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Ostapenko D, Solomon MJ. APC Cdh1-mediated degradation of Cdh1 is necessary for faithful meiotic chromosome segregation in S. cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601619. [PMID: 39005361 PMCID: PMC11245022 DOI: 10.1101/2024.07.01.601619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The Anaphase-Promoting Complex/Cyclosome (APC/C) is a ubiquitin ligase that promotes the ubiquitination and subsequent degradation of numerous cell cycle regulators during mitosis and in G1. Proteins are recruited to the APC/C by activator proteins such as Cdh1. During the cell cycle, Cdh1 is subject to precise regulation so that substrates are not degraded prematurely. We have explored the regulation of Cdh1 during the developmental transition into meiosis and sporulation in the budding yeast S. cerevisiae. Transition to sporulation medium triggers the degradation of Cdh1. Cdh1 degradation is mediated by the APC/C itself in a "trans" mechanism in which one molecule of Cdh1 recruits a second molecule of Cdh1 to the APC/C for ubiquitination. Degradation requires an intact glucose-sensing SNF1 protein kinase complex (orthologous to the mammalian AMPK nutritional sensor), which directly phosphorylates Cdh1 on Ser-200 within an unstructured N-terminal region. In the absence of phosphorylation, expression of a Cdh1-S200A mutant is fully stabilized, leading to chromosome instability and loss of viability. We hypothesize that Cdh1 degradation is necessary for the preservation of cell cycle regulators and chromosome cohesion proteins between the reductional and equational meiotic divisions, which occur without the intervening Gap or S phases found in mitotic cell cycles.
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Affiliation(s)
- Denis Ostapenko
- Yale University, Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, New Haven, CT 06520-8114
| | - Mark J. Solomon
- Yale University, Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, New Haven, CT 06520-8114
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2
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Mecklenburg N, Kowalczyk I, Witte F, Görne J, Laier A, Mamo TM, Gonschior H, Lehmann M, Richter M, Sporbert A, Purfürst B, Hübner N, Hammes A. Identification of disease-relevant modulators of the SHH pathway in the developing brain. Development 2021; 148:272000. [PMID: 34463328 DOI: 10.1242/dev.199307] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Pathogenic gene variants in humans that affect the sonic hedgehog (SHH) pathway lead to severe brain malformations with variable penetrance due to unknown modifier genes. To identify such modifiers, we established novel congenic mouse models. LRP2-deficient C57BL/6N mice suffer from heart outflow tract defects and holoprosencephaly caused by impaired SHH activity. These defects are fully rescued on a FVB/N background, indicating a strong influence of modifier genes. Applying comparative transcriptomics, we identified Pttg1 and Ulk4 as candidate modifiers upregulated in the rescue strain. Functional analyses showed that ULK4 and PTTG1, both microtubule-associated proteins, are positive regulators of SHH signaling, rendering the pathway more resilient to disturbances. In addition, we characterized ULK4 and PTTG1 as previously unidentified components of primary cilia in the neuroepithelium. The identification of genes that powerfully modulate the penetrance of genetic disturbances affecting the brain and heart is likely relevant to understanding the variability in human congenital disorders.
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Affiliation(s)
- Nora Mecklenburg
- Disorders of the Nervous System, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Izabela Kowalczyk
- Disorders of the Nervous System, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Franziska Witte
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Jessica Görne
- Disorders of the Nervous System, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Alena Laier
- Disorders of the Nervous System, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Tamrat M Mamo
- Disorders of the Nervous System, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Hannes Gonschior
- Cellular Imaging, Light Microscopy, Leibniz-Research Institute for Molecular Pharmacology (FMP), 13125 Berlin, Germany
| | - Martin Lehmann
- Cellular Imaging, Light Microscopy, Leibniz-Research Institute for Molecular Pharmacology (FMP), 13125 Berlin, Germany
| | - Matthias Richter
- Advanced Light Microscopy Technology Platform, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Anje Sporbert
- Advanced Light Microscopy Technology Platform, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Bettina Purfürst
- Electron microscopy technology platform, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany.,Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.,Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Annette Hammes
- Disorders of the Nervous System, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
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3
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A modular approach for modeling the cell cycle based on functional response curves. PLoS Comput Biol 2021; 17:e1009008. [PMID: 34379640 PMCID: PMC8382204 DOI: 10.1371/journal.pcbi.1009008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/23/2021] [Accepted: 07/19/2021] [Indexed: 12/02/2022] Open
Abstract
Modeling biochemical reactions by means of differential equations often results in systems with a large number of variables and parameters. As this might complicate the interpretation and generalization of the obtained results, it is often desirable to reduce the complexity of the model. One way to accomplish this is by replacing the detailed reaction mechanisms of certain modules in the model by a mathematical expression that qualitatively describes the dynamical behavior of these modules. Such an approach has been widely adopted for ultrasensitive responses, for which underlying reaction mechanisms are often replaced by a single Hill function. Also time delays are usually accounted for by using an explicit delay in delay differential equations. In contrast, however, S-shaped response curves, which by definition have multiple output values for certain input values and are often encountered in bistable systems, are not easily modeled in such an explicit way. Here, we extend the classical Hill function into a mathematical expression that can be used to describe both ultrasensitive and S-shaped responses. We show how three ubiquitous modules (ultrasensitive responses, S-shaped responses and time delays) can be combined in different configurations and explore the dynamics of these systems. As an example, we apply our strategy to set up a model of the cell cycle consisting of multiple bistable switches, which can incorporate events such as DNA damage and coupling to the circadian clock in a phenomenological way. Bistability plays an important role in many biochemical processes and typically emerges from complex interaction patterns such as positive and double negative feedback loops. Here, we propose to theoretically study the effect of bistability in a larger interaction network. We explicitly incorporate a functional expression describing an S-shaped input-output curve in the model equations, without the need for considering the underlying biochemical events. This expression can be converted into a functional module for an ultrasensitive response, and a time delay is easily included as well. Exploiting the fact that several of these modules can easily be combined in larger networks, we construct a cell cycle model consisting of multiple bistable switches and show how this approach can account for a number of known properties of the cell cycle.
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4
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Fonseca-García C, Nava N, Lara M, Quinto C. An NADPH oxidase regulates carbon metabolism and the cell cycle during root nodule symbiosis in common bean (Phaseolus vulgaris). BMC PLANT BIOLOGY 2021; 21:274. [PMID: 34130630 PMCID: PMC8207584 DOI: 10.1186/s12870-021-03060-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/20/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Rhizobium-legume symbiosis is a specific, coordinated interaction that results in the formation of a root nodule, where biological nitrogen fixation occurs. NADPH oxidases, or Respiratory Burst Oxidase Homologs (RBOHs) in plants, are enzymes that generate superoxide (O2 •-). Superoxide produces other reactive oxygen species (ROS); these ROS regulate different stages of mutualistic interactions. For example, changes in ROS levels are thought to induce ROS scavenging, cell wall remodeling, and changes in phytohormone homeostasis during symbiotic interactions. In common bean (Phaseolus vulgaris), PvRbohB plays a key role in the early stages of nodulation. RESULTS In this study, to explore the role of PvRbohB in root nodule symbiosis, we analyzed transcriptomic data from the roots of common bean under control conditions (transgenic roots without construction) and roots with downregulated expression of PvRbohB (by RNA interference) non-inoculated and inoculated with R. tropici. Our results suggest that ROS produced by PvRBOHB play a central role in infection thread formation and nodule organogenesis through crosstalk with flavonoids, carbon metabolism, cell cycle regulation, and the plant hormones auxin and cytokinin during the early stages of this process. CONCLUSIONS Our findings provide important insight into the multiple roles of ROS in regulating rhizobia-legume symbiosis.
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Affiliation(s)
- Citlali Fonseca-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, Cuernavaca, Morelos, Colonia Chamilpa Mexico
| | - Noreide Nava
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, Cuernavaca, Morelos, Colonia Chamilpa Mexico
| | - Miguel Lara
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, Cuernavaca, Morelos, Colonia Chamilpa Mexico
| | - Carmen Quinto
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, Cuernavaca, Morelos, Colonia Chamilpa Mexico
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5
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Kazemi-Sefat GE, Keramatipour M, Talebi S, Kavousi K, Sajed R, Kazemi-Sefat NA, Mousavizadeh K. The importance of CDC27 in cancer: molecular pathology and clinical aspects. Cancer Cell Int 2021; 21:160. [PMID: 33750395 PMCID: PMC7941923 DOI: 10.1186/s12935-021-01860-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
Background CDC27 is one of the core components of Anaphase Promoting complex/cyclosome. The main role of this protein is defined at cellular division to control cell cycle transitions. Here we review the molecular aspects that may affect CDC27 regulation from cell cycle and mitosis to cancer pathogenesis and prognosis. Main text It has been suggested that CDC27 may play either like a tumor suppressor gene or oncogene in different neoplasms. Divergent variations in CDC27 DNA sequence and alterations in transcription of CDC27 have been detected in different solid tumors and hematological malignancies. Elevated CDC27 expression level may increase cell proliferation, invasiveness and metastasis in some malignancies. It has been proposed that CDC27 upregulation may increase stemness in cancer stem cells. On the other hand, downregulation of CDC27 may increase the cancer cell survival, decrease radiosensitivity and increase chemoresistancy. In addition, CDC27 downregulation may stimulate efferocytosis and improve tumor microenvironment. Conclusion CDC27 dysregulation, either increased or decreased activity, may aggravate neoplasms. CDC27 may be suggested as a prognostic biomarker in different malignancies. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-01860-9.
