin ligase adaptor protein SPOP binds Geminin at endogenous level and regulates DNA replication. SPOP promotes K27-linked non-degradative poly-ubiquitination of Geminin at lysine residues 100 and 127. This poly-ubiquitination of Geminin prevents DNA replication over-firing by indirectly blocking the association of Cdt1 with the MCM protein complex, an interaction required for DNA unwinding and replication. SPOP is frequently mutated in certain human cancer types and implicated in tumorigenesis. We show that cancer-associated SPOP mutations impair Geminin K27-linked poly-ubiquitination and induce replication origin over-firing and re-replication. The replication stress caused by SPOP mutations triggers replication catastrophe and cell death upon ATR inhibition. Our results reveal a tumor suppressor role of SPOP in preventing DNA replication over-firing and genome instability and suggest that SPOP-mutated tumors may be susceptible to ATR inhibitor therapy. Geminin-Cdt1 plays essential roles in the regulation of DNA replication. Here the authors reveal that the CULLIN3 E3 ubiquitin ligase adaptor protein SPOP prevents DNA replication over-firing and genome instability by affecting Geminin ubiquitination.
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17
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Ahmadi SE, Rahimi S, Zarandi B, Chegeni R, Safa M. MYC: a multipurpose oncogene with prognostic and therapeutic implications in blood malignancies. J Hematol Oncol 2021; 14:121. [PMID: 34372899 PMCID: PMC8351444 DOI: 10.1186/s13045-021-01111-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/12/2021] [Indexed: 12/17/2022] Open
Abstract
MYC oncogene is a transcription factor with a wide array of functions affecting cellular activities such as cell cycle, apoptosis, DNA damage response, and hematopoiesis. Due to the multi-functionality of MYC, its expression is regulated at multiple levels. Deregulation of this oncogene can give rise to a variety of cancers. In this review, MYC regulation and the mechanisms by which MYC adjusts cellular functions and its implication in hematologic malignancies are summarized. Further, we also discuss potential inhibitors of MYC that could be beneficial for treating hematologic malignancies.
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Affiliation(s)
- Seyed Esmaeil Ahmadi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Rahimi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Bahman Zarandi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rouzbeh Chegeni
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL, USA.
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
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18
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Zhang H. Regulation of DNA Replication Licensing and Re-Replication by Cdt1. Int J Mol Sci 2021; 22:ijms22105195. [PMID: 34068957 PMCID: PMC8155957 DOI: 10.3390/ijms22105195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022] Open
Abstract
In eukaryotic cells, DNA replication licensing is precisely regulated to ensure that the initiation of genomic DNA replication in S phase occurs once and only once for each mitotic cell division. A key regulatory mechanism by which DNA re-replication is suppressed is the S phase-dependent proteolysis of Cdt1, an essential replication protein for licensing DNA replication origins by loading the Mcm2-7 replication helicase for DNA duplication in S phase. Cdt1 degradation is mediated by CRL4Cdt2 ubiquitin E3 ligase, which further requires Cdt1 binding to proliferating cell nuclear antigen (PCNA) through a PIP box domain in Cdt1 during DNA synthesis. Recent studies found that Cdt2, the specific subunit of CRL4Cdt2 ubiquitin E3 ligase that targets Cdt1 for degradation, also contains an evolutionarily conserved PIP box-like domain that mediates the interaction with PCNA. These findings suggest that the initiation and elongation of DNA replication or DNA damage-induced repair synthesis provide a novel mechanism by which Cdt1 and CRL4Cdt2 are both recruited onto the trimeric PCNA clamp encircling the replicating DNA strands to promote the interaction between Cdt1 and CRL4Cdt2. The proximity of PCNA-bound Cdt1 to CRL4Cdt2 facilitates the destruction of Cdt1 in response to DNA damage or after DNA replication initiation to prevent DNA re-replication in the cell cycle. CRL4Cdt2 ubiquitin E3 ligase may also regulate the degradation of other PIP box-containing proteins, such as CDK inhibitor p21 and histone methylase Set8, to regulate DNA replication licensing, cell cycle progression, DNA repair, and genome stability by directly interacting with PCNA during DNA replication and repair synthesis.
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Affiliation(s)
- Hui Zhang
- Department of Chemistry and Biochemistry, Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 South Maryland Parkway, Box 454003, Las Vegas, NV 89154, USA
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19
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Replication initiation: Implications in genome integrity. DNA Repair (Amst) 2021; 103:103131. [PMID: 33992866 DOI: 10.1016/j.dnarep.2021.103131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 02/01/2023]
Abstract
In every cell cycle, billions of nucleotides need to be duplicated within hours, with extraordinary precision and accuracy. The molecular mechanism by which cells regulate the replication event is very complicated, and the entire process begins way before the onset of S phase. During the G1 phase of the cell cycle, cells prepare by assembling essential replication factors to establish the pre-replicative complex at origins, sites that dictate where replication would initiate during S phase. During S phase, the replication process is tightly coupled with the DNA repair system to ensure the fidelity of replication. Defects in replication and any error must be recognized by DNA damage response and checkpoint signaling pathways in order to halt the cell cycle before cells are allowed to divide. The coordination of these processes throughout the cell cycle is therefore critical to achieve genomic integrity and prevent diseases. In this review, we focus on the current understanding of how the replication initiation events are regulated to achieve genome stability.
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20
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Zeng T, Guan Y, Li YK, Wu Q, Tang XJ, Zeng X, Ling H, Zou J. The DNA replication regulator MCM6: An emerging cancer biomarker and target. Clin Chim Acta 2021; 517:92-98. [PMID: 33609557 DOI: 10.1016/j.cca.2021.02.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 01/07/2023]
Abstract
MCM6 is a significant DNA replication regulator that plays a crucial role in sustaining the cell cycle. In many cancer cells, MCM6 expression is enhanced. For example, persistently increased expression of MCM6 promotes the formation, development and progression of hepatocellular carcinoma (HCC). Up- and down-regulation studies have indicated that MCM6 regulates cell cycle, proliferation, metastasis, immune response and the maintenance of the DNA replication system. MCM6 can also regulate downstream signaling such as MEK/ERK thus promoting carcinogenesis. Accordingly, MCM6 may represent a sensitive and specific biomarker to predict adverse progression and poor outcome. Furthermore, inhibition of MCM6 may be an effective cancer treatment. The present review summarizes the latest results on the inactivating and activating functions of MCM6, underlining its function in carcinogenesis. Further studies of the carcinogenic functions of MCM6 may provide novel insight into cancer biology and shed light on new approaches for cancer diagnosis and treatment.
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Affiliation(s)
- Tian Zeng
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, PR China
| | - Yang Guan
- Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi 330000, PR China
| | - Yu-Kun Li
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, PR China
| | - Qing Wu
- Department of Digestive Medical, The Affiliated Nanhua Hospital, University of South China, Hengyang 421002, PR China
| | - Xiao-Jun Tang
- Department of Spinal Surgery, The Second Affiliated Hospital of University of South China, Hengyang, Hunan 421001, PR China
| | - Xin Zeng
- Department of Histology and Embryology, Chongqing Three Gorges Medical College, Wanzhou, Chongqing 404000, PR China
| | - Hui Ling
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, PR China.
| | - Juan Zou
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, PR China.
