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Fajish G, Challa K, Salim S, Vp A, Mwaniki S, Zhang R, Fujita Y, Ito M, Nishant KT, Shinohara A. DNA double-strand breaks regulate the cleavage-independent release of Rec8-cohesin during yeast meiosis. Genes Cells 2024; 29:86-98. [PMID: 37968127 DOI: 10.1111/gtc.13081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023]
Abstract
The mitotic cohesin complex necessary for sister chromatid cohesion and chromatin loop formation shows local and global association to chromosomes in response to DNA double-strand breaks (DSBs). Here, by genome-wide binding analysis of the meiotic cohesin with Rec8, we found that the Rec8-localization profile along chromosomes is altered from middle to late meiotic prophase I with cleavage-independent dissociation. Each Rec8-binding site on the chromosome axis follows a unique alternation pattern with dissociation and probably association. Centromeres showed altered Rec8 binding in late prophase I relative to mid-prophase I, implying chromosome remodeling of the regions. Rec8 dissociation ratio per chromosome is correlated well with meiotic DSB density. Indeed, the spo11 mutant deficient in meiotic DSB formation did not change the distribution of Rec8 along chromosomes in late meiotic prophase I. These suggest the presence of a meiosis-specific regulatory pathway for the global binding of Rec8-cohesin in response to DSBs.
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Affiliation(s)
- Ghanim Fajish
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kiran Challa
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Sagar Salim
- School of Biology, Indian Institute of Science, Education and Research, Thiruvananthapuram, India
| | - Ajith Vp
- School of Biology, Indian Institute of Science, Education and Research, Thiruvananthapuram, India
| | - Stephen Mwaniki
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Ruihao Zhang
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Yurika Fujita
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Masaru Ito
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Koodali T Nishant
- School of Biology, Indian Institute of Science, Education and Research, Thiruvananthapuram, India
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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2
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Yang C, Ge Y, Zang Y, Xu M, Jin L, Wang Y, Xu X, Xue B, Wang Z, Wang L. CDC20 promotes radioresistance of prostate cancer by activating Twist1 expression. Apoptosis 2023; 28:1584-1595. [PMID: 37535214 DOI: 10.1007/s10495-023-01877-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2023] [Indexed: 08/04/2023]
Abstract
Currently, radiotherapy is one of the most attractive treatments for prostate cancer (PCa) patients. However, radioresistance remains a challenging issue and the underlying mechanism is unknown. Growing evidence has demonstrated that CDC20 (Cell division cycle protein 20) plays a pivotal role in a variety of tumors, including PCa. Here, GEPIA database mining and western blot analysis showed that higher expression of CDC20 was observed in PCa tissues and cells. We demonstrated that the expression of CDC20 was increased in PCa cells by irradiation, and knockdown of CDC20 resulted in inhibition of cell proliferation, migration, tumor formation, induced cell apoptosis and increased radiosensitivity in PCa in vitro and in vivo. Furthermore, we observed that CDC20 regulated Twist1 pathway, influencing cell proliferation and migration. These results suggest that targeting CDC20 and Twist1 may be an effective way to improve the radiosensitivity of PCa.
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Affiliation(s)
- Chuanlai Yang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China
- Scientific Research Department, The Second Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China
| | - Yuegang Ge
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China
- Institute of Radiotherapy and Oncology, Soochow University, Suzhou, 215006, Jiangsu, China
| | - Yachen Zang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China
| | - Ming Xu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China
| | - Lu Jin
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China
| | - Yang Wang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China
| | - Xinyu Xu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China
| | - Boxin Xue
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China
| | - Zhiwei Wang
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, 233003, Anhui, China.
| | - Lixia Wang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China.
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3
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Ivessa AS, Singh S. The increase in cell death rates in caloric restricted cells of the yeast helicase mutant rrm3 is Sir complex dependent. Sci Rep 2023; 13:17832. [PMID: 37857740 PMCID: PMC10587150 DOI: 10.1038/s41598-023-45125-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
Calorie restriction (CR), which is a reduction in calorie intake without malnutrition, usually extends lifespan and improves tissue integrity. This report focuses on the relationship between nuclear genomic instability and dietary-restriction and its effect on cell survival. We demonstrate that the cell survival rates of the genomic instability yeast mutant rrm3 change under metabolic restricted conditions. Rrm3 is a DNA helicase, chromosomal replication slows (and potentially stalls) in its absence with increased rates at over 1400 natural pause sites including sites within ribosomal DNA and tRNA genes. Whereas rrm3 mutant cells have lower cell death rates compared to wild type (WT) in growth medium containing normal glucose levels (i.e., 2%), under CR growth conditions cell death rates increase in the rrm3 mutant to levels, which are higher than WT. The silent-information-regulatory (Sir) protein complex and mitochondrial oxidative stress are required for the increase in cell death rates in the rrm3 mutant when cells are transferred from growth medium containing 2% glucose to CR-medium. The Rad53 checkpoint protein is highly phosphorylated in the rrm3 mutant in response to genomic instability in growth medium containing 2% glucose. Under CR, Rad53 phosphorylation is largely reduced in the rrm3 mutant in a Sir-complex dependent manner. Since CR is an adjuvant treatment during chemotherapy, which may target genomic instability in cancer cells, our studies may gain further insight into how these therapy strategies can be improved.
