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Escorcia W, Tripathi VP, Yuan JP, Forsburg SL. A visual atlas of meiotic protein dynamics in living fission yeast. Open Biol 2021; 11:200357. [PMID: 33622106 PMCID: PMC8061692 DOI: 10.1098/rsob.200357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Meiosis is a carefully choreographed dynamic process that re-purposes proteins from somatic/vegetative cell division, as well as meiosis-specific factors, to carry out the differentiation and recombination pathway common to sexually reproducing eukaryotes. Studies of individual proteins from a variety of different experimental protocols can make it difficult to compare details between them. Using a consistent protocol in otherwise wild-type fission yeast cells, this report provides an atlas of dynamic protein behaviour of representative proteins at different stages during normal zygotic meiosis in fission yeast. This establishes common landmarks to facilitate comparison of different proteins and shows that initiation of S phase likely occurs prior to nuclear fusion/karyogamy.
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Affiliation(s)
- Wilber Escorcia
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA.,Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 45207, USA
| | - Vishnu P Tripathi
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Ji-Ping Yuan
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Susan L Forsburg
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
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2
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Novák B, Tyson JJ. Computational modeling of chromosome re-replication in mutant strains of fission yeast. Mol Biol Cell 2021; 32:830-841. [PMID: 33534609 PMCID: PMC8108527 DOI: 10.1091/mbc.e20-09-0610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Typically cells replicate their genome only once per division cycle, but under some circumstances, both natural and unnatural, cells synthesize an overabundance of DNA, either in a disorganized manner (“overreplication”) or by a systematic doubling of chromosome number (“endoreplication”). These variations on the theme of DNA replication and division have been studied in strains of fission yeast, Schizosaccharomyces pombe, carrying mutations that interfere with the function of mitotic cyclin-dependent kinase (Cdk1:Cdc13) without impeding the roles of DNA-replication loading factor (Cdc18) and S-phase cyclin-dependent kinase (Cdk1:Cig2). Some of these mutations support endoreplication, and some overreplication. In this paper, we propose a dynamical model of the interactions among the proteins governing DNA replication and cell division in fission yeast. By computational simulations of the mathematical model, we account for the observed phenotypes of these re-replicating mutants, and by theoretical analysis of the dynamical system, we provide insight into the molecular distinctions between overreplicating and endoreplicating cells. In the case of induced overproduction of regulatory proteins, our model predicts that cells first switch from normal mitotic cell cycles to growth-controlled endoreplication, and ultimately to disorganized overreplication, parallel to the slow increase of protein to very high levels.
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Affiliation(s)
- Béla Novák
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - John J Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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3
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Active Replication Checkpoint Drives Genome Instability in Fission Yeast mcm4 Mutant. Mol Cell Biol 2020; 40:MCB.00033-20. [PMID: 32341083 DOI: 10.1128/mcb.00033-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/17/2020] [Indexed: 02/07/2023] Open
Abstract
Upon replication fork arrest, the replication checkpoint kinase Cds1 is stimulated to preserve genome integrity. Robust activation of Cds1 in response to hydroxyurea prevents the endonuclease Mus81 from cleaving the stalled replication fork inappropriately. However, we find that the response is different in temperature-sensitive mcm4 mutants, affecting a subunit of the MCM replicative helicase. We show that Cds1 inhibition of Mus81 promotes genomic instability and allows mcm4-dg cells to evade cell cycle arrest. Cds1 regulation of Mus81 activity also contributes to the formation of the replication stress-induced DNA damage markers replication protein A (RPA) and Ku. These results identify a surprising role for Cds1 in driving DNA damage and disrupted chromosomal segregation under certain conditions of replication stress.
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Checkpoint Regulation of Nuclear Tos4 Defines S Phase Arrest in Fission Yeast. G3-GENES GENOMES GENETICS 2020; 10:255-266. [PMID: 31719112 PMCID: PMC6945033 DOI: 10.1534/g3.119.400726] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
From yeast to humans, the cell cycle is tightly controlled by regulatory networks that regulate cell proliferation and can be monitored by dynamic visual markers in living cells. We have observed S phase progression by monitoring nuclear accumulation of the FHA-containing DNA binding protein Tos4, which is expressed in the G1/S phase transition. We use Tos4 localization to distinguish three classes of DNA replication mutants: those that arrest with an apparent 1C DNA content and accumulate Tos4 at the restrictive temperature; those that arrest with an apparent 2C DNA content, that do not accumulate Tos4; and those that proceed into mitosis despite a 1C DNA content, again without Tos4 accumulation. Our data indicate that Tos4 localization in these conditions is responsive to checkpoint kinases, with activation of the Cds1 checkpoint kinase promoting Tos4 retention in the nucleus, and activation of the Chk1 damage checkpoint promoting its turnover. Tos4 localization therefore allows us to monitor checkpoint-dependent activation that responds to replication failure in early vs. late S phase.