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21
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Rapsomaniki MA, Maxouri S, Nathanailidou P, Garrastacho MR, Giakoumakis NN, Taraviras S, Lygeros J, Lygerou Z. In silico analysis of DNA re-replication across a complete genome reveals cell-to-cell heterogeneity and genome plasticity. NAR Genom Bioinform 2021; 3:lqaa112. [PMID: 33554116 PMCID: PMC7846089 DOI: 10.1093/nargab/lqaa112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/15/2020] [Accepted: 01/20/2021] [Indexed: 01/06/2023] Open
Abstract
DNA replication is a complex and remarkably robust process: despite its inherent uncertainty, manifested through stochastic replication timing at a single-cell level, multiple control mechanisms ensure its accurate and timely completion across a population. Disruptions in these mechanisms lead to DNA re-replication, closely connected to genomic instability and oncogenesis. Here, we present a stochastic hybrid model of DNA re-replication that accurately portrays the interplay between discrete dynamics, continuous dynamics and uncertainty. Using experimental data on the fission yeast genome, model simulations show how different regions respond to re-replication and permit insight into the key mechanisms affecting re-replication dynamics. Simulated and experimental population-level profiles exhibit a good correlation along the genome, robust to model parameters, validating our approach. At a single-cell level, copy numbers of individual loci are affected by intrinsic properties of each locus, in cis effects from adjoining loci and in trans effects from distant loci. In silico analysis and single-cell imaging reveal that cell-to-cell heterogeneity is inherent in re-replication and can lead to genome plasticity and a plethora of genotypic variations.
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Affiliation(s)
- Maria Anna Rapsomaniki
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - Stella Maxouri
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - Patroula Nathanailidou
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | | | | | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - John Lygeros
- Automatic Control Laboratory, ETH Zurich, 8092 Zurich, Switzerland
| | - Zoi Lygerou
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
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22
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Novák B, Tyson JJ. Computational modeling of chromosome re-replication in mutant strains of fission yeast. Mol Biol Cell 2021; 32:830-841. [PMID: 33534609 PMCID: PMC8108527 DOI: 10.1091/mbc.e20-09-0610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Typically cells replicate their genome only once per division cycle, but under some circumstances, both natural and unnatural, cells synthesize an overabundance of DNA, either in a disorganized manner (“overreplication”) or by a systematic doubling of chromosome number (“endoreplication”). These variations on the theme of DNA replication and division have been studied in strains of fission yeast, Schizosaccharomyces pombe, carrying mutations that interfere with the function of mitotic cyclin-dependent kinase (Cdk1:Cdc13) without impeding the roles of DNA-replication loading factor (Cdc18) and S-phase cyclin-dependent kinase (Cdk1:Cig2). Some of these mutations support endoreplication, and some overreplication. In this paper, we propose a dynamical model of the interactions among the proteins governing DNA replication and cell division in fission yeast. By computational simulations of the mathematical model, we account for the observed phenotypes of these re-replicating mutants, and by theoretical analysis of the dynamical system, we provide insight into the molecular distinctions between overreplicating and endoreplicating cells. In the case of induced overproduction of regulatory proteins, our model predicts that cells first switch from normal mitotic cell cycles to growth-controlled endoreplication, and ultimately to disorganized overreplication, parallel to the slow increase of protein to very high levels.
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Affiliation(s)
- Béla Novák
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - John J Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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23
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Xu N, You Y, Liu C, Balasov M, Lun LT, Geng Y, Fung CP, Miao H, Tian H, Choy TT, Shi X, Fan Z, Zhou B, Akhmetova K, Din RU, Yang H, Hao Q, Qian P, Chesnokov I, Zhu G. Structural basis of DNA replication origin recognition by human Orc6 protein binding with DNA. Nucleic Acids Res 2020; 48:11146-11161. [PMID: 32986843 PMCID: PMC7641730 DOI: 10.1093/nar/gkaa751] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 08/18/2020] [Accepted: 09/19/2020] [Indexed: 01/08/2023] Open
Abstract
The six-subunit origin recognition complex (ORC), a DNA replication initiator, defines the localization of the origins of replication in eukaryotes. The Orc6 subunit is the smallest and the least conserved among ORC subunits. It is required for DNA replication and essential for viability in all species. Orc6 in metazoans carries a structural homology with transcription factor TFIIB and can bind DNA on its own. Here, we report a solution structure of the full-length human Orc6 (HsOrc6) alone and in a complex with DNA. We further showed that human Orc6 is composed of three independent domains: N-terminal, middle and C-terminal (HsOrc6-N, HsOrc6-M and HsOrc6-C). We also identified a distinct DNA-binding domain of human Orc6, named as HsOrc6-DBD. The detailed analysis of the structure revealed novel amino acid clusters important for the interaction with DNA. Alterations of these amino acids abolish DNA-binding ability of Orc6 and result in reduced levels of DNA replication. We propose that Orc6 is a DNA-binding subunit of human/metazoan ORC and may play roles in targeting, positioning and assembling the functional ORC at the origins.
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Affiliation(s)
- Naining Xu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- Department of Oral and Maxillofacial Surgery, Peking University ShenzhenHospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Yingying You
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Changdong Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Maxim Balasov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Lee Tung Lun
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Yanyan Geng
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Chun Po Fung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Haitao Miao
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Honglei Tian
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - To To Choy
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Xiao Shi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Zhuming Fan
- School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong SAR, 00000, China
| | - Bo Zhou
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Katarina Akhmetova
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Rahman Ud Din
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Hongyu Yang
- Department of Oral and Maxillofacial Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University, Shenzhen, 518036, China
| | - Quan Hao
- School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong SAR, 00000, China
| | - Peiyuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Igor Chesnokov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
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CRL4 Ubiquitin Pathway and DNA Damage Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:225-239. [PMID: 31898231 DOI: 10.1007/978-981-15-1025-0_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
DNA damage occurs in a human cell at an average frequency of 10,000 incidences per day by means of external and internal culprits, damage that triggers sequential cellular responses and stalls the cell cycle while activating specific DNA repair pathways. Failure to remove DNA lesions would compromise genomic integrity, leading to human diseases such as cancer and premature aging. If DNA damage is extensive and cannot be repaired, cells undergo apoptosis. DNA damage response (DDR) often entails posttranslational modifications of key DNA repair and DNA damage checkpoint proteins, including phosphorylation and ubiquitination. Cullin-RING ligase 4 (CRL4) enzyme has been found to target multiple DDR proteins for ubiquitination. In this chapter, we will discuss key repair and checkpoint proteins that are subject to ubiquitin-dependent regulation by members of the CRL4 family during ultraviolet light (UV)-induced DNA damage.
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25
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Jung IJ, Ahn JW, Jung S, Hwang JE, Hong MJ, Choi HI, Kim JB. Overexpression of rice jacalin-related mannose-binding lectin (OsJAC1) enhances resistance to ionizing radiation in Arabidopsis. BMC PLANT BIOLOGY 2019; 19:561. [PMID: 31852472 PMCID: PMC6921557 DOI: 10.1186/s12870-019-2056-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/26/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Jacalin-related lectins in plants are important in defense signaling and regulate growth, development, and response to abiotic stress. We characterized the function of a rice mannose-binding jacalin-related lectin (OsJAC1) in the response to DNA damage from gamma radiation. RESULTS Time- and dose-dependent changes of OsJAC1 expression in rice were detected in response to gamma radiation. To identify OsJAC1 function, OsJAC1-overexpressing transgenic Arabidopsis plants were generated. Interestingly, OsJAC1 overexpression conferred hyper-resistance to gamma radiation in these plants. Using comparative transcriptome analysis, genes related to pathogen defense were identified among 22 differentially expressed genes in OsJAC1-overexpressing Arabidopsis lines following gamma irradiation. Furthermore, expression profiles of genes associated with the plant response to DNA damage were determined in these transgenic lines, revealing expression changes of important DNA damage checkpoint and perception regulatory components, namely MCMs, RPA, ATM, and MRE11. CONCLUSIONS OsJAC1 overexpression may confer hyper-resistance to gamma radiation via activation of DNA damage perception and DNA damage checkpoints in Arabidopsis, implicating OsJAC1 as a key player in DNA damage response in plants. This study is the first report of a role for mannose-binding jacalin-related lectin in DNA damage.
