1
|
Chauhan AS, Jhujh SS, Stewart GS. E3 ligases: a ubiquitous link between DNA repair, DNA replication and human disease. Biochem J 2024; 481:923-944. [PMID: 38985307 DOI: 10.1042/bcj20240124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Maintenance of genome stability is of paramount importance for the survival of an organism. However, genomic integrity is constantly being challenged by various endogenous and exogenous processes that damage DNA. Therefore, cells are heavily reliant on DNA repair pathways that have evolved to deal with every type of genotoxic insult that threatens to compromise genome stability. Notably, inherited mutations in genes encoding proteins involved in these protective pathways trigger the onset of disease that is driven by chromosome instability e.g. neurodevelopmental abnormalities, neurodegeneration, premature ageing, immunodeficiency and cancer development. The ability of cells to regulate the recruitment of specific DNA repair proteins to sites of DNA damage is extremely complex but is primarily mediated by protein post-translational modifications (PTMs). Ubiquitylation is one such PTM, which controls genome stability by regulating protein localisation, protein turnover, protein-protein interactions and intra-cellular signalling. Over the past two decades, numerous ubiquitin (Ub) E3 ligases have been identified to play a crucial role not only in the initiation of DNA replication and DNA damage repair but also in the efficient termination of these processes. In this review, we discuss our current understanding of how different Ub E3 ligases (RNF168, TRAIP, HUWE1, TRIP12, FANCL, BRCA1, RFWD3) function to regulate DNA repair and replication and the pathological consequences arising from inheriting deleterious mutations that compromise the Ub-dependent DNA damage response.
Collapse
Affiliation(s)
- Anoop S Chauhan
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Satpal S Jhujh
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| |
Collapse
|
2
|
Li N, Gao N. A commentary of "Initial DNA melting in human DNA replication initiation": Top 10 Scientific Advances of 2023, China. FUNDAMENTAL RESEARCH 2024; 4:701-703. [PMID: 38933211 PMCID: PMC11197563 DOI: 10.1016/j.fmre.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 03/20/2024] [Indexed: 06/28/2024] Open
Affiliation(s)
- Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
3
|
Wu X, Li Z, Wang ZQ, Xu X. The neurological and non-neurological roles of the primary microcephaly-associated protein ASPM. Front Neurosci 2023; 17:1242448. [PMID: 37599996 PMCID: PMC10436222 DOI: 10.3389/fnins.2023.1242448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
Primary microcephaly (MCPH), is a neurological disorder characterized by small brain size that results in numerous developmental problems, including intellectual disability, motor and speech delays, and seizures. Hitherto, over 30 MCPH causing genes (MCPHs) have been identified. Among these MCPHs, MCPH5, which encodes abnormal spindle-like microcephaly-associated protein (ASPM), is the most frequently mutated gene. ASPM regulates mitotic events, cell proliferation, replication stress response, DNA repair, and tumorigenesis. Moreover, using a data mining approach, we have confirmed that high levels of expression of ASPM correlate with poor prognosis in several types of tumors. Here, we summarize the neurological and non-neurological functions of ASPM and provide insight into its implications for the diagnosis and treatment of MCPH and cancer.
Collapse
Affiliation(s)
- Xingxuan Wu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Zheng Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Zhao-Qi Wang
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| |
Collapse
|
4
|
Song HY, Shen R, Mahasin H, Guo YN, Wang DG. DNA replication: Mechanisms and therapeutic interventions for diseases. MedComm (Beijing) 2023; 4:e210. [PMID: 36776764 PMCID: PMC9899494 DOI: 10.1002/mco2.210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 02/09/2023] Open
Abstract
Accurate and integral cellular DNA replication is modulated by multiple replication-associated proteins, which is fundamental to preserve genome stability. Furthermore, replication proteins cooperate with multiple DNA damage factors to deal with replication stress through mechanisms beyond their role in replication. Cancer cells with chronic replication stress exhibit aberrant DNA replication and DNA damage response, providing an exploitable therapeutic target in tumors. Numerous evidence has indicated that posttranslational modifications (PTMs) of replication proteins present distinct functions in DNA replication and respond to replication stress. In addition, abundant replication proteins are involved in tumorigenesis and development, which act as diagnostic and prognostic biomarkers in some tumors, implying these proteins act as therapeutic targets in clinical. Replication-target cancer therapy emerges as the times require. In this context, we outline the current investigation of the DNA replication mechanism, and simultaneously enumerate the aberrant expression of replication proteins as hallmark for various diseases, revealing their therapeutic potential for target therapy. Meanwhile, we also discuss current observations that the novel PTM of replication proteins in response to replication stress, which seems to be a promising strategy to eliminate diseases.