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5
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Shen KF, Forsburg SL. Overlapping Roles in Chromosome Segregation for Heterochromatin Protein 1 (Swi6) and DDK in Schizosaccharomyces pombe. Genetics 2019; 212:417-430. [PMID: 31000521 PMCID: PMC6553818 DOI: 10.1534/genetics.119.302125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/10/2019] [Indexed: 12/23/2022] Open
Abstract
Fission yeast Swi6 is a human HP1 homolog that plays important roles in multiple cellular processes. In addition to its role in maintaining heterochromatin silencing, Swi6 is required for cohesin enrichment at the pericentromere. Loss of Swi6 leads to abnormal mitosis, including defects in the establishment of bioriented sister kinetochores and microtubule attachment. Swi6 interacts with Dfp1, a regulatory subunit of DBF4-dependent kinase (DDK), and failure to recruit Dfp1 to the pericentromere results in late DNA replication. Using the dfp1-3A mutant allele, which specifically disrupts Swi6-Dfp1 association, we investigated how interaction between Swi6 and Dfp1 affects chromosome dynamics. We find that disrupting the interaction between Swi6 and Dfp1 delays mitotic progression in a spindle assembly checkpoint-dependent manner. Artificially tethering Dfp1 back to the pericentromere is sufficient to restore normal spindle length and rescue segregation defects in swi6-deleted cells. However, Swi6 is necessary for centromeric localization of Rad21-GFP independent of DDK. Our data indicate that DDK contributes to mitotic chromosome segregation in pathways that partly overlap with, but can be separated from both, Swi6 and the other HP1 homolog, Chp2.
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Affiliation(s)
- Kuo-Fang Shen
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-2910
| | - Susan L Forsburg
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-2910
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6
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Rubio A, García-Blanco N, Vázquez-Bolado A, Belén Suárez M, Moreno S. Nutritional cell cycle reprogramming reveals that inhibition of Cdk1 is required for proper MBF-dependent transcription. J Cell Sci 2018; 131:jcs.218743. [PMID: 30154212 DOI: 10.1242/jcs.218743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/20/2018] [Indexed: 01/22/2023] Open
Abstract
In nature, cells and in particular unicellular microorganisms are exposed to a variety of nutritional environments. Fission yeast cells cultured in nitrogen-rich media grow fast, divide with a large size and show a short G1 and a long G2. However, when cultured in nitrogen-poor media, they exhibit reduced growth rate and cell size and a long G1 and a short G2. In this study, we compared the phenotypes of cells lacking the highly conserved cyclin-dependent kinase (Cdk) inhibitor Rum1 and the anaphase-promoting complex/cyclosome (APC/C) activator Ste9 in nitrogen-rich and nitrogen-poor media. Rum1 and Ste9 are dispensable for cell division in nitrogen-rich medium. However, in nitrogen-poor medium they are essential for generating a proper wave of MluI cell-cycle box binding factor (MBF)-dependent transcription at the end of G1, which is crucial for promoting a successful S phase. Mutants lacking Rum1 and Ste9 showed premature entry into S phase and a reduced wave of MBF-dependent transcription, leading to replication stress, DNA damage and G2 cell cycle arrest. This work demonstrates how reprogramming the cell cycle by changing the nutritional environment may reveal new roles for cell cycle regulators.