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Affiliation(s)
- In Jung Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
| | - Sera Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
| | - Jung Eun Hwang
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, 33657 Republic of Korea
| | - Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
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26
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Hitora Y, Takada K, Ise Y, Woo SP, Inoue S, Mori N, Takikawa H, Nakamukai S, Okada S, Matsunaga S. Metachromins X and Y from a marine sponge Spongia sp. and their effects on cell cycle progression. Bioorg Med Chem 2019; 28:115233. [PMID: 31848114 DOI: 10.1016/j.bmc.2019.115233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 02/06/2023]
Abstract
New sesquiterpene quinones, metachromins X (1) and Y (2), together with the known metachromins C (3), J (4), and T (5), were isolated as inhibitors of cell cycle progression in the HeLa/Fucci2 cells. The structure of 1 was assigned by spectroscopic data and confirmed by a total synthesis. The planar structure of 2 was determined by interpretation of spectroscopic data, whereas its absolute configuration was analyzed by a combination of chiral HPLC and CD spectroscopy. Metachromins X (1) and C (3) arrested the cell cycle progression of HeLa/Fucci2 cells at S/G2/M phase.
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Affiliation(s)
- Yuki Hitora
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kentaro Takada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Yuji Ise
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima-cho, Toba-shi, Mie 517-0004, Japan
| | - Sau Pinn Woo
- Center for Marine and Coastal Studies, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
| | - Seiya Inoue
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bukyo-ku, Tokyo 113-8657, Japan
| | - Naoki Mori
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bukyo-ku, Tokyo 113-8657, Japan
| | - Hirosato Takikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bukyo-ku, Tokyo 113-8657, Japan
| | - Shohei Nakamukai
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan. .-tokyo.ac.jp
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27
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Mazian MA, Suenaga N, Ishii T, Hayashi A, Shiomi Y, Nishitani H. A DNA-binding domain in the C-terminal region of Cdt2 enhances the DNA synthesis-coupled CRL4Cdt2 ubiquitin ligase activity for Cdt1. J Biochem 2019; 165:505-516. [PMID: 30649446 DOI: 10.1093/jb/mvz001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
The Cullin-RING ubiquitin ligase CRL4Cdt2 maintains genome integrity by mediating the cell cycle- and DNA damage-dependent degradation of proteins such as Cdt1, p21 and Set8. Human Cdt2 has two regions, a conserved N-terminal seven WD40 repeat region and a less conserved C-terminal region. Here, we showed that the N-terminal region is sufficient for complex formation with CRL4, but the C-terminal region is required for the full ubiquitin ligase activity. UV irradiation-induced polyubiquitination and degradation of Cdt1 were impaired in Cdt2 (N-terminus only)-expressing cells. Deletion and mutation analysis identified a domain in the C-terminal region that increased ubiquitination activity and displayed DNA-binding activity. The identified domain mediated binding to double-stranded DNA and showed higher affinity binding to single-stranded DNA. As the ligase activity of CRL4Cdt2 depends on proliferating cell nuclear antigen (PCNA) loading onto DNA, the present results suggest that the DNA-binding domain facilitates the CRL4Cdt2-mediated recognition and ubiquitination of substrates bound to PCNA on chromatin.
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Affiliation(s)
- Muadz Ahmad Mazian
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
| | - Naohiro Suenaga
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
| | - Takashi Ishii
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
| | - Akiyo Hayashi
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
| | - Yasushi Shiomi
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
| | - Hideo Nishitani
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
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Nurse P, Hayles J. Using genetics to understand biology. Heredity (Edinb) 2019; 123:4-13. [PMID: 31189902 PMCID: PMC6781147 DOI: 10.1038/s41437-019-0209-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/16/2022] Open
Affiliation(s)
- Paul Nurse
- The Francis Crick Institute, 1, Midland Road, London, NW1 1AT, UK
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Minichromosome Maintenance Proteins Cooperate with LANA during the G 1/S Phase of the Cell Cycle To Support Viral DNA Replication. J Virol 2019; 93:JVI.02256-18. [PMID: 30651368 DOI: 10.1128/jvi.02256-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/13/2019] [Indexed: 12/11/2022] Open
Abstract
Latency-associated nuclear antigen (LANA) is essential for maintaining the viral genome by regulating replication and segregation of the viral episomes. The virus maintains 50 to 100 episomal copies during latency and replicates in synchrony with the cellular DNA of the infected cells. Since virus lacks its own replication machinery, it utilizes the cellular proteins for replication and maintenance, and LANA has been shown to make many of these proteins available for replication by directly recruiting them to the viral origin of replication within the terminal repeat (TR) region. Our studies identified members of the minichromosome maintenance (MCM) complex as potential LANA-interacting proteins. Here, we show that LANA specifically interacts with the components of the MCM complex, primarily during the G1/S phase of the cell cycle. MCM3 and -4 of the MCM complex specifically bound to the amino-terminal domain, while MCM6 bound to both the amino- and carboxyl-terminal domains of LANA. The MCM binding region in the N-terminal domain mapped to the chromatin binding domain (CBD). LANA with point mutations in the carboxyl-terminal domain identified an MCM6 binding domain, and overexpression of that domain (amino acids [aa] 1100 to 1150) abolished TR replication. Introduction of a peptide encompassing the LANA aa 1104 to 1123 reduced MCM6 association with LANA and TR replication. Moreover, a recombinant Kaposi's sarcoma-associated herpesvirus (KSHV) expressing LANA with a deletion of aa 1100 to 1150 (BAC16Δ1100-1150, where BAC is bacmid) showed reduced replication and persistence of viral genome copies compared to levels with the wild-type BAC16. Additionally, the role of MCMs in viral replication was confirmed by depleting MCMs and assaying transient and long-term maintenance of the viral episomes. The recruitment of MCMs to the replication origins through LANA was demonstrated through chromatin immunoprecipitation and isolation of proteins on nascent replicated DNA (iPOND). These data clearly show the role of MCMs in latent DNA replication and the potential for targeting the C-terminal domain of LANA to block viral persistence.IMPORTANCE LANA-mediated latent DNA replication is essential for efficient maintenance of KSHV episomes in the host. During latency, virus relies on the host cellular machinery for replication, which occurs in synchrony with the cellular DNA. LANA interacts with the components of multiple cellular pathways, including cellular replication machinery, and recruits them to the viral origin for DNA replication. In this study, we characterize the interactions between LANA and minichromosome maintenance (MCM) proteins, members of the cellular replication complex. We demonstrated a cell cycle-dependent interaction between LANA and MCMs and determined their importance for viral genome replication and maintenance through biochemical assays. In addition, we mapped a 50-amino acid region in LANA which was capable of abrogating the association of MCM6 with LANA and blocking DNA replication. We also detected LANA along with MCMs at the replication forks using a novel approach, isolation of proteins on nascent DNA (iPOND).
