1
|
Schmit MM, Baxley RM, Wang L, Hinderlie P, Kaufman M, Simon E, Raju A, Miller JS, Bielinsky AK. A critical threshold of MCM10 is required to maintain genome stability during differentiation of induced pluripotent stem cells into natural killer cells. Open Biol 2024; 14:230407. [PMID: 38262603 PMCID: PMC10805602 DOI: 10.1098/rsob.230407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/23/2023] [Indexed: 01/25/2024] Open
Abstract
Natural killer (NK) cell deficiency (NKD) is a rare disease in which NK cell function is reduced, leaving affected individuals susceptible to repeated viral infections and cancer. Recently, a patient with NKD was identified carrying compound heterozygous variants of MCM10 (minichromosome maintenance protein 10), an essential gene required for DNA replication, that caused a significant decrease in the amount of functional MCM10. NKD in this patient presented as loss of functionally mature late-stage NK cells. To understand how MCM10 deficiency affects NK cell development, we generated MCM10 heterozygous (MCM10+/-) induced pluripotent stem cell (iPSC) lines. Analyses of these cell lines demonstrated that MCM10 was haploinsufficient, similar to results in other human cell lines. Reduced levels of MCM10 in mutant iPSCs was associated with impaired clonogenic survival and increased genomic instability, including micronuclei formation and telomere erosion. The severity of these phenotypes correlated with the extent of MCM10 depletion. Significantly, MCM10+/- iPSCs displayed defects in NK cell differentiation, exhibiting reduced yields of hematopoietic stem cells (HSCs). Although MCM10+/- HSCs were able to give rise to lymphoid progenitors, these did not generate mature NK cells. The lack of mature NK cells coincided with telomere erosion, suggesting that NKD caused by these MCM10 variants arose from the accumulation of genomic instability including degradation of chromosome ends.
Collapse
Affiliation(s)
- Megan M. Schmit
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ryan M. Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Liangjun Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Peter Hinderlie
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Marissa Kaufman
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Emily Simon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Anjali Raju
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jeffrey S. Miller
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
2
|
Jones ML, Aria V, Baris Y, Yeeles JTP. How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication. Mol Cell 2023; 83:2911-2924.e16. [PMID: 37506699 PMCID: PMC10501992 DOI: 10.1016/j.molcel.2023.06.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023]
Abstract
During eukaryotic DNA replication, Pol α-primase generates primers at replication origins to start leading-strand synthesis and every few hundred nucleotides during discontinuous lagging-strand replication. How Pol α-primase is targeted to replication forks to prime DNA synthesis is not fully understood. Here, by determining cryoelectron microscopy (cryo-EM) structures of budding yeast and human replisomes containing Pol α-primase, we reveal a conserved mechanism for the coordination of priming by the replisome. Pol α-primase binds directly to the leading edge of the CMG (CDC45-MCM-GINS) replicative helicase via a complex interaction network. The non-catalytic PRIM2/Pri2 subunit forms two interfaces with CMG that are critical for in vitro DNA replication and yeast cell growth. These interactions position the primase catalytic subunit PRIM1/Pri1 directly above the exit channel for lagging-strand template single-stranded DNA (ssDNA), revealing why priming occurs efficiently only on the lagging-strand template and elucidating a mechanism for Pol α-primase to overcome competition from RPA to initiate primer synthesis.
Collapse
Affiliation(s)
- Morgan L Jones
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Valentina Aria
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Yasemin Baris
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | |
Collapse
|
3
|
Nasheuer HP, Onwubiko NO. Lagging Strand Initiation Processes in DNA Replication of Eukaryotes-Strings of Highly Coordinated Reactions Governed by Multiprotein Complexes. Genes (Basel) 2023; 14:genes14051012. [PMID: 37239371 DOI: 10.3390/genes14051012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
In their influential reviews, Hanahan and Weinberg coined the term 'Hallmarks of Cancer' and described genome instability as a property of cells enabling cancer development. Accurate DNA replication of genomes is central to diminishing genome instability. Here, the understanding of the initiation of DNA synthesis in origins of DNA replication to start leading strand synthesis and the initiation of Okazaki fragment on the lagging strand are crucial to control genome instability. Recent findings have provided new insights into the mechanism of the remodelling of the prime initiation enzyme, DNA polymerase α-primase (Pol-prim), during primer synthesis, how the enzyme complex achieves lagging strand synthesis, and how it is linked to replication forks to achieve optimal initiation of Okazaki fragments. Moreover, the central roles of RNA primer synthesis by Pol-prim in multiple genome stability pathways such as replication fork restart and protection of DNA against degradation by exonucleases during double-strand break repair are discussed.
Collapse
Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, Arts & Science Building, Main Concourse, School of Biological and Chemical Sciences, Biochemistry, University of Galway, Distillery Road, H91 TK33 Galway, Ireland
| | - Nichodemus O Onwubiko
- Centre for Chromosome Biology, Arts & Science Building, Main Concourse, School of Biological and Chemical Sciences, Biochemistry, University of Galway, Distillery Road, H91 TK33 Galway, Ireland
| |
Collapse
|
4
|
Li Y, Li X, Cournoyer P, Choudhuri S, Yu X, Guo L, Chen S. Cannabidiol-induced transcriptomic changes and cellular senescence in human Sertoli cells. Toxicol Sci 2023; 191:227-238. [PMID: 36519830 PMCID: PMC10123764 DOI: 10.1093/toxsci/kfac131] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cannabidiol (CBD), one of the major cannabinoids in the plant Cannabis sativa L., is the active ingredient in a drug approved for the treatment of seizures associated with certain childhood-onset epileptic disorders. CBD has been shown to induce male reproductive toxicity in multiple animal models. We previously reported that CBD inhibits cellular proliferation in the mouse Sertoli cell line TM4 and in primary human Sertoli cells. In this study, using a transcriptomic approach with mRNA-sequencing analysis, we identified molecular mechanisms underlying CBD-induced cytotoxicity in primary human Sertoli cells. Analysis of differentially expressed genes demonstrated that DNA replication, cell cycle, and DNA repair were the most significantly affected pathways. We confirmed the concentration-dependent changes in the expression of key genes in these pathways using real-time PCR. mRNA sequencing showed upregulation of a group of genes tightly associated with the senescence-associated secretory phenotype (SASP) and with the activation of the p53 signaling pathway, a key upstream event in cellular senescence. Prolonged treatment of 10 μM CBD-induced cellular senescence, as evidenced by the stable cessation of proliferation and the activation of senescence-associated β-galactosidase (SA-β-gal), 2 hallmarks of senescence. Additionally, using real-time PCR and Western blotting assays, we observed that CBD treatment increased the expression of p16, an important marker of cellular senescence. Taken together, our results show that CBD exposure disturbs various interrelated signaling pathways and induces cellular senescence in primary human Sertoli cells.
Collapse
Affiliation(s)
- Yuxi Li
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Xilin Li
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | | | - Supratim Choudhuri
- Office of Food Additive Safety, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA
| | - Xiaozhong Yu
- College of Nursing, University of New Mexico, Albuquerque, NM 87131, USA
| | - Lei Guo
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Si Chen
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| |
Collapse
|
5
|
Xiang S, Reed DR, Alexandrow MG. The CMG helicase and cancer: a tumor "engine" and weakness with missing mutations. Oncogene 2023; 42:473-90. [PMID: 36522488 DOI: 10.1038/s41388-022-02572-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
The replicative Cdc45-MCM-GINS (CMG) helicase is a large protein complex that functions in the DNA melting and unwinding steps as a component of replisomes during DNA replication in mammalian cells. Although the CMG performs this important role in cell growth, the CMG is not a simple bystander in cell cycle events. Components of the CMG, specifically the MCM precursors, are also involved in maintaining genomic stability by regulating DNA replication fork speeds, facilitating recovery from replicative stresses, and preventing consequential DNA damage. Given these important functions, MCM/CMG complexes are highly regulated by growth factors such as TGF-ß1 and by signaling factors such as Myc, Cyclin E, and the retinoblastoma protein. Mismanagement of MCM/CMG complexes when these signaling mediators are deregulated, and in the absence of the tumor suppressor protein p53, leads to increased genomic instability and is a contributor to tumorigenic transformation and tumor heterogeneity. The goal of this review is to provide insight into the mechanisms and dynamics by which the CMG is regulated during its assembly and activation in mammalian genomes, and how errors in CMG regulation due to oncogenic changes promote tumorigenesis. Finally, and most importantly, we highlight the emerging understanding of the CMG helicase as an exploitable vulnerability and novel target for therapeutic intervention in cancer.
Collapse
|
6
|
Zhao X, Wang J, Jin D, Cheng J, Chen H, Li Z, Wang Y, Lou H, Zhu JK, Du X, Gong Z. AtMCM10 promotes DNA replication-coupled nucleosome assembly in Arabidopsis. J Integr Plant Biol 2023; 65:203-222. [PMID: 36541721 DOI: 10.1111/jipb.13438] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Minichromosome Maintenance protein 10 (MCM10) is essential for DNA replication initiation and DNA elongation in yeasts and animals. Although the functions of MCM10 in DNA replication and repair have been well documented, the detailed mechanisms for MCM10 in these processes are not well known. Here, we identified AtMCM10 gene through a forward genetic screening for releasing a silenced marker gene. Although plant MCM10 possesses a similar crystal structure as animal MCM10, AtMCM10 is not essential for plant growth or development in Arabidopsis. AtMCM10 can directly bind to histone H3-H4 and promotes nucleosome assembly in vitro. The nucleosome density is decreased in Atmcm10, and most of the nucleosome density decreased regions in Atmcm10 are also regulated by newly synthesized histone chaperone Chromatin Assembly Factor-1 (CAF-1). Loss of both AtMCM10 and CAF-1 is embryo lethal, indicating that AtMCM10 and CAF-1 are indispensable for replication-coupled nucleosome assembly. AtMCM10 interacts with both new and parental histones. Atmcm10 mutants have lower H3.1 abundance and reduced H3K27me1/3 levels with releasing some silenced transposons. We propose that AtMCM10 deposits new and parental histones during nucleosome assembly, maintaining proper epigenetic modifications and genome stability during DNA replication.
Collapse
Affiliation(s)
- Xinjie Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dan Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hui Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yu Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jian-Kang Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Science, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuan Du
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, 518060, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| |
Collapse
|
7
|
Kang Z, Fu P, Alcivar AL, Fu H, Redon C, Foo TK, Zuo Y, Ye C, Baxley R, Madireddy A, Buisson R, Bielinsky AK, Zou L, Shen Z, Aladjem MI, Xia B. BRCA2 associates with MCM10 to suppress PRIMPOL-mediated repriming and single-stranded gap formation after DNA damage. Nat Commun 2021; 12:5966. [PMID: 34645815 PMCID: PMC8514439 DOI: 10.1038/s41467-021-26227-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/23/2021] [Indexed: 11/28/2022] Open
Abstract
The BRCA2 tumor suppressor protects genome integrity by promoting homologous recombination-based repair of DNA breaks, stability of stalled DNA replication forks and DNA damage-induced cell cycle checkpoints. BRCA2 deficient cells display the radio-resistant DNA synthesis (RDS) phenotype, however the mechanism has remained elusive. Here we show that cells without BRCA2 are unable to sufficiently restrain DNA replication fork progression after DNA damage, and the underrestrained fork progression is due primarily to Primase-Polymerase (PRIMPOL)-mediated repriming of DNA synthesis downstream of lesions, leaving behind single-stranded DNA gaps. Moreover, we find that BRCA2 associates with the essential DNA replication factor MCM10 and this association suppresses PRIMPOL-mediated repriming and ssDNA gap formation, while having no impact on the stability of stalled replication forks. Our findings establish an important function for BRCA2, provide insights into replication fork control during the DNA damage response, and may have implications in tumor suppression and therapy response. Tumor suppressor BRCA2 is known to stabilize and restart stalled DNA replication forks. Here the authors show that BRCA2 is recruited to the replication fork through its interaction with MCM10 and inhibits Primase-Polymerase-mediated repriming, lesion bypass and single strand DNA gap formation after DNA damage.