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Affiliation(s)
- Angela Rubio
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain.,Department of Microbiology and Genetics, University of Salamanca, 37007 Salamanca. Spain
| | - Natalia García-Blanco
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain.,Department of Microbiology and Genetics, University of Salamanca, 37007 Salamanca. Spain
| | - Alicia Vázquez-Bolado
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain.,Department of Microbiology and Genetics, University of Salamanca, 37007 Salamanca. Spain
| | - María Belén Suárez
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain.,Department of Microbiology and Genetics, University of Salamanca, 37007 Salamanca. Spain
| | - Sergio Moreno
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
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Knockleby J, Kim BJ, Mehta A, Lee H. Cdk1-mediated phosphorylation of Cdc7 suppresses DNA re-replication. Cell Cycle 2016; 15:1494-505. [PMID: 27105124 PMCID: PMC4934051 DOI: 10.1080/15384101.2016.1176658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 03/23/2016] [Accepted: 04/06/2016] [Indexed: 12/18/2022] Open
Abstract
To maintain genetic stability, the entire mammalian genome must replicate only once per cell cycle. This is largely achieved by strictly regulating the stepwise formation of the pre-replication complex (pre-RC), followed by the activation of individual origins of DNA replication by Cdc7/Dbf4 kinase. However, the mechanism how Cdc7 itself is regulated in the context of cell cycle progression is poorly understood. Here we report that Cdc7 is phosphorylated by a Cdk1-dependent manner during prometaphase on multiple sites, resulting in its dissociation from origins. In contrast, Dbf4 is not removed from origins in prometaphase, nor is it degraded as cells exit mitosis. Our data thus demonstrates that constitutive phosphorylation of Cdc7 at Cdk1 recognition sites, but not the regulation of Dbf4, prevents the initiation of DNA replication in normally cycling cells and under conditions that promote re-replication in G2/M. As cells exit mitosis, PP1α associates with and dephosphorylates Cdc7. Together, our data support a model where Cdc7 (de)phosphorylation is the molecular switch for the activation and inactivation of DNA replication in mitosis, directly connecting Cdc7 and PP1α/Cdk1 to the regulation of once-per-cell cycle DNA replication in mammalian cells.
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Affiliation(s)
- James Knockleby
- Tumour Biology Group, Advanced Medical Research Institute of Canada, Health Sciences North, Sudbury, Ontario, Canada
| | - Byung Ju Kim
- Tumour Biology Group, Advanced Medical Research Institute of Canada, Health Sciences North, Sudbury, Ontario, Canada
| | - Avani Mehta
- Tumour Biology Group, Advanced Medical Research Institute of Canada, Health Sciences North, Sudbury, Ontario, Canada
| | - Hoyun Lee
- Tumour Biology Group, Advanced Medical Research Institute of Canada, Health Sciences North, Sudbury, Ontario, Canada
- Departments of Medicine, the Faculty of Medicine, the University of Ottawa, Ottawa, Ontario, Canada
- Northern Ontario School of Medicine, Sudbury, Ontario, Canada
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8
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Gaspa L, González-Medina A, Hidalgo E, Ayté J. A functional genome-wide genetic screening identifies new pathways controlling the G1/S transcriptional wave. Cell Cycle 2016; 15:720-9. [PMID: 26890608 DOI: 10.1080/15384101.2016.1148839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The Schizosaccharomyces pombe MBF complex activates the transcription of genes required for DNA synthesis and S phase. The MBF complex contains several proteins, including the core components Cdc10, Res1 and Res2, the co-repressor proteins Yox1 and Nrm1 and the co-activator Rep2. It has recently been shown how MBF is regulated when either the DNA damage or the DNA synthesis checkpoints are activated. However, how MBF is regulated in a normal unperturbed cell cycle is still not well understood. We have set up a genome-wide genomic screen searching for global regulators of MBF. We have crossed our knock-out collection library with a reporter strain that allows the measurement of MBF activity in live cells by flow cytometry. We confirm previously known regulators of MBF and show that COP9/signalosome and tRNA methyltransferases also regulate MBF activity.
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Affiliation(s)
- Laura Gaspa
- a Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra , Barcelona , Spain
| | | | - Elena Hidalgo
- a Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra , Barcelona , Spain
| | - José Ayté
- a Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra , Barcelona , Spain
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9
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Green MD, Sabatinos SA, Forsburg SL. Microscopy techniques to examine DNA replication in fission yeast. Methods Mol Biol 2015; 1300:13-41. [PMID: 25916703 DOI: 10.1007/978-1-4939-2596-4_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Temporal and spatial visualization of replication proteins and associated structures within the narrow confines of a yeast nucleus is technically challenging. Choosing the appropriate method depends upon the parameters of the experiment, the nature of the molecules to be observed, and the hypothesis to be tested. In this chapter, we review three broad types of visualization: whole-cell fluorescence or immunofluorescence, which is useful for questions of timing and chromatin association; nuclear spreads, which provide greater resolution within the chromatin for co-localization and region-specific effects; and chromatin fibers, which allow observation of labeled proteins and newly synthesized DNA on a linear chromosome. We also suggest a mounting procedure for live fission yeast with fluorescent proteins. We discuss applications of these protocols and some considerations for choosing methods and fluorophores.