Collapse
Affiliation(s)
- Hao-Yun Song
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - Rong Shen
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - Hamid Mahasin
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - Ya-Nan Guo
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - De-Gui Wang
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| |
Collapse
|
5
|
A DNA replication-independent function of pre-replication complex genes during cell invasion in C. elegans. PLoS Biol 2022; 20:e3001317. [PMID: 35192608 PMCID: PMC8863262 DOI: 10.1371/journal.pbio.3001317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/01/2021] [Indexed: 11/19/2022] Open
Abstract
Cell invasion is an initiating event during tumor cell metastasis and an essential process during development. A screen of C. elegans orthologs of genes overexpressed in invasive human melanoma cells has identified several components of the conserved DNA pre-replication complex (pre-RC) as positive regulators of anchor cell (AC) invasion. The pre-RC genes function cell-autonomously in the G1-arrested AC to promote invasion, independently of their role in licensing DNA replication origins in proliferating cells. While the helicase activity of the pre-RC is necessary for AC invasion, the downstream acting DNA replication initiation factors are not required. The pre-RC promotes the invasive fate by regulating the expression of extracellular matrix genes and components of the PI3K signaling pathway. Increasing PI3K pathway activity partially suppressed the AC invasion defects caused by pre-RC depletion, suggesting that the PI3K pathway is one critical pre-RC target. We propose that the pre-RC, or a part of it, acts in the postmitotic AC as a transcriptional regulator that facilitates the switch to an invasive phenotype.
Collapse
|
6
|
Ivanova A, Atemin A, Uzunova S, Danovski G, Aleksandrov R, Stoynov S, Nedelcheva-Veleva M. The Effect of Dia2 Protein Deficiency on the Cell Cycle, Cell Size, and Recruitment of Ctf4 Protein in Saccharomyces cerevisiae. Molecules 2021; 27:97. [PMID: 35011329 PMCID: PMC8746418 DOI: 10.3390/molecules27010097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/13/2023] Open
Abstract
Cells have evolved elaborate mechanisms to regulate DNA replication machinery and cell cycles in response to DNA damage and replication stress in order to prevent genomic instability and cancer. The E3 ubiquitin ligase SCFDia2 in S. cerevisiae is involved in the DNA replication and DNA damage stress response, but its effect on cell growth is still unclear. Here, we demonstrate that the absence of Dia2 prolongs the cell cycle by extending both S- and G2/M-phases while, at the same time, activating the S-phase checkpoint. In these conditions, Ctf4-an essential DNA replication protein and substrate of Dia2-prolongs its binding to the chromatin during the extended S- and G2/M-phases. Notably, the prolonged cell cycle when Dia2 is absent is accompanied by a marked increase in cell size. We found that while both DNA replication inhibition and an absence of Dia2 exerts effects on cell cycle duration and cell size, Dia2 deficiency leads to a much more profound increase in cell size and a substantially lesser effect on cell cycle duration compared to DNA replication inhibition. Our results suggest that the increased cell size in dia2∆ involves a complex mechanism in which the prolonged cell cycle is one of the driving forces.
Collapse
Affiliation(s)
| | | | | | | | | | - Stoyno Stoynov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G., Bonchev Str. Bl.21, 1113 Sofia, Bulgaria; (A.I.); (A.A.); (S.U.); (G.D.); (R.A.)
| | - Marina Nedelcheva-Veleva
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G., Bonchev Str. Bl.21, 1113 Sofia, Bulgaria; (A.I.); (A.A.); (S.U.); (G.D.); (R.A.)
| |
Collapse
|
7
|
Das S, Caballero M, Kolesnikova T, Zhimulev I, Koren A, Nordman J. Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila. Genetics 2021; 219:6369517. [PMID: 34740250 PMCID: PMC8570783 DOI: 10.1093/genetics/iyab147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022] Open
Abstract
Regulation of DNA replication and copy number is necessary to promote genome stability and maintain cell and tissue function. DNA replication is regulated temporally in a process known as replication timing (RT). Rap1-interacting factor 1 (Rif1) is a key regulator of RT and has a critical function in copy number control in polyploid cells. Previously, we demonstrated that Rif1 functions with SUUR to inhibit replication fork progression and promote underreplication (UR) of specific genomic regions. How Rif1-dependent control of RT factors into its ability to promote UR is unknown. By applying a computational approach to measure RT in Drosophila polyploid cells, we show that SUUR and Rif1 have differential roles in controlling UR and RT. Our findings reveal that Rif1 acts to promote late replication, which is necessary for SUUR-dependent underreplication. Our work provides new insight into the process of UR and its links to RT.