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Affiliation(s)
- Golnaz Ensieh Kazemi-Sefat
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Shahid Hemmat Highway, P.O. Box: 14665-354, Tehran, 14496-14535, Iran
| | - Mohammad Keramatipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Talebi
- Department of Medical Genetics, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Roya Sajed
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Shahid Hemmat Highway, P.O. Box: 14665-354, Tehran, 14496-14535, Iran
| | | | - Kazem Mousavizadeh
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Shahid Hemmat Highway, P.O. Box: 14665-354, Tehran, 14496-14535, Iran. .,Cellular and Molecular Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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6
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Howell RSM, Klemm C, Thorpe PH, Csikász-Nagy A. Unifying the mechanism of mitotic exit control in a spatiotemporal logical model. PLoS Biol 2020; 18:e3000917. [PMID: 33180788 PMCID: PMC7685450 DOI: 10.1371/journal.pbio.3000917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 11/24/2020] [Accepted: 10/09/2020] [Indexed: 11/18/2022] Open
Abstract
The transition from mitosis into the first gap phase of the cell cycle in budding yeast is controlled by the Mitotic Exit Network (MEN). The network interprets spatiotemporal cues about the progression of mitosis and ensures that release of Cdc14 phosphatase occurs only after completion of key mitotic events. The MEN has been studied intensively; however, a unified understanding of how localisation and protein activity function together as a system is lacking. In this paper, we present a compartmental, logical model of the MEN that is capable of representing spatial aspects of regulation in parallel to control of enzymatic activity. We show that our model is capable of correctly predicting the phenotype of the majority of mutants we tested, including mutants that cause proteins to mislocalise. We use a continuous time implementation of the model to demonstrate that Cdc14 Early Anaphase Release (FEAR) ensures robust timing of anaphase, and we verify our findings in living cells. Furthermore, we show that our model can represent measured cell-cell variation in Spindle Position Checkpoint (SPoC) mutants. This work suggests a general approach to incorporate spatial effects into logical models. We anticipate that the model itself will be an important resource to experimental researchers, providing a rigorous platform to test hypotheses about regulation of mitotic exit.
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Affiliation(s)
- Rowan S M Howell
- The Francis Crick Institute, London, United Kingdom.,Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Cinzia Klemm
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Peter H Thorpe
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Attila Csikász-Nagy
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom.,Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
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7
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Khondker S, Kajjo S, Chandler-Brown D, Skotheim J, Rudner A, Ikui AE. PP2A Cdc55 dephosphorylates Pds1 and inhibits spindle elongation in S. cerevisiae. J Cell Sci 2020; 133:jcs243766. [PMID: 32591482 PMCID: PMC7406319 DOI: 10.1242/jcs.243766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/11/2020] [Indexed: 11/20/2022] Open
Abstract
PP2ACdc55 (the form of protein phosphatase 2A containing Cdc55) regulates cell cycle progression by reversing cyclin-dependent kinase (CDK)- and polo-like kinase (Cdc5)-dependent phosphorylation events. In S. cerevisiae, Cdk1 phosphorylates securin (Pds1), which facilitates Pds1 binding and inhibits separase (Esp1). During anaphase, Esp1 cleaves the cohesin subunit Scc1 and promotes spindle elongation. Here, we show that PP2ACdc55 directly dephosphorylates Pds1 both in vivo and in vitro Pds1 hyperphosphorylation in a cdc55 deletion mutant enhanced the Pds1-Esp1 interaction, which played a positive role in Pds1 nuclear accumulation and in spindle elongation. We also show that nuclear PP2ACdc55 plays a role during replication stress to inhibit spindle elongation. This pathway acted independently of the known Mec1, Swe1 or spindle assembly checkpoint (SAC) checkpoint pathways. We propose a model where Pds1 dephosphorylation by PP2ACdc55 disrupts the Pds1-Esp1 protein interaction and inhibits Pds1 nuclear accumulation, which prevents spindle elongation, a process that is elevated during replication stress.
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Affiliation(s)
- Shoily Khondker
- Biology Department, Brooklyn College, The City University of New York, Brooklyn, NY 11238, USA
- Biology Program, CUNY Graduate Center, New York, NY 10016, USA
| | - Sam Kajjo
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | | | - Jan Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Adam Rudner
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Amy E. Ikui
- Biology Department, Brooklyn College, The City University of New York, Brooklyn, NY 11238, USA
- Biology Program, CUNY Graduate Center, New York, NY 10016, USA
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8
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Wen Z, Zhu H, Zhang A, Lin J, Zhang G, Liu D, Xiao Y, Ye C, Sun D, Wu B, Zhang J, Gao J. Cdc14a has a role in spermatogenesis, sperm maturation and male fertility. Exp Cell Res 2020; 395:112178. [PMID: 32679235 DOI: 10.1016/j.yexcr.2020.112178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 07/07/2020] [Accepted: 07/11/2020] [Indexed: 11/29/2022]
Abstract
Cdc14a is an evolutionarily conserved dual-specific protein phosphatase, and it plays different roles in different organisms. Cdc14a mutations in human have been reported to cause male infertility, while the specific role of Cdc14a in regulation of the male reproductive system remains elusive. In the present study, we established a knockout mouse model to study the function of Cdc14a in male reproductive system. Cdc14a-/- male mice were subfertile and they could only produce very few offspring. The number of sperm was decreased, the sperm motility was impaired, and the proportion of sperm with abnormal morphology was elevated in Cdc14a-/- mice. When we mated Cdc14a-/- male mice with wild-type (WT) female mice, fertilized eggs could be found in female fallopian tubes, however, the majority of these embryos died during development. Some empty spaces were observed in seminiferous tubule of Cdc14a-/- testes. Compared with WT male mice, the proportions of pachytene spermatocytes were increased and germ cells stained with γH2ax were decreased in Cdc14a-/- male mice, indicating that knockout of Cdc14a inhibited meiotic initiation. Subsequently, we analyzed the expression levels of some substrate proteins of Cdc14a, including Cdc25a, Wee1, and PR-Set7, and compared those with WT testes, in which the expression levels of these proteins were significantly increased in Cdc14a-/- testes. Our results revealed that Cdc14a-/- male mice are highly subfertile, and Cdc14a is essential for normal spermatogenesis and sperm function.
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Affiliation(s)
- Zongzhuang Wen
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, 250100, PR China
| | - Haixia Zhu
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, 250100, PR China
| | - Aizhen Zhang
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, 250100, PR China
| | - Jing Lin
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, 250100, PR China
| | - Guangkai Zhang
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, 250100, PR China
| | - Dongyue Liu
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, 250100, PR China
| | - Yu Xiao
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, 250100, PR China
| | - Chao Ye
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, 250100, PR China
| | - Daqing Sun
- Department of Pediatric Surgery, Tianjin Medical University General Hospital, Tianjin, 300041, PR China.
| | - Bin Wu
- Department of Reproductive Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250100, PR China.
| | - Jian Zhang
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, 250100, PR China.
| | - Jiangang Gao
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, 250100, PR China.
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9
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Jackman M, Marcozzi C, Barbiero M, Pardo M, Yu L, Tyson AL, Choudhary JS, Pines J. Cyclin B1-Cdk1 facilitates MAD1 release from the nuclear pore to ensure a robust spindle checkpoint. J Cell Biol 2020; 219:e201907082. [PMID: 32236513 PMCID: PMC7265330 DOI: 10.1083/jcb.201907082] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 02/05/2020] [Accepted: 03/06/2020] [Indexed: 11/22/2022] Open
Abstract
How the cell rapidly and completely reorganizes its architecture when it divides is a problem that has fascinated researchers for almost 150 yr. We now know that the core regulatory machinery is highly conserved in eukaryotes, but how these multiple protein kinases, protein phosphatases, and ubiquitin ligases are coordinated in space and time to remodel the cell in a matter of minutes remains a major question. Cyclin B1-Cdk is the primary kinase that drives mitotic remodeling; here we show that it is targeted to the nuclear pore complex (NPC) by binding an acidic face of the kinetochore checkpoint protein, MAD1, where it coordinates NPC disassembly with kinetochore assembly. Localized cyclin B1-Cdk1 is needed for the proper release of MAD1 from the embrace of TPR at the nuclear pore so that it can be recruited to kinetochores before nuclear envelope breakdown to maintain genomic stability.
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10
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Zhao Y, Wang D, Zhang Z, Lu Y, Yang X, Ouyang Q, Tang C, Li F. Critical slowing down and attractive manifold: A mechanism for dynamic robustness in the yeast cell-cycle process. Phys Rev E 2020; 101:042405. [PMID: 32422801 DOI: 10.1103/physreve.101.042405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 01/13/2020] [Indexed: 11/07/2022]
Abstract
Biological processes that execute complex multiple functions, such as the cell cycle, must ensure the order of sequential events and maintain dynamic robustness against various fluctuations. Here, we examine the mechanisms and fundamental structure that achieve these properties in the cell cycle of the budding yeast Saccharomyces cerevisiae. We show that this process behaves like an excitable system containing three well-decoupled saddle-node bifurcations to execute DNA replication and mitosis events. The yeast cell-cycle regulatory network can be divided into three modules-the G1/S phase, early M phase, and late M phase-wherein both positive feedback loops in each module and interactions among modules play important roles. Specifically, when the cell-cycle process operates near the critical points of the saddle-node bifurcations, a critical slowing down effect takes place. Such interregnum then allows for an attractive manifold and sufficient duration for cell-cycle events, within which to assess the completion of DNA replication and mitosis, e.g., spindle assembly. Moreover, such arrangement ensures that any fluctuation in an early module or event will not transmit to a later module or event. Thus, our results suggest a possible dynamical mechanism of the cell-cycle process to ensure event order and dynamic robustness and give insight into the evolution of eukaryotic cell-cycle processes.