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Affiliation(s)
- Marc D Green
- Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, RRI 108, Los Angeles, CA, 90089-2910, USA,
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10
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Hipp K, Rau P, Schäfer B, Gronenborn B, Jeske H. The RXL motif of the African cassava mosaic virus Rep protein is necessary for rereplication of yeast DNA and viral infection in plants. Virology 2014; 462-463:189-98. [PMID: 24999043 DOI: 10.1016/j.virol.2014.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/02/2014] [Accepted: 06/04/2014] [Indexed: 01/17/2023]
Abstract
Geminiviruses, single-stranded DNA plant viruses, encode a replication-initiator protein (Rep) that is indispensable for virus replication. A potential cyclin interaction motif (RXL) in the sequence of African cassava mosaic virus Rep may be an alternative link to cell cycle controls to the known interaction with plant homologs of retinoblastoma protein (pRBR). Mutation of this motif abrogated rereplication in fission yeast induced by expression of wildtype Rep suggesting that Rep interacts via its RXL motif with one or several yeast proteins. The RXL motif is essential for viral infection of Nicotiana benthamiana plants, since mutation of this motif in infectious clones prevented any symptomatic infection. The cell-cycle link (Clink) protein of a nanovirus (faba bean necrotic yellows virus) was investigated that activates the cell cycle by binding via its LXCXE motif to pRBR. Expression of wildtype Clink and a Clink mutant deficient in pRBR-binding did not trigger rereplication in fission yeast.
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Affiliation(s)
- Katharina Hipp
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Peter Rau
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Benjamin Schäfer
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Bruno Gronenborn
- Institut des Sciences du Végétal, CNRS, 91198 Gif-sur-Yvette, France
| | - Holger Jeske
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany.
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11
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Borg M, Rutley N, Kagale S, Hamamura Y, Gherghinoiu M, Kumar S, Sari U, Esparza-Franco MA, Sakamoto W, Rozwadowski K, Higashiyama T, Twell D. An EAR-Dependent Regulatory Module Promotes Male Germ Cell Division and Sperm Fertility in Arabidopsis. THE PLANT CELL 2014; 26:2098-2113. [PMID: 24876252 PMCID: PMC4079371 DOI: 10.1105/tpc.114.124743] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The production of the sperm cells in angiosperms requires coordination of cell division and cell differentiation. In Arabidopsis thaliana, the germline-specific MYB protein DUO1 integrates these processes, but the regulatory hierarchy in which DUO1 functions is unknown. Here, we identify an essential role for two germline-specific DUO1 target genes, DAZ1 and DAZ2, which encode EAR motif-containing C2H2-type zinc finger proteins. We show that DAZ1/DAZ2 are required for germ cell division and for the proper accumulation of mitotic cyclins. Importantly, DAZ1/DAZ2 are sufficient to promote G2- to M-phase transition and germ cell division in the absence of DUO1. DAZ1/DAZ2 are also required for DUO1-dependent cell differentiation and are essential for gamete fusion at fertilization. We demonstrate that the two EAR motifs in DAZ1/DAZ2 mediate their function in the male germline and are required for transcriptional repression and for physical interaction with the corepressor TOPLESS. Our findings uncover an essential module in a regulatory hierarchy that drives mitotic transition in male germ cells and implicates gene repression pathways in sperm cell formation and fertility.
