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Liu Y, Han T, Xu Z, Wu J, Zhou J, Guo J, Miao R, Xing Y, Ge D, Bai Y, Hu D. CDC45 promotes the stemness and metastasis in lung adenocarcinoma by affecting the cell cycle. J Transl Med 2024; 22:335. [PMID: 38589907 PMCID: PMC11000299 DOI: 10.1186/s12967-024-05038-5] [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: 10/30/2023] [Accepted: 02/24/2024] [Indexed: 04/10/2024] Open
Abstract
OBJECTIVE This study aimed to assess the functions of cell division cycle protein 45 (CDC45) in Non-small cell lung cancer (NSCLC) cancer and its effects on stemness and metastasis. METHODS Firstly, differentially expressed genes related to lung cancer metastasis and stemness were screened by differential analysis and lasso regression. Then, in vitro, experiments such as colony formation assay, scratch assay, and transwell assay were conducted to evaluate the impact of CDC45 knockdown on the proliferation and migration abilities of lung cancer cells. Western blotting was used to measure the expression levels of related proteins and investigate the regulation of CDC45 on the cell cycle. Finally, in vivo model with subcutaneous injection of lung cancer cells was performed to verify the effect of CDC45 on tumor growth. RESULTS This study identified CDC45 as a key gene potentially influencing tumor stemness and lymph node metastasis. Knockdown of CDC45 not only suppressed the proliferation and migration abilities of lung cancer cells but also caused cell cycle arrest at the G2/M phase. Further analysis revealed a negative correlation between CDC45 and cell cycle-related proteins, stemness-related markers, and tumor mutations. Mouse experiments confirmed that CDC45 knockdown inhibited tumor growth. CONCLUSION As a novel regulator of stemness, CDC45 plays a role in regulating lung cancer cell proliferation, migration, and cell cycle. Therefore, CDC45 may serve as a potential target for lung cancer treatment and provide a reference for further mechanistic research and therapeutic development.
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Affiliation(s)
- Yafeng Liu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, People's Republic of China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Tao Han
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, People's Republic of China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Zhi Xu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, People's Republic of China
| | - Jing Wu
- Joint Research Center for Occupational Medicine and Health of IHM, School of Medicine, Anhui University of Science and Technology, Huainan, People's Republic of China.
| | - Jiawei Zhou
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, People's Republic of China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Jianqiang Guo
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, People's Republic of China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Rui Miao
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, People's Republic of China
| | - Yingru Xing
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, People's Republic of China
- Department of Clinical Laboratory, Anhui Zhongke Gengjiu Hospital, Hefei, People's Republic of China
| | - Deyong Ge
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, People's Republic of China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Ying Bai
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, People's Republic of China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China.
| | - Dong Hu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, People's Republic of China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China.
- Key Laboratory of Industrial Dust Prevention and Control & Occupational Safety and Health of the Ministry of Education, Anhui University of Science and Technology, Huainan, People's Republic of China.
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Clavijo-Buriticá DC, Sosa CC, Heredia RC, Mosquera AJ, Álvarez A, Medina J, Quimbaya M. Use of Arabidopsis thaliana as a model to understand specific carcinogenic events: Comparison of the molecular machinery associated with cancer-hallmarks in plants and humans. Heliyon 2023; 9:e15367. [PMID: 37101642 PMCID: PMC10123165 DOI: 10.1016/j.heliyon.2023.e15367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/28/2023] Open
Abstract
Model organisms are fundamental in cancer research given that they rise the possibility to characterize in a quantitative-objective fashion the organisms as a whole in ways that are infeasible in humans. From this perspective, model organisms with short generation times and established protocols for genetic manipulation allow the understanding of basic biology principles that might guide carcinogenic onset. The cancer-hallmarks (CHs) approach, a modular perspective for cancer understanding, stands that underlying the variability among different cancer types, critical events support the carcinogenic origin and progression. Thus, CHs as interconnected genetic circuitry, have a causal effect over cancer biogenesis and might represent a comparison scaffold among model organisms to identify and characterize evolutionarily conserved modules to understand cancer. Nevertheless, the identification of novel cancer regulators by comparative genomics approaches relies on selecting specific biological processes or related signaling cascades that limit the type of detected regulators, even more, holistic analysis from a systemic perspective is absent. Similarly, although the plant Arabidopsis thaliana has been used as a model organism to dissect specific disease-associated mechanisms, given the evolutionary distance between plants and humans, a general concern about the utility of using A. thaliana as a cancer model persists. In the present research, we take advantage of the CHs paradigm as a framework to establish a functional systemic comparison between plants and humans, that allowed the identification not only of specific novel key genetic regulators, but also, biological processes, metabolic systems, and genetic modules that might contribute to the neoplastic transformation. We propose five cancer-hallmarks that overlapped in conserved mechanisms and processes between Arabidopsis and human and thus, represent mechanisms which study can be prioritized in A. thaliana as an alternative model for cancer research. Additionally, derived from network analyses and machine learning strategies, a new set of potential candidate genes that might contribute to neoplastic transformation is described. These findings postulate A. thaliana as a suitable model to dissect, not all, but specific cancer properties, highlighting the importance of using alternative complementary models to understand carcinogenesis.
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Affiliation(s)
| | - Chrystian C. Sosa
- Pontificia Universidad Javeriana Cali, Department of Natural Sciences and Mathematics, Cali, Colombia
- Grupo de Investigación en Evolución, Ecología y Conservación EECO, Programa de Biología, Facultad de Ciencias Básicas y Tecnologías, Universidad del Quindío, Armenia, Colombia
| | - Rafael Cárdenas Heredia
- Pontificia Universidad Javeriana Cali, Department of Natural Sciences and Mathematics, Cali, Colombia
| | - Arlen James Mosquera
- Pontificia Universidad Javeriana Cali, Department of Natural Sciences and Mathematics, Cali, Colombia
| | - Andrés Álvarez
- Pontificia Universidad Javeriana Cali, Department of Natural Sciences and Mathematics, Cali, Colombia
| | - Jan Medina
- Pontificia Universidad Javeriana Cali, Department of Natural Sciences and Mathematics, Cali, Colombia
| | - Mauricio Quimbaya
- Pontificia Universidad Javeriana Cali, Department of Natural Sciences and Mathematics, Cali, Colombia
- Corresponding author.
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3
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Xu X, Chang CW, Li M, Omabe K, Le N, Chen YH, Liang F, Liu Y. DNA replication initiation factor RECQ4 possesses a role in antagonizing DNA replication initiation. Nat Commun 2023; 14:1233. [PMID: 36871012 PMCID: PMC9985596 DOI: 10.1038/s41467-023-36968-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Deletion of the conserved C-terminus of the Rothmund-Thomson syndrome helicase RECQ4 is highly tumorigenic. However, while the RECQ4 N-terminus is known to facilitate DNA replication initiation, the function of its C-terminus remains unclear. Using an unbiased proteomic approach, we identify an interaction between the RECQ4 N-terminus and the anaphase-promoting complex/cyclosome (APC/C) on human chromatin. We further show that this interaction stabilizes APC/C co-activator CDH1 and enhances APC/C-dependent degradation of the replication inhibitor Geminin, allowing replication factors to accumulate on chromatin. In contrast, the function is blocked by the RECQ4 C-terminus, which binds to protein inhibitors of APC/C. A cancer-prone, C-terminal-deleted RECQ4 mutation increases origin firing frequency, accelerates G1/S transition, and supports abnormally high DNA content. Our study reveals a role of the human RECQ4 C-terminus in antagonizing its N-terminus, thereby suppressing replication initiation, and this suppression is impaired by oncogenic mutations.
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Affiliation(s)
- Xiaohua Xu
- Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, CA, 92008, USA
| | - Chou-Wei Chang
- Vesigen Therapeutics, 790 Memorial Drive, Suite 103, Cambridge, MA, 02139, USA
| | - Min Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Kenneth Omabe
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Nhung Le
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Yi-Hsuan Chen
- Department of Computer Science, University of Southern California, Los Angeles, CA, 90089, USA
| | - Feng Liang
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, 90089, USA
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA.
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Archaea as a Model System for Molecular Biology and Biotechnology. Biomolecules 2023; 13:biom13010114. [PMID: 36671499 PMCID: PMC9855744 DOI: 10.3390/biom13010114] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.