Collapse
Affiliation(s)
- Souradip Das
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Madison Caballero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Tatyana Kolesnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,Laboratory of Structural, Functional and Comparative Genomics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Igor Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,Laboratory of Structural, Functional and Comparative Genomics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jared Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| |
Collapse
|
8
|
Khan YA, White KI, Brunger AT. The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines. Crit Rev Biochem Mol Biol 2021; 57:156-187. [PMID: 34632886 DOI: 10.1080/10409238.2021.1979460] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. Typically, AAA+ proteins transduce chemical energy from the hydrolysis of ATP into mechanical energy through conformational change, which can drive a variety of biological processes. AAA+ proteins operate in a variety of cellular contexts with diverse functions including disassembly of SNARE proteins, protein quality control, DNA replication, ribosome assembly, and viral replication. This breadth of function illustrates both the importance of AAA+ proteins in health and disease and emphasizes the importance of understanding conserved mechanisms of chemo-mechanical energy transduction. This review is divided into three major portions. First, the core AAA+ fold is presented. Next, the seven different clades of AAA+ proteins and structural details and reclassification pertaining to proteins in each clade are described. Finally, two well-known AAA+ proteins, NSF and its close relative p97, are reviewed in detail.
Collapse
Affiliation(s)
- Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| |
Collapse
|
9
|
MCMs in Cancer: Prognostic Potential and Mechanisms. Anal Cell Pathol (Amst) 2020; 2020:3750294. [PMID: 32089988 PMCID: PMC7023756 DOI: 10.1155/2020/3750294] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/25/2020] [Indexed: 12/17/2022] Open
Abstract
Enabling replicative immortality and uncontrolled cell cycle are hallmarks of cancer cells. Minichromosome maintenance proteins (MCMs) exhibit helicase activity in replication initiation and play vital roles in controlling replication times within a cell cycle. Overexpressed MCMs are detected in various cancerous tissues and cancer cell lines. Previous studies have proposed MCMs as promising proliferation markers in cancers, while the prognostic values remain controversial and the underlying mechanisms remain unascertained. This review provides an overview of the significant findings regarding the cellular and tumorigenic functions of the MCM family. Besides, current evidence of the prognostic roles of MCMs is retrospectively reviewed. This work also offers insight into the mechanisms of MCMs prompting carcinogenesis and adverse prognosis, providing information for future research. Finally, MCMs in liver cancer are specifically discussed, and future perspectives are provided.
Collapse
|
10
|
Kalogeropoulou A, Lygerou Z, Taraviras S. Cortical Development and Brain Malformations: Insights From the Differential Regulation of Early Events of DNA Replication. Front Cell Dev Biol 2019; 7:29. [PMID: 30915332 PMCID: PMC6421272 DOI: 10.3389/fcell.2019.00029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/20/2019] [Indexed: 12/27/2022] Open
Abstract
During the development of the cortex distinct populations of Neural Stem Cells (NSCs) are defined by differences in their cell cycle duration, self-renewal capacity and transcriptional profile. A key difference across the distinct populations of NSCs is the length of G1 phase, where the licensing of the DNA replication origins takes place by the assembly of a pre-replicative complex. Licensing of DNA replication is a process that is adapted accordingly to the cell cycle length of NSCs to secure the timed duplication of the genome. Moreover, DNA replication should be efficiently coordinated with ongoing transcription for the prevention of conflicts that would impede the progression of both processes, compromising the normal course of development. In the present review we discuss how the differential regulation of the licensing and initiation of DNA replication in different cortical NSCs populations is integrated with the properties of these stem cells populations. Moreover, we examine the implication of the initial steps of DNA replication in the pathogenetic mechanisms of neurodevelopmental defects and Zika virus-related microcephaly, highlighting the significance of the differential regulation of DNA replication during brain development.