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Affiliation(s)
- Michael Borg
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Nicholas Rutley
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Sateesh Kagale
- Agriculture and Agri-Food Canada, Saskatoon SK S7N OX2, Canada
| | - Yuki Hamamura
- JST, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Mihai Gherghinoiu
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Sanjeev Kumar
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Ugur Sari
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | | | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | | | - Tetsuya Higashiyama
- JST, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - David Twell
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
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12
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Mechanism of chromosomal DNA replication initiation and replication fork stabilization in eukaryotes. SCIENCE CHINA-LIFE SCIENCES 2014; 57:482-7. [PMID: 24699916 DOI: 10.1007/s11427-014-4631-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 09/18/2013] [Indexed: 10/25/2022]
Abstract
Chromosomal DNA replication is one of the central biological events occurring inside cells. Due to its large size, the replication of genomic DNA in eukaryotes initiates at hundreds to tens of thousands of sites called DNA origins so that the replication could be completed in a limited time. Further, eukaryotic DNA replication is sophisticatedly regulated, and this regulation guarantees that each origin fires once per S phase and each segment of DNA gets duplication also once per cell cycle. The first step of replication initiation is the assembly of pre-replication complex (pre-RC). Since 1973, four proteins, Cdc6/Cdc18, MCM, ORC and Cdt1, have been extensively studied and proved to be pre-RC components. Recently, a novel pre-RC component called Sap1/Girdin was identified. Sap1/Girdin is required for loading Cdc18/Cdc6 to origins for pre-RC assembly in the fission yeast and human cells, respectively. At the transition of G1 to S phase, pre-RC is activated by the two kinases, cyclindependent kinase (CDK) and Dbf4-dependent kinase (DDK), and subsequently, RPA, primase-polα, PCNA, topoisomerase, Cdc45, polδ, and polɛ are recruited to DNA origins for creating two bi-directional replication forks and initiating DNA replication. As replication forks move along chromatin DNA, they frequently stall due to the presence of a great number of replication barriers on chromatin DNA, such as secondary DNA structures, protein/DNA complexes, DNA lesions, gene transcription. Stalled forks must require checkpoint regulation for their stabilization. Otherwise, stalled forks will collapse, which results in incomplete DNA replication and genomic instability. This short review gives a concise introduction regarding the current understanding of replication initiation and replication fork stabilization.
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13
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Yadav MP, Padmanabhan S, Tripathi VP, Mishra RK, Dubey DD. Analysis of stress-induced duplex destabilization (SIDD) properties of replication origins, genes and intergenes in the fission yeast, Schizosaccharomyces pombe. BMC Res Notes 2012; 5:643. [PMID: 23163955 PMCID: PMC3533806 DOI: 10.1186/1756-0500-5-643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 11/12/2012] [Indexed: 11/24/2022] Open
Abstract
Background Replication and transcription, the two key functions of DNA, require unwinding of the DNA double helix. It has been shown that replication origins in the budding yeast, Saccharomyces cerevisiae contain an easily unwound stretch of DNA. We have used a recently developed method for determining the locations and degrees of stress-induced duplex destabilization (SIDD) for all the reported replication origins in the genome of the fission yeast, Schizosaccharomyces pombe. Results We have found that the origins are more susceptible to SIDD as compared to the non-origin intergenic regions (NOIRs) and genes. SIDD analysis of many known origins in other eukaryotes suggests that SIDD is a common property of replication origins. Interestingly, the previously shown deletion-dependent changes in the activities of the origins of the ura4 origin region on chromosome 3 are paralleled by changes in SIDD properties, suggesting SIDD’s role in origin activity. SIDD profiling following in silico deletions of some origins suggests that many of the closely spaced S. pombe origins could be clusters of two or three weak origins, similar to the ura4 origin region. Conclusion SIDD appears to be a highly conserved, functionally important property of replication origins in S. pombe and other organisms. The distinctly low SIDD scores of origins and the long range effects of genetic alterations on SIDD properties provide a unique predictive potential to the SIDD analysis. This could be used in exploring different aspects of structural and functional organization of origins including interactions between closely spaced origins.
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Affiliation(s)
- Mukesh P Yadav
- Department of Biotechnology, Veer Bahadur Singh Purvanchal University, Jaunpur, Uttar Pradesh 222001, India
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14
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Nowack M, Harashima H, Dissmeyer N, Zhao X, Bouyer D, Weimer A, De Winter F, Yang F, Schnittger A. Genetic Framework of Cyclin-Dependent Kinase Function in Arabidopsis. Dev Cell 2012; 22:1030-40. [DOI: 10.1016/j.devcel.2012.02.015] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 12/15/2011] [Accepted: 02/29/2012] [Indexed: 10/28/2022]
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15
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Salvado B, Karathia H, Chimenos AU, Vilaprinyo E, Omholt S, Sorribas A, Alves R. Methods for and results from the study of design principles in molecular systems. Math Biosci 2011; 231:3-18. [DOI: 10.1016/j.mbs.2011.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 01/24/2011] [Accepted: 02/10/2011] [Indexed: 12/27/2022]
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16
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Kiang L, Heichinger C, Watt S, Bähler J, Nurse P. Specific replication origins promote DNA amplification in fission yeast. J Cell Sci 2010; 123:3047-51. [PMID: 20736315 DOI: 10.1242/jcs.067470] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To ensure equal replication of the genome in every eukaryotic cell cycle, replication origins fire only once each S phase and do not fire after passive replication. Failure in these controls can lead to local amplification, contributing to genome instability and the development of cancer. To identify features of replication origins important for such amplification, we have investigated origin firing and local genome amplification in the presence of excess helicase loaders Cdc18 and Cdt1 in fission yeast. We find that S phase controls are attenuated and coordination of origin firing is lost, resulting in local amplification. Specific origins are necessary for amplification but act only within a permissive chromosomal context. Origins associated with amplification are highly AT-rich, fire efficiently and early during mitotic S phase, and are located in large intergenic regions. We propose that these features predispose replication origins to re-fire within a single S phase, or to remain active after passive replication.