Collapse
Affiliation(s)
- Zhihua Kang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Pan Fu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Department of Clinical Microbiology Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Allen L Alcivar
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Bristol-Myers Squibb Company, Bloomsbury, NJ, 08804, USA
| | - Haiqing Fu
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Christophe Redon
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Tzeh Keong Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Yamei Zuo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Caiyong Ye
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,School of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Ryan Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Advaitha Madireddy
- Department of Pediatric Hematology/Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Remi Buisson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Zhiyuan Shen
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
| |
Collapse
|
8
|
Chen YR, Li YT, Wang MQ, Zhu SL. Prognostic significance and function of MCM10 in human hepatocellular carcinoma. Future Oncol 2021; 17:4457-4470. [PMID: 34350781 DOI: 10.2217/fon-2021-0225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To investigate the role of MCM10, a conserved replication factor, in hepatocellular carcinoma (HCC). Methods: We used data from 364 HCC patients in the Cancer Genome Atlas database and conducted in vitro experiments to confirm the role of MCM10. Results: High MCM10 expression correlated with poor HCC patient outcome and was an independent prognosticator for HCC. Time-dependent receiver operating characteristic curve analysis found that the sequential trend of MCM10 for survival was not inferior to that of the tumor node metastasis stage. The MCM10 model had a higher C-index than the non-MCM10 model, indicating that incorporating MCM10 into a multivariate model improves the model's prognostic accuracy for HCC. Genetic alterations of MCM10 prominently correlated with an unfavorable HCC outcome. Conclusion: Our findings strongly suggest using the MCM10 gene as a prognostic indicator in HCC.
Collapse
Affiliation(s)
- Yi-Ru Chen
- Department of Gastroenterology & Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yi-Ting Li
- Department of General Practice, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mei-Qian Wang
- Department of Gastroenterology & Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Sen-Lin Zhu
- Department of Gastroenterology & Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| |
Collapse
|
9
|
Zhang P, Zhu C, Geng Y, Wang Y, Yang Y, Liu Q, Guo W, Chachar S, Riaz A, Yan S, Yang L, Yi K, Wu C, Gu X. Rice and Arabidopsis homologs of yeast CHROMOSOME TRANSMISSION FIDELITY PROTEIN 4 commonly interact with Polycomb complexes but exert divergent regulatory functions. Plant Cell 2021; 33:1417-1429. [PMID: 33647940 PMCID: PMC8254485 DOI: 10.1093/plcell/koab047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/29/2021] [Indexed: 05/02/2023]
Abstract
Both genetic and epigenetic information must be transferred from mother to daughter cells during cell division. The mechanisms through which information about chromatin states and epigenetic marks like histone 3 lysine 27 trimethylation (H3K27me3) are transferred have been characterized in animals; these processes are less well understood in plants. Here, based on characterization of a dwarf rice (Oryza sativa) mutant (dwarf-related wd40 protein 1, drw1) deficient for yeast CTF4 (CHROMOSOME TRANSMISSION FIDELITY PROTEIN 4), we discovered that CTF4 orthologs in plants use common cellular machinery yet accomplish divergent functional outcomes. Specifically, drw1 exhibited no flowering-related phenotypes (as in the putatively orthologous Arabidopsis thaliana eol1 mutant), but displayed cell cycle arrest and DNA damage responses. Mechanistically, we demonstrate that DRW1 sustains normal cell cycle progression by modulating the expression of cell cycle inhibitors KIP-RELATED PROTEIN 1 (KRP1) and KRP5, and show that these effects are mediated by DRW1 binding their promoters and increasing H3K27me3 levels. Thus, although CTF4 orthologs ENHANCER OF LHP1 1 (EOL1) in Arabidopsis and DRW1 in rice are both expressed uniquely in dividing cells, commonly interact with several Polycomb complex subunits, and promote H3K27me3 deposition, we now know that their regulatory functions diverged substantially during plant evolution. Moreover, our work experimentally illustrates specific targets of CTF4/EOL1/DRW1, their protein-proteininteraction partners, and their chromatin/epigenetic effects in plants.
Collapse
Affiliation(s)
- Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunmei Zhu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuke Geng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ying Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sadaruddin Chachar
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Adeel Riaz
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuangyong Yan
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Liwen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Keke Yi
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Author for correspondence: (K.Y.), (C.W.), (X.G.)
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Author for correspondence: (K.Y.), (C.W.), (X.G.)
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Author for correspondence: (K.Y.), (C.W.), (X.G.)
| |
Collapse
|
10
|
Lin YC, Prasanth SG. Replication initiation: Implications in genome integrity. DNA Repair (Amst) 2021; 103:103131. [PMID: 33992866 DOI: 10.1016/j.dnarep.2021.103131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 02/01/2023]
Abstract
In every cell cycle, billions of nucleotides need to be duplicated within hours, with extraordinary precision and accuracy. The molecular mechanism by which cells regulate the replication event is very complicated, and the entire process begins way before the onset of S phase. During the G1 phase of the cell cycle, cells prepare by assembling essential replication factors to establish the pre-replicative complex at origins, sites that dictate where replication would initiate during S phase. During S phase, the replication process is tightly coupled with the DNA repair system to ensure the fidelity of replication. Defects in replication and any error must be recognized by DNA damage response and checkpoint signaling pathways in order to halt the cell cycle before cells are allowed to divide. The coordination of these processes throughout the cell cycle is therefore critical to achieve genomic integrity and prevent diseases. In this review, we focus on the current understanding of how the replication initiation events are regulated to achieve genome stability.
Collapse
|
11
|
Mace EM, Paust S, Conte MI, Baxley RM, Schmit MM, Patil SL, Guilz NC, Mukherjee M, Pezzi AE, Chmielowiec J, Tatineni S, Chinn IK, Akdemir ZC, Jhangiani SN, Muzny DM, Stray-Pedersen A, Bradley RE, Moody M, Connor PP, Heaps AG, Steward C, Banerjee PP, Gibbs RA, Borowiak M, Lupski JR, Jolles S, Bielinsky AK, Orange JS. Human NK cell deficiency as a result of biallelic mutations in MCM10. J Clin Invest 2020; 130:5272-5286. [PMID: 32865517 PMCID: PMC7524476 DOI: 10.1172/jci134966] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
Human natural killer cell deficiency (NKD) arises from inborn errors of immunity that lead to impaired NK cell development, function, or both. Through the understanding of the biological perturbations in individuals with NKD, requirements for the generation of terminally mature functional innate effector cells can be elucidated. Here, we report a cause of NKD resulting from compound heterozygous mutations in minichromosomal maintenance complex member 10 (MCM10) that impaired NK cell maturation in a child with fatal susceptibility to CMV. MCM10 has not been previously associated with monogenic disease and plays a critical role in the activation and function of the eukaryotic DNA replisome. Through evaluation of patient primary fibroblasts, modeling patient mutations in fibroblast cell lines, and MCM10 knockdown in human NK cell lines, we have shown that loss of MCM10 function leads to impaired cell cycle progression and induction of DNA damage-response pathways. By modeling MCM10 deficiency in primary NK cell precursors, including patient-derived induced pluripotent stem cells, we further demonstrated that MCM10 is required for NK cell terminal maturation and acquisition of immunological system function. Together, these data define MCM10 as an NKD gene and provide biological insight into the requirement for the DNA replisome in human NK cell maturation and function.
Collapse
Affiliation(s)
- Emily M. Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Silke Paust
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, California, USA
| | - Matilde I. Conte
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Ryan M. Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Megan M. Schmit
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sagar L. Patil
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Nicole C. Guilz
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Malini Mukherjee
- Center for Human Immunobiology, Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics
| | - Ashley E. Pezzi
- Center for Human Immunobiology, Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics
| | - Jolanta Chmielowiec
- Center for Cell and Gene Therapy, and
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Swetha Tatineni
- Department of Pediatrics
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Ivan K. Chinn
- Department of Pediatrics
- Department of Molecular and Human Genetics and
| | | | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Donna M. Muzny
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo, Norway
| | - Rachel E. Bradley
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Mo Moody
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Philip P. Connor
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Adrian G. Heaps
- Department of Virology and Immunology, North Cumbria University Hospitals, Carlisle, United Kingdom
| | - Colin Steward
- Department of Paediatric Haematology, Oncology and Bone Marrow Transplantation, Bristol Royal Hospital for Children, Bristol, United Kingdom
| | - Pinaki P. Banerjee
- Center for Human Immunobiology, Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Malgorzata Borowiak
- Center for Cell and Gene Therapy, and
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas, USA
- Adam Mickiewicz University, Poznan, Poland
- McNair Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - James R. Lupski
- Department of Pediatrics
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | - Stephen Jolles
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Anja K. Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jordan S. Orange
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| |
Collapse
|
12
|
Singh B, Bisht KK, Upadhyay U, Kushwaha AC, Nanda JS, Srivastava S, Saini JK, Klar AJS, Singh J. Role of Cdc23/Mcm10 in generating the ribonucleotide imprint at the mat1 locus in fission yeast. Nucleic Acids Res 2019; 47:3422-3433. [PMID: 30759238 PMCID: PMC6468313 DOI: 10.1093/nar/gkz092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 01/31/2019] [Accepted: 02/10/2019] [Indexed: 01/28/2023] Open
Abstract
The developmental asymmetry of fission yeast daughter cells derives from inheriting ‘older Watson’ versus ‘older Crick’ DNA strand from the parental cell, strands that are complementary but not identical with each other. A novel DNA strand-specific ‘imprint’, installed during DNA replication at the mating-type locus (mat1), imparts competence for cell type inter-conversion to one of the two chromosome replicas. The catalytic subunit of DNA Polymerase α (Polα) has been implicated in the imprinting process. Based on its known biochemical function, Polα might install the mat1 imprint during lagging strand synthesis. The nature of the imprint is not clear: it is either a nick or a ribonucleotide insertion. Our investigations do not support a direct role of Polα in nicking through putative endonuclease domains but confirm its indirect role in installing an alkali-labile moiety as the imprint. While ruling out the role of the primase subunit of Polα holoenzyme, we find that mutations in the Polα-recruitment and putative primase homology domain in Mcm10/Cdc23 abrogate the ribonucleotide imprint formation. These results, while confirming the ribonucleotide nature of the imprint suggest the possibility of a direct role of Mcm10/Cdc23 in installing it in cooperation with Polα and Swi1.