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Affiliation(s)
- Yao Zhao
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Dedi Wang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Zhiwen Zhang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xiaojing Yang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Qi Ouyang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Chao Tang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Fangting Li
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
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11
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Wasserman D, Nachum S, Cohen M, Enrico TP, Noach-Hirsh M, Parasol J, Zomer-Polak S, Auerbach N, Sheinberger-Chorni E, Nevenzal H, Levi-Dadon N, Wang X, Lahmi R, Michaely E, Gerber D, Emanuele MJ, Tzur A. Cell cycle oscillators underlying orderly proteolysis of E2F8. Mol Biol Cell 2020; 31:725-740. [PMID: 31995441 PMCID: PMC7185961 DOI: 10.1091/mbc.e19-12-0725] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
E2F8 is a transcriptional repressor that antagonizes E2F1 at the crossroads of the cell cycle, apoptosis, and cancer. Previously, we discovered that E2F8 is a direct target of the APC/C ubiquitin ligase. Nevertheless, it remains unknown how E2F8 is dynamically controlled throughout the entirety of the cell cycle. Here, using newly developed human cell-free systems that recapitulate distinct inter-mitotic and G1 phases and a continuous transition from prometaphase to G1, we reveal an interlocking dephosphorylation switch coordinating E2F8 degradation with mitotic exit and the activation of APC/CCdh1. Further, we uncover differential proteolysis rates for E2F8 at different points within G1 phase, accounting for its accumulation in late G1 while APC/CCdh1 is still active. Finally, we demonstrate that the F-box protein Cyclin F regulates E2F8 in G2-phase. Altogether, our data define E2F8 regulation throughout the cell cycle, illuminating an extensive coordination between phosphorylation, ubiquitination and transcription in mammalian cell cycle.
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Affiliation(s)
- Danit Wasserman
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Sapir Nachum
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Meital Cohen
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Taylor P Enrico
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Meirav Noach-Hirsh
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Jasmin Parasol
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Sarit Zomer-Polak
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Naomi Auerbach
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Evelin Sheinberger-Chorni
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Hadas Nevenzal
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Nofar Levi-Dadon
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Xianxi Wang
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Roxane Lahmi
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Efrat Michaely
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Doron Gerber
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Michael J Emanuele
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Amit Tzur
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
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12
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Bansal S, Tiwari S. Mechanisms for the temporal regulation of substrate ubiquitination by the anaphase-promoting complex/cyclosome. Cell Div 2019; 14:14. [PMID: 31889987 PMCID: PMC6927175 DOI: 10.1186/s13008-019-0057-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/04/2019] [Indexed: 12/16/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a multi-subunit, multifunctional ubiquitin ligase that controls the temporal degradation of numerous cell cycle regulatory proteins to direct the unidirectional cell cycle phases. Several different mechanisms contribute to ensure the correct order of substrate modification by the APC/C complex. Recent advances in biochemical, biophysical and structural studies of APC/C have provided a deep mechanistic insight into the working of this complex ubiquitin ligase. This complex displays remarkable conformational flexibility in response to various binding partners and post-translational modifications, which together regulate substrate selection and catalysis of APC/C. Apart from this, various features and modifications of the substrates also influence their recognition and affinity to APC/C complex. Ultimately, temporal degradation of substrates depends on the kind of ubiquitin modification received, the processivity of APC/C, and other extrinsic mechanisms. This review discusses our current understanding of various intrinsic and extrinsic mechanisms responsible for 'substrate ordering' by the APC/C complex.
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Affiliation(s)
- Shivangee Bansal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Swati Tiwari
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
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13
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Stallaert W, Kedziora KM, Chao HX, Purvis JE. Bistable switches as integrators and actuators during cell cycle progression. FEBS Lett 2019; 593:2805-2816. [PMID: 31566708 DOI: 10.1002/1873-3468.13628] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/20/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022]
Abstract
Progression through the cell cycle is driven by bistable switches-specialized molecular circuits that govern transitions from one cellular state to another. Although the mechanics of bistable switches are relatively well understood, it is less clear how cells integrate multiple sources of molecular information to engage these switches. Here, we describe how bistable switches act as hubs of information processing and examine how variability, competition, and inheritance of molecular signals determine the timing of the Rb-E2F bistable switch that controls cell cycle entry. Bistable switches confer both robustness and plasticity to cell cycle progression, ensuring that cell cycle events are performed completely and in the correct order, while still allowing flexibility to cope with ongoing stress and changing environmental conditions.
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Affiliation(s)
- Wayne Stallaert
- Department of Genetics, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Katarzyna M Kedziora
- Department of Genetics, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Hui Xiao Chao
- Department of Genetics, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jeremy E Purvis
- Department of Genetics, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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14
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O'Connor KC. Molecular Profiles of Cell-to-Cell Variation in the Regenerative Potential of Mesenchymal Stromal Cells. Stem Cells Int 2019; 2019:5924878. [PMID: 31636675 PMCID: PMC6766122 DOI: 10.1155/2019/5924878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022] Open
Abstract
Cell-to-cell variation in the regenerative potential of mesenchymal stromal cells (MSCs) impedes the translation of MSC therapies into clinical practice. Cellular heterogeneity is ubiquitous across MSC cultures from different species and tissues. This review highlights advances to elucidate molecular profiles that identify cell subsets with specific regenerative properties in heterogeneous MSC cultures. Cell surface markers and global signatures are presented for proliferation and differentiation potential, as well as immunomodulation and trophic properties. Key knowledge gaps are discussed as potential areas of future research. Molecular profiles of MSC heterogeneity have the potential to enable unprecedented control over the regenerative potential of MSC therapies through the discovery of new molecular targets and as quality attributes to develop robust and reproducible biomanufacturing processes. These advances would have a positive impact on the nascent field of MSC therapeutics by accelerating the development of therapies with more consistent and effective treatment outcomes.
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Affiliation(s)
- Kim C. O'Connor
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana, USA
- Center for Stem Cell Research and Regenerative Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
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15
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Sparapani S, Bachewich C. Characterization of a novel separase-interacting protein and candidate new securin, Eip1p, in the fungal pathogen Candida albicans. Mol Biol Cell 2019; 30:2469-2489. [PMID: 31411946 PMCID: PMC6743357 DOI: 10.1091/mbc.e18-11-0696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 07/03/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
Proper chromosome segregation is crucial for maintaining genomic stability and dependent on separase, a conserved and essential cohesin protease. Securins are key regulators of separases, but remain elusive in many organisms due to sequence divergence. Here, we demonstrate that the separase homologue Esp1p in the ascomycete Candida albicans, an important pathogen of humans, is essential for chromosome segregation. However, C. albicans lacks a sequence homologue of securins found in model ascomycetes. We sought a functional homologue through identifying Esp1p interacting factors. Affinity purification of Esp1p and mass spectrometry revealed Esp1p-Interacting Protein1 (Eip1p)/Orf19.955p, an uncharacterized protein specific to Candida species. Functional analyses demonstrated that Eip1p is important for chromosome segregation but not essential, and modulated in an APCCdc20-dependent manner, similar to securins. Eip1p is strongly enriched in response to methyl methanesulfate (MMS) or hydroxyurea (HU) treatment, and its depletion partially suppresses an MMS or HU-induced metaphase block. Further, Eip1p depletion reduces Mcd1p/Scc1p, a cohesin subunit and separase target. Thus, Eip1p may function as a securin. However, other defects in Eip1p-depleted cells suggest additional roles. Overall, the results introduce a candidate new securin, provide an approach for identifying these divergent proteins, reveal a putative anti-fungal therapeutic target, and highlight variations in mitotic regulation in eukaryotes.
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Affiliation(s)
- Samantha Sparapani
- Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada
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16
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Interplay between Phosphatases and the Anaphase-Promoting Complex/Cyclosome in Mitosis. Cells 2019; 8:cells8080814. [PMID: 31382469 PMCID: PMC6721574 DOI: 10.3390/cells8080814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 12/14/2022] Open
Abstract
Accurate division of cells into two daughters is a process that is vital to propagation of life. Protein phosphorylation and selective degradation have emerged as two important mechanisms safeguarding the delicate choreography of mitosis. Protein phosphatases catalyze dephosphorylation of thousands of sites on proteins, steering the cells through establishment of the mitotic phase and exit from it. A large E3 ubiquitin ligase, the anaphase-promoting complex/cyclosome (APC/C) becomes active during latter stages of mitosis through G1 and marks hundreds of proteins for destruction. Recent studies have revealed the complex interregulation between these two classes of enzymes. In this review, we highlight the direct and indirect mechanisms by which phosphatases and the APC/C mutually influence each other to ensure accurate spatiotemporal and orderly progression through mitosis, with a particular focus on recent insights and conceptual advances.