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Affiliation(s)
- Lee Kiang
- Laboratory of Yeast Genetics and Cell Biology, The Rockefeller University, 1230 York Avenue, Box 5, New York, NY 10065, USA.
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17
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Persistent telomere damage induces bypass of mitosis and tetraploidy. Cell 2010; 141:81-93. [PMID: 20371347 DOI: 10.1016/j.cell.2010.01.031] [Citation(s) in RCA: 227] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 12/09/2009] [Accepted: 01/15/2010] [Indexed: 12/31/2022]
Abstract
Tetraploidization has been proposed as an intermediate step toward aneuploidy in human cancer but a general mechanism for the induction of tetraploidy during tumorigenesis is lacking. We report that tetraploidization occurs in p53-deficient cells experiencing a prolonged DNA damage signal due to persistent telomere dysfunction. Live-cell imaging revealed that these cells have an extended G2 due to ATM/ATR- and Chk1/Chk2-mediated inhibition of Cdk1/CyclinB and eventually bypass mitosis. Despite their lack of mitosis, the cells showed APC/Cdh1-dependent degradation of the replication inhibitor geminin, followed by accumulation of Cdt1, which is required for origin licensing. Cells then entered a second S phase resulting in whole-genome reduplication and tetraploidy. Upon restoration of telomere protection, these tetraploid cells resumed cell division cycles and proliferated. These observations suggest a general mechanism for the induction of tetraploidization in the early stages of tumorigenesis when telomere dysfunction can result from excessive telomere shortening.
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Kim JA, Lee J, Margolis RL, Fotedar R. SP600125 suppresses Cdk1 and induces endoreplication directly from G2 phase, independent of JNK inhibition. Oncogene 2010; 29:1702-16. [PMID: 20062077 PMCID: PMC3145494 DOI: 10.1038/onc.2009.464] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 10/14/2009] [Accepted: 10/22/2009] [Indexed: 12/20/2022]
Abstract
Cell cycle controls ensure that DNA replication (S phase) follows mitosis resulting in two precise copies of the genome. A failure of the control mechanisms can result in multiple rounds of DNA replication without cell division. In endoreplication, cells with replicated genomes bypass mitosis, then replicate their DNA again, resulting in polyploidy. Endoreplication from G2 phase lacks all hallmarks of mitosis. Using synchronized cells, we show that the c-Jun N-terminal kinase (JNK) inhibitor, SP600125, prevents the entry of cells into mitosis and leads to endoreplication of DNA from G2 phase. We show that cells proceed from G2 phase to replicate their DNA in the absence of mitosis. This effect of SP600125 is independent of its suppression of JNK activity. Instead, the inhibitory effect of SP600125 on mitotic entry predominantly occurs upstream of Aurora A kinase and Polo-like kinase 1, resulting in a failure to remove the inhibitory phosphorylation of Cdk1. Importantly, our results directly show that the inhibition of Cdk1 activity and the persistence of Cdk2 activity in G2 cells induces endoreplication without mitosis. Furthermore, endoreplication from G2 phase is independent of p53 control.
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Affiliation(s)
- JA Kim
- Sidney Kimmel Cancer Center, San Diego, CA, USA
| | - J Lee
- Sidney Kimmel Cancer Center, San Diego, CA, USA
| | - RL Margolis
- Sidney Kimmel Cancer Center, San Diego, CA, USA
- Burnham Institute for Medical Research, La Jolla, CA, USA
| | - R Fotedar
- Sidney Kimmel Cancer Center, San Diego, CA, USA
- Burnham Institute for Medical Research, La Jolla, CA, USA
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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