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5
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Wang X, Liang C, Li A, Cheng G, Long F, Khan R, Wang J, Zhang Y, Wu S, Wang Y, Qiu J, Mei C, Yang W, Zan L. RNA-Seq and lipidomics reveal different adipogenic processes between bovine perirenal and intramuscular adipocytes. Adipocyte 2022; 11:448-462. [PMID: 35941812 PMCID: PMC9367662 DOI: 10.1080/21623945.2022.2106051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Adipogenesis involves complex interactions between transcription and metabolic signalling. Exploration of the developmental characteristics of intramuscular adipocyte will provide targets for enhancing beef cattle marbling without increasing obesity. Few reports have compared bovine perirenal and intramuscular adipocyte transcriptomes using the combined analysis of transcriptomes and lipid metabolism to explore differences in adipogenic characteristics. We identified perirenal preadipocytes (PRA) and intramuscular preadipocytes (IMA) in Qinchuan cattle. We found that IMA were highly prolific in the early stages of adipogenesis, while PRA shows a stronger adipogenic ability in the terminal differentiation. Bovine perirenal and intramuscular adipocytes were detected through the combined analysis of the transcriptome and metabolome. More triglyceride was found to be upregulated in perirenal adipocytes; however, more types and amounts of unsaturated fatty acids were detected in intramuscular adipocytes, including eicosapentaenoic acid (20:5 n-3; EPA) and docosahexaenoic acid (22:6 n-3; DHA). Furthermore, differentially expressed genes in perirenal and intramuscular adipocytes were positively correlated with the eicosanoid, phosphatidylcholine (PC), phosphatidyl ethanolamine (PE), and sphingomyelin contents. Associated differential metabolic pathways included the glycerolipid and glycerophospholipid metabolisms. Our research findings provide a basis for the screening of key metabolic pathways or genes and metabolites involved in intramuscular fat production in cattle.
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Affiliation(s)
- Xiaoyu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chengcheng Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Feng Long
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Rajwali Khan
- Department of Livestock Management, the University of Agriculture, Peshawar, Pakistan
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yu Zhang
- Longri Breeding Farm of Sichuan Province, Sichuan, Chengdu, China
| | - Sen Wu
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Qinghai, Xining, China
| | - Yujuan Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ju Qiu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Wucai Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
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6
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He Z, Wang X, Yang Z, Jiang Y, Li L, Wang X, Song Z, Wang X, Wan J, Jiang S, Zhang N, Cui R. Expression and prognosis of CDC45 in cervical cancer based on the GEO database. PeerJ 2021; 9:e12114. [PMID: 34557356 PMCID: PMC8420875 DOI: 10.7717/peerj.12114] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/15/2021] [Indexed: 12/24/2022] Open
Abstract
Cervical cancer is one of the most common malignant tumors in women, and its morbidity and mortality are increasing year by year worldwide. Therefore, an urgent and challenging task is to identify potential biomarkers for cervical cancer. This study aims to identify the hub genes based on the GEO database and then validate their prognostic values in cervical cancer by multiple databases. By analysis, we obtained 83 co-expressed differential genes from the GEO database (GSE63514, GSE67522 and GSE39001). GO and KEGG enrichment analysis showed that these 83 co-expressed it mainly involved differential genes in DNA replication, cell division, cell cycle, etc.. The PPI network was constructed and top 10 genes with protein-protein interaction were selected. Then, we validated ten genes using some databases such as TCGA, GTEx and oncomine. Survival analysis demonstrated significant differences in CDC45, RFC4, TOP2A. Differential expression analysis showed that these genes were highly expressed in cervical cancer tissues. Furthermore, univariate and multivariate cox regression analysis indicated that CDC45 and clinical stage IV were independent prognostic factors for cervical cancer. In addition, the HPA database validated the protein expression level of CDC45 in cervical cancer. Further studies investigated the relationship between CDC45 and tumor-infiltrating immune cells via CIBERSORT. Finally, gene set enrichment analysis (GSEA) showed CDC45 related genes were mainly enriched in cell cycle, chromosome, catalytic activity acting on DNA, etc. These results suggested CDC45 may be a potential biomarker associated with the prognosis of cervical cancer.
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Affiliation(s)
- Zikang He
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Xiaojin Wang
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Zhiming Yang
- Department of Clinical Laboratory, Handan Central Hospital, Handan, China
| | - Ying Jiang
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Luhui Li
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Xingyun Wang
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Zheyao Song
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Xiuli Wang
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China.,Department of Clinical Laboratory, The Seventh Hospital in Qiqihar, Qiqihar, China
| | - Jiahui Wan
- Department of Clinical Laboratory, Harbin Public Security Hospital, Harbin, China
| | - Shijun Jiang
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China.,Department of Clinical Laboratory, Daqing Medical College, Daqing, China
| | - Naiwen Zhang
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Rongjun Cui
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
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7
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Cabral D, Forero Ballesteros H, de Melo BP, Lourenço-Tessutti IT, Simões de Siqueira KM, Obicci L, Grossi-de-Sa MF, Hemerly AS, de Almeida Engler J. The Armadillo BTB Protein ABAP1 Is a Crucial Player in DNA Replication and Transcription of Nematode-Induced Galls. FRONTIERS IN PLANT SCIENCE 2021; 12:636663. [PMID: 33995437 PMCID: PMC8121025 DOI: 10.3389/fpls.2021.636663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
The biogenesis of root-knot nematode (Meloidogyne spp.)-induced galls requires the hyperactivation of the cell cycle with controlled balance of mitotic and endocycle programs to keep its homeostasis. To better understand gall functioning and to develop new control strategies for this pest, it is essential to find out how the plant host cell cycle programs are responding and integrated during the nematode-induced gall formation. This work investigated the spatial localization of a number of gene transcripts involved in the pre-replication complex during DNA replication in galls and report their akin colocation with the cell cycle S-phase regulator Armadillo BTB Arabidopsis Protein 1 (ABAP1). ABAP1 is a negative regulator of pre-replication complex controlling DNA replication of genes involved in control of cell division and proliferation; therefore, its function has been investigated during gall ontogenesis. Functional analysis was performed upon ABAP1 knockdown and overexpression in Arabidopsis thaliana. We detected ABAP1 promoter activity and localized ABAP1 protein in galls during development, and its overexpression displayed significantly reduced gall sizes containing atypical giant cells. Profuse ABAP1 expression also impaired gall induction and hindered nematode reproduction. Remarkably, ABAP1 knockdown likewise negatively affected gall and nematode development, suggesting its involvement in the feeding site homeostasis. Microscopy analysis of cleared and nuclei-stained whole galls revealed that ABAP1 accumulation resulted in aberrant giant cells displaying interconnected nuclei filled with enlarged heterochromatic regions. Also, imbalanced ABAP1 expression caused changes in expression patterns of genes involved in the cell division control as demonstrated by qRT-PCR. CDT1a, CDT1b, CDKA;1, and CYCB1;1 mRNA levels were significantly increased in galls upon ABAP1 overexpression, possibly contributing to the structural changes in galls during nematode infection. Overall, data obtained in galls reinforced the role of ABAP1 controlling DNA replication and mitosis and, consequently, cell proliferation. ABAP1 expression might likely take part of a highly ordered mechanism balancing of cell cycle control to prevent gall expansion. ABAP1 expression might prevent galls to further expand, limiting excessive mitotic activity. Our data strongly suggest that ABAP1 as a unique plant gene is an essential component for cell cycle regulation throughout gall development during nematode infection and is required for feeding site homeostasis.
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Affiliation(s)
- Danila Cabral
- INRAE, Université Côte d’Azur, CNRS, ISA, Sophia Antipolis, France
| | - Helkin Forero Ballesteros
- INRAE, Université Côte d’Azur, CNRS, ISA, Sophia Antipolis, France
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Paes de Melo
- INRAE, Université Côte d’Azur, CNRS, ISA, Sophia Antipolis, France
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Isabela Tristan Lourenço-Tessutti
- INRAE, Université Côte d’Azur, CNRS, ISA, Sophia Antipolis, France
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | | | - Luciana Obicci
- INRAE, Université Côte d’Azur, CNRS, ISA, Sophia Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | - Adriana S. Hemerly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Guo J, Bai Y, Chen Z, Mo J, Li Q, Sun H, Zhang Q. Transcriptomic analysis suggests the inhibition of DNA damage repair in green alga Raphidocelis subcapitata exposed to roxithromycin. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 201:110737. [PMID: 32505758 DOI: 10.1016/j.ecoenv.2020.110737] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
Macrolide antibiotics are common contaminants in the aquatic environment. They are toxic to a wide range of primary producers, inhibiting the algal growth and further hindering the delivery of several ecosystem services. Yet the molecular mechanisms of macrolides in algae remain undetermined. The objectives of this study were therefore to: 1. evaluate whether macrolides at the environmentally relevant level inhibit the growth of algae; and 2. test the hypothesis that macrolides bind to ribosome and inhibit protein translocation in algae, as it does in bacteria. In this study, transcriptomic analysis was applied to elucidate the toxicological mechanism in a model green alga Raphidocelis subcapitata treated with 5 and 90 μg L-1 of a typical macrolide roxithromycin (ROX). While exposure to ROX at 5 μg L-1 for 7 days did not affect algal growth and the transciptome, ROX at 90 μg L-1 resulted in 45% growth inhibition and 2306 (983 up- and 1323 down-regulated) DEGs, which were primarily enriched in the metabolism of energy, lipid, vitamins, and DNA replication and repair pathways. Nevertheless, genes involved in pathways in relation to translation and protein translocation and processing were dysregulated. Surprisingly, we found that genes involved in the base excision repair process were mostly repressed, suggesting that ROX may be genotoxic and cause DNA damage in R. subcapitata. Taken together, ROX was unlikely to pose a threat to green algae in the environment and the mode of action of macrolides in bacteria may not be directly extrapolated to green algae.