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17
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Bouftas N, Wassmann K. Cycling through mammalian meiosis: B-type cyclins in oocytes. Cell Cycle 2019; 18:1537-1548. [PMID: 31208271 PMCID: PMC6619999 DOI: 10.1080/15384101.2019.1632139] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/17/2019] [Accepted: 05/24/2019] [Indexed: 12/15/2022] Open
Abstract
B-type cyclins in association with Cdk1 mediate key steps of mitosis and meiosis, by phosphorylating a plethora of substrates. Progression through the meiotic cell cycle requires the execution of two cell divisions named meiosis I and II without intervening S-phase, to obtain haploid gametes. These two divisions are highly asymmetric in the large oocyte. Chromosome segregation in meiosis I and sister chromatid segregation in meiosis II requires the sharp, switch-like inactivation of Cdk1 activity, which is brought about by degradation of B-type cyclins and counteracting phosphatases. Importantly and contrary to mitosis, inactivation of Cdk1 must not allow S-phase to take place at exit from meiosis I. Here, we describe recent studies on the regulation of translation and degradation of B-type cyclins in mouse oocytes, and how far their roles are redundant or specific, with a special focus on the recently discovered oocyte-specific role of cyclin B3.
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Affiliation(s)
- Nora Bouftas
- Institut de Biologie Paris Seine (IBPS), Sorbonne Université, Paris, France
- CNRS UMR7622 Developmental Biology Lab, Sorbonne Université, Paris, France
| | - Katja Wassmann
- Institut de Biologie Paris Seine (IBPS), Sorbonne Université, Paris, France
- CNRS UMR7622 Developmental Biology Lab, Sorbonne Université, Paris, France
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18
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Karasu ME, Bouftas N, Keeney S, Wassmann K. Cyclin B3 promotes anaphase I onset in oocyte meiosis. J Cell Biol 2019; 218:1265-1281. [PMID: 30723090 PMCID: PMC6446836 DOI: 10.1083/jcb.201808091] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/26/2018] [Accepted: 12/17/2018] [Indexed: 12/11/2022] Open
Abstract
Cyclins control the switch-like cell cycle transitions that orchestrate orderly duplication and segregation of genomes. Karasu et al. delineate an essential function for mouse cyclin B3 for anaphase onset in the first meiotic division of oocytes. Meiosis poses unique challenges because two rounds of chromosome segregation must be executed without intervening DNA replication. Mammalian cells express numerous temporally regulated cyclins, but how these proteins collaborate to control meiosis remains poorly understood. Here, we show that female mice genetically ablated for cyclin B3 are viable—indicating that the protein is dispensable for mitotic divisions—but are sterile. Mutant oocytes appear normal until metaphase I but then display a highly penetrant failure to transition to anaphase I. They arrest with hallmarks of defective anaphase-promoting complex/cyclosome (APC/C) activation, including no separase activity, high CDK1 activity, and high cyclin B1 and securin levels. Partial APC/C activation occurs, however, as exogenously expressed APC/C substrates can be degraded. Cyclin B3 forms active kinase complexes with CDK1, and meiotic progression requires cyclin B3–associated kinase activity. Cyclin B3 homologues from frog, zebrafish, and fruit fly rescue meiotic progression in cyclin B3–deficient mouse oocytes, indicating conservation of the biochemical properties and possibly cellular functions of this germline-critical cyclin.
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Affiliation(s)
- Mehmet E Karasu
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY.,Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Nora Bouftas
- Institut de Biologie Paris Seine, Sorbonne Université, Paris, France.,Developmental Biology Lab, Sorbonne Université, Centre National de la Recherche Scientifique UMR7622, Paris, France
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY .,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY.,Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Katja Wassmann
- Institut de Biologie Paris Seine, Sorbonne Université, Paris, France .,Developmental Biology Lab, Sorbonne Université, Centre National de la Recherche Scientifique UMR7622, Paris, France
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19
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Gérard C, Gonze D, Goldbeter A. Revisiting a skeleton model for the mammalian cell cycle: From bistability to Cdk oscillations and cellular heterogeneity. J Theor Biol 2018; 461:276-290. [PMID: 30352237 DOI: 10.1016/j.jtbi.2018.10.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 02/07/2023]
Abstract
A network of cyclin-dependent kinases (Cdks) regulated by multiple negative and positive feedback loops controls progression in the mammalian cell cycle. We previously proposed a detailed computational model for this network, which consists of four coupled Cdk modules. Both this detailed model and a reduced, skeleton version show that the Cdk network is capable of temporal self-organization in the form of sustained Cdk oscillations, which correspond to the orderly progression along the different cell cycle phases G1, S (DNA replication), G2 and M (mitosis). We use the skeleton model to revisit the role of positive feedback (PF) loops on the dynamics of the mammalian cell cycle by showing that the multiplicity of PF loops extends the range of bistability in the isolated Cdk modules controlling the G1/S and G2/M transitions. Resorting to stochastic simulations we show that, through their effect on the range of bistability, multiple PF loops enhance the robustness of Cdk oscillations with respect to molecular noise. The model predicts that a rise in the total level of Cdk1 also enlarges the domain of bistability in the isolated Cdk modules as well as the range of oscillations in the full Cdk network. Surprisingly, stochastic simulations indicate that Cdk1 overexpression reduces the robustness of Cdk oscillations towards molecular noise; this result is due to the increased distance between the two branches of the bistable switch at higher levels of Cdk1. At intermediate levels of growth factor stochastic simulations show that cells may randomly switch between cell cycle arrest and cell proliferation, as a consequence of fluctuations. In the presence of Cdk1 overexpression, these transitions occur even at low levels of growth factor. Extending stochastic simulations from single cells to cell populations suggests that stochastic switches between cell cycle arrest and proliferation may provide a source of heterogeneity in a cell population, as observed in cancer cells characterized by Cdk1 overexpression.
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Affiliation(s)
- Claude Gérard
- Unité de Chronobiologie théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus Plaine, CP 231, B-1050 Brussels, Belgium
| | - Didier Gonze
- Unité de Chronobiologie théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus Plaine, CP 231, B-1050 Brussels, Belgium
| | - Albert Goldbeter
- Unité de Chronobiologie théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus Plaine, CP 231, B-1050 Brussels, Belgium.
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20
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Konishi M, Shindo N, Komiya M, Tanaka K, Itoh T, Hirota T. Quantitative analyses of the metaphase-to-anaphase transition reveal differential kinetic regulation for securin and cyclin B1. Biomed Res 2018; 39:75-85. [PMID: 29669986 DOI: 10.2220/biomedres.39.75] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Separation of sister chromatids is a drastic and irreversible step in the cell cycle. The key biochemistry behind this event is the proteolysis mediated by the ubiquitin ligase called the anaphase promoting complex, or APC/C. Securin and cyclin B1 are the two established substrates for APC/C whose degradation releases separase and inactivates cyclin B1-dependent kinase 1 (cdk1), respectively, at the metaphase-to-anaphase transition. In this study, we have combined biochemical quantifications with mathematical simulations to characterize the kinetic regulation of securin and cyclin B1, in the cytoplasmic and chromosomal compartments, and found that they are differentially distributed and degraded with different rates. Modeling their interaction with separase predicted that activation timing of separase well coincides with the decline of securin-separase concentration in the cytoplasm. Notably, it also coincides with the peak of cyclin B1-separase level on chromosomes, which appeared crucial to coordinate the timing for separase activation and cdk1 inhibition. We have also conducted phosphoproteomic analysis and identified Ki67 as a chromosomal cdk1 substrate whose dephosphorylation is facilitated by cyclin B1-separase interaction in anaphase.
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Affiliation(s)
- Makoto Konishi
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research (JFCR).,Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Norihisa Shindo
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research (JFCR)
| | - Masataka Komiya
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Kozo Tanaka
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University
| | - Takehiko Itoh
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Toru Hirota
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research (JFCR)
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21
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The threshold of an excitable system serves as a control mechanism for noise filtering during chemotaxis. PLoS One 2018; 13:e0201283. [PMID: 30059517 PMCID: PMC6066244 DOI: 10.1371/journal.pone.0201283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 06/18/2018] [Indexed: 01/29/2023] Open
Abstract
Chemotaxis, the migration of cells in the direction of a chemical gradient, is of utmost importance in various biological processes. In recent years, research has demonstrated that the underlying mechanism that controls cell migration is an excitable network. One of the properties that characterizes excitability is the presence of a threshold for activation. Here, we show that excitable systems possess noise filtering capabilities that enable faster and more efficient directed migration compared to other systems that also include a threshold, such as ultrasensitive switches. We demonstrate that this filtering ability is a consequence of the varying responses of excitable systems to step and pulse stimuli. Whereas the response to step inputs is determined solely by the magnitude of the stimulus, for pulse stimuli, the response depends on both the magnitude and duration of the stimulus. We then show that these two forms of threshold behavior can be decoupled from one another, allowing finer control in chemotaxis. Finally, we use a simple model of chemotaxis to demonstrate that cells that rely on an excitable system display faster and more effective directed migration that a hypothetical cell guided by an ultra-sensitive switch.
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22
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Affiliation(s)
- Patrick L. Ferree
- Department of Cell Biology; Duke University Medical Center; Durham NC USA
| | - Stefano Di Talia
- Department of Cell Biology; Duke University Medical Center; Durham NC USA
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23
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Alfieri C, Zhang S, Barford D. Visualizing the complex functions and mechanisms of the anaphase promoting complex/cyclosome (APC/C). Open Biol 2017; 7:170204. [PMID: 29167309 PMCID: PMC5717348 DOI: 10.1098/rsob.170204] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/10/2017] [Indexed: 12/17/2022] Open
Abstract
The anaphase promoting complex or cyclosome (APC/C) is a large multi-subunit E3 ubiquitin ligase that orchestrates cell cycle progression by mediating the degradation of important cell cycle regulators. During the two decades since its discovery, much has been learnt concerning its role in recognizing and ubiquitinating specific proteins in a cell-cycle-dependent manner, the mechanisms governing substrate specificity, the catalytic process of assembling polyubiquitin chains on its target proteins, and its regulation by phosphorylation and the spindle assembly checkpoint. The past few years have witnessed significant progress in understanding the quantitative mechanisms underlying these varied APC/C functions. This review integrates the overall functions and properties of the APC/C with mechanistic insights gained from recent cryo-electron microscopy (cryo-EM) studies of reconstituted human APC/C complexes.