Collapse
Affiliation(s)
- Balveer Singh
- Institute of Genetics and Development of Rennes, Faculte de Medecine, Campus santé de Villejean, 2 avenue du Professor Leon Bernard, CS 34317, 35043 Rennes Cedex, France
| | - Kamlesh K Bisht
- Translational Discovery Biology, (Immuno-Oncology), Bristol-Myers Squibb Route 206 & Province Line Road, Princeton, NJ 08543, USA
| | - Udita Upadhyay
- Department of Anesthesiology, RMSB 8022, 1600 NW, 10th Ave., Miami, FL 33136, USA
| | | | - Jagpreet Singh Nanda
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Suchita Srivastava
- QC Division, Central Research Institute, Kasauli, Himachal Pradesh 173204, India
| | - Jai Kumar Saini
- Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Amar J S Klar
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Building 539, Room 154, Frederick, MD 21702-1201, USA
| | - Jagmohan Singh
- Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| |
Collapse
|
13
|
Paulson CN, John K, Baxley RM, Kurniawan F, Orellana K, Francis R, Sobeck A, Eichman BF, Chazin WJ, Aihara H, Georg GI, Hawkinson JE, Bielinsky AK. The anti-parasitic agent suramin and several of its analogues are inhibitors of the DNA binding protein Mcm10. Open Biol 2019; 9:190117. [PMID: 31409229 PMCID: PMC6731595 DOI: 10.1098/rsob.190117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Minichromosome maintenance protein 10 (Mcm10) is essential for DNA unwinding by the replisome during S phase. It is emerging as a promising anti-cancer target as MCM10 expression correlates with tumour progression and poor clinical outcomes. Here we used a competition-based fluorescence polarization (FP) high-throughput screening (HTS) strategy to identify compounds that inhibit Mcm10 from binding to DNA. Of the five active compounds identified, only the anti-parasitic agent suramin exhibited a dose-dependent decrease in replication products in an in vitro replication assay. Structure–activity relationship evaluation identified several suramin analogues that inhibited ssDNA binding by the human Mcm10 internal domain and full-length Xenopus Mcm10, including analogues that are selective for Mcm10 over human RPA. Binding of suramin analogues to Mcm10 was confirmed by surface plasmon resonance (SPR). SPR and FP affinity determinations were highly correlated, with a similar rank between affinity and potency for killing colon cancer cells. Suramin analogue NF157 had the highest human Mcm10 binding affinity (FP Ki 170 nM, SPR KD 460 nM) and cell activity (IC50 38 µM). Suramin and its analogues are the first identified inhibitors of Mcm10 and probably block DNA binding by mimicking the DNA sugar phosphate backbone due to their extended, polysulfated anionic structures.
Collapse
Affiliation(s)
- Carolyn N Paulson
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery & Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, USA
| | - Kristen John
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery & Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, USA
| | - Ryan M Baxley
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Fredy Kurniawan
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kayo Orellana
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rawle Francis
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery & Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, USA
| | - Alexandra Sobeck
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brandt F Eichman
- Departments of Biological Sciences and Biochemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gunda I Georg
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery & Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, USA
| | - Jon E Hawkinson
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery & Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
14
|
Mueller SH, Spenkelink LM, van Oijen AM. When proteins play tag: the dynamic nature of the replisome. Biophys Rev 2019; 11:641-651. [PMID: 31273608 PMCID: PMC6682189 DOI: 10.1007/s12551-019-00569-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/24/2019] [Indexed: 02/06/2023] Open
Abstract
DNA replication, or the copying of DNA, is a fundamental process to all life. The system of proteins that carries out replication, the replisome, encounters many roadblocks on its way. An inability of the replisome to properly overcome these roadblocks will negatively affect genomic integrity which in turn can lead to disease. Over the past decades, efforts by many researchers using a broad array of approaches have revealed roles for many different proteins during the initial response of the replisome upon encountering roadblocks. Here, we revisit what is known about DNA replication and the effect of roadblocks during DNA replication across different organisms. We also address how advances in single-molecule techniques have changed our view of the replisome from a highly stable machine with behavior dictated by deterministic principles to a dynamic system that is controlled by stochastic processes. We propose that these dynamics will play crucial roles in roadblock bypass. Further single-molecule studies of this bypass will, therefore, be essential to facilitate the in-depth investigation of multi-protein complexes that is necessary to understand complicated collisions on the DNA.
Collapse
Affiliation(s)
- Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia.
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales, 2522, Australia.
| |
Collapse
|
15
|
Abstract
Several decades of research have identified Mcm10 hanging around the replisome making several critical contacts with a number of proteins but with no real disclosed function. Recently, the O'Donnell laboratory has been better able to map the interactions of Mcm10 with a larger Cdc45/GINS/MCM (CMG) unwinding complex placing it at the front of the replication fork. They have shown biochemically that Mcm10 has the impressive ability to strip off single-strand binding protein (RPA) and reanneal complementary DNA strands. This has major implications in controlling DNA unwinding speed as well as responding to various situations where fork reversal is needed. This work opens up a number of additional facets discussed here revolving around accessing the DNA junction for different molecular purposes within a crowded replisome. Abbreviations: alt-NHEJ: Alternative Nonhomologous End-Joining; CC: Coli-Coil motif; CMG: Cdc45/GINS/MCM2-7; CMGM: Cdc45/GINS/Mcm2-7/Mcm10; CPT: Camptothecin; CSB: Cockayne Syndrome Group B protein; CTD: C-Terminal Domain; DSB: Double-Strand Break; DSBR: Double-Strand Break Repair; dsDNA: Double-Stranded DNA; GINS: go-ichi-ni-san, Sld5-Psf1-Psf2-Psf3; HJ Dis: Holliday Junction dissolution; HJ Res: Holliday Junction resolution; HR: Homologous Recombination; ICL: Interstrand Cross-Link; ID: Internal Domain; MCM: Minichromosomal Maintenance; ND: Not Determined; NTD: N-Terminal Domain; PCNA: Proliferating Cell Nuclear Antigen; RPA: Replication Protein A; SA: Strand Annealing; SE: Strand Exchange; SEW: Steric Exclusion and Wrapping; ssDNA: Single-Stranded DNA; TCR: Transcription-Coupled Repair; TOP1: Topoisomerase.
Collapse
Affiliation(s)
- Robert M Brosh
- a Laboratory of Molecular Gerontology , National Institute on Aging, National Institutes of Health , Baltimore , MD USA
| | - Michael A Trakselis
- b Department of Chemistry and Biochemistry , Baylor University , Waco , TX , USA
| |
Collapse
|
16
|
Allahyar A, Ubels J, de Ridder J. A data-driven interactome of synergistic genes improves network-based cancer outcome prediction. PLoS Comput Biol 2019; 15:e1006657. [PMID: 30726216 PMCID: PMC6380593 DOI: 10.1371/journal.pcbi.1006657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 02/19/2019] [Accepted: 11/20/2018] [Indexed: 12/13/2022] Open
Abstract
Robustly predicting outcome for cancer patients from gene expression is an important challenge on the road to better personalized treatment. Network-based outcome predictors (NOPs), which considers the cellular wiring diagram in the classification, hold much promise to improve performance, stability and interpretability of identified marker genes. Problematically, reports on the efficacy of NOPs are conflicting and for instance suggest that utilizing random networks performs on par to networks that describe biologically relevant interactions. In this paper we turn the prediction problem around: instead of using a given biological network in the NOP, we aim to identify the network of genes that truly improves outcome prediction. To this end, we propose SyNet, a gene network constructed ab initio from synergistic gene pairs derived from survival-labelled gene expression data. To obtain SyNet, we evaluate synergy for all 69 million pairwise combinations of genes resulting in a network that is specific to the dataset and phenotype under study and can be used to in a NOP model. We evaluated SyNet and 11 other networks on a compendium dataset of >4000 survival-labelled breast cancer samples. For this purpose, we used cross-study validation which more closely emulates real world application of these outcome predictors. We find that SyNet is the only network that truly improves performance, stability and interpretability in several existing NOPs. We show that SyNet overlaps significantly with existing gene networks, and can be confidently predicted (~85% AUC) from graph-topological descriptions of these networks, in particular the breast tissue-specific network. Due to its data-driven nature, SyNet is not biased to well-studied genes and thus facilitates post-hoc interpretation. We find that SyNet is highly enriched for known breast cancer genes and genes related to e.g. histological grade and tamoxifen resistance, suggestive of a role in determining breast cancer outcome.
Collapse
Affiliation(s)
- Amin Allahyar
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Joske Ubels
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Skyline DX, Rotterdam
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam
| | - Jeroen de Ridder
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
17
|
Tsao WC, Eckert KA. Detours to Replication: Functions of Specialized DNA Polymerases during Oncogene-induced Replication Stress. Int J Mol Sci 2018; 19:ijms19103255. [PMID: 30347795 PMCID: PMC6214091 DOI: 10.3390/ijms19103255] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 01/10/2023] Open
Abstract
Incomplete and low-fidelity genome duplication contribute to genomic instability and cancer development. Difficult-to-Replicate Sequences, or DiToRS, are natural impediments in the genome that require specialized DNA polymerases and repair pathways to complete and maintain faithful DNA synthesis. DiToRS include non B-DNA secondary structures formed by repetitive sequences, for example within chromosomal fragile sites and telomeres, which inhibit DNA replication under endogenous stress conditions. Oncogene activation alters DNA replication dynamics and creates oncogenic replication stress, resulting in persistent activation of the DNA damage and replication stress responses, cell cycle arrest, and cell death. The response to oncogenic replication stress is highly complex and must be tightly regulated to prevent mutations and tumorigenesis. In this review, we summarize types of known DiToRS and the experimental evidence supporting replication inhibition, with a focus on the specialized DNA polymerases utilized to cope with these obstacles. In addition, we discuss different causes of oncogenic replication stress and its impact on DiToRS stability. We highlight recent findings regarding the regulation of DNA polymerases during oncogenic replication stress and the implications for cancer development.
Collapse
Affiliation(s)
- Wei-Chung Tsao
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
| | - Kristin A Eckert
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
| |
Collapse
|
18
|
Abstract
Cohesion is established in S-phase through the action of key replisome factors as replication forks engage cohesin molecules. By holding sister chromatids together, cohesion critically assists both an equal segregation of the duplicated genetic material and an efficient repair of DNA breaks. Nonetheless, the molecular events leading the entrapment of nascent chromatids by cohesin during replication are only beginning to be understood. The authors describe here the essential structural features of the cohesin complex in connection to its ability to associate DNA molecules and review the current knowledge on the architectural-functional organization of the eukaryotic replisome, significantly advanced by recent biochemical and structural studies. In light of this novel insight, the authors discuss the mechanisms proposed to assist interfacing of replisomes with chromatin-bound cohesin complexes and elaborate on models for nascent chromatids entrapment by cohesin in the environment of the replication fork.