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Affiliation(s)
- Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Yi Bai
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Zhi Chen
- Department of Building, Civil and Environmental Engineering, Concordia University, Montreal, H3G 1M8, Canada
| | - Jiezhang Mo
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Qi Li
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Haotian Sun
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Qiang Zhang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China.
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9
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Pan L, Wang X, Yang L, Zhao L, Zhai L, Xu J, Yang Y, Mao Y, Cheng S, Xiao T, Tan M. Proteomic and Phosphoproteomic Maps of Lung Squamous Cell Carcinoma From Chinese Patients. Front Oncol 2020; 10:963. [PMID: 32612956 PMCID: PMC7308564 DOI: 10.3389/fonc.2020.00963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 12/29/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is one of the leading causes of tumor-driven deaths in the world. To date, studies on the tumor heterogeneity of LUSC at genomic level have only revealed limited therapeutic benefits. Therefore, system-wide research of LUSC at proteomic level may further improve precision medicine strategies on individual demands. To this end, we performed proteomic and phosphoproteomic study for LUSC samples of 25 Chinese patients. From our results, two subgroups (Cluster I and II) based on proteomic data were identified, which were associated with distinct molecular characteristics and clinicopathologic features. Combined with phosphoproteomic data, our result showed that spliceosome pathway was enriched in Cluster I, while focal adhesion pathway, immune-related pathways and Ras signaling pathway were enriched in Cluster II. In addition, we found that lymph node metastasis (LNM) was associated with our proteomic subgroups and cell cycle pathway was enriched in patients with LNM. Further analysis showed that MCM2, a DNA replication licensing factor involved in cell cycle pathway, was highly expressed in patients with poor prognosis, which was further proved by immunohistochemistry (IHC) analysis. In summary, our study provided a resource of the proteomic and phosphoproteomic features of LUSC in Chinese patients.
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Affiliation(s)
- Lulu Pan
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Xijun Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Longhai Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Cardiothoracic Surgery, Shenzhen University General Hospital/Shenzhen University Clinical Medical Academy, Shenzhen, China
| | - Lei Zhao
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Linhui Zhai
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Junyu Xu
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yikun Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yousheng Mao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Minjia Tan
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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10
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Post-Translational Modifications of the Mini-Chromosome Maintenance Proteins in DNA Replication. Genes (Basel) 2019; 10:genes10050331. [PMID: 31052337 PMCID: PMC6563057 DOI: 10.3390/genes10050331] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/26/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
The eukaryotic mini-chromosome maintenance (MCM) complex, composed of MCM proteins 2-7, is the core component of the replisome that acts as the DNA replicative helicase to unwind duplex DNA and initiate DNA replication. MCM10 tightly binds the cell division control protein 45 homolog (CDC45)/MCM2-7/ DNA replication complex Go-Ichi-Ni-San (GINS) (CMG) complex that stimulates CMG helicase activity. The MCM8-MCM9 complex may have a non-essential role in activating the pre-replicative complex in the gap 1 (G1) phase by recruiting cell division cycle 6 (CDC6) to the origin recognition complex (ORC). Each MCM subunit has a distinct function achieved by differential post-translational modifications (PTMs) in both DNA replication process and response to replication stress. Such PTMs include phosphorylation, ubiquitination, small ubiquitin-like modifier (SUMO)ylation, O-N-acetyl-D-glucosamine (GlcNAc)ylation, and acetylation. These PTMs have an important role in controlling replication progress and genome stability. Because MCM proteins are associated with various human diseases, they are regarded as potential targets for therapeutic development. In this review, we summarize the different PTMs of the MCM proteins, their involvement in DNA replication and disease development, and the potential therapeutic implications.
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11
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Mughal MJ, Mahadevappa R, Kwok HF. DNA replication licensing proteins: Saints and sinners in cancer. Semin Cancer Biol 2018; 58:11-21. [PMID: 30502375 DOI: 10.1016/j.semcancer.2018.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/08/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022]
Abstract
DNA replication is all-or-none process in the cell, meaning, once the DNA replication begins it proceeds to completion. Hence, to achieve maximum control of DNA replication, eukaryotic cells employ a multi-subunit initiator protein complex known as "pre-replication complex or DNA replication licensing complex (DNA replication LC). This complex involves multiple proteins which are origin-recognition complex family proteins, cell division cycle-6, chromatin licensing and DNA replication factor 1, and minichromosome maintenance family proteins. Higher-expression of DNA replication LC proteins appears to be an early event during development of cancer since it has been a common hallmark observed in a wide variety of cancers such as oesophageal, laryngeal, pulmonary, mammary, colorectal, renal, urothelial etc. However, the exact mechanisms leading to the abnormally high expression of DNA replication LC have not been clearly deciphered. Increased expression of DNA replication LC leads to licensing and/or firing of multiple origins thereby inducing replication stress and genomic instability. Therapeutic approaches where the reduction in the activity of DNA replication LC was achieved either by siRNA or shRNA techniques, have shown increased sensitivity of cancer cell lines towards the anti-cancer drugs such as cisplatin, 5-Fluorouracil, hydroxyurea etc. Thus, the expression level of DNA replication LC within the cell determines a cell's fate thereby creating a paradox where DNA replication LC acts as both "Saint" and "Sinner". With a potential to increase sensitivity to chemotherapy drugs, DNA replication LC proteins have prospective clinical importance in fighting cancer. Hence, in this review, we will shed light on importance of DNA replication LC with an aim to use DNA replication LC in diagnosis and prognosis of cancer in patients as well as possible therapeutic targets for cancer therapy.
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Affiliation(s)
- Muhammad Jameel Mughal
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau
| | - Ravikiran Mahadevappa
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau
| | - Hang Fai Kwok
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau.
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12
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Bennetzen MV, Kosar M, Bunkenborg J, Payne MR, Bartkova J, Lindström MS, Lukas J, Andersen JS, Bartek J, Larsen DH. DNA damage-induced dynamic changes in abundance and cytosol-nuclear translocation of proteins involved in translational processes, metabolism, and autophagy. Cell Cycle 2018; 17:2146-2163. [PMID: 30196736 DOI: 10.1080/15384101.2018.1515552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Ionizing radiation (IR) causes DNA double-strand breaks (DSBs) and activates a versatile cellular response regulating DNA repair, cell-cycle progression, transcription, DNA replication and other processes. In recent years proteomics has emerged as a powerful tool deepening our understanding of this multifaceted response. In this study we use SILAC-based proteomics to specifically investigate dynamic changes in cytoplasmic protein abundance after ionizing radiation; we present in-depth bioinformatics analysis and show that levels of proteins involved in autophagy (cathepsins and other lysosomal proteins), proteasomal degradation (Ubiquitin-related proteins), energy metabolism (mitochondrial proteins) and particularly translation (ribosomal proteins and translation factors) are regulated after cellular exposure to ionizing radiation. Downregulation of no less than 68 ribosomal proteins shows rapid changes in the translation pattern after IR. Additionally, we provide evidence of compartmental cytosol-nuclear translocation of numerous DNA damage related proteins using protein correlation profiling. In conclusion, these results highlight unexpected cytoplasmic processes actively orchestrated after genotoxic insults and protein translocation from the cytoplasm to the nucleus as a fundamental regulatory mechanism employed to aid cell survival and preservation of genome integrity.
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Affiliation(s)
- Martin V Bennetzen
- a Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense M , Denmark
| | - Martin Kosar
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark
| | - Jakob Bunkenborg
- a Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense M , Denmark
| | - Mark Ronald Payne
- c National Institute of Aquatic Resources , Technical University of Denmark , Lyngby , Denmark
| | - Jirina Bartkova
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark.,d Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology , Karolinska Institutet , Solna , Sweden
| | - Mikael S Lindström
- d Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology , Karolinska Institutet , Solna , Sweden
| | - Jiri Lukas
- e Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research , Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen , Denmark
| | - Jens S Andersen
- a Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense M , Denmark
| | - Jiri Bartek
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark.,d Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology , Karolinska Institutet , Solna , Sweden
| | - Dorthe Helena Larsen
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark.,f Nucleolar Stress and Disease Group, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark
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13
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Zhang T, Meng J, Liu X, Zhang X, Peng X, Cheng Z, Zhang F. ING5 differentially regulates protein lysine acetylation and promotes p300 autoacetylation. Oncotarget 2017; 9:1617-1629. [PMID: 29416718 PMCID: PMC5788586 DOI: 10.18632/oncotarget.22176] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 10/11/2017] [Indexed: 02/06/2023] Open
Abstract
ING5 belongs to the Inhibitor of Growth (ING) candidate tumor suppressor family. Previously, we have shown that ING5 inhibits invasiveness of lung cancer cells by downregulating EMT-inducing genes. However, the underlying mechanisms remain unclear. The aim of the study was to use integrated approach involving SILAC labeling and mass spectrometry-based quantitative proteomics to quantify dynamic changes of acetylation regulated by ING5 in lung cancer cells. Here, we have found that ING5 has a profound influence on protein lysine acetylation with 163 acetylation peptides on 122 proteins significantly upregulated and 100 acetylation peptides on 72 proteins downregulated by ING5 overexpression. Bioinfomatic analysis revealed that the acetylated proteins upregulated by ING5 located preferentially in nucleus to cytoplasm and were significantly enriched in transcription cofactor activity, chromatin binding and DNA binding functions; while those downregulated by ING5 located preferentially in cytoplasm rather than nucleus and were functionally enriched in metabolism, suggesting diverse functions of ING5 through differentially regulating protein acetylation. Interestingly, we found ING5 overexpression promotes p300 autoacetylation at K1555, K1558 and K1560 within p300 HAT domain, and two novel sites K1647 and K1794, leading to activation of p300 HAT activity, which was confirmed by accelerated acetylation of p300 target proteins, p53 at k382 and histone H3 at K18. A specific p300 HAT inhibitor C646 impaired ING5-increased acetylation of H3K18 and p53K382, and subsequent expression of p21 and Bax. In conclusion, our results reveal the lysine acetylome regulated by ING5 and provide new insights into mechanisms of ING5 in the regulation of gene expression, metabolism and other cellular functions.