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30
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Cheung MH, Amin A, Wu R, Qin Y, Zou L, Yu Z, Liang C. Human NOC3 is essential for DNA replication licensing in human cells. Cell Cycle 2019; 18:605-620. [PMID: 30741601 DOI: 10.1080/15384101.2019.1578522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Noc3p (Nucleolar Complex-associated protein) is an essential protein in budding yeast DNA replication licensing. Noc3p mediates the loading of Cdc6p and MCM proteins onto replication origins during the M-to-G1 transition by interacting with ORC (Origin Recognition Complex) and MCM (Minichromosome Maintenance) proteins. FAD24 (Factor for Adipocyte Differentiation, clone number 24), the human homolog of Noc3p (hNOC3), was previously reported to play roles in the regulation of DNA replication and proliferation in human cells. However, the role of hNOC3 in replication licensing was unclear. Here we report that hNOC3 physically interacts with multiple human pre-replicative complex (pre-RC) proteins and associates with known replication origins throughout the cell cycle. Moreover, knockdown of hNOC3 in HeLa cells abrogates the chromatin association of other pre-RC proteins including hCDC6 and hMCM, leading to DNA replication defects and eventual apoptosis in an abortive S-phase. In comparison, specific inhibition of the ribosome biogenesis pathway by preventing pre-rRNA synthesis, does not lead to any cell cycle or DNA replication defect or apoptosis in the same timeframe as the hNOC3 knockdown experiments. Our findings strongly suggest that hNOC3 plays an essential role in pre-RC formation and the initiation of DNA replication independent of its potential role in ribosome biogenesis in human cells.
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Affiliation(s)
- Man-Hei Cheung
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China.,c Shenzhen-PKU-HKUST Medical Center , Biomedical Research Institute , Shenzhen , China
| | - Aftab Amin
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China.,d School of Chinese Medicine , Hong Kong Baptist University , Hong Kong , China
| | - Rentian Wu
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China
| | - Yan Qin
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China
| | - Lan Zou
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,e Intelgen Limited , Hong Kong-Guangzhou-Foshan , China
| | - Zhiling Yu
- d School of Chinese Medicine , Hong Kong Baptist University , Hong Kong , China
| | - Chun Liang
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China.,c Shenzhen-PKU-HKUST Medical Center , Biomedical Research Institute , Shenzhen , China.,e Intelgen Limited , Hong Kong-Guangzhou-Foshan , China
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Premature activation of Cdk1 leads to mitotic events in S phase and embryonic lethality. Oncogene 2018; 38:998-1018. [PMID: 30190546 PMCID: PMC6756125 DOI: 10.1038/s41388-018-0464-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/15/2018] [Accepted: 07/27/2018] [Indexed: 01/08/2023]
Abstract
Cell cycle regulation, especially faithful DNA replication and mitosis, are crucial to maintain genome stability. Cyclin-dependent kinase (CDK)/cyclin complexes drive most processes in cellular proliferation. In response to DNA damage, cell cycle surveillance mechanisms enable normal cells to arrest and undergo repair processes. Perturbations in genomic stability can lead to tumor development and suggest that cell cycle regulators could be effective targets in anticancer therapy. However, many clinical trials ended in failure due to off-target effects of the inhibitors used. Here, we investigate in vivo the importance of WEE1- and MYT1-dependent inhibitory phosphorylation of mammalian CDK1. We generated Cdk1AF knockin mice, in which two inhibitory phosphorylation sites are replaced by the non-phosphorylatable amino acids T14A/Y15F. We uncovered that monoallelic expression of CDK1AF is early embryonic lethal in mice and induces S phase arrest accompanied by γH2AX and DNA damage checkpoint activation in mouse embryonic fibroblasts (MEFs). The chromosomal fragmentation in Cdk1AF MEFs does not rely on CDK2 and is partly caused by premature activation of MUS81-SLX4 structure-specific endonuclease complexes, as well as untimely onset of chromosome condensation followed by nuclear lamina disassembly. We provide evidence that tumor development in liver expressing CDK1AF is inhibited. Interestingly, the regulatory mechanisms that impede cell proliferation in CDK1AF expressing cells differ partially from the actions of the WEE1 inhibitor, MK-1775, with p53 expression determining the sensitivity of cells to the drug response. Thus, our work highlights the importance of improved therapeutic strategies for patients with various cancer types and may explain why some patients respond better to WEE1 inhibitors.
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32
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Du Y, Lu T, Huang S, Ren F, Cui G, Chen J. Somatic mutation landscape of a meningioma and its pulmonary metastasis. Cancer Commun (Lond) 2018; 38:16. [PMID: 29764516 PMCID: PMC5993143 DOI: 10.1186/s40880-018-0291-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/25/2018] [Indexed: 01/06/2023] Open
Abstract
Background Extracranial metastasis (ENM) of meningiomas is extremely rare, and typically occurs several years after a primary tumor is diagnosed. However, the genetic changes underlying ENM events have not yet been investigated. Case presentation A 58-year-old male patient was sent to the emergency room of our hospital because of a sudden fall. Magnetic resonance imaging detected a mass at the right frontal sagittal sinus. He underwent tumor resection and recovered well, but post-operative computed tomography revealed three lumps on the right side of his chest. Thoracic surgery was performed to remove two of the lumps. Pathological findings revealed that the brain and lung tumors were grade I meningiomas. The patient received no additional radiation or chemotherapy post-surgery, and there was no sign of tumor recurrence in the brain or progression of the remaining lump in the chest 1 year after surgery. We performed whole exome sequencing of the patient’s blood, primary brain tumor, and lung metastatic tumor tissues to identify somatic genetic alterations that had occurred during ENM. This revealed that a frameshift deletion of the neurofibromin 2 gene likely drove formation of the meningioma. Surprisingly, we found that the brain tumor was relatively homogeneous and contained only one dominant clone; both the pulmonary metastasis and the original brain tumor were derived from the same clone, and no obvious additional driver mutations were detected in the metastatic tumor. Conclusion Although ENM of meningiomas is very rare, brain tumor cells appear to be more adaptable to tissue microenvironments outside of the central nervous system than was commonly thought.
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Affiliation(s)
- Yaran Du
- Institute of Functional Nano and Soft Materials (FUNSOM) & Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, 215123, P. R. China
| | - Ting Lu
- Department of Neurosurgery, First Affiliated Hospital of Soochow University, Suzhou, 215006, P. R. China
| | - Song Huang
- National Institute of Biological Sciences, Beijing, 102206, P. R. China
| | - Fangfang Ren
- Department of Biochemistry and Molecular Biology, Soochow University Medical College, Suzhou, 215123, P. R. China
| | - Gang Cui
- Department of Neurosurgery, First Affiliated Hospital of Soochow University, Suzhou, 215006, P. R. China
| | - Jian Chen
- Institute of Functional Nano and Soft Materials (FUNSOM) & Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, 215123, P. R. China.
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Bøe CA, Håland TW, Boye E, Syljuåsen RG, Grallert B. A novel role for ATR/Rad3 in G1 phase. Sci Rep 2018; 8:6880. [PMID: 29720710 PMCID: PMC5931961 DOI: 10.1038/s41598-018-25238-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/12/2018] [Indexed: 12/29/2022] Open
Abstract
Checkpoint kinases are important in cellular surveillance pathways that help cells to cope with DNA damage and protect their genomes. In cycling cells, DNA replication is one of the most sensitive processes and therefore all organisms carefully regulate replication initiation and progression. The checkpoint kinase ATR plays important roles both in response to DNA damage and replication stress, and ATR inhibitors are currently in clinical trials for cancer treatment. Therefore, it is important to understand the roles of ATR in detail. Here we show that the fission yeast homologue Rad3 and the human ATR regulate events also in G1 phase in an unperturbed cell cycle. Rad3Δ mutants or human cells exposed to ATR inhibitor in G1 enter S phase prematurely, which results in increased DNA damage. Furthermore, ATR inhibition in a single G1 reduces clonogenic survival, demonstrating that long-term effects of ATR inhibition during G1 are deleterious for the cell. Interestingly, ATR inhibition through G1 and S phase reduces survival in an additive manner, strongly arguing that different functions of ATR are targeted in the different cell-cycle phases. We propose that potential effects of ATR inhibitors in G1 should be considered when designing future treatment protocols with such inhibitors.