Collapse
Affiliation(s)
| | - Zoi Lygerou
- Department of General Biology, Medical School, University of Patras, Patras, Greece
| | - Stavros Taraviras
- Department of Physiology, Medical School, University of Patras, Patras, Greece
| |
Collapse
|
11
|
Yamamoto K, Makino N, Nagai M, Honma Y, Araki H, Ushimaru T. TORC1 signaling regulates DNA replication via DNA replication protein levels. Biochem Biophys Res Commun 2018; 505:1128-1133. [DOI: 10.1016/j.bbrc.2018.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/04/2018] [Indexed: 02/07/2023]
|
12
|
Munden A, Rong Z, Sun A, Gangula R, Mallal S, Nordman JT. Rif1 inhibits replication fork progression and controls DNA copy number in Drosophila. eLife 2018; 7:e39140. [PMID: 30277458 PMCID: PMC6185109 DOI: 10.7554/elife.39140] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/01/2018] [Indexed: 12/22/2022] Open
Abstract
Control of DNA copy number is essential to maintain genome stability and ensure proper cell and tissue function. In Drosophila polyploid cells, the SNF2-domain-containing SUUR protein inhibits replication fork progression within specific regions of the genome to promote DNA underreplication. While dissecting the function of SUUR's SNF2 domain, we identified an interaction between SUUR and Rif1. Rif1 has many roles in DNA metabolism and regulates the replication timing program. We demonstrate that repression of DNA replication is dependent on Rif1. Rif1 localizes to active replication forks in a partially SUUR-dependent manner and directly regulates replication fork progression. Importantly, SUUR associates with replication forks in the absence of Rif1, indicating that Rif1 acts downstream of SUUR to inhibit fork progression. Our findings uncover an unrecognized function of the Rif1 protein as a regulator of replication fork progression.
Collapse
Affiliation(s)
- Alexander Munden
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
| | - Zhan Rong
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
| | - Amanda Sun
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
| | - Rama Gangula
- Department of MedicineVanderbilt University School of MedicineNashvilleUnited States
| | - Simon Mallal
- Department of MedicineVanderbilt University School of MedicineNashvilleUnited States
- Department of Pathology, Microbiology and ImmunologyVanderbilt University School of MedicineNashvilleUnited States
| | - Jared T Nordman
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
| |
Collapse
|
13
|
Hernández-Carralero E, Cabrera E, Alonso-de Vega I, Hernández-Pérez S, Smits VAJ, Freire R. Control of DNA Replication Initiation by Ubiquitin. Cells 2018; 7:E146. [PMID: 30241373 PMCID: PMC6211026 DOI: 10.3390/cells7100146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic cells divide by accomplishing a program of events in which the replication of the genome is a fundamental part. To ensure all cells have an accurate copy of the genome, DNA replication occurs only once per cell cycle and is controlled by numerous pathways. A key step in this process is the initiation of DNA replication in which certain regions of DNA are marked as competent to replicate. Moreover, initiation of DNA replication needs to be coordinated with other cell cycle processes. At the molecular level, initiation of DNA replication relies, among other mechanisms, upon post-translational modifications, including the conjugation and hydrolysis of ubiquitin. An example is the precise control of the levels of the DNA replication initiation protein Cdt1 and its inhibitor Geminin by ubiquitin-mediated proteasomal degradation. This control ensures that DNA replication occurs with the right timing during the cell cycle, thereby avoiding re-replication events. Here, we review the events that involve ubiquitin signalling during DNA replication initiation, and how they are linked to human disease.