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Affiliation(s)
- Tao Zhang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Jin Meng
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China.,Department of Pharmacy, No. 309 Hospital of PLA, Beijing 100091, China
| | - Xinli Liu
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Xutao Zhang
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Xiaojun Peng
- Department of Bioinformatics, Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Zhongyi Cheng
- Department of Bioinformatics, Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Feng Zhang
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
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14
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Ghith A, Ismail NS, Youssef K, Abouzid KA. Medicinal Attributes of Thienopyrimidine Based Scaffold Targeting Tyrosine Kinases and Their Potential Anticancer Activities. Arch Pharm (Weinheim) 2017; 350. [DOI: 10.1002/ardp.201700242] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/14/2017] [Accepted: 09/05/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Amna Ghith
- Faculty of Pharmaceutical Sciences and Pharmaceutical Industries; Department of Pharmaceutical Chemistry; Future University in Egypt; Cairo Egypt
| | - Nasser S.M. Ismail
- Faculty of Pharmaceutical Sciences and Pharmaceutical Industries; Department of Pharmaceutical Chemistry; Future University in Egypt; Cairo Egypt
| | - Khairia Youssef
- Faculty of Pharmaceutical Sciences and Pharmaceutical Industries; Department of Pharmaceutical Chemistry; Future University in Egypt; Cairo Egypt
| | - Khaled A.M. Abouzid
- Faculty of Pharmacy; Department of Pharmaceutical Chemistry; Ain Shams University; Abbassia, Cairo Egypt
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15
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Breviscapine (BVP) inhibits prostate cancer progression through damaging DNA by minichromosome maintenance protein-7 (MCM-7) modulation. Biomed Pharmacother 2017. [PMID: 28628830 DOI: 10.1016/j.biopha.2017.06.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Naturally occurring compounds are reported as effective candidates for prevention and treatment of various cancers. Breviscapine (BVP) is a mixture of flavonoid glycosides, derived from the Chinese herbs. Previous researches have indicated that BVP has comprehensive pharmacological functions. However, little is known about whether BVP has preventive effects on human prostate cancer. Here, we attempted to explore if BVP inhibits human prostate cancer in vitro and in vivo in a comprehensive manner. We found that BVP triggered cytotoxicity in prostate cancer cell lines dose-dependently. BVP-induced DNA damage caused the cell cycle arrest and apoptosis and further induced cell death. High expression of MCM-7 was reduced in BVP-treated cancer cells and tumor tissues, and also the DNA damage response marker of γH2AX is down-regulated by BVP, associated with MCM-7 expression through regulating retinoblastoma protein (Rb) and checkpoint control proteins expression. Additionally, BVP induced apoptotic response in prostate cancer cells and tumors via activating Caspase-3 and PARP. In vivo studies indicated that BVP impeded tumor growth in xenograft animal models. In conclusion, our data indicates that breviscapine (BVP) can be further explored for its potential, which might be used in human prostate cancer therapeutics.
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16
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Brasil JN, Costa CNM, Cabral LM, Ferreira PCG, Hemerly AS. The plant cell cycle: Pre-Replication complex formation and controls. Genet Mol Biol 2017; 40:276-291. [PMID: 28304073 PMCID: PMC5452130 DOI: 10.1590/1678-4685-gmb-2016-0118] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 08/16/2016] [Indexed: 01/07/2023] Open
Abstract
The multiplication of cells in all living organisms requires a tight regulation of DNA replication. Several mechanisms take place to ensure that the DNA is replicated faithfully and just once per cell cycle in order to originate through mitoses two new daughter cells that contain exactly the same information from the previous one. A key control mechanism that occurs before cells enter S phase is the formation of a pre-replication complex (pre-RC) that is assembled at replication origins by the sequential association of the origin recognition complex, followed by Cdt1, Cdc6 and finally MCMs, licensing DNA to start replication. The identification of pre-RC members in all animal and plant species shows that this complex is conserved in eukaryotes and, more importantly, the differences between kingdoms might reflect their divergence in strategies on cell cycle regulation, as it must be integrated and adapted to the niche, ecosystem, and the organism peculiarities. Here, we provide an overview of the knowledge generated so far on the formation and the developmental controls of the pre-RC mechanism in plants, analyzing some particular aspects in comparison to other eukaryotes.
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Affiliation(s)
- Juliana Nogueira Brasil
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Centro Universitário Christus, Fortaleza, CE, Brazil
| | - Carinne N Monteiro Costa
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Luiz Mors Cabral
- Departamento de Biologia Celular e Molecular, Universidade Federal Fluminense, Niteroi, RJ, Brazil
| | - Paulo C G Ferreira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Adriana S Hemerly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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17
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Xu X, Wang JT, Li M, Liu Y. TIMELESS Suppresses the Accumulation of Aberrant CDC45·MCM2-7·GINS Replicative Helicase Complexes on Human Chromatin. J Biol Chem 2016; 291:22544-22558. [PMID: 27587400 PMCID: PMC5077192 DOI: 10.1074/jbc.m116.719963] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 08/31/2016] [Indexed: 07/24/2023] Open
Abstract
The replication licensing factor CDC6 recruits the MCM2-7 replicative helicase to the replication origin, where MCM2-7 is activated to initiate DNA replication. MCM2-7 is activated by both the CDC7-Dbf4 kinase and cyclin-dependent kinase and via interactions with CDC45 and go-ichi-ni-san complex (GINS) to form the CDC45·MCM2-7·GINS (CMG) helicase complex. TIMELESS (TIM) is important for the subsequent coupling of CMG activity to DNA polymerases for efficient DNA synthesis. However, the mechanism by which TIM regulates CMG activity for proper replication fork progression remains unclear. Here we show that TIM interacts with MCM2-7 prior to the initiation of DNA replication. TIM depletion in various human cell lines results in the accumulation of aberrant CMG helicase complexes on chromatin. Importantly, the presence of these abnormal CMG helicase complexes is not restricted to cells undergoing DNA synthesis. Furthermore, even though these aberrant CMG complexes interact with the DNA polymerases on human chromatin, these complexes are not phosphorylated properly by cyclin-dependent kinase/CDC7-Dbf4 kinase and exhibit reduced DNA unwinding activity. This phenomenon coincides with a significant accumulation of the p27 and p21 replication inhibitors, reduced chromatin association of CDC6 and cyclin E, and a delay in S phase entry. Our results provide the first evidence that TIM is required for the correct chromatin association of the CMG complex to allow efficient DNA replication.
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Affiliation(s)
- Xiaohua Xu
- From the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010-3000
| | - Jiin-Tarng Wang
- From the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010-3000
| | - Min Li
- From the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010-3000
| | - Yilun Liu
- From the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010-3000
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18
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Abstract
Whole-exome sequencing has emerged as a fast and effective tool for the elucidation of genetic defects underlying both rare and common human diseases. Increased availability and decreased costs of next-generation sequencing have enabled investigators to use this approach not only in individual patients with rare diseases, but also to screen large cohorts or populations for the genetic determinants of diseases. Within the field of endocrinology, exome sequencing has led to major advancements in our understanding of many disorders including adrenal disease, growth and puberty disorders and type 2 diabetes mellitus, as well as a multitude of rare genetic syndromes with prominent endocrine involvement. In this Review, we provide an overview of these new insights and discuss the role that exome sequencing is expected to have in endocrine research and future clinical practice.