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Affiliation(s)
- Cathrine A Bøe
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Tine W Håland
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Erik Boye
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Randi G Syljuåsen
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
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Nukina K, Hayashi A, Shiomi Y, Sugasawa K, Ohtsubo M, Nishitani H. Mutations at multiple CDK phosphorylation consensus sites on Cdt2 increase the affinity of CRL4 Cdt2 for PCNA and its ubiquitination activity in S phase. Genes Cells 2018; 23:200-213. [PMID: 29424068 DOI: 10.1111/gtc.12563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/09/2018] [Indexed: 12/22/2022]
Abstract
CRL4Cdt2 ubiquitin ligase plays an important role maintaining genome integrity during the cell cycle. A recent report suggested that Cdk1 negatively regulates CRL4Cdt2 activity through phosphorylation of its receptor, Cdt2, but the involvement of phosphorylation remains unclear. To address this, we mutated all CDK consensus phosphorylation sites located in the C-terminal half region of Cdt2 (Cdt2-18A) and examined the effect on substrate degradation. We show that both cyclinA/Cdk2 and cyclinB/Cdk1 phosphorylated Cdt2 in vitro and that phosphorylation was reduced by the 18A mutation both in vitro and in vivo. The 18A mutation increased the affinity of Cdt2 to PCNA, and a high amount of Cdt2-18A was colocalized with PCNA foci during S phase in comparison with Cdt2-WT. Poly-ubiquitination activity to Cdt1 was concomitantly enhanced in cells expressing Cdt2-18A. Other CRL4Cdt2 substrates, Set8 and thymine DNA glycosylase, begin to accumulate around late S phase to G2 phase, but the accumulation was prevented in Cdt2-18A cells. Furthermore, mitotic degradation of Cdt1 after UV irradiation was induced in these cells. Our results suggest that CDK-mediated phosphorylation of Cdt2 inactivates its ubiquitin ligase activity by reducing its affinity to PCNA, an important strategy for regulating the levels of key proteins in the cell cycle.
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Affiliation(s)
- Kohei Nukina
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo, Japan
| | - Akiyo Hayashi
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo, Japan
| | - Yasushi Shiomi
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo, Japan
| | | | - Motoaki Ohtsubo
- Department of Food and Fermentation Science, Faculty of Food Science and Nutrition, Beppu University, Beppu, Oita, Japan
| | - Hideo Nishitani
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo, Japan
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35
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Matson JP, Dumitru R, Coryell P, Baxley RM, Chen W, Twaroski K, Webber BR, Tolar J, Bielinsky AK, Purvis JE, Cook JG. Rapid DNA replication origin licensing protects stem cell pluripotency. eLife 2017; 6:30473. [PMID: 29148972 PMCID: PMC5720591 DOI: 10.7554/elife.30473] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/16/2017] [Indexed: 11/24/2022] Open
Abstract
Complete and robust human genome duplication requires loading minichromosome maintenance (MCM) helicase complexes at many DNA replication origins, an essential process termed origin licensing. Licensing is restricted to G1 phase of the cell cycle, but G1 length varies widely among cell types. Using quantitative single-cell analyses, we found that pluripotent stem cells with naturally short G1 phases load MCM much faster than their isogenic differentiated counterparts with long G1 phases. During the earliest stages of differentiation toward all lineages, MCM loading slows concurrently with G1 lengthening, revealing developmental control of MCM loading. In contrast, ectopic Cyclin E overproduction uncouples short G1 from fast MCM loading. Rapid licensing in stem cells is caused by accumulation of the MCM loading protein, Cdt1. Prematurely slowing MCM loading in pluripotent cells not only lengthens G1 but also accelerates differentiation. Thus, rapid origin licensing is an intrinsic characteristic of stem cells that contributes to pluripotency maintenance. From red blood cells to nerve cells, animals’ bodies contain many different types of specialized cells. These all begin as stem cells, which have the potential to divide and make more stem cells or to specialize. All dividing cells must first unwind their DNA so that it can be copied. To achieve this, cells load DNA-unwinding enzymes called helicases onto their DNA during the part of the cell cycle known as G1 phase. Cells must load enough helicase enzymes to ensure that their DNA is copied completely and in time. Stem cells divide faster than their specialized descendants, and have a much shorter G1 phase too. Yet these cells still manage to load enough helicases to copy their DNA. Little is known about how the amount, rate and timing of helicase loading varies between cells that divide at different speeds. Now Matson et al. have measured how quickly helicase enzymes are loaded onto DNA in individual human cells, including stem cells and specialized or “differentiated” cells. Stem cells loaded helicases rapidly to make up for the short time they spent in G1 phase, while differentiated cells loaded the enzymes more slowly. Measuring how the loading rate changed when stem cells were triggered to specialize showed that helicase loading slowed as the G1 phase got longer. Matson et al. found that the levels of key proteins required for helicase loading correlated with the rates of loading. Altering the levels of the proteins changed how quickly the enzymes were loaded and how the cells behaved – for example, slowing down the loading of helicases made the stem cells specialize quicker. These findings show that the processes of cell differentiation and DNA replication are closely linked. This study and future ones will help scientists understand what is happening during early animal development, when specialization first takes place, as well as what has gone wrong in cancer cells, which also divide quickly. A better understanding of this process also helps in regenerative medicine – where one of the challenges is to make enough specialized cells to transplant into a patient with tissue damage without those cells becoming cancerous.
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Affiliation(s)
- Jacob Peter Matson
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, United States
| | - Raluca Dumitru
- Human Pluripotent Stem Cell Core Facility, The University of North Carolina, Chapel Hill, United States
| | - Philip Coryell
- Department of Genetics, The University of North Carolina, Chapel Hill, United States
| | - Ryan M Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, The University of Minnesota, Minneapolis, United States
| | - Weili Chen
- Stem Cell Institute, University of Minnesota, Minnesota, United States
| | - Kirk Twaroski
- Stem Cell Institute, University of Minnesota, Minnesota, United States
| | - Beau R Webber
- Stem Cell Institute, University of Minnesota, Minnesota, United States
| | - Jakub Tolar
- Stem Cell Institute, University of Minnesota, Minnesota, United States
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, The University of Minnesota, Minneapolis, United States
| | - Jeremy E Purvis
- Department of Genetics, The University of North Carolina, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
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36
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ATR kinase inhibition induces unscheduled origin firing through a Cdc7-dependent association between GINS and And-1. Nat Commun 2017; 8:1392. [PMID: 29123096 PMCID: PMC5680267 DOI: 10.1038/s41467-017-01401-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/13/2017] [Indexed: 11/09/2022] Open
Abstract
ATR kinase activity slows replication forks and prevents origin firing in damaged cells. Here we describe proteomic analyses that identified mechanisms through which ATR kinase inhibitors induce unscheduled origin firing in undamaged cells. ATR-Chk1 inhibitor-induced origin firing is mediated by Cdc7 kinase through previously undescribed phosphorylations on GINS that induce an association between GINS and And-1. ATR-Chk1 inhibitor-induced origin firing is blocked by prior exposure to DNA damaging agents showing that the prevention of origin firing does not require ongoing ATR activity. In contrast, ATR-Chk1 inhibitor-induced origins generate additional replication forks that are targeted by subsequent exposure to DNA damaging agents. Thus, the sequence of administration of an ATR kinase inhibitor and a DNA damaging agent impacts the DNA damage induced by the combination. Our experiments identify competing ATR and Cdc7 kinase-dependent mechanisms at replication origins in human cells.