Collapse
Affiliation(s)
- Sara Villa-Hernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 928040 Madrid, Spain
| | - Rodrigo Bermejo
- Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 928040 Madrid, Spain
| |
Collapse
|
19
|
Mahadevappa R, Neves H, Yuen SM, Jameel M, Bai Y, Yuen HF, Zhang SD, Zhu Y, Lin Y, Kwok HF. DNA Replication Licensing Protein MCM10 Promotes Tumor Progression and Is a Novel Prognostic Biomarker and Potential Therapeutic Target in Breast Cancer. Cancers (Basel) 2018; 10:cancers10090282. [PMID: 30135378 PMCID: PMC6162382 DOI: 10.3390/cancers10090282] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/17/2018] [Accepted: 08/20/2018] [Indexed: 12/20/2022] Open
Abstract
Breast cancer is one of the most common malignancies in women worldwide. In breast cancer, the cell proliferation rate is known to influence the cancer malignancy. Recent studies have shown that DNA replication initiation/licensing factors are involved in cancer cell proliferation as well as cancer cell migration and invasion. Licensing factors have also been reported as important prognostic markers in lung, prostrate, and bladder cancers. Here, we studied the role of MCM10, a novel licensing factor, in breast cancer progression. From the public database, NCBI, we investigated six independent breast cancer patient cohorts, totaling 1283 patients. We observed a significant association between high MCM10 mRNA expression with tumor grading and patients’ survival time. Most importantly, using breast cancer cohorts with available treatment information, we also demonstrated that a high level of MCM10 is associated with a better response to conventional treatment. Similarly, in in vitro studies, the expression level of MCM10 in breast cancer cell lines is significantly higher compared to paired normal breast epithelium cells. Knockdown of MCM10 expression in the cancer cell line showed significantly decreased tumorigenic properties such as cell proliferation, migration and anchorage independence. The MCF7 breast cancer cell line, after MCM10 expression knockdown, showed significantly decreased tumorigenic properties such as cell proliferation, migration, and anchorage independent growth. Mechanistically, MCM10 expression is observed to be regulated by an Estrogen Receptor (ER) signaling pathway, where its expression is suppressed by the inhibition of the ER or serum withdrawal. Our results suggest that MCM10 plays an important role in breast cancer progression and is a potential prognostic/predictive biomarker and therapeutic target for breast cancer patients.
Collapse
Affiliation(s)
- Ravikiran Mahadevappa
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau, China.
| | - Henrique Neves
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau, China.
| | - Shun Ming Yuen
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau, China.
| | - Muhammad Jameel
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau, China.
| | - Yuchen Bai
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau, China.
| | - Hiu-Fung Yuen
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Londonderry BT47 6SB, UK.
| | - Youzhi Zhu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.
| | - Yao Lin
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China.
| | - Hang Fai Kwok
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau, China.
| |
Collapse
|
20
|
Abstract
Proper regulation of DNA replication ensures the faithful transmission of genetic material essential for optimal cellular and organismal physiology. Central to this regulation is the activity of a set of enzymes that induce or reverse posttranslational modifications of various proteins critical for the initiation, progression, and termination of DNA replication. This is particularly important when DNA replication proceeds in cancer cells with elevated rates of genomic instability and increased proliferative capacities. Here, we describe how DNA replication in mammalian cells is regulated via the activity of the ubiquitin-proteasome system as well as the consequence of derailed ubiquitylation signaling involved in this important cellular activity.
Collapse
|
21
|
Stewart PA, Khamis ZI, Zhau HE, Duan P, Li Q, Chung LWK, Sang QXA. Upregulation of minichromosome maintenance complex component 3 during epithelial-to-mesenchymal transition in human prostate cancer. Oncotarget 2018; 8:39209-39217. [PMID: 28424404 PMCID: PMC5503607 DOI: 10.18632/oncotarget.16835] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 03/08/2017] [Indexed: 01/13/2023] Open
Abstract
Metastasis is often associated with epithelial-to-mesenchymal transition (EMT). To understand the molecular mechanisms of this process, we conducted proteomic analysis of androgen-repressed cancer of the prostate (ARCaP), an experimental model of metastatic human prostate cancer. The protein signatures of epithelial (ARCaPE) and mesenchymal (ARCaPM) cells were consistent with their phenotypes. Importantly, the expression of mini-chromosome maintenance 3 (MCM3) protein, a crucial subunit of DNA helicase, was significantly higher in ARCaPM cells than that of ARCaPE cells. This increased MCM3 protein expression level was verified using Western blot analysis of the ARCaP cell lineages. Furthermore, immunohistochemical analysis of MCM3 protein levels in human prostate tissue specimens showed elevated expression in bone metastasis and advanced human prostate cancer tissue samples. Subcutaneous injection experiments using ARCaPE and ARCaPM cells in a mouse model also revealed increased MCM3 protein levels in mesenchymal-derived tumors. This study identifies MCM3 as an upregulated molecule in mesenchymal phenotype of human prostate cancer cells and advanced human prostate cancer specimens, suggesting MCM3 may be a new potential drug target for prostate cancer treatment.
Collapse
Affiliation(s)
- Paul A Stewart
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL, United States of America
| | - Zahraa I Khamis
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL, United States of America.,Laboratory of Cancer Biology and Molecular Immunology, Department of Biochemistry, Faculty of Sciences, Lebanese University, Beirut, Lebanon
| | - Haiyen E Zhau
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Peng Duan
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Quanlin Li
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Leland W K Chung
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Qing-Xiang Amy Sang
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL, United States of America.,Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States of America
| |
Collapse
|
22
|
Kang S, Kang MS, Ryu E, Myung K. Eukaryotic DNA replication: Orchestrated action of multi-subunit protein complexes. Mutat Res 2018; 809:58-69. [PMID: 28501329 DOI: 10.1016/j.mrfmmm.2017.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/13/2017] [Accepted: 04/30/2017] [Indexed: 06/07/2023]
Abstract
Genome duplication is an essential process to preserve genetic information between generations. The eukaryotic cell cycle is composed of functionally distinct phases: G1, S, G2, and M. One of the key replicative proteins that participate at every stage of DNA replication is the Mcm2-7 complex, a replicative helicase. In the G1 phase, inactive Mcm2-7 complexes are loaded on the replication origins by replication-initiator proteins, ORC and Cdc6. Two kinases, S-CDK and DDK, convert the inactive origin-loaded Mcm2-7 complex to an active helicase, the CMG complex in the S phase. The activated CMG complex begins DNA unwinding and recruits enzymes essential for DNA synthesis to assemble a replisome at the replication fork. After completion of DNA synthesis, the inactive CMG complex on the replicated DNA is removed from chromatin to terminate DNA replication. In this review, we will discuss the structure, function, and regulation of the molecular machines involved in each step of DNA replication.
Collapse
Affiliation(s)
- Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea.
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; School of Life Sciences, Ulsan National Institute for Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; School of Life Sciences, Ulsan National Institute for Science and Technology, Ulsan 44919, Republic of Korea
| |
Collapse
|
23
|
Abstract
In this Review, Riera et al. review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2–7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability.
Collapse
Affiliation(s)
- Alberto Riera
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Marta Barbon
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Medical Research Council (MRC) London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
| | - Yasunori Noguchi
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - L Maximilian Reuter
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Sarah Schneider
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Christian Speck
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Medical Research Council (MRC) London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
| |
Collapse
|
24
|
Zhang W, Yeung CHL, Wu L, Yuen KWY. E3 ubiquitin ligase Bre1 couples sister chromatid cohesion establishment to DNA replication in Saccharomyces cerevisiae. eLife 2017; 6:28231. [PMID: 29058668 PMCID: PMC5699866 DOI: 10.7554/elife.28231] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 10/22/2017] [Indexed: 12/12/2022] Open
Abstract
Bre1, a conserved E3 ubiquitin ligase in Saccharomyces cerevisiae, together with its interacting partner Lge1, are responsible for histone H2B monoubiquitination, which regulates transcription, DNA replication, and DNA damage response and repair, ensuring the structural integrity of the genome. Deletion of BRE1 or LGE1 also results in whole chromosome instability. We discovered a novel role for Bre1, Lge1 and H2Bub1 in chromosome segregation and sister chromatid cohesion. Bre1’s function in G1 and S phases contributes to cohesion establishment, but it is not required for cohesion maintenance in G2 phase. Bre1 is dispensable for the loading of cohesin complex to chromatin in G1, but regulates the localization of replication factor Mcm10 and cohesion establishment factors Ctf4, Ctf18 and Eco1 to early replication origins in G1 and S phases, and promotes cohesin subunit Smc3 acetylation for cohesion stabilization. H2Bub1 epigenetically marks the origins, potentially signaling the coupling of DNA replication and cohesion establishment. Most of the DNA in a cell is stored in structures called chromosomes. During every cell cycle, each cell needs to replicate its chromosomes, hold the two chromosome copies (also known as “sister chromatids”) together before cell division, and distribute them equally to the two new cells. Each step must be executed accurately otherwise the new cells will have extra or missing chromosomes – a condition that is seen in many cancer cells and that can cause embryos to die. Since these processes are so essential to life, they are highly similar in a range of species, from single-celled organisms such as yeast to multicellular organisms like humans. However, it was not clear when and how sister chromatids first join together, or how this process is linked to DNA replication. The DNA in the sister chromatids is wrapped around proteins called histones to form a structure known as chromatin. An enzyme called Bre1 plays roles in gene transcription and DNA replication and repair by adding ubiquitin molecules to a histone called H2B. Now, by using genetic, molecular and cell biological approaches to study baker and brewer yeast cells, Zhang et al. show that the activity of Bre1 helps to hold sister chromatids together. Specifically, Bre1 recruits proteins to the chromatin before and during DNA replication, which help to initiate replication and to establish cohesion between the sister chromatids. The ubiquitin molecule attached to H2B by Bre1 is also essential for establishing cohesion, acting as a mark that helps to link the two processes. In the future it will be worthwhile to investigate whether genetic mutations that prevent sister chromatids adhering to each other is a major cause of the chromosome abnormalities seen in cancer cells. This knowledge may be useful for diagnosing cancers. Drugs that prevent the activity of Bre1 and other proteins involved in holding together sister chromatids could also be developed as potential cancer treatments that kill cancer cells by causing instability in their number of chromosomes.
Collapse
Affiliation(s)
- Wei Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | | | - Liwen Wu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
25
|
Zhang W, Yeung CHL, Wu L, Yuen KWY. E3 ubiquitin ligase Bre1 couples sister chromatid cohesion establishment to DNA replication in Saccharomyces cerevisiae. eLife 2017; 6:28231. [PMID: 29058668 DOI: 10.7554/elife.28231.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 10/22/2017] [Indexed: 05/25/2023] Open
Abstract
Bre1, a conserved E3 ubiquitin ligase in Saccharomyces cerevisiae, together with its interacting partner Lge1, are responsible for histone H2B monoubiquitination, which regulates transcription, DNA replication, and DNA damage response and repair, ensuring the structural integrity of the genome. Deletion of BRE1 or LGE1 also results in whole chromosome instability. We discovered a novel role for Bre1, Lge1 and H2Bub1 in chromosome segregation and sister chromatid cohesion. Bre1's function in G1 and S phases contributes to cohesion establishment, but it is not required for cohesion maintenance in G2 phase. Bre1 is dispensable for the loading of cohesin complex to chromatin in G1, but regulates the localization of replication factor Mcm10 and cohesion establishment factors Ctf4, Ctf18 and Eco1 to early replication origins in G1 and S phases, and promotes cohesin subunit Smc3 acetylation for cohesion stabilization. H2Bub1 epigenetically marks the origins, potentially signaling the coupling of DNA replication and cohesion establishment.