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Affiliation(s)
- Christiaan de Bruin
- Cincinnati Children's Hospital Medical Center, Division of Endocrinology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Andrew Dauber
- Cincinnati Children's Hospital Medical Center, Division of Endocrinology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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19
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Maya-Mendoza A, Merchut-Maya JM, Bartkova J, Bartek J, Streuli CH, Jackson DA. Immortalised breast epithelia survive prolonged DNA replication stress and return to cycle from a senescent-like state. Cell Death Dis 2014; 5:e1351. [PMID: 25058425 PMCID: PMC4123104 DOI: 10.1038/cddis.2014.315] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/09/2014] [Accepted: 06/11/2014] [Indexed: 12/20/2022]
Abstract
Mammalian cells have mechanisms to counteract the effects of metabolic and exogenous stresses, many of that would be mutagenic if ignored. Damage arising during DNA replication is a major source of mutagenesis. The extent of damage dictates whether cells undergo transient cell cycle arrest and damage repair, senescence or apoptosis. Existing dogma defines these alternative fates as distinct choices. Here we show that immortalised breast epithelial cells are able to survive prolonged S phase arrest and subsequently re-enter cycle after many days of being in an arrested, senescence-like state. Prolonged cell cycle inhibition in fibroblasts induced DNA damage response and cell death. However, in immortalised breast epithelia, efficient S phase arrest minimised chromosome damage and protected sufficient chromatin-bound replication licensing complexes to allow cell cycle re-entry. We propose that our observation could have implications for the design of drug therapies for breast cancer.
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Affiliation(s)
- A Maya-Mendoza
- 1] Faculty of Life Sciences and Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, UK [2] Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark
| | - J M Merchut-Maya
- Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark
| | - J Bartkova
- Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark
| | - J Bartek
- 1] Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark [2] Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, CZ-779 00 Olomouc, Czech Republic
| | - C H Streuli
- Faculty of Life Sciences and Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - D A Jackson
- Faculty of Life Sciences and Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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20
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Ishino Y, Ishino S. Rapid progress of DNA replication studies in Archaea, the third domain of life. SCIENCE CHINA-LIFE SCIENCES 2012; 55:386-403. [PMID: 22645083 DOI: 10.1007/s11427-012-4324-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 04/20/2012] [Indexed: 02/04/2023]
Abstract
Archaea, the third domain of life, are interesting organisms to study from the aspects of molecular and evolutionary biology. Archaeal cells have a unicellular ultrastructure without a nucleus, resembling bacterial cells, but the proteins involved in genetic information processing pathways, including DNA replication, transcription, and translation, share strong similarities with those of Eukaryota. Therefore, archaea provide useful model systems to understand the more complex mechanisms of genetic information processing in eukaryotic cells. Moreover, the hyperthermophilic archaea provide very stable proteins, which are especially useful for the isolation of replisomal multicomplexes, to analyze their structures and functions. This review focuses on the history, current status, and future directions of archaeal DNA replication studies.
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Affiliation(s)
- Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan.
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21
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Ishino S, Fujino S, Tomita H, Ogino H, Takao K, Daiyasu H, Kanai T, Atomi H, Ishino Y. Biochemical and genetical analyses of the three mcm genes from the hyperthermophilic archaeon, Thermococcus kodakarensis. Genes Cells 2011; 16:1176-89. [PMID: 22093166 DOI: 10.1111/j.1365-2443.2011.01562.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In eukaryotes, the replicative DNA helicase 'core' is the minichromosome maintenance (Mcm) complex (MCM), forming a heterohexameric complex consisting of six subunits (Mcm2-7). Recent studies showed that the CMG (Cdc45-MCM-GINS) complex is the actual helicase body in the replication fork progression complex. In Archaea, Thermococcus kodakarensis harbors three genes encoding the Mcm homologs on its genome, contrary to most archaea, which have only one homolog. It is thus, of high interest, whether and how these three Mcms share their functions in DNA metabolism in this hyperthermophile. Here, we report the biochemical properties of two of these proteins, TkoMcm1 and TkoMcm3. In addition, their physical and functional interactions with GINS, possibly an essential factor for the initiation and elongation process of DNA replication, are presented through in vitro ATPase and helicase assays, and an in vivo immunoprecipitation assay. Gene disruption and product quantification analyses suggested that TkoMcm3 is essential for cell growth and plays a key role as the main DNA helicase in DNA replication, whereas TkoMcm1 also shares some function in the cells.
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Affiliation(s)
- Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Hakozaki, Higashi-ku, Fukuoka, Japan
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22
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Perna D, Fagà G, Verrecchia A, Gorski MM, Barozzi I, Narang V, Khng J, Lim KC, Sung WK, Sanges R, Stupka E, Oskarsson T, Trumpp A, Wei CL, Müller H, Amati B. Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts. Oncogene 2011; 31:1695-709. [PMID: 21860422 PMCID: PMC3324106 DOI: 10.1038/onc.2011.359] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The transition from quiescence to proliferation is a key regulatory step that can be induced by serum stimulation in cultured fibroblasts. The transcription factor Myc is directly induced by serum mitogens and drives a secondary gene expression program that remains largely unknown. Using mRNA profiling, we identify close to 300 Myc-dependent serum response (MDSR) genes, which are induced by serum in a Myc-dependent manner in mouse fibroblasts. Mapping of genomic Myc-binding sites by ChIP-seq technology revealed that most MDSR genes were directly targeted by Myc, but represented a minor fraction (5.5%) of all Myc-bound promoters (which were 22.4% of all promoters). Other target loci were either induced by serum in a Myc-independent manner, were not significantly regulated or were negatively regulated. MDSR gene products were involved in a variety of processes, including nucleotide biosynthesis, ribosome biogenesis, DNA replication and RNA control. Of the 29 MDSR genes targeted by RNA interference, three showed a requirement for cell-cycle entry upon serum stimulation and 11 for long-term proliferation and/or survival. Hence, proper coordination of key regulatory and biosynthetic pathways following mitogenic stimulation relies upon the concerted regulation of multiple Myc-dependent genes.
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Affiliation(s)
- D Perna
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Milan, Italy
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23
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Murphy DM, Buckley PG, Bryan K, Watters KM, Koster J, van Sluis P, Molenaar J, Versteeg R, Stallings RL. Dissection of the oncogenic MYCN transcriptional network reveals a large set of clinically relevant cell cycle genes as drivers of neuroblastoma tumorigenesis. Mol Carcinog 2010; 50:403-11. [PMID: 21557326 DOI: 10.1002/mc.20722] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 11/19/2010] [Indexed: 01/11/2023]
Abstract
Amplification of the oncogenic transcription factor MYCN plays a major role in the pathogenesis of several pediatric cancers, including neuroblastoma, medulloblastoma, and rhabodomyosarcoma. For neuroblastoma, MYCN amplification is the most powerful genetic predictor of poor patient survival, yet the mechanism by which MYCN drives tumorigenesis is only partially understood. To gain an insight into the distribution of MYCN binding and to identify clinically relevant MYCN target genes, we performed an integrated analysis of MYCN ChIP-chip and mRNA expression using the MYCN repressible SHEP-21N neuroblastoma cell line. We hypothesized that genes exclusively MYCN bound in SHEP-21N cells over-expressing MYCN would be enriched for direct targets which contribute to the process of disease progression. Integrated analysis revealed that MYCN drives tumorigenesis predominantly as a positive regulator of target gene transcription. A high proportion of genes (24%) that are MYCN bound and up-regulated in the SHEP-21N model are significantly associated with poor overall patient survival (OS) in a set of 88 tumors. In contrast, the proportion of genes down-regulated when bound by MYCN in the SHEP-21N model and which are significantly associated with poor overall patient survival when under-expressed in primary tumors was significantly lower (5%). Gene ontology analysis determined a highly statistically significant enrichment for cell cycle related genes within the over-expressed MYCN target group which were also associated with poor OS. We conclude that the over-expression of MYCN leads to aberrant binding and over-expression of genes associated with cell cycle regulation which are significantly correlated with poor OS and MYCN amplification.
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Affiliation(s)
- Derek M Murphy
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, Dublin, Ireland
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Rodriguez-Acebes S, Proctor I, Loddo M, Wollenschlaeger A, Rashid M, Falzon M, Prevost AT, Sainsbury R, Stoeber K, Williams GH. Targeting DNA replication before it starts: Cdc7 as a therapeutic target in p53-mutant breast cancers. THE AMERICAN JOURNAL OF PATHOLOGY 2010; 177:2034-45. [PMID: 20724597 DOI: 10.2353/ajpath.2010.100421] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Treatment options for triple-receptor negative (ER-/PR-/Her2-) and Her2-overexpressing (ER-/PR-/Her2+) breast cancers with acquired or de novo resistance are limited, and metastatic disease remains incurable. Targeting of growth signaling networks is often constrained by pathway redundancy or growth-independent cancer cell cycles. The cell-cycle protein Cdc7 regulates S phase by promoting DNA replication. This essential kinase acts as a convergence point for upstream growth signaling pathways and is therefore an attractive therapeutic target. We show that increased Cdc7 expression during mammary tumorigenesis is linked to Her2-overexpressing and triple-negative subtypes, accelerated cell cycle progression (P < 0.001), arrested tumor differentiation (P < 0.001), genomic instability (P = 0.019), increasing NPI score (P < 0.001), and reduced disease-free survival (HR = 1.98 [95% CI: 1.27-3.10]; P = 0.003), thus implicating its deregulation in the development of aggressive disease. Targeting Cdc7 with RNAi, we demonstrate that p53-mutant Her2-overexpressing and triple-negative breast cancer cell lines undergo an abortive S phase and apoptotic cell death due to loss of a p53-dependent Cdc7-inhibition checkpoint. In contrast, untransformed breast epithelial cells arrest in G1, remain viable, and are able to resume cell proliferation on recovery of Cdc7 kinase activity. Thus, Cdc7 appears to represent a potent and highly specific anticancer target in Her2-overexpressing and triple-negative breast cancers. Emerging Cdc7 kinase inhibitors may therefore significantly broaden the therapeutic armamentarium for treatment of the aggressive p53-mutant breast cancer subtypes identified in this study.