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37
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Riera A, Barbon M, Noguchi Y, Reuter LM, Schneider S, Speck C. From structure to mechanism-understanding initiation of DNA replication. Genes Dev 2017; 31:1073-1088. [PMID: 28717046 PMCID: PMC5538431 DOI: 10.1101/gad.298232.117] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this Review, Riera et al. review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2–7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability.
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Affiliation(s)
- Alberto Riera
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Marta Barbon
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Medical Research Council (MRC) London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
| | - Yasunori Noguchi
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - L Maximilian Reuter
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Sarah Schneider
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Christian Speck
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Medical Research Council (MRC) London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
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38
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Abstract
Semiconservative DNA replication has provided an elegant solution to the fundamental problem of how life is able to proliferate in a way that allows cells, organisms, and populations to survive and replicate many times over. Somewhat lost, however, in our admiration for this mechanism is an appreciation for the asymmetries that occur in the process of DNA replication. As we discuss in this review, these asymmetries arise as a consequence of the structure of the DNA molecule and the enzymatic mechanism of DNA synthesis. Increasing evidence suggests that asymmetries in DNA replication are able to play a central role in the processes of adaptation and evolution by shaping the mutagenic landscape of cells. Additionally, in eukaryotes, recent work has demonstrated that the inherent asymmetries in DNA replication may play an important role in the process of chromatin replication. As chromatin plays an essential role in defining cell identity, asymmetries generated during the process of DNA replication may play critical roles in cell fate decisions related to patterning and development.
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Affiliation(s)
- Jonathan Snedeker
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218; , ,
| | - Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218; , ,
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218; , ,
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39
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Pai CC, Kishkevich A, Deegan RS, Keszthelyi A, Folkes L, Kearsey SE, De León N, Soriano I, de Bruin RAM, Carr AM, Humphrey TC. Set2 Methyltransferase Facilitates DNA Replication and Promotes Genotoxic Stress Responses through MBF-Dependent Transcription. Cell Rep 2017; 20:2693-2705. [PMID: 28903048 PMCID: PMC5608972 DOI: 10.1016/j.celrep.2017.08.058] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 06/10/2017] [Accepted: 08/17/2017] [Indexed: 11/24/2022] Open
Abstract
Chromatin modification through histone H3 lysine 36 methylation by the SETD2 tumor suppressor plays a key role in maintaining genome stability. Here, we describe a role for Set2-dependent H3K36 methylation in facilitating DNA replication and the transcriptional responses to both replication stress and DNA damage through promoting MluI cell-cycle box (MCB) binding factor (MBF)-complex-dependent transcription in fission yeast. Set2 loss leads to reduced MBF-dependent ribonucleotide reductase (RNR) expression, reduced deoxyribonucleoside triphosphate (dNTP) synthesis, altered replication origin firing, and a checkpoint-dependent S-phase delay. Accordingly, prolonged S phase in the absence of Set2 is suppressed by increasing dNTP synthesis. Furthermore, H3K36 is di- and tri-methylated at these MBF gene promoters, and Set2 loss leads to reduced MBF binding and transcription in response to genotoxic stress. Together, these findings provide new insights into how H3K36 methylation facilitates DNA replication and promotes genotoxic stress responses in fission yeast.
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Affiliation(s)
- Chen-Chun Pai
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK.
| | - Anastasiya Kishkevich
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6B, UK
| | - Rachel S Deegan
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Andrea Keszthelyi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex BN1 9RQ, UK
| | - Lisa Folkes
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Stephen E Kearsey
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Nagore De León
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Ignacio Soriano
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | | | - Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex BN1 9RQ, UK
| | - Timothy C Humphrey
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK.
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40
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Nuclear DNA Replication in Trypanosomatids: There Are No Easy Methods for Solving Difficult Problems. Trends Parasitol 2017; 33:858-874. [PMID: 28844718 PMCID: PMC5662062 DOI: 10.1016/j.pt.2017.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 01/09/2023]
Abstract
In trypanosomatids, etiological agents of devastating diseases, replication is robust and finely controlled to maintain genome stability and function in stressful environments. However, these parasites encode several replication protein components and complexes that show potentially variant composition compared with model eukaryotes. This review focuses on the advances made in recent years regarding the differences and peculiarities of the replication machinery in trypanosomatids, including how such divergence might affect DNA replication dynamics and the replication stress response. Comparing the DNA replication machinery and processes of parasites and their hosts may provide a foundation for the identification of targets that can be used in the development of chemotherapies to assist in the eradication of diseases caused by these pathogens. In trypanosomatids, DNA replication is tightly controlled by protein complexes that diverge from those of model eukaryotes. There is no consensus for the number of replication origins used by trypanosomatids; how their replication dynamics compares with that of model organisms is the subject of debate. The DNA replication rate in trypanosomatids is similar to, but slightly higher than, that of model eukaryotes, which may be related to chromatin structure and function. Recent data suggest that the origin recognition complex in trypanosomatids closely resembles the multisubunit eukaryotic model. The absence of fundamental replication-associated proteins in trypanosomatids suggests that new signaling pathways may be present in these parasites to direct DNA replication and the replicative stress response.
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41
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Izumi M, Mizuno T, Yanagi KI, Sugimura K, Okumura K, Imamoto N, Abe T, Hanaoka F. The Mcm2-7-interacting domain of human mini-chromosome maintenance 10 (Mcm10) protein is important for stable chromatin association and origin firing. J Biol Chem 2017. [PMID: 28646110 DOI: 10.1074/jbc.m117.779371] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The protein mini-chromosome maintenance 10 (Mcm10) was originally identified as an essential yeast protein in the maintenance of mini-chromosome plasmids. Subsequently, Mcm10 has been shown to be required for both initiation and elongation during chromosomal DNA replication. However, it is not fully understood how the multiple functions of Mcm10 are coordinated or how Mcm10 interacts with other factors at replication forks. Here, we identified and characterized the Mcm2-7-interacting domain in human Mcm10. The interaction with Mcm2-7 required the Mcm10 domain that contained amino acids 530-655, which overlapped with the domain required for the stable retention of Mcm10 on chromatin. Expression of truncated Mcm10 in HeLa cells depleted of endogenous Mcm10 via siRNA revealed that the Mcm10 conserved domain (amino acids 200-482) is essential for DNA replication, whereas both the conserved and the Mcm2-7-binding domains were required for its full activity. Mcm10 depletion reduced the initiation frequency of DNA replication and interfered with chromatin loading of replication protein A, DNA polymerase (Pol) α, and proliferating cell nuclear antigen, whereas the chromatin loading of Cdc45 and Pol ϵ was unaffected. These results suggest that human Mcm10 is bound to chromatin through the interaction with Mcm2-7 and is primarily involved in the initiation of DNA replication after loading of Cdc45 and Pol ϵ.