Collapse
Affiliation(s)
- Esperanza Hernández-Carralero
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Elisa Cabrera
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Ignacio Alonso-de Vega
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Santiago Hernández-Pérez
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
| | - Veronique A J Smits
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| |
Collapse
|
14
|
Li S, Xu Z, Xu J, Zuo L, Yu C, Zheng P, Gan H, Wang X, Li L, Sharma S, Chabes A, Li D, Wang S, Zheng S, Li J, Chen X, Sun Y, Xu D, Han J, Chan K, Qi Z, Feng J, Li Q. Rtt105 functions as a chaperone for replication protein A to preserve genome stability. EMBO J 2018; 37:embj.201899154. [PMID: 30065069 DOI: 10.15252/embj.201899154] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/28/2018] [Accepted: 07/06/2018] [Indexed: 02/05/2023] Open
Abstract
Generation of single-stranded DNA (ssDNA) is required for the template strand formation during DNA replication. Replication Protein A (RPA) is an ssDNA-binding protein essential for protecting ssDNA at replication forks in eukaryotic cells. While significant progress has been made in characterizing the role of the RPA-ssDNA complex, how RPA is loaded at replication forks remains poorly explored. Here, we show that the Saccharomyces cerevisiae protein regulator of Ty1 transposition 105 (Rtt105) binds RPA and helps load it at replication forks. Cells lacking Rtt105 exhibit a dramatic reduction in RPA loading at replication forks, compromised DNA synthesis under replication stress, and increased genome instability. Mechanistically, we show that Rtt105 mediates the RPA-importin interaction and also promotes RPA binding to ssDNA directly in vitro, but is not present in the final RPA-ssDNA complex. Single-molecule studies reveal that Rtt105 affects the binding mode of RPA to ssDNA These results support a model in which Rtt105 functions as an RPA chaperone that escorts RPA to the nucleus and facilitates its loading onto ssDNA at replication forks.
Collapse
Affiliation(s)
- Shuqi Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Zhiyun Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jiawei Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Linyu Zuo
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chuanhe Yu
- Department of Pediatrics and Department of Genetics and Development, Institute for Cancer Genetics, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Pu Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Haiyun Gan
- Department of Pediatrics and Department of Genetics and Development, Institute for Cancer Genetics, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Xuezheng Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Longtu Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Sushma Sharma
- Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Andrei Chabes
- Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Di Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Sheng Wang
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Sihao Zheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Jinbao Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Junhong Han
- Division of Abdominal Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and National Collaborative Center for Biotherapy, Chengdu, China
| | - Kuiming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Zhi Qi
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jianxun Feng
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China .,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Qing Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China .,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| |
Collapse
|
15
|
Bellelli R, Borel V, Logan C, Svendsen J, Cox DE, Nye E, Metcalfe K, O'Connell SM, Stamp G, Flynn HR, Snijders AP, Lassailly F, Jackson A, Boulton SJ. Polε Instability Drives Replication Stress, Abnormal Development, and Tumorigenesis. Mol Cell 2018; 70:707-721.e7. [PMID: 29754823 PMCID: PMC5972231 DOI: 10.1016/j.molcel.2018.04.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 01/08/2023]
Abstract
DNA polymerase ε (POLE) is a four-subunit complex and the major leading strand polymerase in eukaryotes. Budding yeast orthologs of POLE3 and POLE4 promote Polε processivity in vitro but are dispensable for viability in vivo. Here, we report that POLE4 deficiency in mice destabilizes the entire Polε complex, leading to embryonic lethality in inbred strains and extensive developmental abnormalities, leukopenia, and tumor predisposition in outbred strains. Comparable phenotypes of growth retardation and immunodeficiency are also observed in human patients harboring destabilizing mutations in POLE1. In both Pole4-/- mouse and POLE1 mutant human cells, Polε hypomorphy is associated with replication stress and p53 activation, which we attribute to inefficient replication origin firing. Strikingly, removing p53 is sufficient to rescue embryonic lethality and all developmental abnormalities in Pole4 null mice. However, Pole4-/-p53+/- mice exhibit accelerated tumorigenesis, revealing an important role for controlled CMG and origin activation in normal development and tumor prevention.