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Affiliation(s)
- Sara Rodriguez-Acebes
- Department of Pathology, Wolfson Institute for Biomedical Research, University College London, London, UK
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Bonda DJ, Evans TA, Santocanale C, Llosá JC, Viña J, Bajic VP, Castellani RJ, Siedlak SL, Perry G, Smith MA, Lee HG. Evidence for the progression through S-phase in the ectopic cell cycle re-entry of neurons in Alzheimer disease. Aging (Albany NY) 2010; 1:382-8. [PMID: 19946466 PMCID: PMC2783633 DOI: 10.18632/aging.100044] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Aberrant neuronal re-entry into the cell cycle is emerging as a potential
pathological mechanism in Alzheimer disease (AD). However, while cyclins,
cyclin dependent kinases (CDKs), and other mitotic factors are ectopically
expressed in neurons, many of these proteins are also involved in other
pathological and physiological processes, generating continued debate on
whether such markers are truly indicative of a bona fide cell cycle
process. To address this issue, here we analyzed one of the minichromosome
maintenance (Mcm) proteins that plays a role in DNA replication and becomes
phosphorylated by the S-phase promoting CDKs and Cdc7 during DNA synthesis.
We found phosphorylated Mcm2 (pMcm2) markedly associated with neurofibrillary
tangles, neuropil threads, and dystrophic neurites in AD but not in
aged-matched controls. These data not only provide further evidence for
cell cycle aberrations in AD, but the cytoplasmic, rather than nuclear,
localization of pMcm2 suggests an abnormal cellular distribution of this
important replication factor in AD that may explain resultant cell cycle
stasis and consequent neuronal degeneration.
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Affiliation(s)
- David J Bonda
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
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26
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Masai H, Matsumoto S, You Z, Yoshizawa-Sugata N, Oda M. Eukaryotic chromosome DNA replication: where, when, and how? Annu Rev Biochem 2010; 79:89-130. [PMID: 20373915 DOI: 10.1146/annurev.biochem.052308.103205] [Citation(s) in RCA: 370] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA replication is central to cell proliferation. Studies in the past six decades since the proposal of a semiconservative mode of DNA replication have confirmed the high degree of conservation of the basic machinery of DNA replication from prokaryotes to eukaryotes. However, the need for replication of a substantially longer segment of DNA in coordination with various internal and external signals in eukaryotic cells has led to more complex and versatile regulatory strategies. The replication program in higher eukaryotes is under a dynamic and plastic regulation within a single cell, or within the cell population, or during development. We review here various regulatory mechanisms that control the replication program in eukaryotes and discuss future directions in this dynamic field.
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Affiliation(s)
- Hisao Masai
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan.
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Akita M, Adachi A, Takemura K, Yamagami T, Matsunaga F, Ishino Y. Cdc6/Orc1 from Pyrococcus furiosus may act as the origin recognition protein and Mcm helicase recruiter. Genes Cells 2010; 15:537-52. [PMID: 20384788 DOI: 10.1111/j.1365-2443.2010.01402.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Archaea have one or more Cdc6/Orc1 proteins, which share sequence similarities with eukaryotic Cdc6 and Orc1. These proteins are involved in the initiation process of DNA replication, although their specific function has not been elucidated, except for origin recognition and binding. We showed that the Cdc6/Orc1 protein from the hyperthermophilic archaeon Pyrococcus furiosus specifically binds to the oriC region in the whole genome. However, it remains unclear how this initiator protein specifically recognizes the oriC region and how the Mcm helicase is recruited to oriC. In the current study, we characterized the biochemical properties of Cdc6/Orc1 in P. furiosus. The ATPase activity of the Cdc6/Orc1 protein was completely suppressed by binding to DNA containing the origin recognition box (ORB). Limited proteolysis and DNase I-footprint experiments suggested that the Cdc6/Orc1 protein changes its conformation on the ORB sequence in the presence of ATP. This conformational change may have an unknown, important function in the initiation process. Results from an in vitro recruiting assay indicated that Mcm is recruited onto the oriC region in a Cdc6/Orc1-dependent, but not ATP-dependent, manner. However, some other function is required for the functional loading of this helicase to start the unwinding of the replication fork DNA.
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Affiliation(s)
- Masaki Akita
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
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Abstract
The Mcm2-7 complex serves as the eukaryotic replicative helicase, the molecular motor that both unwinds duplex DNA and powers fork progression during DNA replication. Consistent with its central role in this process, much prior work has illustrated that Mcm2-7 loading and activation are landmark events in the regulation of DNA replication. Unlike any other hexameric helicase, Mcm2-7 is composed of six unique and essential subunits. Although the unusual oligomeric nature of this complex has long hampered biochemical investigations, recent advances with both the eukaryotic as well as the simpler archaeal Mcm complexes provide mechanistic insight into their function. In contrast to better-studied homohexameric helicases, evidence suggests that the six Mcm2-7 complex ATPase active sites are functionally distinct and are likely specialized to accommodate the regulatory constraints of the eukaryotic process.
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29
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Tan BCM, Liu H, Lin CL, Lee SC. Functional cooperation between FACT and MCM is coordinated with cell cycle and differential complex formation. J Biomed Sci 2010; 17:11. [PMID: 20156367 PMCID: PMC2848000 DOI: 10.1186/1423-0127-17-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 02/16/2010] [Indexed: 11/18/2022] Open
Abstract
Background Functional cooperation between FACT and the MCM helicase complex constitutes an integral step during DNA replication initiation. However, mode of regulation that underlies the proper functional interaction of FACT and MCM is poorly understood. Methods & Results Here we present evidence indicating that such interaction is coordinated with cell cycle progression and differential complex formation. We first demonstrate the existence of two distinct FACT-MCM subassemblies, FACT-MCM2/4/6/7 and FACT-MCM2/3/4/5. Both complexes possess DNA unwinding activity and are subject to cell cycle-dependent enzymatic regulation. Interestingly, analysis of functional attributes further suggests that they act at distinct, and possibly sequential, steps during origin establishment and replication initiation. Moreover, we show that the phosphorylation profile of the FACT-associated MCM4 undergoes a cell cycle-dependent change, which is directly correlated with the catalytic activity of the FACT-MCM helicase complexes. Finally, at the quaternary structure level, physical interaction between FACT and MCM complexes is generally dependent on persistent cell cycle and further stabilized upon S phase entry. Cessation of mitotic cycle destabilizes the complex formation and likely leads to compromised coordination and activities. Conclusions Together, our results correlate FACT-MCM functionally and temporally with S phase and DNA replication. They further demonstrate that enzymatic activities intrinsically important for DNA replication are tightly controlled at various levels, thereby ensuring proper progression of, as well as exit from, the cell cycle and ultimately euploid gene balance.
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Affiliation(s)
- Bertrand Chin-Ming Tan
- Department of Life Science, College of Medicine, Chang Gung Univeristy, Taoyuan, Taiwan.
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30
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Development of quantitative and high-throughput assays of polyomavirus and papillomavirus DNA replication. Virology 2010; 399:65-76. [PMID: 20079917 DOI: 10.1016/j.virol.2009.12.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 11/17/2009] [Accepted: 12/17/2009] [Indexed: 11/23/2022]
Abstract
Polyoma- and papillomaviruses genome replication is initiated by the binding of large T antigen (LT) and of E1 and E2, respectively, at the viral origin (ori). Replication of an ori-containing plasmid occurs in cells transiently expressing these viral proteins and is typically quantified by Southern blotting or PCR. To facilitate the study of SV40 and HPV31 DNA replication, we developed cellular assays in which transient replication of the ori-plasmid is quantified using a firefly luciferase gene located in cis to the ori. Under optimized conditions, replication of the SV40 and HPV31 ori-plasmids resulted in a 50- and 150-fold increase in firefly luciferase levels, respectively. These results were validated using replication-defective mutants of LT, E1 and E2 and with inhibitors of DNA replication and cell-cycle progression. These quantitative and high-throughput assays should greatly facilitate the study of SV40 and HPV31 DNA replication and the identification of small-molecule inhibitors of this process.