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Affiliation(s)
- Masako Izumi
- Accelerator Applications Research Group, Nishina Center for Accelerator-Based Science, Wako, Saitama 351-0198, Japan.
| | - Takeshi Mizuno
- Cellular Dynamics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | | | - Kazuto Sugimura
- Department of Life Science, Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | - Katsuzumi Okumura
- Department of Life Science, Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Tomoko Abe
- Accelerator Applications Research Group, Nishina Center for Accelerator-Based Science, Wako, Saitama 351-0198, Japan
| | - Fumio Hanaoka
- Department of Life Science, Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan; Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki 305-8577, Japan
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42
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Hizume K, Kominami H, Kobayashi K, Yamada H, Araki H. Flexible DNA Path in the MCM Double Hexamer Loaded on DNA. Biochemistry 2017; 56:2435-2445. [DOI: 10.1021/acs.biochem.6b00922] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kohji Hizume
- Division
of Microbial Genetics, National Institute of Genetics, Mishima 411-8540, Japan
- Department
of Genetics, School of Life Science, the Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Hiroaki Kominami
- Department
of Electronic Science and Engineering, Kyoto University, Kyoto University
Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Kei Kobayashi
- Department
of Electronic Science and Engineering, Kyoto University, Kyoto University
Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Hirofumi Yamada
- Department
of Electronic Science and Engineering, Kyoto University, Kyoto University
Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Hiroyuki Araki
- Division
of Microbial Genetics, National Institute of Genetics, Mishima 411-8540, Japan
- Department
of Genetics, School of Life Science, the Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
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43
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Tang XF, Chen XY, Zhang CD, Li YF, Liu TH, Zhou XL, Wang L, Zhang Q, Chen P, Lu C, Pan MH. Two Geminin homologs regulate DNA replication in silkworm, Bombyx mori. Cell Cycle 2017; 16:830-840. [PMID: 28379781 DOI: 10.1080/15384101.2017.1282582] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
DNA replication is rigorously controlled in cells to ensure that the genome duplicates exactly once per cell cycle. Geminin is a small nucleoprotein, which prevents DNA rereplication by directly binding to and inhibiting the DNA replication licensing factor, Cdt1. In this study, we have identified 2 Geminin genes, BmGeminin1 and BmGeminn2, in silkworm, Bombyx mori. These genes contain the Geminin conserved coiled-coil domain and are periodically localized in the nucleus during the S-G2 phase but are degraded at anaphase in mitosis. Both BmGeminin1 and BmGeminin2 are able to homodimerize and interact with BmCdt1 in cells. In addition, BmGeminin1 and BmGeminin2 can interact with each other. Overexpression of BmGeminin1 affects cell cycle progression: cell cycle is arrested in S phase, and RNA interference of BmGeminin1 leads to rereplication. In contrast, overexpression or knockdown of BmGeminin2 with RNAi did not significantly affect cell cycle, while more rereplication occurred when BmGeminin1 and BmGeminin2 together were knocked down in cells than when only BmGeminin1 was knocked down. These data suggest that both BmGeminin1 and BmGeminin2 are involved in the regulation of DNA replication. These findings provide insight into the function of Geminin and contribute to our understanding of the regulation mechanism of cell cycle in silkworm.
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Affiliation(s)
- Xiao-Fang Tang
- a State Key Laboratory of Silkworm Genome Biology , Southwest University , Chongqing , China
| | - Xiang-Yun Chen
- a State Key Laboratory of Silkworm Genome Biology , Southwest University , Chongqing , China.,b Basic Medical School , Guiyang College of Traditional Chinese Medicine , Guiyang , China
| | - Chun-Dong Zhang
- a State Key Laboratory of Silkworm Genome Biology , Southwest University , Chongqing , China.,c Department of Biochemistry and Molecular Biology , Chongqing Medical University , Chongqing , China
| | - Yao-Feng Li
- a State Key Laboratory of Silkworm Genome Biology , Southwest University , Chongqing , China.,b Basic Medical School , Guiyang College of Traditional Chinese Medicine , Guiyang , China
| | - Tai-Hang Liu
- a State Key Laboratory of Silkworm Genome Biology , Southwest University , Chongqing , China
| | - Xiao-Lin Zhou
- a State Key Laboratory of Silkworm Genome Biology , Southwest University , Chongqing , China
| | - La Wang
- a State Key Laboratory of Silkworm Genome Biology , Southwest University , Chongqing , China
| | - Qian Zhang
- a State Key Laboratory of Silkworm Genome Biology , Southwest University , Chongqing , China
| | - Peng Chen
- a State Key Laboratory of Silkworm Genome Biology , Southwest University , Chongqing , China.,d Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry , Southwest University , Chongqing , China
| | - Cheng Lu
- a State Key Laboratory of Silkworm Genome Biology , Southwest University , Chongqing , China.,d Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry , Southwest University , Chongqing , China
| | - Min-Hui Pan
- a State Key Laboratory of Silkworm Genome Biology , Southwest University , Chongqing , China.,d Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry , Southwest University , Chongqing , China
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44
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Abstract
Cellular DNA replication factories depend on ring-shaped hexameric helicases to aid DNA synthesis by processively unzipping the parental DNA helix. Replicative helicases are loaded onto DNA by dedicated initiator, loader, and accessory proteins during the initiation of DNA replication in a tightly regulated, multistep process. We discuss here the molecular choreography of DNA replication initiation across the three domains of life, highlighting similarities and differences in the strategies used to deposit replicative helicases onto DNA and to melt the DNA helix in preparation for replisome assembly. Although initiators and loaders are phylogenetically related, the mechanisms they use for accomplishing similar tasks have diverged considerably and in an unpredictable manner.
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Affiliation(s)
- Franziska Bleichert
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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45
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Tanaka M, Takahara M, Nukina K, Hayashi A, Sakai W, Sugasawa K, Shiomi Y, Nishitani H. Mismatch repair proteins recruited to ultraviolet light-damaged sites lead to degradation of licensing factor Cdt1 in the G1 phase. Cell Cycle 2017; 16:673-684. [PMID: 28278049 DOI: 10.1080/15384101.2017.1295179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Cdt1 is rapidly degraded by CRL4Cdt2 E3 ubiquitin ligase after UV (UV) irradiation. Previous reports revealed that the nucleotide excision repair (NER) pathway is responsible for the rapid Cdt1-proteolysis. Here, we show that mismatch repair (MMR) proteins are also involved in the degradation of Cdt1 after UV irradiation in the G1 phase. First, compared with the rapid (within ∼15 min) degradation of Cdt1 in normal fibroblasts, Cdt1 remained stable for ∼30 min in NER-deficient XP-A cells, but was degraded within ∼60 min. The delayed degradation was also dependent on PCNA and CRL4Cdt2. The MMR proteins Msh2 and Msh6 were recruited to the UV-damaged sites of XP-A cells in the G1 phase. Depletion of these factors with small interfering RNAs prevented Cdt1 degradation in XP-A cells. Similar to the findings in XP-A cells, depletion of XPA delayed Cdt1 degradation in normal fibroblasts and U2OS cells, and co-depletion of Msh6 further prevented Cdt1 degradation. Furthermore, depletion of Msh6 alone delayed Cdt1 degradation in both cell types. When Cdt1 degradation was attenuated by high Cdt1 expression, repair synthesis at the damaged sites was inhibited. Our findings demonstrate that UV irradiation induces multiple repair pathways that activate CRL4Cdt2 to degrade its target proteins in the G1 phase of the cell cycle, leading to efficient repair of DNA damage.