Collapse
Affiliation(s)
| | - Valerie Borel
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Clare Logan
- MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | | | - Danielle E Cox
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Emma Nye
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Kay Metcalfe
- Department of Genetic Medicine, St Mary's Hospital, Oxford Road, Manchester, M13 OJH, UK
| | - Susan M O'Connell
- Department of Paediatrics, Cork University Hospital, Wilton, Cork T12 DC4A, Ireland
| | - Gordon Stamp
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Helen R Flynn
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | | | - Andrew Jackson
- MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| |
Collapse
|
16
|
V S V, K R, V N S, Sara George P, K C, K J, S T, Sujathan K. DNA Replication Licensing Proteins for Early Detection of Lung Cancer. Asian Pac J Cancer Prev 2017; 18:3041-3047. [PMID: 29172277 PMCID: PMC5773789 DOI: 10.22034/apjcp.2017.18.11.3041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background: To identify and characterize malignant and premalignant cells in sputum and matched tissue samples with reference to expression of minichromosome maintenance proteins (MCM2, MCM5) and cell division cycle protein 6 (CDC 6) and to assess their potential as biomarkers of premalignant and malignant lesions of the lung and associations with clinicopathological features. Methods: Expression of MCM2, MCM5 and 6 proteins in sputum samples and corresponding tissues was assessed by immunocytochemistry, and correlated with histological findings. Results: For characterization of malignant, metaplastic or dysplastic cells, CDC6 protein had the highest sensitivity of 87.7%. All the three markers together had a sensitivity of 94.4%. Furthermore these proteins could be employed to assess the proliferative potential of precancerous or atypical cells, as overexpression increasing with the stage of disease and degree of metastasis. Conclusion: The assessed markers can be utilized in routine cytopathology laboratories to supplement conventional morphological evaluation so that the sensitivity of sputum cytology can be enhanced. Potential applications in predicting the clinical behavior of lung lesions and predicting prognosis and survival deserve further attention.
Collapse
Affiliation(s)
- Veena V S
- Division of Pathology, Regional Cancer Centre, Medical College Campus, Thiruvananthapuram, India
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Li J, Liu J, Liang Z, He F, Yang L, Li P, Jiang Y, Wang B, Zhou C, Wang Y, Ren Y, Yang J, Zhang J, Luo Z, Vaziri C, Liu P. Simvastatin and Atorvastatin inhibit DNA replication licensing factor MCM7 and effectively suppress RB-deficient tumors growth. Cell Death Dis 2017; 8:e2673. [PMID: 28300827 PMCID: PMC5386551 DOI: 10.1038/cddis.2017.46] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 12/13/2022]
Abstract
Loss or dysfunction of tumor suppressor retinoblastoma (RB) is a common feature in various tumors, and contributes to cancer cell stemness and drug resistance to cancer therapy. However, the strategy to suppress or eliminate Rb-deficient tumor cells remains unclear. In the present study, we accidentally found that reduction of DNA replication licensing factor MCM7 induced more apoptosis in RB-deficient tumor cells than in control tumor cells. Moreover, after a drug screening and further studies, we demonstrated that statin drug Simvastatin and Atorvastatin were able to inhibit MCM7 and RB expressions. Further study showed that Simvastatin and Atorvastatin induced more chromosome breaks and gaps of Rb-deficient tumor cells than control tumor cells. In vivo results showed that Simvastatin and Atorvastatin significantly suppressed Rb-deficient tumor growth than control in xenograft mouse models. The present work demonstrates that ‘old' lipid-lowering drugs statins are novel weapons against RB-deficient tumors due to their effects on suppressing MCM7 protein levels.
Collapse
Affiliation(s)
- Juan Li
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Jie Liu
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Zheyong Liang
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Fang He
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Lu Yang
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Pingping Li
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Yina Jiang
- Department of Pathology, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Bo Wang
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Can Zhou
- Department of Breast Surgery, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Yaochun Wang
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Yu Ren
- Department of Breast Surgery, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Jin Yang
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Jianmin Zhang
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo 14263, NY 14263, USA
| | - Zhijun Luo
- Department of Biochemistry, Boston University School of Medicine, Boston 02118, MA, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Peijun Liu
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| |
Collapse
|
18
|
Sun J, Yuan Z, Bai L, Li H. Cryo-EM of dynamic protein complexes in eukaryotic DNA replication. Protein Sci 2017; 26:40-51. [PMID: 27589669 PMCID: PMC5192969 DOI: 10.1002/pro.3033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/27/2016] [Accepted: 08/29/2016] [Indexed: 12/21/2022]
Abstract
DNA replication in Eukaryotes is a highly dynamic process that involves several dozens of proteins. Some of these proteins form stable complexes that are amenable to high-resolution structure determination by cryo-EM, thanks to the recent advent of the direct electron detector and powerful image analysis algorithm. But many of these proteins associate only transiently and flexibly, precluding traditional biochemical purification. We found that direct mixing of the component proteins followed by 2D and 3D image sorting can capture some very weakly interacting complexes. Even at 2D average level and at low resolution, EM images of these flexible complexes can provide important biological insights. It is often necessary to positively identify the feature-of-interest in a low resolution EM structure. We found that systematically fusing or inserting maltose binding protein (MBP) to selected proteins is highly effective in these situations. In this chapter, we describe the EM studies of several protein complexes involved in the eukaryotic DNA replication over the past decade or so. We suggest that some of the approaches used in these studies may be applicable to structural analysis of other biological systems.