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Abstract
Eukaryotic initiation of DNA replication is a tightly regulated process. In the yeasts, S-phase-specific cyclin Cdk1 complex as well as Dfb4-Cdc7 kinase phosphorylate the initiation factors Sld2 and Sld3. These factors form a ternary complex with another initiation factor Dbp11 in their phosphorylated state, and associate with the origin of replication. This complex mediates the loading of Cdc45. A second complex called GINS and consisting of Sld5 and Psf1, 2 and 3 is also loaded onto the origin during the initiation process, in an interdependent manner with the Sld2/Sld3/Dpb11 complex. Both complexes cooperate in the recruitment of the replicative DNA polymerases, thus executing the initiation and subsequent establishment of the replication fork. Cdc45 and GINS are essential, well-conserved factors that are retained at the elongating replication fork. They form a stable helicase complex with MCM2-7 and mediate its contact to the replicative DNA polymerases. In contrast, the Sld2/Sld3/Dpb11 complex critical for the initiation is not retained by the elongating replication fork. Sld2 displays limited homology to the amino-terminal region of RecQL4 helicase, which may represent its metazoan orthologue, whereas Sld3 homologues have been identified only in fungi. Dbp11 and its fission yeast homologue Cut5 are members of a large family of BRCT-containing proteins including human TopBP1 and fruit fly Mus101. Similar principles of regulation apply also to human initiation of DNA replication, despite obvious differences in the detailed mechanisms. The regulatory initiation cascade is intimately intertwined with the cell cycle apparatus as well as the checkpoint control.
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Affiliation(s)
- Helmut Pospiech
- Leibniz Institute for Age Research - Fritz Lipmann Institute, D-07745 Jena, Germany
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32
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Kulkarni AA, Kingsbury SR, Tudzarova S, Hong HK, Loddo M, Rashid M, Rodriguez-Acebes S, Prevost AT, Ledermann JA, Stoeber K, Williams GH. Cdc7 kinase is a predictor of survival and a novel therapeutic target in epithelial ovarian carcinoma. Clin Cancer Res 2009; 15:2417-25. [PMID: 19318489 DOI: 10.1158/1078-0432.ccr-08-1276] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PURPOSE There is a lack of prognostic and predictive biomarkers in epithelial ovarian carcinoma, and the targeting of oncogenic signaling pathways has had limited impact on patient survival in this highly heterogeneous disease. The origin licensing machinery, which renders chromosomes competent for DNA replication, acts as a convergence point for upstream signaling pathways. We tested the hypothesis that Cdc7 kinase, a core component of the licensing machinery, is predictive of clinical outcome and may constitute a novel therapeutic target in epithelial ovarian carcinoma. EXPERIMENTAL DESIGN A total of 143 cases of ovarian cancer and 5 cases of normal ovary were analyzed for Cdc7 protein expression dynamics and clinicopathologic features. To assess the therapeutic potential of Cdc7, expression was down-regulated by RNA interference in SKOV-3 and Caov-3 ovarian cancer cells. RESULTS Increased Cdc7 protein levels were significantly associated with arrested tumor differentiation (P = 0.004), advanced clinical stage (P = 0.01), genomic instability (P < 0.001), and accelerated cell cycle progression. Multivariate analysis shows that Cdc7 predicts disease-free survival independent of patient age, tumor grade and stage (hazard ratio, 2.03; confidence interval, 1.53-2.68; P < 0.001), with the hazard ratio for relapse increasing to 10.90 (confidence interval, 4.07-29.17) for the stages 3 to 4/upper Cdc7 tertile group relative to stages 1 to 2/lower Cdc7 tertile tumors. In SKOV-3 and Caov-3 cells, Cdc7 siRNA knockdown triggered high levels of apoptosis, whereas untransformed cells arrest in G(1) phase and remain viable. CONCLUSIONS Our findings show that Cdc7 kinase predicts survival and is a potent anticancer target in epithelial ovarian carcinoma, highlighting its potential as a predictor of susceptibility to small molecule kinase inhibitors currently in development.
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Affiliation(s)
- Anjana A Kulkarni
- Department of Pathology and Cancer Institute, Cancer Institute, University College London, London, United Kingdom
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33
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Abstract
Papillomaviruses establish persistent infection in the dividing, basal epithelial cells of the host. The viral genome is maintained as a circular, double-stranded DNA, extrachromosomal element within these cells. Viral genome amplification occurs only when the epithelial cells differentiate and viral particles are shed in squames that are sloughed from the surface of the epithelium. There are three modes of replication in the papillomavirus life cycle. Upon entry, in the establishment phase, the viral genome is amplified to a low copy number. In the second maintenance phase, the genome replicates in dividing cells at a constant copy number, in synchrony with the cellular DNA. And finally, in the vegetative or productive phase, the viral DNA is amplified to a high copy number in differentiated cells and is destined to be packaged in viral capsids. This review discusses the cis elements and protein factors required for each stage of papillomavirus replication.
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Affiliation(s)
- Alison A McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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34
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High mobility group box associated with cell proliferation appears to play an important role in hepatocellular carcinogenesis in rats and humans. Toxicology 2008; 255:160-70. [PMID: 19041683 DOI: 10.1016/j.tox.2008.10.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 10/20/2008] [Accepted: 10/21/2008] [Indexed: 11/22/2022]
Abstract
To identify genes important in hepatocellular carcinogenesis, especially processes involved in malignant transformation, we focused on differences in gene expression between adenomas and carcinomas by DNA microarray. Eighty-one genes for which expression was specific in carcinomas were analyzed using Ingenuity Pathway Analysis software and Gene Ontology, and found to be associated with TP53 and regulators of cell proliferation. In the genes associated with TP53, we selected high mobility group box (HMGB) for detailed analysis. Immunohistochemistry revealed expression of HMGBs in carcinomas to be significantly higher than in other lesions among both human and rat liver, and a positive correlation between HMGBs and TP53 was detected in rat carcinomas. Knock-down of HMGB 2 expression in a rat hepatocellular carcinoma cell line by RNAi resulted in inhibition of cell growth, although no effects on invasion were evident in vitro. These results suggest that acquisition of malignant potential in the liver requires specific signaling pathways related to high cell proliferation associated with TP53. In particular, HMGBs appear to have an important role for progression and cell proliferation associated with loss of TP53 function in rat and in human hepatocarcinogenesis.
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Pruitt SC, Bailey KJ, Freeland A. Reduced Mcm2 expression results in severe stem/progenitor cell deficiency and cancer. Stem Cells 2007; 25:3121-32. [PMID: 17717065 DOI: 10.1634/stemcells.2007-0483] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mcm2 is a component of the DNA replication licensing complex that marks DNA replication origins during G1 of the cell cycle for use in the subsequent S-phase. It is expressed in stem/progenitor cells in a variety of regenerative tissues in mammals. Here, we have used the Mcm2 gene to develop a transgenic mouse in which somatic stem/progenitor cells can be genetically modified in the adult. In these mice, a tamoxifen-inducible form of Cre recombinase is integrated 3' to the Mcm2 coding sequence and expressed via an internal ribosome entry site (IRES). Heterozygous Mcm2(IRES-CreERT2/wild-type (wt)) mice are phenotypically indistinguishable from wild-type at least through 1 year of age. In bigenic Mcm2(IRES-CreERT2/wt); Z/EG reporter mice, tamoxifen-dependent enhanced green fluorescence protein expression is inducible in a wide variety of somatic stem cells and their progeny. However, in Mcm2(IRES-CreERT2/IRES-CreERT2) homozygous embryos or mouse embryonic fibroblasts, Mcm2 is reduced to approximately one-third of wild-type levels. Despite the fact that these mice develop normally and are asymptomatic as young adults, life span is greatly reduced, with most surviving to only approximately 10-12 weeks of age. They demonstrate severe deficiencies in the proliferative cell compartments of a variety of tissues, including the subventricular zone of the brain, muscle, and intestinal crypts. However, the immediate cause of death in most of these animals is cancer, where the majority develop lymphomas. These studies directly demonstrate that deficiencies in the function of the core DNA replication machinery that are compatible with development and survival nonetheless result in a chronic phenotype leading to stem cell deficiency in multiple tissues and cancer. Disclosure of potential conflicts of interest is found at the end of this article.
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Affiliation(s)
- Steven C Pruitt
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, New York 14263, USA.
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36
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Lau E, Tsuji T, Guo L, Lu SH, Jiang W. The role of pre‐replicative complex (pre‐RC) components in oncogenesis. FASEB J 2007; 21:3786-94. [PMID: 17690155 DOI: 10.1096/fj.07-8900rev] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Normal DNA replication is stringently regulated to ensure a timely occurrence no more than once per cell cycle. Abrogation of the exquisite control mechanisms that maintain this process results in detrimental gains and losses of genomic DNA commonly seen in cancer and developmental defects. Replication initiation proteins, known as prereplicative complex (pre-RC) proteins, serve as a primary level of regulation, controlling when DNA replication can begin. Unsurprisingly, several pre-RC proteins are overexpressed in cancer and serve as good tumor markers. However, their direct correlation with increasing tumor grade and poor prognosis has posed a long-standing question: Are pre-RC proteins oncogenic? Recently, a growing body of data indicates that deregulation of individual pre-RC proteins, either by overexpression or functional deficiency in several organismal models, results in significant and consistently perturbed cell cycle regulation, genomic instability, and, potentially, tumorigenesis. In this review, we examine this broad range of evidence suggesting that pre-RC proteins play roles during oncogenesis that are more than simply indicative of proliferation, supporting the notion that pre-RC proteins may potentially have significant diagnostic and therapeutic value.