Collapse
Affiliation(s)
- Wei Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | | | - Liwen Wu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
26
|
Perez-Arnaiz P, Bruck I, Colbert MK, Kaplan DL. An intact Mcm10 coiled-coil interaction surface is important for origin melting, helicase assembly and the recruitment of Pol-α to Mcm2-7. Nucleic Acids Res 2017; 45:7261-7275. [PMID: 28510759 PMCID: PMC5499591 DOI: 10.1093/nar/gkx438] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/03/2017] [Indexed: 11/16/2022] Open
Abstract
Mcm10 is an essential eukaryotic factor required for DNA replication. The replication fork helicase is composed of Cdc45, Mcm2–7 and GINS (CMG). DDK is an S-phase-specific kinase required for replication initiation, and the DNA primase-polymerase in eukaryotes is pol α. Mcm10 forms oligomers in vitro, mediated by the coiled-coil domain at the N-terminal region of the protein. We characterized an Mcm10 mutant at the N-terminal Domain (NTD), Mcm10-4A, defective for self-interaction. We found that the Mcm10-4A mutant was defective for stimulating DDK phosphorylation of Mcm2, binding to eighty-nucleotide ssDNA, and recruiting pol α to Mcm2–7 in vitro. Expression of wild-type levels of mcm10-4A resulted in severe growth and DNA replication defects in budding yeast cells, with diminished DDK phosphorylation of Mcm2. We then expressed the mcm10-4A in mcm5-bob1 mutant cells to bypass the defects mediated by diminished stimulation of DDK phosphorylation of Mcm2. Expression of wild-type levels of mcm10-4A in mcm5-bob1 mutant cells resulted in severe growth and DNA replication defects, along with diminished RPA signal at replication origins. We also detected diminished GINS and pol-α recruitment to the Mcm2–7 complex. We conclude that an intact Mcm10 coiled-coil interaction surface is important for origin melting, helicase assembly, and the recruitment of pol α to Mcm2–7.
Collapse
Affiliation(s)
- Patricia Perez-Arnaiz
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, FL 32306, USA
| | - Irina Bruck
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, FL 32306, USA
| | - Max K Colbert
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, FL 32306, USA
| | - Daniel L Kaplan
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, FL 32306, USA
| |
Collapse
|
27
|
Vo N, Anh Suong DN, Yoshino N, Yoshida H, Cotterill S, Yamaguchi M. Novel roles of HP1a and Mcm10 in DNA replication, genome maintenance and photoreceptor cell differentiation. Nucleic Acids Res 2017; 45:1233-1254. [PMID: 28180289 PMCID: PMC5388399 DOI: 10.1093/nar/gkw1174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 11/04/2016] [Accepted: 11/13/2016] [Indexed: 01/21/2023] Open
Abstract
Both Mcm10 and HP1a are known to be required for DNA replication. However, underlying mechanism is not clarified yet especially for HP1. Knockdown of both HP1a and Mcm10 genes inhibited the progression of S phase in Drosophila eye imaginal discs. Proximity Ligation Assay (PLA) demonstrated that HP1a is in close proximity to DNA replication proteins including Mcm10, RFC140 and DNA polymerase ε 255 kDa subunit in S-phase. This was further confirmed by co-immunoprecipitation assay. The PLA signals between Mcm10 and HP1a are specifically observed in the mitotic cycling cells, but not in the endocycling cells. Interestingly, many cells in the posterior regions of eye imaginal discs carrying a double knockdown of Mcm10 and HP1a induced ectopic DNA synthesis and DNA damage without much of ectopic apoptosis. Therefore, the G1-S checkpoint may be affected by knockdown of both proteins. This event was also the case with other HP family proteins such as HP4 and HP6. In addition, both Mcm10 and HP1a are required for differentiation of photoreceptor cells R1, R6 and R7. Further analyses on several developmental genes involved in the photoreceptor cell differentiation suggest that a role of both proteins is mediated by regulation of the lozenge gene.
Collapse
Affiliation(s)
- Nicole Vo
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan.,The Center for Advanced Insect Research, Kyoto Institute of Technology, Kyoto, Japan
| | - Dang Ngoc Anh Suong
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan.,The Center for Advanced Insect Research, Kyoto Institute of Technology, Kyoto, Japan
| | - Natsuki Yoshino
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan.,The Center for Advanced Insect Research, Kyoto Institute of Technology, Kyoto, Japan
| | - Hideki Yoshida
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan.,The Center for Advanced Insect Research, Kyoto Institute of Technology, Kyoto, Japan
| | - Sue Cotterill
- Department of Basic Medical Sciences, St Georges, University of London, London, UK
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan.,The Center for Advanced Insect Research, Kyoto Institute of Technology, Kyoto, Japan
| |
Collapse
|
28
|
Langston LD, Mayle R, Schauer GD, Yurieva O, Zhang D, Yao NY, Georgescu RE, O'Donnell ME. Mcm10 promotes rapid isomerization of CMG-DNA for replisome bypass of lagging strand DNA blocks. eLife 2017; 6:e29118. [PMID: 28869037 PMCID: PMC5599239 DOI: 10.7554/elife.29118] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/03/2017] [Indexed: 12/18/2022] Open
Abstract
Replicative helicases in all cell types are hexameric rings that unwind DNA by steric exclusion in which the helicase encircles the tracking strand only and excludes the other strand from the ring. This mode of translocation allows helicases to bypass blocks on the strand that is excluded from the central channel. Unlike other replicative helicases, eukaryotic CMG helicase partially encircles duplex DNA at a forked junction and is stopped by a block on the non-tracking (lagging) strand. This report demonstrates that Mcm10, an essential replication protein unique to eukaryotes, binds CMG and greatly stimulates its helicase activity in vitro. Most significantly, Mcm10 enables CMG and the replisome to bypass blocks on the non-tracking DNA strand. We demonstrate that bypass occurs without displacement of the blocks and therefore Mcm10 must isomerize the CMG-DNA complex to achieve the bypass function.
Collapse
Affiliation(s)
- Lance D Langston
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | - Ryan Mayle
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | | | - Olga Yurieva
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | | | - Nina Y Yao
- The Rockefeller UniversityNew YorkUnited States
| | - Roxana E Georgescu
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | - Mike E O'Donnell
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| |
Collapse
|
29
|
Lõoke M, Maloney MF, Bell SP. Mcm10 regulates DNA replication elongation by stimulating the CMG replicative helicase. Genes Dev 2017; 31:291-305. [PMID: 28270517 PMCID: PMC5358725 DOI: 10.1101/gad.291336.116] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/31/2017] [Indexed: 11/25/2022]
Abstract
Activation of the Mcm2-7 replicative DNA helicase is the committed step in eukaryotic DNA replication initiation. Although Mcm2-7 activation requires binding of the helicase-activating proteins Cdc45 and GINS (forming the CMG complex), an additional protein, Mcm10, drives initial origin DNA unwinding by an unknown mechanism. We show that Mcm10 binds a conserved motif located between the oligonucleotide/oligosaccharide fold (OB-fold) and A subdomain of Mcm2. Although buried in the interface between these domains in Mcm2-7 structures, mutations predicted to separate the domains and expose this motif restore growth to conditional-lethal MCM10 mutant cells. We found that, in addition to stimulating initial DNA unwinding, Mcm10 stabilizes Cdc45 and GINS association with Mcm2-7 and stimulates replication elongation in vivo and in vitro. Furthermore, we identified a lethal allele of MCM10 that stimulates initial DNA unwinding but is defective in replication elongation and CMG binding. Our findings expand the roles of Mcm10 during DNA replication and suggest a new model for Mcm10 function as an activator of the CMG complex throughout DNA replication.
Collapse
Affiliation(s)
- Marko Lõoke
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA
| | - Michael F Maloney
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA.,Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA
| | - Stephen P Bell
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA
| |
Collapse
|
30
|
Neves H, Kwok HF. In sickness and in health: The many roles of the minichromosome maintenance proteins. Biochim Biophys Acta Rev Cancer 2017; 1868:295-308. [DOI: 10.1016/j.bbcan.2017.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/29/2017] [Accepted: 06/01/2017] [Indexed: 01/09/2023]
|
31
|
Izumi M, Mizuno T, Yanagi KI, Sugimura K, Okumura K, Imamoto N, Abe T, Hanaoka F. The Mcm2-7-interacting domain of human mini-chromosome maintenance 10 (Mcm10) protein is important for stable chromatin association and origin firing. J Biol Chem 2017. [PMID: 28646110 DOI: 10.1074/jbc.m117.779371] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The protein mini-chromosome maintenance 10 (Mcm10) was originally identified as an essential yeast protein in the maintenance of mini-chromosome plasmids. Subsequently, Mcm10 has been shown to be required for both initiation and elongation during chromosomal DNA replication. However, it is not fully understood how the multiple functions of Mcm10 are coordinated or how Mcm10 interacts with other factors at replication forks. Here, we identified and characterized the Mcm2-7-interacting domain in human Mcm10. The interaction with Mcm2-7 required the Mcm10 domain that contained amino acids 530-655, which overlapped with the domain required for the stable retention of Mcm10 on chromatin. Expression of truncated Mcm10 in HeLa cells depleted of endogenous Mcm10 via siRNA revealed that the Mcm10 conserved domain (amino acids 200-482) is essential for DNA replication, whereas both the conserved and the Mcm2-7-binding domains were required for its full activity. Mcm10 depletion reduced the initiation frequency of DNA replication and interfered with chromatin loading of replication protein A, DNA polymerase (Pol) α, and proliferating cell nuclear antigen, whereas the chromatin loading of Cdc45 and Pol ϵ was unaffected. These results suggest that human Mcm10 is bound to chromatin through the interaction with Mcm2-7 and is primarily involved in the initiation of DNA replication after loading of Cdc45 and Pol ϵ.
Collapse
Affiliation(s)
- Masako Izumi
- Accelerator Applications Research Group, Nishina Center for Accelerator-Based Science, Wako, Saitama 351-0198, Japan.
| | - Takeshi Mizuno
- Cellular Dynamics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | | | - Kazuto Sugimura
- Department of Life Science, Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | - Katsuzumi Okumura
- Department of Life Science, Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Tomoko Abe
- Accelerator Applications Research Group, Nishina Center for Accelerator-Based Science, Wako, Saitama 351-0198, Japan
| | - Fumio Hanaoka
- Department of Life Science, Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan; Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki 305-8577, Japan
| |
Collapse
|
32
|
Evrony GD, Cordero DR, Shen J, Partlow JN, Yu TW, Rodin RE, Hill RS, Coulter ME, Lam ATN, Jayaraman D, Gerrelli D, Diaz DG, Santos C, Morrison V, Galli A, Tschulena U, Wiemann S, Martel MJ, Spooner B, Ryu SC, Elhosary PC, Richardson JM, Tierney D, Robinson CA, Chibbar R, Diudea D, Folkerth R, Wiebe S, Barkovich AJ, Mochida GH, Irvine J, Lemire EG, Blakley P, Walsh CA. Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome. Genome Res 2017. [PMID: 28630177 PMCID: PMC5538549 DOI: 10.1101/gr.219899.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
While next-generation sequencing has accelerated the discovery of human disease genes, progress has been largely limited to the “low hanging fruit” of mutations with obvious exonic coding or canonical splice site impact. In contrast, the lack of high-throughput, unbiased approaches for functional assessment of most noncoding variants has bottlenecked gene discovery. We report the integration of transcriptome sequencing (RNA-seq), which surveys all mRNAs to reveal functional impacts of variants at the transcription level, into the gene discovery framework for a unique human disease, microcephaly-micromelia syndrome (MMS). MMS is an autosomal recessive condition described thus far in only a single First Nations population and causes intrauterine growth restriction, severe microcephaly, craniofacial anomalies, skeletal dysplasia, and neonatal lethality. Linkage analysis of affected families, including a very large pedigree, identified a single locus on Chromosome 21 linked to the disease (LOD > 9). Comprehensive genome sequencing did not reveal any pathogenic coding or canonical splicing mutations within the linkage region but identified several nonconserved noncoding variants. RNA-seq analysis detected aberrant splicing in DONSON due to one of these noncoding variants, showing a causative role for DONSON disruption in MMS. We show that DONSON is expressed in progenitor cells of embryonic human brain and other proliferating tissues, is co-expressed with components of the DNA replication machinery, and that Donson is essential for early embryonic development in mice as well, suggesting an essential conserved role for DONSON in the cell cycle. Our results demonstrate the utility of integrating transcriptomics into the study of human genetic disease when DNA sequencing alone is not sufficient to reveal the underlying pathogenic mutation.