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Affiliation(s)
- Claudio Alfieri
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Suyang Zhang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Barford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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24
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de Los Santos-Velázquez AI, de Oya IG, Manzano-López J, Monje-Casas F. Late rDNA Condensation Ensures Timely Cdc14 Release and Coordination of Mitotic Exit Signaling with Nucleolar Segregation. Curr Biol 2017; 27:3248-3263.e5. [PMID: 29056450 DOI: 10.1016/j.cub.2017.09.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/16/2017] [Accepted: 09/13/2017] [Indexed: 12/28/2022]
Abstract
The nucleolus plays a pivotal role in multiple key cellular processes. An illustrative example is the regulation of mitotic exit in Saccharomyces cerevisiae through the nucleolar sequestration of the Cdc14 phosphatase. The peculiar structure of the nucleolus, however, has also its drawbacks. The repetitive nature of the rDNA gives rise to cohesion-independent linkages whose resolution in budding yeast requires the Cdc14-dependent inhibition of rRNA transcription, which facilitates condensin accessibility to this locus. Thus, the rDNA condenses and segregates later than most other yeast genomic regions. Here, we show that defective function of a small nucleolar ribonucleoprotein particle (snoRNP) assembly factor facilitates condensin accessibility to the rDNA and induces nucleolar hyper-condensation. Interestingly, this increased compaction of the nucleolus interferes with the proper release of Cdc14 from this organelle. This observation provides an explanation for the delayed rDNA condensation in budding yeast, which is necessary to efficiently coordinate timely Cdc14 release and mitotic exit with nucleolar compaction and segregation.
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Affiliation(s)
- Ana Isabel de Los Santos-Velázquez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Inés G de Oya
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Javier Manzano-López
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Fernando Monje-Casas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain.
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25
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Davey NE, Morgan DO. Building a Regulatory Network with Short Linear Sequence Motifs: Lessons from the Degrons of the Anaphase-Promoting Complex. Mol Cell 2017; 64:12-23. [PMID: 27716480 DOI: 10.1016/j.molcel.2016.09.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The anaphase-promoting complex or cyclosome (APC/C) is a ubiquitin ligase that polyubiquitinates specific substrates at precise times in the cell cycle, thereby triggering the events of late mitosis in a strict order. The robust substrate specificity of the APC/C prevents the potentially deleterious degradation of non-APC/C substrates and also averts the cell-cycle errors and genomic instability that could result from mistimed degradation of APC/C targets. The APC/C recognizes short linear sequence motifs, or degrons, on its substrates. The specific and timely modification and degradation of APC/C substrates is likely to be modulated by variations in degron sequence and context. We discuss the extensive affinity, specificity, and selectivity determinants encoded in APC/C degrons, and we describe some of the extrinsic mechanisms that control APC/C-substrate recognition. As an archetype for protein motif-driven regulation of cell function, the APC/C-substrate interaction provides insights into the general properties of post-translational regulatory systems.
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Affiliation(s)
- Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
| | - David O Morgan
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.
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26
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Deneke VE, Melbinger A, Vergassola M, Di Talia S. Waves of Cdk1 Activity in S Phase Synchronize the Cell Cycle in Drosophila Embryos. Dev Cell 2017; 38:399-412. [PMID: 27554859 DOI: 10.1016/j.devcel.2016.07.023] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/13/2016] [Accepted: 07/26/2016] [Indexed: 01/16/2023]
Abstract
Embryos of most metazoans undergo rapid and synchronous cell cycles following fertilization. While diffusion is too slow for synchronization of mitosis across large spatial scales, waves of Cdk1 activity represent a possible process of synchronization. However, the mechanisms regulating Cdk1 waves during embryonic development remain poorly understood. Using biosensors of Cdk1 and Chk1 activities, we dissect the regulation of Cdk1 waves in the Drosophila syncytial blastoderm. We show that Cdk1 waves are not controlled by the mitotic switch but by a double-negative feedback between Cdk1 and Chk1. Using mathematical modeling and surgical ligations, we demonstrate a fundamental distinction between S phase Cdk1 waves, which propagate as active trigger waves in an excitable medium, and mitotic Cdk1 waves, which propagate as passive phase waves. Our findings show that in Drosophila embryos, Cdk1 positive feedback serves primarily to ensure the rapid onset of mitosis, while wave propagation is regulated by S phase events.
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Affiliation(s)
- Victoria E Deneke
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Anna Melbinger
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Massimo Vergassola
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
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27
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Yang Y, Zhang Y, Li WJ, Jiang Y, Zhu Z, Hu H, Li W, Wu JW, Wang ZX, Dong MQ, Huang S, Ou G. Spectraplakin Induces Positive Feedback between Fusogens and the Actin Cytoskeleton to Promote Cell-Cell Fusion. Dev Cell 2017; 41:107-120.e4. [DOI: 10.1016/j.devcel.2017.03.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/18/2017] [Accepted: 03/10/2017] [Indexed: 10/25/2022]
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Zou Y, Qiu G, Jiang L, Cai Z, Sun W, Hu H, Lu C, Jin W, Hu G. Overexpression of ubiquitin specific proteases 44 promotes the malignancy of glioma by stabilizing tumor-promoter securin. Oncotarget 2017; 8:58231-58246. [PMID: 28938551 PMCID: PMC5601647 DOI: 10.18632/oncotarget.16447] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/28/2017] [Indexed: 12/20/2022] Open
Abstract
Ubiquitin specific peptidase 44 (USP44) has been identified as an important component of spindle assemble checkpoint (SAC) to prevent the formation of aneuploidy. However, recent study raised a controversy about the effect of USP44 in tumor. Here, we first confirmed the intranuclear localization of USP44 by testing several specific antibodies to recognize endogenous USP44. Then, data from IHC and qRT-PCR assay indicated that the high expression of USP44 existed in high-grade glioma tissues and signified a poor prognosis. Knockdown of USP44 inhibited proliferation, migration and invasion, induced apoptosis, and arrested cell cycle in G2/M phase in the established glioma cell lines. Down-regulation of oncoprotein securin was detected in USP44 deficient cells, and the interaction of endogenous USP44 and securin was confirmed by immunoprecipitation in U251MG cells, which indicated that securin was a substrate of USP44, and might be stabilized by USP44. In vivo, knockdown of USP44 inhibited the tumorigenicity of U87MG cells significantly. Consequently, our findings suggested that overexpression of USP44 could enhance the malignancy of glioma via securin. USP44 might serve as a predictive biomarker, and the USP44-securin pathway might provide a new therapeutic strategy for the treatment of glioma.
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Affiliation(s)
- Yongxiang Zou
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, PR China
| | - Guanzhong Qiu
- Department of Neurosurgery, General Hospital of Jinan Military Command, Jinan, PR China
| | - Lei Jiang
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, PR China
| | - Zheng Cai
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, PR China
| | - Wei Sun
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, PR China
| | - Hongkang Hu
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, PR China
| | - Chengyin Lu
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, PR China
| | - Weilin Jin
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, Key Laboratory for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electronic Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Guohan Hu
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, PR China
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29
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Kamenz J, Hauf S. Time To Split Up: Dynamics of Chromosome Separation. Trends Cell Biol 2017; 27:42-54. [DOI: 10.1016/j.tcb.2016.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/14/2016] [Accepted: 07/29/2016] [Indexed: 11/16/2022]
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Roles of SMC Complexes During T Lymphocyte Development and Function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 106:17-42. [DOI: 10.1016/bs.apcsb.2016.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Abstract
The mitotic checkpoint is a specialized signal transduction pathway that contributes to the fidelity of chromosome segregation. The signaling of the checkpoint originates from defective kinetochore-microtubule interactions and leads to formation of the mitotic checkpoint complex (MCC), a highly potent inhibitor of the Anaphase Promoting Complex/Cyclosome (APC/C)—the E3 ubiquitin ligase essential for anaphase onset. Many important questions concerning the MCC and its interaction with APC/C have been intensively investigated and debated in the past 15 years, such as the exact composition of the MCC, how it is assembled during a cell cycle, how it inhibits APC/C, and how the MCC is disassembled to allow APC/C activation. These efforts have culminated in recently reported structure models for human MCC:APC/C supra-complexes at near-atomic resolution that shed light on multiple aspects of the mitotic checkpoint mechanisms. However, confusing statements regarding the MCC are still scattered in the literature, making it difficult for students and scientists alike to obtain a clear picture of MCC composition, structure, function and dynamics. This review will comb through some of the most popular concepts or misconceptions about the MCC, discuss our current understandings, present a synthesized model on regulation of CDC20 ubiquitination, and suggest a few future endeavors and cautions for next phase of MCC research.