Collapse
Affiliation(s)
- Jingchuan Sun
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
| | - Zuanning Yuan
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
- The Biochemistry and Structural Biology ProgramStony Brook UniversityStony BrookNew York11794
| | - Lin Bai
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
| | - Huilin Li
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
| |
Collapse
|
19
|
Abstract
DNA replication origins strikingly differ between eukaryotic species and cell types. Origins are localized and can be highly efficient in budding yeast, are randomly located in early fly and frog embryos, which do not transcribe their genomes, and are clustered in broad (10-100 kb) non-transcribed zones, frequently abutting transcribed genes, in mammalian cells. Nonetheless, in all cases, origins are established during the G1-phase of the cell cycle by the loading of double hexamers of the Mcm 2-7 proteins (MCM DHs), the core of the replicative helicase. MCM DH activation in S-phase leads to origin unwinding, polymerase recruitment, and initiation of bidirectional DNA synthesis. Although MCM DHs are initially loaded at sites defined by the binding of the origin recognition complex (ORC), they ultimately bind chromatin in much greater numbers than ORC and only a fraction are activated in any one S-phase. Data suggest that the multiplicity and functional redundancy of MCM DHs provide robustness to the replication process and affect replication time and that MCM DHs can slide along the DNA and spread over large distances around the ORC. Recent studies further show that MCM DHs are displaced along the DNA by collision with transcription complexes but remain functional for initiation after displacement. Therefore, eukaryotic DNA replication relies on intrinsically mobile and flexible origins, a strategy fundamentally different from bacteria but conserved from yeast to human. These properties of MCM DHs likely contribute to the establishment of broad, intergenic replication initiation zones in higher eukaryotes.
Collapse
Affiliation(s)
- Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Superieure (IBENS), Ecole Normale Superieure, PSL Research University, Paris, France
| |
Collapse
|
20
|
Wei L, Zhao X. A new MCM modification cycle regulates DNA replication initiation. Nat Struct Mol Biol 2016; 23:209-16. [PMID: 26854664 PMCID: PMC4823995 DOI: 10.1038/nsmb.3173] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 01/06/2016] [Indexed: 01/16/2023]
Abstract
The MCM DNA helicase is a central regulatory target during genome replication. MCM is kept inactive during G1, and it initiates replication after being activated in S phase. During this transition, the only known chemical change to MCM is the gain of multisite phosphorylation that promotes cofactor recruitment. Because replication initiation is intimately linked to multiple biological cues, additional changes to MCM can provide further regulatory points. Here, we describe a yeast MCM SUMOylation cycle that regulates replication. MCM subunits undergo SUMOylation upon loading at origins in G1 before MCM phosphorylation. MCM SUMOylation levels then decline as MCM phosphorylation levels rise, thus suggesting an inhibitory role of MCM SUMOylation during replication. Indeed, increasing MCM SUMOylation impairs replication initiation, partly through promoting the recruitment of a phosphatase that decreases MCM phosphorylation and activation. We propose that MCM SUMOylation counterbalances kinase-based regulation, thus ensuring accurate control of replication initiation.
Collapse
Affiliation(s)
- Lei Wei
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
21
|
Nordman JT, Kozhevnikova EN, Verrijzer CP, Pindyurin AV, Andreyeva EN, Shloma VV, Zhimulev IF, Orr-Weaver TL. DNA copy-number control through inhibition of replication fork progression. Cell Rep 2014; 9:841-9. [PMID: 25437540 DOI: 10.1016/j.celrep.2014.10.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/29/2014] [Accepted: 09/30/2014] [Indexed: 01/15/2023] Open
Abstract
Proper control of DNA replication is essential to ensure faithful transmission of genetic material and prevent chromosomal aberrations that can drive cancer progression and developmental disorders. DNA replication is regulated primarily at the level of initiation and is under strict cell-cycle regulation. Importantly, DNA replication is highly influenced by developmental cues. In Drosophila, specific regions of the genome are repressed for DNA replication during differentiation by the SNF2 domain-containing protein SUUR through an unknown mechanism. We demonstrate that SUUR is recruited to active replication forks and mediates the repression of DNA replication by directly inhibiting replication fork progression instead of functioning as a replication fork barrier. Mass spectrometry identification of SUUR-associated proteins identified the replicative helicase member CDC45 as a SUUR-associated protein, supporting a role for SUUR directly at replication forks. Our results reveal that control of eukaryotic DNA copy number can occur through the inhibition of replication fork progression.