Collapse
Affiliation(s)
- Gilad D Evrony
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Dwight R Cordero
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.,Laboratory of Molecular Medicine, Partners Personalized Medicine, Cambridge, Massachusetts 02139, USA
| | - Jennifer N Partlow
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Timothy W Yu
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Michael E Coulter
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Anh-Thu N Lam
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Divya Jayaraman
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Dianne Gerrelli
- Institute of Child Health, University College London, London WC1N 1EH, United Kingdom
| | - Diana G Diaz
- Institute of Child Health, University College London, London WC1N 1EH, United Kingdom
| | - Chloe Santos
- Institute of Child Health, University College London, London WC1N 1EH, United Kingdom
| | - Victoria Morrison
- Institute of Child Health, University College London, London WC1N 1EH, United Kingdom
| | - Antonella Galli
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Ulrich Tschulena
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - M Jocelyne Martel
- Department of Obstetrics and Gynecology, University of Saskatchewan College of Medicine, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Betty Spooner
- Northern Medical Services, University of Saskatchewan College of Medicine, Saskatoon, Saskatchewan S7K 0L4, Canada
| | - Steven C Ryu
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Princess C Elhosary
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jillian M Richardson
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Danielle Tierney
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Christopher A Robinson
- Department of Pathology, Royal University Hospital, University of Saskatchewan, Saskatoon, Saskatchewan S7N 0W8, Canada
| | - Rajni Chibbar
- Department of Pathology, Royal University Hospital, University of Saskatchewan, Saskatoon, Saskatchewan S7N 0W8, Canada
| | - Dana Diudea
- Department of Pathology, Royal University Hospital, University of Saskatchewan, Saskatoon, Saskatchewan S7N 0W8, Canada
| | - Rebecca Folkerth
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sheldon Wiebe
- Department of Medical Imaging, Royal University Hospital, University of Saskatchewan, Saskatoon, Saskatchewan S7N 0W8, Canada
| | - A James Barkovich
- Department of Radiology, University of California San Francisco, San Francisco, California 94143, USA
| | - Ganeshwaran H Mochida
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - James Irvine
- Northern Medical Services, University of Saskatchewan College of Medicine, Saskatoon, Saskatchewan S7K 0L4, Canada.,Population Health Unit, Mamawetan Churchill River and Keewatin-Yatthé Health Regions, and Athabasca Health Authority, La Ronge, Saskatchewan S0J 1L0, Canada
| | - Edmond G Lemire
- Department of Pediatrics, Royal University Hospital, University of Saskatchewan, Saskatoon, Saskatchewan S7N 0W8, Canada
| | - Patricia Blakley
- Department of Pediatrics, Royal University Hospital, University of Saskatchewan, Saskatoon, Saskatchewan S7N 0W8, Canada
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| |
Collapse
|
33
|
Abstract
The accurate and complete replication of genomic DNA is essential for all life. In eukaryotic cells, the assembly of the multi-enzyme replisomes that perform replication is divided into stages that occur at distinct phases of the cell cycle. Replicative DNA helicases are loaded around origins of DNA replication exclusively during G1 phase. The loaded helicases are then activated during S phase and associate with the replicative DNA polymerases and other accessory proteins. The function of the resulting replisomes is monitored by checkpoint proteins that protect arrested replisomes and inhibit new initiation when replication is inhibited. The replisome also coordinates nucleosome disassembly, assembly, and the establishment of sister chromatid cohesion. Finally, when two replisomes converge they are disassembled. Studies in Saccharomyces cerevisiae have led the way in our understanding of these processes. Here, we review our increasingly molecular understanding of these events and their regulation.
Collapse
|
34
|
Zhu C, Yamaguchi K, Ohsugi T, Terakado Y, Noguchi R, Ikenoue T, Furukawa Y. Identification of FERM domain-containing protein 5 as a novel target of β-catenin/TCF7L2 complex. Cancer Sci 2017; 108:612-619. [PMID: 28117551 PMCID: PMC5406541 DOI: 10.1111/cas.13174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 01/13/2017] [Accepted: 01/18/2017] [Indexed: 01/08/2023] Open
Abstract
Deregulation of the canonical Wnt signaling pathway plays an important role in human tumorigenesis through the accumulation of β‐catenin and subsequent transactivation of TCF7L2. Although some of the consequences associated with the accumulated β‐catenin have been clarified, the comprehensive effect of activated β‐catenin/TCF7L2 transcriptional complex on tumorigenesis remains to be elucidated. To understand the precise molecular mechanisms underlying colorectal cancer, we searched for genes regulated by the complex in colorectal tumors. We performed expression profile analysis of HCT116 and SW480 colon cancer cells treated with β‐catenin siRNAs, and ChIP‐sequencing using anti‐TCF7L2 antibody. Combination of these data with public microarray data of LS174 cells with a dominant‐negative form of TCF7L2 identified a total of 11 candidate genes. In this paper, we focused on FERM domain‐containing protein 5 (FRMD5), and confirmed that it is regulated by both β‐catenin and TCF7L2. An additional reporter assay disclosed that a region in intron1 transcriptionally regulated the expression of FRMD5. ChIP assay also corroborated that TCF7L2 associates with this region. These data suggested that FRMD5 is a novel direct target of the β‐catenin/TCF7L2 complex.
Collapse
Affiliation(s)
- Chi Zhu
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomoyuki Ohsugi
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yumi Terakado
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Rei Noguchi
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tsuneo Ikenoue
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
35
|
Baxley RM, Bielinsky AK. Mcm10: A Dynamic Scaffold at Eukaryotic Replication Forks. Genes (Basel) 2017; 8:E73. [PMID: 28218679 DOI: 10.3390/genes8020073] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/09/2017] [Accepted: 02/09/2017] [Indexed: 12/13/2022] Open
Abstract
To complete the duplication of large genomes efficiently, mechanisms have evolved that coordinate DNA unwinding with DNA synthesis and provide quality control measures prior to cell division. Minichromosome maintenance protein 10 (Mcm10) is a conserved component of the eukaryotic replisome that contributes to this process in multiple ways. Mcm10 promotes the initiation of DNA replication through direct interactions with the cell division cycle 45 (Cdc45)-minichromosome maintenance complex proteins 2-7 (Mcm2-7)-go-ichi-ni-san GINS complex proteins, as well as single- and double-stranded DNA. After origin firing, Mcm10 controls replication fork stability to support elongation, primarily facilitating Okazaki fragment synthesis through recruitment of DNA polymerase-α and proliferating cell nuclear antigen. Based on its multivalent properties, Mcm10 serves as an essential scaffold to promote DNA replication and guard against replication stress. Under pathological conditions, Mcm10 is often dysregulated. Genetic amplification and/or overexpression of MCM10 are common in cancer, and can serve as a strong prognostic marker of poor survival. These findings are compatible with a heightened requirement for Mcm10 in transformed cells to overcome limitations for DNA replication dictated by altered cell cycle control. In this review, we highlight advances in our understanding of when, where and how Mcm10 functions within the replisome to protect against barriers that cause incomplete replication.
Collapse
|
36
|
Abstract
Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation - from selecting replication start sites to replicative helicase loading and activation - and describe how these events are often distinctly regulated across different eukaryotic model organisms.
Collapse
Affiliation(s)
- Matthew W Parker
- a Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Michael R Botchan
- b Department of Molecular and Cell Biology , University of California Berkeley , Berkeley , CA , USA
| | - James M Berger
- a Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| |
Collapse
|
37
|
Bruck I, Dhingra N, Kaplan DL. A Positive Amplification Mechanism Involving a Kinase and Replication Initiation Factor Helps Assemble the Replication Fork Helicase. J Biol Chem 2017; 292:3062-3073. [PMID: 28082681 DOI: 10.1074/jbc.m116.772368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/11/2017] [Indexed: 01/09/2023] Open
Abstract
The assembly of the replication fork helicase during S phase is key to the initiation of DNA replication in eukaryotic cells. One step in this assembly in budding yeast is the association of Cdc45 with the Mcm2-7 heterohexameric ATPase, and a second step is the assembly of the tetrameric GINS (GG-Ichi-Nii-San) complex with Mcm2-7. Dbf4-dependent kinase (DDK) and S-phase cyclin-dependent kinase (S-CDK) are two S phase-specific kinases that phosphorylate replication proteins during S phase, and Dpb11, Sld2, Sld3, Pol ϵ, and Mcm10 are factors that are also required for replication initiation. However, the exact roles of these initiation factors in assembly of the replication fork helicase remain unclear. We show here that Dpb11 stimulates DDK phosphorylation of the minichromosome maintenance complex protein Mcm4 alone and also of the Mcm2-7 complex and the dsDNA-loaded Mcm2-7 complex. We further demonstrate that Dpb11 can directly recruit DDK to Mcm4. A DDK phosphomimetic mutant of Mcm4 bound Dpb11 with substantially higher affinity than wild-type Mcm4, suggesting a mechanism to recruit Dpb11 to DDK-phosphorylated Mcm2-7. Furthermore, dsDNA-loaded Mcm2-7 harboring the DDK phosphomimetic Mcm4 mutant bound GINS in the presence of Dpb11, suggesting a mechanism for how GINS is recruited to Mcm2-7. We isolated a mutant of Dpb11 that is specifically defective for binding to Mcm4. This mutant, when expressed in budding yeast, diminished cell growth and DNA replication, substantially decreased Mcm4 phosphorylation, and decreased association of GINS with replication origins. We conclude that Dpb11 functions with DDK and Mcm4 in a positive amplification mechanism to trigger the assembly of the replication fork helicase.
Collapse
Affiliation(s)
- Irina Bruck
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306
| | - Nalini Dhingra
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306
| | - Daniel L Kaplan
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306.
| |
Collapse
|
38
|
Yeeles JTP, Janska A, Early A, Diffley JFX. How the Eukaryotic Replisome Achieves Rapid and Efficient DNA Replication. Mol Cell 2017; 65:105-116. [PMID: 27989442 PMCID: PMC5222725 DOI: 10.1016/j.molcel.2016.11.017] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/17/2016] [Accepted: 11/07/2016] [Indexed: 01/15/2023]
Abstract
The eukaryotic replisome is a molecular machine that coordinates the Cdc45-MCM-GINS (CMG) replicative DNA helicase with DNA polymerases α, δ, and ε and other proteins to copy the leading- and lagging-strand templates at rates between 1 and 2 kb min-1. We have now reconstituted this sophisticated machine with purified proteins, beginning with regulated CMG assembly and activation. We show that replisome-associated factors Mrc1 and Csm3/Tof1 are crucial for in vivo rates of replisome progression. Additionally, maximal rates only occur when DNA polymerase ε catalyzes leading-strand synthesis together with its processivity factor PCNA. DNA polymerase δ can support leading-strand synthesis, but at slower rates. DNA polymerase δ is required for lagging-strand synthesis, but surprisingly also plays a role in establishing leading-strand synthesis, before DNA polymerase ε engagement. We propose that switching between these DNA polymerases also contributes to leading-strand synthesis under conditions of replicative stress.