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Affiliation(s)
- Song-Tao Liu
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft St., Toledo, OH 43606, USA
| | - Hang Zhang
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft St., Toledo, OH 43606, USA
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32
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Araujo AR, Gelens L, Sheriff RSM, Santos SDM. Positive Feedback Keeps Duration of Mitosis Temporally Insulated from Upstream Cell-Cycle Events. Mol Cell 2016; 64:362-375. [PMID: 27768873 PMCID: PMC5077699 DOI: 10.1016/j.molcel.2016.09.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/09/2016] [Accepted: 09/14/2016] [Indexed: 10/27/2022]
Abstract
Cell division is characterized by a sequence of events by which a cell gives rise to two daughter cells. Quantitative measurements of cell-cycle dynamics in single cells showed that despite variability in G1-, S-, and G2 phases, duration of mitosis is short and remarkably constant. Surprisingly, there is no correlation between cell-cycle length and mitotic duration, suggesting that mitosis is temporally insulated from variability in earlier cell-cycle phases. By combining live cell imaging and computational modeling, we showed that positive feedback is the molecular mechanism underlying the temporal insulation of mitosis. Perturbing positive feedback gave rise to a sluggish, variable entry and progression through mitosis and uncoupled duration of mitosis from variability in cell cycle length. We show that positive feedback is important to keep mitosis short, constant, and temporally insulated and anticipate it might be a commonly used regulatory strategy to create modularity in other biological systems.
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Affiliation(s)
- Ana Rita Araujo
- Quantitative Cell Biology Lab, MRC-Clinical Sciences Centre (CSC), London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium
| | - Rahuman S M Sheriff
- Quantitative Cell Biology Lab, MRC-Clinical Sciences Centre (CSC), London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; European Bioinformatics Institute, EMBL-EBI, Hinxton, Cambridge CB10 1SD, UK
| | - Silvia D M Santos
- Quantitative Cell Biology Lab, MRC-Clinical Sciences Centre (CSC), London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
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33
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Deneke VE, Melbinger A, Vergassola M, Di Talia S. Waves of Cdk1 Activity in S Phase Synchronize the Cell Cycle in Drosophila Embryos. Dev Cell 2016. [PMID: 27554859 DOI: 10.1016/j.devcel.2016.07.0240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Embryos of most metazoans undergo rapid and synchronous cell cycles following fertilization. While diffusion is too slow for synchronization of mitosis across large spatial scales, waves of Cdk1 activity represent a possible process of synchronization. However, the mechanisms regulating Cdk1 waves during embryonic development remain poorly understood. Using biosensors of Cdk1 and Chk1 activities, we dissect the regulation of Cdk1 waves in the Drosophila syncytial blastoderm. We show that Cdk1 waves are not controlled by the mitotic switch but by a double-negative feedback between Cdk1 and Chk1. Using mathematical modeling and surgical ligations, we demonstrate a fundamental distinction between S phase Cdk1 waves, which propagate as active trigger waves in an excitable medium, and mitotic Cdk1 waves, which propagate as passive phase waves. Our findings show that in Drosophila embryos, Cdk1 positive feedback serves primarily to ensure the rapid onset of mitosis, while wave propagation is regulated by S phase events.
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Affiliation(s)
- Victoria E Deneke
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Anna Melbinger
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Massimo Vergassola
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
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Ferree PL, Deneke VE, Di Talia S. Measuring time during early embryonic development. Semin Cell Dev Biol 2016; 55:80-8. [PMID: 26994526 PMCID: PMC4903905 DOI: 10.1016/j.semcdb.2016.03.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/15/2016] [Indexed: 11/27/2022]
Abstract
In most metazoans, embryonic development is orchestrated by a precise series of cellular behaviors. Understanding how such events are regulated to achieve a stereotypical temporal progression is a fundamental problem in developmental biology. In this review, we argue that studying the regulation of the cell cycle in early embryonic development will reveal novel principles of how embryos accurately measure time. We will discuss the strategies that have emerged from studying early development of Drosophila embryos. By comparing the development of flies to that of other metazoans, we will highlight both conserved and alternative mechanisms to generate precision during embryonic development.
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Affiliation(s)
- Patrick L Ferree
- Department of Cell Biology, Duke University Medical Center, Durham NC, United States
| | - Victoria E Deneke
- Department of Cell Biology, Duke University Medical Center, Durham NC, United States
| | - Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham NC, United States.
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35
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Yuan K, O'Farrell PH. TALE-light imaging reveals maternally guided, H3K9me2/3-independent emergence of functional heterochromatin in Drosophila embryos. Genes Dev 2016; 30:579-93. [PMID: 26915820 PMCID: PMC4782051 DOI: 10.1101/gad.272237.115] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/26/2016] [Indexed: 11/25/2022]
Abstract
In this study, Yuan and O'Farrell investigated how heterochromatin is established during development. Using new methodology for live imaging that allows spatial and temporal resolution of heterochromatin formation during normal Drosophila embryogenesis, they show that a maternal signal can act transgenerationally to influence the formation of heterochromatin on a satellite sequence. Metazoans start embryogenesis with a relatively naïve genome. The transcriptionally inert, late-replicating heterochromatic regions, including the constitutive heterochromatin on repetitive sequences near centromeres and telomeres, need to be re-established during development. To explore the events initiating heterochromatin formation and examine their temporal control, sequence specificity, and immediate regulatory consequence, we established a live imaging approach that enabled visualization of steps in heterochromatin emergence on specific satellite sequences during the mid-blastula transition (MBT) in Drosophila. Unexpectedly, only a subset of satellite sequences, including the 359-base-pair (bp) repeat sequence, recruited HP1a at the MBT. The recruitment of HP1a to the 359-bp repeat was dependent on HP1a's chromoshadow domain but not its chromodomain and was guided by maternally provided signals. HP1a recruitment to the 359-bp repeat was required for its programmed shift to later replication, and ectopic recruitment of HP1a was sufficient to delay replication timing of a different repeat. Our results reveal that emergence of constitutive heterochromatin follows a stereotyped developmental program in which different repetitive sequences use distinct interactions and independent pathways to arrive at a heterochromatic state. This differential emergence of heterochromatin on various repetitive sequences changes their replication order and remodels the DNA replication schedule during embryonic development.
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Affiliation(s)
- Kai Yuan
- Department of Biochemistry, University of California at San Francisco, San Francisco, California 94158, USA
| | - Patrick H O'Farrell
- Department of Biochemistry, University of California at San Francisco, San Francisco, California 94158, USA
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36
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Van Roey K, Davey NE. Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation. Cell Commun Signal 2015; 13:45. [PMID: 26626130 PMCID: PMC4666095 DOI: 10.1186/s12964-015-0123-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/24/2015] [Indexed: 01/01/2023] Open
Abstract
A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. Although these regulatory modules are physicochemically distinct, they share an evolutionary plasticity that has facilitated a rapid growth of their use and resulted in their ubiquity in complex organisms. The ease of motif acquisition simplifies access to basal housekeeping functions, facilitates the co-regulation of multiple biomolecules allowing them to respond in a coordinated manner to changes in the cell state, and supports the integration of multiple signals for combinatorial decision-making. Consequently, motifs are indispensable for temporal, spatial, conditional and basal regulation at the transcriptional, post-transcriptional and post-translational level. In this review, we highlight that many of the key regulatory pathways of the cell are recruited by motifs and that the ease of motif acquisition has resulted in large networks of co-regulated biomolecules. We discuss how co-operativity allows simple static motifs to perform the conditional regulation that underlies decision-making in higher eukaryotic biological systems. We observe that each gene and its products have a unique set of DNA, RNA or protein motifs that encode a regulatory program to define the logical circuitry that guides the life cycle of these biomolecules, from transcription to degradation. Finally, we contrast the regulatory properties of protein motifs and the regulatory elements of DNA and (pre-)mRNAs, advocating that co-regulation, co-operativity, and motif-driven regulatory programs are common mechanisms that emerge from the use of simple, evolutionarily plastic regulatory modules.
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Affiliation(s)
- Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany.
- Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050, Brussels, Belgium.
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
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37
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Lyu L, Whitcomb EA, Jiang S, Chang ML, Gu Y, Duncan MK, Cvekl A, Wang WL, Limi S, Reneker LW, Shang F, Du L, Taylor A. Unfolded-protein response-associated stabilization of p27(Cdkn1b) interferes with lens fiber cell denucleation, leading to cataract. FASEB J 2015; 30:1087-95. [PMID: 26590164 DOI: 10.1096/fj.15-278036] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/02/2015] [Indexed: 12/21/2022]
Abstract
Failure of lens fiber cell denucleation (LFCD) is associated with congenital cataracts, but the pathobiology awaits elucidation. Recent work has suggested that mechanisms that direct the unidirectional process of LFCD are analogous to the cyclic processes associated with mitosis. We found that lens-specific mutations that elicit an unfolded-protein response (UPR) in vivo accumulate p27(Cdkn1b), show cyclin-dependent kinase (Cdk)-1 inhibition, retain their LFC nuclei, and are cataractous. Although a UPR was not detected in lenses expressing K6W-Ub, they also accumulated p27 and showed failed LFCD. Induction of a UPR in human lens epithelial cells (HLECs) also induced accumulation of p27 associated with decreased levels of S-phase kinase-associated protein (Skp)-2, a ubiquitin ligase that regulates mitosis. These cells also showed decreased lamin A/C phosphorylation and metaphase arrest. The suppression of lamin A/C phosphorylation and metaphase transition induced by the UPR was rescued by knockdown of p27. Taken together, these data indicate that accumulation of p27, whether related to the UPR or not, prevents the phosphorylation of lamin A/C and LFCD in maturing LFCs in vivo, as well as in dividing HLECs. The former leads to cataract and the latter to metaphase arrest. These results suggest that accumulation of p27 is a common mechanism underlying retention of LFC nuclei.