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Affiliation(s)
- Miyuki Tanaka
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
| | - Michiyo Takahara
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
| | - Kohei Nukina
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
| | - Akiyo Hayashi
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
| | - Wataru Sakai
- b Biosignal Research Center , Kobe University , Kobe , Hyogo , Japan
| | - Kaoru Sugasawa
- b Biosignal Research Center , Kobe University , Kobe , Hyogo , Japan
| | - Yasushi Shiomi
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
| | - Hideo Nishitani
- a Graduate School of Life Science , University of Hyogo , Kamigori, Ako-gun , Hyogo , Japan
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46
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Guan L, He P, Yang F, Zhang Y, Hu Y, Ding J, Hua Y, Zhang Y, Ye Q, Hu J, Wang T, Jin C, Kong D. Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe. J Biol Chem 2017; 292:6056-6075. [PMID: 28223353 DOI: 10.1074/jbc.m116.767806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 02/17/2017] [Indexed: 11/06/2022] Open
Abstract
A central step in the initiation of chromosomal DNA replication in eukaryotes is the assembly of pre-replicative complex (pre-RC) at late M and early G1 phase of the cell cycles. Since 1973, four proteins or protein complexes, including cell division control protein 6 (Cdc6)/Cdc18, minichromosome maintenance protein complex, origin recognition complex (ORC), and Cdt1, are known components of the pre-RC. Previously, we reported that a non-ORC protein binds to the essential element Δ9 of the Schizosaccharomyces pombe DNA-replication origin ARS3001. In this study, we identified that the non-ORC protein is Sap1. Like ORC, Sap1 binds to DNA origins during cell growth cycles. But unlike ORC, which binds to asymmetric AT-rich sequences through its nine AT-hook motifs, Sap1 preferentially binds to a DNA sequence of 5'-(A/T) n (C/G)(A/T)9-10(G/C)(A/T) n -3' (n ≥ 1). We also found that Sap1 and ORC physically interact. We further demonstrated that Sap1 is required for the assembly of the pre-RC because of its essential role in recruiting Cdc18 to DNA origins. Thus, we conclude that Sap1 is a replication-initiation factor that directly participates in the assembly of the pre-RC. DNA-replication origins in fission yeast are defined by possessing two essential elements with one bound by ORC and the other by Sap1.
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Affiliation(s)
- Ling Guan
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences
| | - Peng He
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences
| | - Fang Yang
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences
| | - Yuan Zhang
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences
| | - Yunfei Hu
- the Beijing Nuclear Magnetic Resonance Center.,the College of Chemistry and Molecular Engineering, and
| | - Jienv Ding
- the Beijing Nuclear Magnetic Resonance Center
| | - Yu Hua
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences
| | - Yi Zhang
- the Beijing Nuclear Magnetic Resonance Center
| | - Qiong Ye
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences
| | - Jiazhi Hu
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences
| | - Tao Wang
- the Department of Biology, South University of Science and Technology of China, 1088 Xueyuan Road, Nanshan District, Shenzhen 518055, Guangdong, China
| | - Changwen Jin
- the Beijing Nuclear Magnetic Resonance Center, .,the College of Chemistry and Molecular Engineering, and.,the Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871 and
| | - Daochun Kong
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences,
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47
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Control of Genome Integrity by RFC Complexes; Conductors of PCNA Loading onto and Unloading from Chromatin during DNA Replication. Genes (Basel) 2017; 8:genes8020052. [PMID: 28134787 PMCID: PMC5333041 DOI: 10.3390/genes8020052] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/21/2017] [Indexed: 11/23/2022] Open
Abstract
During cell division, genome integrity is maintained by faithful DNA replication during S phase, followed by accurate segregation in mitosis. Many DNA metabolic events linked with DNA replication are also regulated throughout the cell cycle. In eukaryotes, the DNA sliding clamp, proliferating cell nuclear antigen (PCNA), acts on chromatin as a processivity factor for DNA polymerases. Since its discovery, many other PCNA binding partners have been identified that function during DNA replication, repair, recombination, chromatin remodeling, cohesion, and proteolysis in cell-cycle progression. PCNA not only recruits the proteins involved in such events, but it also actively controls their function as chromatin assembles. Therefore, control of PCNA-loading onto chromatin is fundamental for various replication-coupled reactions. PCNA is loaded onto chromatin by PCNA-loading replication factor C (RFC) complexes. Both RFC1-RFC and Ctf18-RFC fundamentally function as PCNA loaders. On the other hand, after DNA synthesis, PCNA must be removed from chromatin by Elg1-RFC. Functional defects in RFC complexes lead to chromosomal abnormalities. In this review, we summarize the structural and functional relationships among RFC complexes, and describe how the regulation of PCNA loading/unloading by RFC complexes contributes to maintaining genome integrity.
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48
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Parker MW, Botchan MR, Berger JM. Mechanisms and regulation of DNA replication initiation in eukaryotes. Crit Rev Biochem Mol Biol 2017; 52:107-144. [PMID: 28094588 DOI: 10.1080/10409238.2016.1274717] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation - from selecting replication start sites to replicative helicase loading and activation - and describe how these events are often distinctly regulated across different eukaryotic model organisms.
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Affiliation(s)
- Matthew W Parker
- a Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Michael R Botchan
- b Department of Molecular and Cell Biology , University of California Berkeley , Berkeley , CA , USA
| | - James M Berger
- a Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD , USA
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49
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Sun J, Yuan Z, Bai L, Li H. Cryo-EM of dynamic protein complexes in eukaryotic DNA replication. Protein Sci 2017; 26:40-51. [PMID: 27589669 PMCID: PMC5192969 DOI: 10.1002/pro.3033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/27/2016] [Accepted: 08/29/2016] [Indexed: 12/21/2022]
Abstract
DNA replication in Eukaryotes is a highly dynamic process that involves several dozens of proteins. Some of these proteins form stable complexes that are amenable to high-resolution structure determination by cryo-EM, thanks to the recent advent of the direct electron detector and powerful image analysis algorithm. But many of these proteins associate only transiently and flexibly, precluding traditional biochemical purification. We found that direct mixing of the component proteins followed by 2D and 3D image sorting can capture some very weakly interacting complexes. Even at 2D average level and at low resolution, EM images of these flexible complexes can provide important biological insights. It is often necessary to positively identify the feature-of-interest in a low resolution EM structure. We found that systematically fusing or inserting maltose binding protein (MBP) to selected proteins is highly effective in these situations. In this chapter, we describe the EM studies of several protein complexes involved in the eukaryotic DNA replication over the past decade or so. We suggest that some of the approaches used in these studies may be applicable to structural analysis of other biological systems.
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Affiliation(s)
- Jingchuan Sun
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
| | - Zuanning Yuan
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
- The Biochemistry and Structural Biology ProgramStony Brook UniversityStony BrookNew York11794
| | - Lin Bai
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
| | - Huilin Li
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
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50
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Bai L, Yuan Z, Sun J, Georgescu R, O'Donnell ME, Li H. Architecture of the Saccharomyces cerevisiae Replisome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:207-228. [PMID: 29357060 DOI: 10.1007/978-981-10-6955-0_10] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Eukaryotic replication proteins are highly conserved, and thus study of Saccharomyces cerevisiae replication can inform about this central process in higher eukaryotes including humans. The S. cerevisiae replisome is a large and dynamic assembly comprised of ~50 proteins. The core of the replisome is composed of 31 different proteins including the 11-subunit CMG helicase; RFC clamp loader pentamer; PCNA clamp; the heteroligomeric DNA polymerases ε, δ, and α-primase; and the RPA heterotrimeric single strand binding protein. Many additional protein factors either travel with or transiently associate with these replisome proteins at particular times during replication. In this chapter, we summarize several recent structural studies on the S. cerevisiae replisome and its subassemblies using single particle electron microscopy and X-ray crystallography. These recent structural studies have outlined the overall architecture of a core replisome subassembly and shed new light on the mechanism of eukaryotic replication.
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Affiliation(s)
- Lin Bai
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Zuanning Yuan
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA
- Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY, USA
| | - Jingchuan Sun
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Roxana Georgescu
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA.
- Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY, USA.
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