Collapse
Affiliation(s)
- Jared T Nordman
- Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Elena N Kozhevnikova
- Erasmus University Medical Centre, P.O. Box 1738, 3000 DR Rotterdam, the Netherlands; Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 10, Novosibirsk 630090, Russia
| | - C Peter Verrijzer
- Erasmus University Medical Centre, P.O. Box 1738, 3000 DR Rotterdam, the Netherlands
| | - Alexey V Pindyurin
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 8/2, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia
| | - Evgeniya N Andreyeva
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 8/2, Novosibirsk 630090, Russia
| | - Victor V Shloma
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 8/2, Novosibirsk 630090, Russia
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 8/2, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia
| | - Terry L Orr-Weaver
- Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| |
Collapse
|
22
|
Functional conservation of the pre-sensor one beta-finger hairpin (PS1-hp) structures in mini-chromosome maintenance proteins of Saccharomyces cerevisiae and archaea. G3-GENES GENOMES GENETICS 2014; 4:1319-26. [PMID: 24875627 PMCID: PMC4455780 DOI: 10.1534/g3.114.011668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mini-chromosome maintenance (MCM) proteins form complexes that are required for DNA replication and are highly conserved throughout evolution. The replicative helicase of eukaryotic organisms is composed of the six paralogs MCM2-7, which form a heterohexameric ring structure. In contrast, the structure of the archaean replicative MCM helicase is a single Mcm protein that forms a homohexameric complex. Atomic structures of archaeal MCMs have identified multiple beta-finger structures in Mcm proteins whose in vivo function is unknown. In the present study, we have investigated the physiological role of the pre-sensor 1 beta-hairpin (PS1-hp) beta-fingers of Saccharomyces cerevisiaeMcm4p and Mcm5p in DNA replication initiation and elongation in vivo. The PS1-hp beta-finger mutant of Mcm5p (mcm5-HAT K506A::URA3) has a growth defect at both 18° and 37°. Mutation of the Mcm4p PS1-hp beta-finger (mcm4-HA K658A::TRP1) does not have a growth defect, indicating different functional contributions of the PS1-hp beta-finger structures of different MCM helicase subunits. Both Mcm4p and Mcm5p PS1-hp beta-finger mutants can coimmunoprecipitate Mcm2p, indicating the formation of the hexameric MCM helicase complex. Both PS1-hp beta-finger mutants have a plasmid loss phenotype that is suppressible by origin dosage, indicating a defective replication initiation. Surprisingly, a defect in the binding of PS1-hp MCM mutants to origins of DNA replication was not found by chromatin immunoprecipitation, suggesting a novel interpretation in which the defect is in a subsequent step of DNA strand separation by the MCM helicase. The double mutant mcm4-HA K658A::TRP1mcm5-HAT K506A::URA3 is lethal, displaying a terminal MCM mutant phenotype of large budded cells.
Collapse
|
23
|
O'Donnell M, Langston L, Stillman B. Principles and concepts of DNA replication in bacteria, archaea, and eukarya. Cold Spring Harb Perspect Biol 2013; 5:5/7/a010108. [PMID: 23818497 DOI: 10.1101/cshperspect.a010108] [Citation(s) in RCA: 214] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The accurate copying of genetic information in the double helix of DNA is essential for inheritance of traits that define the phenotype of cells and the organism. The core machineries that copy DNA are conserved in all three domains of life: bacteria, archaea, and eukaryotes. This article outlines the general nature of the DNA replication machinery, but also points out important and key differences. The most complex organisms, eukaryotes, have to coordinate the initiation of DNA replication from many origins in each genome and impose regulation that maintains genomic integrity, not only for the sake of each cell, but for the organism as a whole. In addition, DNA replication in eukaryotes needs to be coordinated with inheritance of chromatin, developmental patterning of tissues, and cell division to ensure that the genome replicates once per cell division cycle.
Collapse
Affiliation(s)
- Michael O'Donnell
- The Rockefeller University and Howard Hughes Medical Institute, New York, New York 10065, USA
| | | | | |
Collapse
|