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Affiliation(s)
- Lei Lyu
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Elizabeth A Whitcomb
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Shuhong Jiang
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Min-Lee Chang
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Yumei Gu
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Melinda K Duncan
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Ales Cvekl
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Wei-Lin Wang
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Saima Limi
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Lixing W Reneker
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Fu Shang
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Linfang Du
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Allen Taylor
- *Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Science, Sichuan University, Sichuan China; Laboratory for Nutrition and Vision Research, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA; Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA; and Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, Missouri, USA
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Lu D, Girard JR, Li W, Mizrak A, Morgan DO. Quantitative framework for ordered degradation of APC/C substrates. BMC Biol 2015; 13:96. [PMID: 26573515 PMCID: PMC4647693 DOI: 10.1186/s12915-015-0205-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/23/2015] [Indexed: 01/07/2023] Open
Abstract
Background During cell-cycle progression, substrates of a single master regulatory enzyme can be modified in a specific order. Here, we used experimental and computational approaches to dissect the quantitative mechanisms underlying the ordered degradation of the substrates of the ubiquitin ligase APC/CCdc20, a key regulator of chromosome segregation in mitosis. Results We show experimentally that the rate of catalysis varies with different substrates of APC/CCdc20. Using a computational model based on multi-step ubiquitination, we then show how changes in the interaction between a single substrate and APC/CCdc20 can alter the timing of degradation onset relative to APC/CCdc20 activation, while ensuring a fast degradation rate. Degradation timing and dynamics depend on substrate affinity for the enzyme as well as the catalytic rate at which the substrate is modified. When two substrates share the same pool of APC/CCdc20, their relative enzyme affinities and rates of catalysis influence the partitioning of APC/CCdc20 among substrates, resulting in substrate competition. Depending on how APC/CCdc20 is partitioned among its substrates, competition can have minor or major effects on the degradation of certain substrates. We show experimentally that increased expression of the early APC/CCdc20 substrate Clb5 does not delay the degradation of the later substrate securin, arguing against a role for competition with Clb5 in establishing securin degradation timing. Conclusions The degradation timing of APC/CCdc20 substrates depends on the multi-step nature of ubiquitination, differences in substrate-APC/CCdc20 interactions, and competition among substrates. Our studies provide a conceptual framework for understanding how ordered modification can be established among substrates of the same regulatory enzyme, and facilitate our understanding of how precise temporal control is achieved by a small number of master regulators to ensure a successful cell division cycle. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0205-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dan Lu
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Juliet R Girard
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Weihan Li
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Arda Mizrak
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - David O Morgan
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA.
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Abstract
The segregation of sister chromatids during mitosis is one of the most easily visualized, yet most remarkable, events during the life cycle of a cell. The accuracy of this process is essential to maintain ploidy during cell duplication. Over the past 20 years, substantial progress has been made in identifying components of both the kinetochore and the mitotic spindle that generate the force to move mitotic chromosomes. Additionally, we now have a reasonable, albeit incomplete, understanding of the molecular and biochemical events that are involved in establishing and dissolving sister-chromatid cohesion. However, it is less well-understood how this dissolution of cohesion occurs synchronously on all chromosomes at the onset of anaphase. At the centre of the action is the anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase that, in association with its activator cell-division cycle protein 20 homologue (Cdc20), is responsible for the destruction of securin. This leads to the activation of separase, a specialized protease that cleaves the kleisin-subunit of the cohesin complex, to relieve cohesion between sister chromatids. APC/C-Cdc20 is also responsible for the destruction of cyclin B and therefore inactivation of the cyclin B-cyclin-dependent kinase 1 (Cdk1). This latter event induces a change in the microtubule dynamics that results in the movement of sister chromatids to spindle poles (anaphase A), spindle elongation (anaphase B) and the onset of cytokinesis. In the present paper, we review the emerging evidence that multiple, spatially and temporally regulated feedback loops ensure anaphase onset is rapid, co-ordinated and irreversible.
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40
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Simpson-Lavy KJ, Zenvirth D, Brandeis M. Phosphorylation and dephosphorylation regulate APC/C(Cdh1) substrate degradation. Cell Cycle 2015; 14:3138-45. [PMID: 26252546 DOI: 10.1080/15384101.2015.1078036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Anaphase Promoting Complex/Cyclosome (APC/C) ubiquitin ligase activated by its G1 specific adaptor protein Cdh1 is a major regulator of the cell cycle. The APC/C(Cdh1) mediates degradation of dozens of proteins, however, the kinetics and requirements for their degradation are largely unknown. We demonstrate that overexpression of the constitutive active CDH1(m11) mutant that is not inhibited by phosphorylation results in mitotic exit in the absence of the FEAR and MEN pathways, and DNA re-replication in the absence of Cdc7 activity. This mode of mitotic exit also reveals additional requirements for APC/C(Cdh1) substrate degradation, which for some substrates such as Pds1 or Clb5 is dephosphorylation, but for others such as Cdc5 is phosphorylation.
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Key Words
- APC/C, Cdc5, Cdc14, Cdh1, Clb5, Dbf4, DNA replication, exit from mitosis, Pds1, substrate phosphorylation, yeast
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Affiliation(s)
- Kobi J Simpson-Lavy
- a The Department of Genetics ; The Alexander Silberman Institute of Life Sciences; The Hebrew University of Jerusalem ; Jerusalem , Israel
| | - Drora Zenvirth
- a The Department of Genetics ; The Alexander Silberman Institute of Life Sciences; The Hebrew University of Jerusalem ; Jerusalem , Israel
| | - Michael Brandeis
- a The Department of Genetics ; The Alexander Silberman Institute of Life Sciences; The Hebrew University of Jerusalem ; Jerusalem , Israel
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Zhang T, Qi ST, Huang L, Ma XS, Ouyang YC, Hou Y, Shen W, Schatten H, Sun QY. Cyclin B3 controls anaphase onset independent of spindle assembly checkpoint in meiotic oocytes. Cell Cycle 2015; 14:2648-54. [PMID: 26125114 DOI: 10.1080/15384101.2015.1064567] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cyclin B3 is a relatively new member of the cyclin family whose functions are little known. We found that depletion of cyclin B3 inhibited metaphase-anaphase transition as indicated by a well-sustained MI spindle and cyclin B1 expression in meiotic oocytes after extended culture. This effect was independent of spindle assembly checkpoint activity, since both Bub3 and BubR1 signals were not observed at kinetochores in MI-arrested cells. The metaphase I arrest was not rescued by either Mad2 knockdown or cdc20 overexpression, but it was rescued by securin RNAi. We conclude that cyclin B3 controls the metaphase-anaphase transition by activating APC/C(cdc20) in meiotic oocytes, a process that does not rely on SAC activity.
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Affiliation(s)
- Teng Zhang
- a Institute of Reproductive Sciences; College of Animal Science and Technology; Qingdao Agricultural University ; Qingdao , China
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Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN. Silence on the relevant literature and errors in implementation. Nat Biotechnol 2015; 33:336-9. [PMID: 25850052 DOI: 10.1038/nbt.3185] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Philippe Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Marc R Birtwistle
- Icahn School of Medicine at Mount Sinai, Dept. of Pharmacology and Systems Therapeutics, New York, New York, USA
| | - Nils Blüthgen
- 1] Institut für Pathologie Charite, Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany. [2] Integrative Research Institute for the Life Sciences, Humboldt University Berlin, Berlin, Germany
| | | | - Kwang-Hyun Cho
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon, Republic of Korea
| | - Carlo Cosentino
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus Salvatore Venuta, Catanzaro, Italy
| | - Alberto de la Fuente
- Department of Biomathematics and Bioinformatics, Institute for Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Jan B Hoek
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Anatoly Kiyatkin
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Walter Kolch
- 1] Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland. [2] Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland. [3] School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | | | - Pedro Mendes
- 1] Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK. [2] School of Computer Science, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK. [3] Center for Quantitative Medicine, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Takashi Naka
- Faculty of Information Science, Kyushu Sangyo University, Higashi-ku, Fukuoka, Japan
| | - Tapesh Santra
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Eduardo Sontag
- Department of Mathematics and Cancer Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
| | - Hans V Westerhoff
- 1] Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK. [2] Molecular Cell Physiology, VU University, Amsterdam, The Netherlands. [3] Synthetic Systems Biology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Boris N Kholodenko
- 1] Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland. [2] Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland. [3] School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
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Godfrey M, Kuilman T, Uhlmann F. Nur1 dephosphorylation confers positive feedback to mitotic exit phosphatase activation in budding yeast. PLoS Genet 2015; 11:e1004907. [PMID: 25569132 PMCID: PMC4287440 DOI: 10.1371/journal.pgen.1004907] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 11/20/2014] [Indexed: 12/16/2022] Open
Abstract
Substrate dephosphorylation by the cyclin-dependent kinase (Cdk)-opposing phosphatase, Cdc14, is vital for many events during budding yeast mitotic exit. Cdc14 is sequestered in the nucleolus through inhibitory binding to Net1, from which it is released in anaphase following Net1 phosphorylation. Initial Net1 phosphorylation depends on Cdk itself, in conjunction with proteins of the Cdc14 Early Anaphase Release (FEAR) network. Later on, the Mitotic Exit Network (MEN) signaling cascade maintains Cdc14 release. An important unresolved question is how Cdc14 activity can increase in early anaphase, while Cdk activity, that is required for Net1 phosphorylation, decreases and the MEN is not yet active. Here we show that the nuclear rim protein Nur1 interacts with Net1 and, in its Cdk phosphorylated form, inhibits Cdc14 release. Nur1 is dephosphorylated by Cdc14 in early anaphase, relieving the inhibition and promoting further Cdc14 release. Nur1 dephosphorylation thus describes a positive feedback loop in Cdc14 phosphatase activation during mitotic exit, required for faithful chromosome segregation and completion of the cell division cycle. During the cell cycle, a specific sequence of events leads to the formation of two daughter cells from one mother cell. Progression through the cell cycle is tightly controlled, with events occurring in the right place at the right time. Exactly how this is achieved is still being elucidated. In budding yeast, the events occurring during the final cell cycle phase – “mitotic exit” – are controlled by the phosphatase Cdc14. It is kept sequestered and inactive until it is needed for mitotic exit, at which time it is rapidly released. In this study, we have identified a new regulator of Cdc14 activity, the protein Nur1. In a series of experiments, we saw that Nur1 acts both upstream and downstream of Cdc14 activation, thereby creating a positive feedback loop. On the one hand, Nur1 contributes to inhibiting Cdc14 until the start of mitotic exit. On the other hand, through the actions of Cdc14 itself, Nur1 is disabled as an opponent of the phosphatase. This creates a robust system, rapidly switching between two opposing states and thus driving forward the mitotic exit transition.