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Affiliation(s)
- Eric Lau
- The Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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37
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Shultz RW, Tatineni VM, Hanley-Bowdoin L, Thompson WF. Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice. PLANT PHYSIOLOGY 2007; 144:1697-714. [PMID: 17556508 PMCID: PMC1949880 DOI: 10.1104/pp.107.101105] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Accepted: 05/29/2007] [Indexed: 05/15/2023]
Abstract
Core DNA replication proteins mediate the initiation, elongation, and Okazaki fragment maturation functions of DNA replication. Although this process is generally conserved in eukaryotes, important differences in the molecular architecture of the DNA replication machine and the function of individual subunits have been reported in various model systems. We have combined genome-wide bioinformatic analyses of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) with published experimental data to provide a comprehensive view of the core DNA replication machinery in plants. Many components identified in this analysis have not been studied previously in plant systems, including the GINS (go ichi ni san) complex (PSF1, PSF2, PSF3, and SLD5), MCM8, MCM9, MCM10, NOC3, POLA2, POLA3, POLA4, POLD3, POLD4, and RNASEH2. Our results indicate that the core DNA replication machinery from plants is more similar to vertebrates than single-celled yeasts (Saccharomyces cerevisiae), suggesting that animal models may be more relevant to plant systems. However, we also uncovered some important differences between plants and vertebrate machinery. For example, we did not identify geminin or RNASEH1 genes in plants. Our analyses also indicate that plants may be unique among eukaryotes in that they have multiple copies of numerous core DNA replication genes. This finding raises the question of whether specialized functions have evolved in some cases. This analysis establishes that the core DNA replication machinery is highly conserved across plant species and displays many features in common with other eukaryotes and some characteristics that are unique to plants.
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Affiliation(s)
- Randall W Shultz
- Department of Plant Biology , North Carolina State University, Raleigh, North Carolina 27695, USA
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38
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Bauerschmidt C, Pollok S, Kremmer E, Nasheuer HP, Grosse F. Interactions of human Cdc45 with the Mcm2-7 complex, the GINS complex, and DNA polymerases delta and epsilon during S phase. Genes Cells 2007; 12:745-58. [PMID: 17573775 DOI: 10.1111/j.1365-2443.2007.01090.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cdc45 is an essential cellular protein that functions in both the initiation and elongation of DNA replication. Here, we analyzed the localization of human Cdc45 and its interactions with other proteins during the cell cycle. Human Cdc45 showed a diffuse distribution in G1 phase, a spot-like pattern in S and G2, and again a diffuse distribution in M phase of the cell cycle. The co-localization of Cdc45 with active replication sites during S phase suggested that the human Cdc45 protein was part of the elongation complex. This view was corroborated by findings that Cdc45 interacted with the elongating DNA polymerases delta and epsilon, with Psf2, which is a component of the GINS complex as well as with Mcm5 and 7, subunits of the putative replicative DNA helicase complex. Hence, Cdc45 may play an important role in elongation of DNA replication by bridging the processive DNA polymerases delta and epsilon with the replicative helicase in the elongating machinery.
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Affiliation(s)
- Christina Bauerschmidt
- Biochemistry Group, Leibniz Institute for Age Research-Fritz-Lipmann-Institute e. V., Beutenbergstrasse 11, D-07745 Jena, Germany
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Fradet-Turcotte A, Vincent C, Joubert S, Bullock PA, Archambault J. Quantitative analysis of the binding of simian virus 40 large T antigen to DNA. J Virol 2007; 81:9162-74. [PMID: 17596312 PMCID: PMC1951407 DOI: 10.1128/jvi.00384-07] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
SV40 large T antigen (T-ag) is a multifunctional protein that successively binds to 5'-GAGGC-3' sequences in the viral origin of replication, melts the origin, unwinds DNA ahead of the replication fork, and interacts with host DNA replication factors to promote replication of the simian virus 40 genome. The transition of T-ag from a sequence-specific binding protein to a nonspecific helicase involves its assembly into a double hexamer whose formation is likely dictated by the propensity of T-ag to oligomerize and its relative affinities for the origin as well as for nonspecific double- and single-stranded DNA. In this study, we used a sensitive assay based on fluorescence anisotropy to measure the affinities of wild-type and mutant forms of the T-ag origin-binding domain (OBD), and of a larger fragment containing the N-terminal domain (N260), for different DNA substrates. We report that the N-terminal domain does not contribute to binding affinity but reduces the propensity of the OBD to self-associate. We found that the OBD binds with different affinities to its four sites in the origin and determined a consensus binding site by systematic mutagenesis of the 5'-GAGGC-3' sequence and of the residue downstream of it, which also contributes to affinity. Interestingly, the OBD also binds to single-stranded DNA with an approximately 10-fold higher affinity than to nonspecific duplex DNA and in a mutually exclusive manner. Finally, we provide evidence that the sequence specificity of full-length T-ag is lower than that of the OBD. These results provide a quantitative basis onto which to anchor our understanding of the interaction of T-ag with the origin and its assembly into a double hexamer.
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Affiliation(s)
- Amélie Fradet-Turcotte
- Laboratory of Molecular Virology, Institut de Recherches Cliniques de Montréal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada
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Nasheuer HP, Pospiech H, Syväoja J. Progress Towards the Anatomy of the Eukaryotic DNA Replication Fork. Genome Integr 2006. [DOI: 10.1007/7050_016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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DePamphilis ML, Blow JJ, Ghosh S, Saha T, Noguchi K, Vassilev A. Regulating the licensing of DNA replication origins in metazoa. Curr Opin Cell Biol 2006; 18:231-9. [PMID: 16650748 DOI: 10.1016/j.ceb.2006.04.001] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Accepted: 04/04/2006] [Indexed: 01/19/2023]
Abstract
Eukaryotic DNA replication is a highly conserved process; the proteins and sequence of events that replicate animal genomes are remarkably similar to those that replicate yeast genomes. Moreover, the assembly of prereplication complexes at DNA replication origins ('DNA licensing') is regulated in all eukaryotes so that no origin fires more than once in a single cell cycle. And yet there are significant differences between species both in the selection of replication origins and in the way in which these origins are licensed to operate. Moreover, these differences impart advantages to multicellular animals and plants that facilitate their development, such as better control over endoreduplication, flexibility in origin selection, and discrimination between quiescent and proliferative states.
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Affiliation(s)
- Melvin L DePamphilis
- National Institute of Child Health and Human Development, National Institutes of Health, Building 6/3A-15, 9000 Rockville Pike, Bethesda, MD 20892-2753, USA.
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Quaglia A, McStay M, Stoeber K, Loddo M, Caplin M, Fanshawe T, Williams G, Dhillon A. Novel markers of cell kinetics to evaluate progression from cirrhosis to hepatocellular carcinoma. Liver Int 2006; 26:424-32. [PMID: 16629645 DOI: 10.1111/j.1478-3231.2006.01242.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
BACKGROUND We investigated cell cycle kinetics of nodular lesions in cirrhosis to differentiate hepatocellular carcinoma (HCC) from its precursor lesions. METHODS Twelve small HCC, 10 regenerative (RN), six large regenerative (LRN), and five dysplastic nodules (DN), identified in explant cirrhotic livers of five consecutive patients transplanted at Royal Free Hospital in 2002. Immunoperoxidase for MCM2, geminin and Ki67 was performed and the percentage of positive cells counted. RESULTS The proportion of cells expressing MCM2 was more than those expressing Ki67, which in turn was more than those expressing geminin (overall median=16%, 2% and 0.5%, respectively, P<0.001). There was a statistically significant trend of increasing Ki67 expression (P=0.006), from RN to HCC; this trend was not statistically significant for geminin (P=0.18) or MCM2 (P=0.51). The median percentage of cells expressing Ki67 was 1% in RN, 0.5% in LRN, 2.2% in DN and 5.4% in HCC. The combination of these markers identified four different cell kinetics patterns: 'resting' (G0 cells: MCM2 -ve, Ki67 -ve, geminin -ve); 'licensed' (MCM2 +ve, Ki67 -ve, geminin -ve); 'slowly growing' (G1 phase arrest, MCM2 +ve, Ki67 +ve, low (0.4%) geminin) and expanding (MCM2 +ve, Ki67 +ve, geminin +ve) nodules. CONCLUSIONS The combination of MCM2, geminin and Ki67 could represent a valuable tool in the understanding of HCC progression in cirrhosis.
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Affiliation(s)
- Alberto Quaglia
- Department of Histopathology, Royal Free and University College Medical School, London, UK.
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