Collapse
Affiliation(s)
- Joseph T P Yeeles
- The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Potters Bar, Hertfordshire EN6 3LD, UK
| | - Agnieska Janska
- The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Potters Bar, Hertfordshire EN6 3LD, UK
| | - Anne Early
- The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Potters Bar, Hertfordshire EN6 3LD, UK
| | - John F X Diffley
- The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Potters Bar, Hertfordshire EN6 3LD, UK.
| |
Collapse
|
39
|
Perez-Arnaiz P, Kaplan DL. An Mcm10 Mutant Defective in ssDNA Binding Shows Defects in DNA Replication Initiation. J Mol Biol 2016; 428:4608-4625. [PMID: 27751725 DOI: 10.1016/j.jmb.2016.10.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/28/2016] [Accepted: 10/07/2016] [Indexed: 11/25/2022]
Abstract
Mcm10 is an essential protein that functions to initiate DNA replication after the formation of the replication fork helicase. In this manuscript, we identified a budding yeast Mcm10 mutant (Mcm10-m2,3,4) that is defective in DNA binding in vitro. Moreover, this Mcm10-m2,3,4 mutant does not stimulate the phosphorylation of Mcm2 by Dbf4-dependent kinase (DDK) in vitro. When we expressed wild-type levels of mcm10-m2,3,4 in budding yeast cells, we observed a severe growth defect and a substantially decreased DNA replication. We also observed a substantially reduced replication protein A- chromatin immunoprecipitation signal at origins of replication, reduced levels of DDK-phosphorylated Mcm2, and diminished Go, Ichi, Ni, and San (GINS) association with Mcm2-7 in vivo. mcm5-bob1 bypasses the growth defect conferred by DDK-phosphodead Mcm2 in budding yeast. However, the growth defect observed by expressing mcm10-m2,3,4 is not bypassed by the mcm5-bob1 mutation. Furthermore, origin melting and GINS association with Mcm2-7 are substantially decreased for cells expressing mcm10-m2,3,4 in the mcm5-bob1 background. Thus, the origin melting and GINS-Mcm2-7 interaction defects we observed for mcm10-m2,3,4 are not explained by decreased Mcm2 phosphorylation by DDK, since the defects persist in an mcm5-bob1 background. These data suggest that DNA binding by Mcm10 is essential for the initiation of DNA replication.
Collapse
Affiliation(s)
- Patricia Perez-Arnaiz
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA
| | - Daniel L Kaplan
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA.
| |
Collapse
|
40
|
Abstract
Minichromosome maintenance protein (Mcm) 10 is a part of the eukaryotic replication machinery and highly conserved throughout evolution. As a multivalent DNA scaffold, Mcm10 coordinates the action of proteins that are indispensable for lagging strand synthesis, such as the replication clamp, proliferating cell nuclear antigen (PCNA). The binding between Mcm10 and PCNA serves an essential function during DNA elongation and is mediated by the ubiquitination of Mcm10. Here we map lysine 372 as the primary attachment site for ubiquitin on S. cerevisiae Mcm10. Moreover, we identify five additional lysines that can be ubiquitinated. Mutation of lysine 372 to arginine ablates ubiquitination of overexpressed protein and causes sensitivity to the replication inhibitor hydroxyurea in cells that are S-phase checkpoint compromised. Together, these findings reveal the high selectivity of the ubiquitination machinery that targets Mcm10 and that ubiquitination has a role in suppressing replication stress. S. cerevisiae Mcm10 is ubiquitinated at lysine 372. Alternative ubiquitination sites exist at five specific lysine residues. The mcm10-K372R mutation synergizes with a 9-1-1 checkpoint deficiency.
Collapse
Affiliation(s)
- Tianji Zhang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, United States of America
| | - Brandy L Fultz
- Department of Natural Sciences, College of Science and Health Professions, Northeastern State University, 3100 East New Orleans Street, Broken Arrow, OK 74014
| | - Sapna Das-Bradoo
- Department of Natural Sciences, College of Science and Health Professions, Northeastern State University, 3100 East New Orleans Street, Broken Arrow, OK 74014
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, United States of America
| |
Collapse
|
41
|
Chadha GS, Gambus A, Gillespie PJ, Blow JJ. Xenopus Mcm10 is a CDK-substrate required for replication fork stability. Cell Cycle 2016; 15:2183-2195. [PMID: 27327991 PMCID: PMC4993430 DOI: 10.1080/15384101.2016.1199305] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/01/2016] [Accepted: 06/03/2016] [Indexed: 12/17/2022] Open
Abstract
During S phase, following activation of the S phase CDKs and the DBF4-dependent kinases (DDK), double hexamers of Mcm2-7 at licensed replication origins are activated to form the core replicative helicase. Mcm10 is one of several proteins that have been implicated from work in yeasts to play a role in forming a mature replisome during the initiation process. Mcm10 has also been proposed to play a role in promoting replisome stability after initiation has taken place. The role of Mcm10 is particularly unclear in metazoans, where conflicting data has been presented. Here, we investigate the role and regulation of Mcm10 in Xenopus egg extracts. We show that Xenopus Mcm10 is recruited to chromatin late in the process of replication initiation and this requires prior action of DDKs and CDKs. We also provide evidence that Mcm10 is a CDK substrate but does not need to be phosphorylated in order to associate with chromatin. We show that in extracts depleted of more than 99% of Mcm10, the bulk of DNA replication still occurs, suggesting that Mcm10 is not required for the process of replication initiation. However, in extracts depleted of Mcm10, the replication fork elongation rate is reduced. Furthermore, the absence of Mcm10 or its phosphorylation by CDK results in instability of replisome proteins on DNA, which is particularly important under conditions of replication stress.
Collapse
Affiliation(s)
- Gaganmeet Singh Chadha
- a Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee , Dundee , UK
| | - Agnieszka Gambus
- a Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee , Dundee , UK
| | - Peter J Gillespie
- a Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee , Dundee , UK
| | - J Julian Blow
- a Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee , Dundee , UK
| |
Collapse
|
42
|
Wang Z, Zhu F. Minichromosome maintenance protein 7 regulates phagocytosis in kuruma shrimp Marsupenaeus japonicas against white spot syndrome virus. Fish Shellfish Immunol 2016; 55:293-303. [PMID: 27276115 DOI: 10.1016/j.fsi.2016.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/26/2016] [Accepted: 06/04/2016] [Indexed: 06/06/2023]
Abstract
Minichromosome maintenance protein (MCM7) belongs to the MCM protein family and participates in the MCM complex by playing a role in the cell replication cycle and chromosome initiation of eukaryotes. Previously, we found that several genes, including MCM7, were over-expressed in Drosophila melanogaster after white spot syndrome virus (WSSV) infection. In this study, we aimed to further research the MCM7 of kuruma shrimp, Marsupenaeus japonicus (mjMCM7) and determine its role in the innate immune system. To this end, we cloned the entire 2307-bp mjMCM7 sequence, including a 1974-bp open reading frame (ORF) encoding a 658-aa-long protein. Real-time PCR showed that the gene was primarily expressed in the hemolymph and hepatopancreas and over-expressed in shrimp challenged with WSSV. Gene function study was carried out by knocking down the expression of MCM7 using small interference RNA (siRNA). The results revealed that β-actin, hemocyanin, prophenoloxidase (proPO) and tumor necrosis factor-α (TNF-α) were up-regulated while the cytoskeleton proteins such as myosin and Rho were significantly down-regulated at 24 h after treatment. The results indicate a possible relationship between mjMCM7 and the innate immune system, and suggest that mjMCM7 may play a role in phagocytosis. After WSSV challenge, WSSV copies and mortality count were both higher in the MCM7-siRNA-treated groups at 60 h after treatment, and the mortality count approached that of the control groups over time. The phagocytosis rate was significantly lower in the MCM7-siRNA-treated group than in the WSSV group. The findings of this study confirm that mjMCM7 positively regulates phagocytosis and plays an important role against WSSV. These results could help researchers to further understand the function of the MCM7 protein and reveal its potential role in the innate immunity of invertebrates.
Collapse
Affiliation(s)
- Zhi Wang
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Fei Zhu
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
| |
Collapse
|
43
|
García-Rodríguez N, Wong RP, Ulrich HD. Functions of Ubiquitin and SUMO in DNA Replication and Replication Stress. Front Genet 2016; 7:87. [PMID: 27242895 PMCID: PMC4865505 DOI: 10.3389/fgene.2016.00087] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/27/2016] [Indexed: 12/14/2022] Open
Abstract
Complete and faithful duplication of its entire genetic material is one of the essential prerequisites for a proliferating cell to maintain genome stability. Yet, during replication DNA is particularly vulnerable to insults. On the one hand, lesions in replicating DNA frequently cause a stalling of the replication machinery, as most DNA polymerases cannot cope with defective templates. This situation is aggravated by the fact that strand separation in preparation for DNA synthesis prevents common repair mechanisms relying on strand complementarity, such as base and nucleotide excision repair, from working properly. On the other hand, the replication process itself subjects the DNA to a series of hazardous transformations, ranging from the exposure of single-stranded DNA to topological contortions and the generation of nicks and fragments, which all bear the risk of inducing genomic instability. Dealing with these problems requires rapid and flexible responses, for which posttranslational protein modifications that act independently of protein synthesis are particularly well suited. Hence, it is not surprising that members of the ubiquitin family, particularly ubiquitin itself and SUMO, feature prominently in controlling many of the defensive and restorative measures involved in the protection of DNA during replication. In this review we will discuss the contributions of ubiquitin and SUMO to genome maintenance specifically as they relate to DNA replication. We will consider cases where the modifiers act during regular, i.e., unperturbed stages of replication, such as initiation, fork progression, and termination, but also give an account of their functions in dealing with lesions, replication stalling and fork collapse.
Collapse
|
44
|
Douglas ME, Diffley JFX. Recruitment of Mcm10 to Sites of Replication Initiation Requires Direct Binding to the Minichromosome Maintenance (MCM) Complex. J Biol Chem 2016; 291:5879-5888. [PMID: 26719337 PMCID: PMC4786722 DOI: 10.1074/jbc.m115.707802] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 12/28/2015] [Indexed: 01/11/2023] Open
Abstract
Mcm10 is required for the initiation of eukaryotic DNA replication and contributes in some unknown way to the activation of the Cdc45-MCM-GINS (CMG) helicase. How Mcm10 is localized to sites of replication initiation is unclear, as current models indicate that direct binding to minichromosome maintenance (MCM) plays a role, but the details and functional importance of this interaction have not been determined. Here, we show that purified Mcm10 can bind both DNA-bound double hexamers and soluble single hexamers of MCM. The binding of Mcm10 to MCM requires the Mcm10 C terminus. Moreover, the binding site for Mcm10 on MCM includes the Mcm2 and Mcm6 subunits and overlaps that for the loading factor Cdt1. Whether Mcm10 recruitment to replication origins depends on CMG helicase assembly has been unclear. We show that Mcm10 recruitment occurs via two modes: low affinity recruitment in the absence of CMG assembly ("G1-like") and high affinity recruitment when CMG assembly takes place ("S-phase-like"). Mcm10 that cannot bind directly to MCM is defective in both modes of recruitment and is unable to support DNA replication. These findings indicate that Mcm10 is localized to replication initiation sites by directly binding MCM through the Mcm10 C terminus.