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Affiliation(s)
- Molly Godfrey
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
| | - Thomas Kuilman
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
- * E-mail:
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Chang L, Barford D. Insights into the anaphase-promoting complex: a molecular machine that regulates mitosis. Curr Opin Struct Biol 2014; 29:1-9. [PMID: 25174288 DOI: 10.1016/j.sbi.2014.08.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/01/2014] [Accepted: 08/05/2014] [Indexed: 12/13/2022]
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a large multimeric complex that functions as a RING domain E3 ubiquitin ligase to regulate ordered transitions through the cell cycle. It does so by controlling the ubiquitin-mediated proteolysis of cell cycle proteins, notably cyclins and securins, whose degradation triggers sister chromatid disjunction and mitotic exit. Regulation of APC/C activity and modulation of its substrate specificity are subject to intricate cell cycle checkpoints and control mechanisms involving the switching of substrate-specifying cofactors, association of regulatory protein complexes and post-translational modifications. This review discusses the recent progress towards understanding the overall architecture of the APC/C, the molecular basis for degron recognition and ubiquitin chain synthesis, and how these activities are regulated.
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Affiliation(s)
- Leifu Chang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Barford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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45
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Han X, Li Z. Comparative analysis of chromosome segregation in human, yeasts and trypanosome. ACTA ACUST UNITED AC 2014; 9:472-480. [PMID: 25844087 DOI: 10.1007/s11515-014-1334-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chromosome segregation is a tightly regulated process through which duplicated genetic materials are equally partitioned into daughter cells. During the past decades, tremendous efforts have been made to understand the molecular mechanism of chromosome segregation using animals and yeasts as model systems. Recently, new insights into chromosome segregation have gradually emerged using trypanosome, an early branching parasitic protozoan, as a model organism. To uncover the unique aspects of chromosome segregation in trypanosome, which potentially could serve as new drug targets for anti-trypanosome chemotherapy, it is necessary to perform a comparative analysis of the chromosome segregation machinery between trypanosome and its human host. Here, we briefly review the current knowledge about chromosome segregation in human and Trypanosoma brucei, with a focus on the regulation of cohesin and securin degradation triggered by the activation of the anaphase promoting complex/cyclosome (APC/C). We also include yeasts in our comparative analysis since some of the original discoveries were made using budding and fission yeasts as the model organisms and, therefore, these could provide hints about the evolution of the machinery. We highlight both common and unique features in these model systems and also provide perspectives for future research in trypanosome.
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Affiliation(s)
- Xianxian Han
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, TX 77030, USA
| | - Ziyin Li
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, TX 77030, USA
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46
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Short B. How mitosis keeps itself in order. J Biophys Biochem Cytol 2014. [PMCID: PMC4195825 DOI: 10.1083/jcb.2071if] [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: 11/22/2022] Open
Abstract
Researchers describe how multiple mechanisms ensure that mitotic proteins are degraded in the correct sequence.
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47
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A million peptide motifs for the molecular biologist. Mol Cell 2014; 55:161-9. [PMID: 25038412 DOI: 10.1016/j.molcel.2014.05.032] [Citation(s) in RCA: 359] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/24/2014] [Accepted: 05/15/2014] [Indexed: 11/22/2022]
Abstract
A molecular description of functional modules in the cell is the focus of many high-throughput studies in the postgenomic era. A large portion of biomolecular interactions in virtually all cellular processes is mediated by compact interaction modules, referred to as peptide motifs. Such motifs are typically less than ten residues in length, occur within intrinsically disordered regions, and are recognized and/or posttranslationally modified by structured domains of the interacting partner. In this review, we suggest that there might be over a million instances of peptide motifs in the human proteome. While this staggering number suggests that peptide motifs are numerous and the most understudied functional module in the cell, it also holds great opportunities for new discoveries.
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48
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Lu D, Hsiao JY, Davey NE, Van Voorhis VA, Foster SA, Tang C, Morgan DO. Multiple mechanisms determine the order of APC/C substrate degradation in mitosis. ACTA ACUST UNITED AC 2014; 207:23-39. [PMID: 25287299 PMCID: PMC4195823 DOI: 10.1083/jcb.201402041] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To ensure proper mitotic progression, robust ordering of the destruction of APC/CCdc20 substrates is driven by the integration of molecular mechanisms ranging from phosphorylation-dependent interaction with substrates to sensing of the status of the spindle assembly checkpoint. The ubiquitin protein ligase anaphase-promoting complex or cyclosome (APC/C) controls mitosis by promoting ordered degradation of securin, cyclins, and other proteins. The mechanisms underlying the timing of APC/C substrate degradation are poorly understood. We explored these mechanisms using quantitative fluorescence microscopy of GFP-tagged APC/CCdc20 substrates in living budding yeast cells. Degradation of the S cyclin, Clb5, begins early in mitosis, followed 6 min later by the degradation of securin and Dbf4. Anaphase begins when less than half of securin is degraded. The spindle assembly checkpoint delays the onset of Clb5 degradation but does not influence securin degradation. Early Clb5 degradation depends on its interaction with the Cdk1–Cks1 complex and the presence of a Cdc20-binding “ABBA motif” in its N-terminal region. The degradation of securin and Dbf4 is delayed by Cdk1-dependent phosphorylation near their Cdc20-binding sites. Thus, a remarkably diverse array of mechanisms generates robust ordering of APC/CCdc20 substrate destruction.
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Affiliation(s)
- Dan Lu
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Jennifer Y Hsiao
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Norman E Davey
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Vanessa A Van Voorhis
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Scott A Foster
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Chao Tang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - David O Morgan
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
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Abstract
Nearly 20% of the budding yeast genome is transcribed periodically during the cell division cycle. The precise temporal execution of this large transcriptional program is controlled by a large interacting network of transcriptional regulators, kinases, and ubiquitin ligases. Historically, this network has been viewed as a collection of four coregulated gene clusters that are associated with each phase of the cell cycle. Although the broad outlines of these gene clusters were described nearly 20 years ago, new technologies have enabled major advances in our understanding of the genes comprising those clusters, their regulation, and the complex regulatory interplay between clusters. More recently, advances are being made in understanding the roles of chromatin in the control of the transcriptional program. We are also beginning to discover important regulatory interactions between the cell-cycle transcriptional program and other cell-cycle regulatory mechanisms such as checkpoints and metabolic networks. Here we review recent advances and contemporary models of the transcriptional network and consider these models in the context of eukaryotic cell-cycle controls.
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50
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Hellmuth S, Böttger F, Pan C, Mann M, Stemmann O. PP2A delays APC/C-dependent degradation of separase-associated but not free securin. EMBO J 2014; 33:1134-47. [PMID: 24781523 DOI: 10.1002/embj.201488098] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The universal triggering event of eukaryotic chromosome segregation is cleavage of centromeric cohesin by separase. Prior to anaphase, most separase is kept inactive by association with securin. Protein phosphatase 2A (PP2A) constitutes another binding partner of human separase, but the functional relevance of this interaction has remained enigmatic. We demonstrate that PP2A stabilizes separase-associated securin by dephosphorylation, while phosphorylation of free securin enhances its polyubiquitylation by the ubiquitin ligase APC/C and proteasomal degradation. Changing PP2A substrate phosphorylation sites to alanines slows degradation of free securin, delays separase activation, lengthens early anaphase, and results in anaphase bridges and DNA damage. In contrast, separase-associated securin is destabilized by introduction of phosphorylation-mimetic aspartates or extinction of separase-associated PP2A activity. G2- or prometaphase-arrested cells suffer from unscheduled activation of separase when endogenous securin is replaced by aspartate-mutant securin. Thus, PP2A-dependent stabilization of separase-associated securin prevents precocious activation of separase during checkpoint-mediated arrests with basal APC/C activity and increases the abruptness and fidelity of sister chromatid separation in anaphase.
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Affiliation(s)
| | | | - Cuiping Pan
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Olaf Stemmann
- Chair of Genetics, University of Bayreuth, Bayreuth, Germany
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