Collapse
Affiliation(s)
- Max E Douglas
- From The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - John F X Diffley
- From The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Hertfordshire EN6 3LD, United Kingdom.
| |
Collapse
|
45
|
Abstract
The initiation of DNA replication is a highly regulated event in eukaryotic cells to ensure that the entire genome is copied once and only once during S phase. The primary target of cellular regulation of eukaryotic DNA replication initiation is the assembly and activation of the replication fork helicase, the 11-subunit assembly that unwinds DNA at a replication fork. The replication fork helicase, called CMG for Cdc45-Mcm2-7, and GINS, assembles in S phase from the constituent Cdc45, Mcm2-7, and GINS proteins. The assembly and activation of the CMG replication fork helicase during S phase is governed by 2 S-phase specific kinases, CDK and DDK. CDK stimulates the interaction between Sld2, Sld3, and Dpb11, 3 initiation factors that are each required for the initiation of DNA replication. DDK, on the other hand, phosphorylates the Mcm2, Mcm4, and Mcm6 subunits of the Mcm2-7 complex. Sld3 recruits Cdc45 to Mcm2-7 in a manner that depends on DDK, and recent work suggests that Sld3 binds directly to Mcm2-7 and also to single-stranded DNA. Furthermore, recent work demonstrates that Sld3 and its human homolog Treslin substantially stimulate DDK phosphorylation of Mcm2. These data suggest that the initiation factor Sld3/Treslin coordinates the assembly and activation of the eukaryotic replication fork helicase by recruiting Cdc45 to Mcm2-7, stimulating DDK phosphorylation of Mcm2, and binding directly to single-stranded DNA as the origin is melted.
Collapse
Affiliation(s)
- Irina Bruck
- a Department of Biomedical Science; Florida State University College of Medicine ; Tallahassee , FL USA
| | - Patricia Perez-Arnaiz
- a Department of Biomedical Science; Florida State University College of Medicine ; Tallahassee , FL USA
| | - Max K Colbert
- a Department of Biomedical Science; Florida State University College of Medicine ; Tallahassee , FL USA
| | - Daniel L Kaplan
- a Department of Biomedical Science; Florida State University College of Medicine ; Tallahassee , FL USA
| |
Collapse
|
46
|
Perez-Arnaiz P, Bruck I, Kaplan DL. Mcm10 coordinates the timely assembly and activation of the replication fork helicase. Nucleic Acids Res 2015; 44:315-29. [PMID: 26582917 PMCID: PMC4705653 DOI: 10.1093/nar/gkv1260] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/02/2015] [Indexed: 11/12/2022] Open
Abstract
Mcm10 is an essential replication factor that is required for DNA replication in eukaryotes. Two key steps in the initiation of DNA replication are the assembly and activation of Cdc45–Mcm2–7-GINS (CMG) replicative helicase. However, it is not known what coordinates helicase assembly with helicase activation. We show in this manuscript, using purified proteins from budding yeast, that Mcm10 directly interacts with the Mcm2–7 complex and Cdc45. In fact, Mcm10 recruits Cdc45 to Mcm2–7 complex in vitro. To study the role of Mcm10 in more detail in vivo we used an auxin inducible degron in which Mcm10 is degraded upon addition of auxin. We show in this manuscript that Mcm10 is required for the timely recruitment of Cdc45 and GINS recruitment to the Mcm2–7 complex in vivo during early S phase. We also found that Mcm10 stimulates Mcm2 phosphorylation by DDK in vivo and in vitro. These findings indicate that Mcm10 plays a critical role in coupling replicative helicase assembly with helicase activation. Mcm10 is first involved in the recruitment of Cdc45 to the Mcm2–7 complex. After Cdc45–Mcm2–7 complex assembly, Mcm10 promotes origin melting by stimulating DDK phosphorylation of Mcm2, which thereby leads to GINS attachment to Mcm2–7.
Collapse
Affiliation(s)
- Patricia Perez-Arnaiz
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, FL 32306, USA
| | - Irina Bruck
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, FL 32306, USA
| | - Daniel L Kaplan
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, FL 32306, USA
| |
Collapse
|
47
|
Becker JR, Pons C, Nguyen HD, Costanzo M, Boone C, Myers CL, Bielinsky AK. Genetic Interactions Implicating Postreplicative Repair in Okazaki Fragment Processing. PLoS Genet 2015; 11:e1005659. [PMID: 26545110 PMCID: PMC4636136 DOI: 10.1371/journal.pgen.1005659] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/19/2015] [Indexed: 01/28/2023] Open
Abstract
Ubiquitination of the replication clamp proliferating cell nuclear antigen (PCNA) at the conserved residue lysine (K)164 triggers postreplicative repair (PRR) to fill single-stranded gaps that result from stalled DNA polymerases. However, it has remained elusive as to whether cells engage PRR in response to replication defects that do not directly impair DNA synthesis. To experimentally address this question, we performed synthetic genetic array (SGA) analysis with a ubiquitination-deficient K164 to arginine (K164R) mutant of PCNA against a library of S. cerevisiae temperature-sensitive alleles. The SGA signature of the K164R allele showed a striking correlation with profiles of mutants deficient in various aspects of lagging strand replication, including rad27Δ and elg1Δ. Rad27 is the primary flap endonuclease that processes 5' flaps generated during lagging strand replication, whereas Elg1 has been implicated in unloading PCNA from chromatin. We observed chronic ubiquitination of PCNA at K164 in both rad27Δ and elg1Δ mutants. Notably, only rad27Δ cells exhibited a decline in cell viability upon elimination of PRR pathways, whereas elg1Δ mutants were not affected. We further provide evidence that K164 ubiquitination suppresses replication stress resulting from defective flap processing during Okazaki fragment maturation. Accordingly, ablation of PCNA ubiquitination increased S phase checkpoint activation, indicated by hyperphosphorylation of the Rad53 kinase. Furthermore, we demonstrate that alternative flap processing by overexpression of catalytically active exonuclease 1 eliminates PCNA ubiquitination. This suggests a model in which unprocessed flaps may directly participate in PRR signaling. Our findings demonstrate that PCNA ubiquitination at K164 in response to replication stress is not limited to DNA synthesis defects but extends to DNA processing during lagging strand replication.
Collapse
Affiliation(s)
- Jordan R. Becker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Hai Dang Nguyen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Michael Costanzo
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| |
Collapse
|
48
|
Reubens MC, Biller MD, Bedsole SE, Hopkins LT, Ables ET, Christensen TW. Mcm10 is required for oogenesis and early embryogenesis in Drosophila. Mech Dev 2015; 138 Pt 3:291-9. [PMID: 26369283 DOI: 10.1016/j.mod.2015.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/27/2015] [Accepted: 09/08/2015] [Indexed: 01/05/2023]
Abstract
Efficient replication of the genome and the establishment of endogenous chromatin states are processes that are essential to eukaryotic life. It is well documented that Mcm10 is intimately linked to both of these important biological processes; therefore, it is not surprising that Mcm10 is commonly misregulated in many human cancers. Most of the research regarding the biological roles of Mcm10 has been performed in single-cell or cell-free in-vitro systems. Though these systems are informative, they are unable to provide information on the cell-specific function of Mcm10 in the context of the tissue and organ systems that comprise multicellular eukaryotes. We therefore sought to identify the potential biological functions of Mcm10 in the context of a complex multicellular organism by continuing our analysis in Drosophila using three novel hypomorphic alleles. Observation of embryonic nuclear morphology and quantification of embryo hatch rates reveal that maternal loading of Mcm10 is required for embryonic nuclear stability, and suggest a role for Mcm10 post zygotic transition. Contrary to the essential nature of Mcm10 depicted in the literature, it does not appear to be required for adult viability in Drosophila if embryonic requirements are met. Although not required for adult somatic viability, analysis of fecundity and ovarian morphology in mutant females suggest that Mcm10 plays a role in maintenance of the female germline. Taken together, our results demonstrate critical roles for Mcm10 during early embryogenesis, and mark the first data linking Mcm10 to female specific reproduction in multicellular eukaryotes.
Collapse
Affiliation(s)
- Michael C Reubens
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Megan D Biller
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Sidney E Bedsole
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Lucas T Hopkins
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Elizabeth T Ables
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Tim W Christensen
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| |
Collapse
|
49
|
Abstract
Posttranslational modification of proteins by means of attachment of a small globular protein ubiquitin (i.e., ubiquitylation) represents one of the most abundant and versatile mechanisms of protein regulation employed by eukaryotic cells. Ubiquitylation influences almost every cellular process and its key role in coordination of the DNA damage response is well established. In this review we focus, however, on the ways ubiquitylation controls the process of unperturbed DNA replication. We summarise the accumulated knowledge showing the leading role of ubiquitin driven protein degradation in setting up conditions favourable for replication origin licensing and S-phase entry. Importantly, we also present the emerging major role of ubiquitylation in coordination of the active DNA replication process: preventing re-replication, regulating the progression of DNA replication forks, chromatin re-establishment and disassembly of the replisome at the termination of replication forks.
Collapse
Affiliation(s)
- Sara Priego Moreno
- School of Cancer Sciences, University of Birmingham, Vincent Drive, B15 2TT, Birmingham, UK
| | - Agnieszka Gambus
- School of Cancer Sciences, University of Birmingham, Vincent Drive, B15 2TT, Birmingham, UK.
| |
Collapse
|
50
|
Romani B, Shaykh Baygloo N, Aghasadeghi MR, Allahbakhshi E. HIV-1 Vpr Protein Enhances Proteasomal Degradation of MCM10 DNA Replication Factor through the Cul4-DDB1[VprBP] E3 Ubiquitin Ligase to Induce G2/M Cell Cycle Arrest. J Biol Chem 2015; 290:17380-9. [PMID: 26032416 DOI: 10.1074/jbc.m115.641522] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/06/2022] Open
Abstract
Human immunodeficiency virus type 1 Vpr is an accessory protein that induces G2/M cell cycle arrest. It is well documented that interaction of Vpr with the Cul4-DDB1[VprBP] E3 ubiquitin ligase is essential for the induction of G2/M arrest. In this study, we show that HIV-1 Vpr indirectly binds MCM10, a eukaryotic DNA replication factor, in a Vpr-binding protein (VprBP) (VprBP)-dependent manner. Binding of Vpr to MCM10 enhanced ubiquitination and proteasomal degradation of MCM10. G2/M-defective mutants of Vpr were not able to deplete MCM10, and we show that Vpr-induced depletion of MCM10 is related to the ability of Vpr to induce G2/M arrest. Our study demonstrates that MCM10 is the natural substrate of the Cul4-DDB1[VprBP] E3 ubiquitin ligase whose degradation is regulated by VprBP, but Vpr enhances the proteasomal degradation of MCM10 by interacting with VprBP.
Collapse
Affiliation(s)
- Bizhan Romani
- From the Department of Biology, Faculty of Science, University of Isfahan, Isfahan 81746-73441, the Cellular and Molecular Research Center (CMRC), Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences (AJUMS), Ahvaz 61357-15794, and
| | - Nima Shaykh Baygloo
- From the Department of Biology, Faculty of Science, University of Isfahan, Isfahan 81746-73441
| | | | - Elham Allahbakhshi
- the Cellular and Molecular Research Center (CMRC), Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences (AJUMS), Ahvaz 61357-15794, and
| |
Collapse
|