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Affiliation(s)
- Andreas S Ivessa
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07101-1709, USA.
| | - Sukhwinder Singh
- Pathology and Laboratory Medicine/Flow Cytometry and Immunology Core Laboratory, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07101-1709, USA
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4
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Liang X, Fu Z, Tang L, Zheng M, Chen D, Liu A, Shi L, Yang L, Shao C, Dong X. PLAGL1 is associated with prognosis and cell proliferation in pancreatic adenocarcinoma. BMC Gastroenterol 2023; 23:2. [PMID: 36600208 PMCID: PMC9811725 DOI: 10.1186/s12876-022-02609-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 12/08/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Emerging evidence has shown the crucial roles of pleomorphic adenoma gene (PLAG) family genes in multiple cancers. However, their functions and mechanisms in pancreatic adenocarcinoma (PAAD) remain poorly understood. METHODS We analyzed the expression levels of PLAG family genes in both The Cancer Genome Atlas (TCGA) database and a Gene Expression Omnibus (GEO) database, and confirmed the results in our three independent cohorts of 382 PAAD tissues and 362 adjacent nontumor pancreatic tissues. Integrated analyses were carried out to explore the function, mechanism and prognostic value of the selected PLAG family gene in PAAD patients. RESULTS By analyzing the TCGA and GEO databases, PLAGL1 was identified to be downregulated in PAAD tissues, and its decreasing levels of both mRNA and protein were verified in our three independent PAAD cohorts. PLAGL1 expression was inversely correlated with clinicopathological factors including the Ki67+ cell rate and pathologic stage. Further GSEA of the TCGA-PAAD cohort demonstrated that multiple signaling pathways implicated in cell proliferation were enriched in the lower PLAGL1 expressing PAAD group. Moreover, we demonstrated that PLAGL1 expression was obviously negatively associated with patients' overall survival outcome in both the TCGA-PAAD cohort and our verification cohorts. Additionally, through MTS and BrdU assays, we further demonstrated in vitro that PLAGL1 had the impact of preventing the proliferation of pancreatic cancer cells. CONCLUSIONS Our present study suggested that downregulated PLAGL1 might act as a biomarker in predicts poor prognosis and one of important factors in increasing cell proliferation in PAAD. This study provides us with a novel prognostic marker and therapeutic strategy for PAAD, which deserves further study.
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Affiliation(s)
- Xing Liang
- grid.429222.d0000 0004 1798 0228Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006 Jiangsu Province China ,grid.73113.370000 0004 0369 1660Department of Pancreatic-Biliary Surgery, Second Affiliated Hospital of Naval Medical University, Fengyang Road 415, Shanghai, 200003 China
| | - Zhiping Fu
- grid.73113.370000 0004 0369 1660Department of Pancreatic-Biliary Surgery, Second Affiliated Hospital of Naval Medical University, Fengyang Road 415, Shanghai, 200003 China
| | - Liang Tang
- grid.73113.370000 0004 0369 1660Department of Pancreatic-Biliary Surgery, Second Affiliated Hospital of Naval Medical University, Fengyang Road 415, Shanghai, 200003 China
| | - Minghui Zheng
- grid.73113.370000 0004 0369 1660Department of Pancreatic-Biliary Surgery, Second Affiliated Hospital of Naval Medical University, Fengyang Road 415, Shanghai, 200003 China
| | - Danlei Chen
- grid.73113.370000 0004 0369 1660Department of Pancreatic-Biliary Surgery, Second Affiliated Hospital of Naval Medical University, Fengyang Road 415, Shanghai, 200003 China
| | - Anan Liu
- grid.73113.370000 0004 0369 1660Department of Pancreatic-Biliary Surgery, Second Affiliated Hospital of Naval Medical University, Fengyang Road 415, Shanghai, 200003 China
| | - Ligang Shi
- grid.73113.370000 0004 0369 1660Department of Pancreatic-Biliary Surgery, Second Affiliated Hospital of Naval Medical University, Fengyang Road 415, Shanghai, 200003 China
| | - Linhua Yang
- grid.16821.3c0000 0004 0368 8293Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Chenghao Shao
- grid.73113.370000 0004 0369 1660Department of Pancreatic-Biliary Surgery, Second Affiliated Hospital of Naval Medical University, Fengyang Road 415, Shanghai, 200003 China
| | - Xiaoqiang Dong
- grid.429222.d0000 0004 1798 0228Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006 Jiangsu Province China
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5
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Yam CQX, Lim HH, Surana U. DNA damage checkpoint execution and the rules of its disengagement. Front Cell Dev Biol 2022; 10:1020643. [PMID: 36274841 PMCID: PMC9582513 DOI: 10.3389/fcell.2022.1020643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Chromosomes are susceptible to damage during their duplication and segregation or when exposed to genotoxic stresses. Left uncorrected, these lesions can result in genomic instability, leading to cells’ diminished fitness, unbridled proliferation or death. To prevent such fates, checkpoint controls transiently halt cell cycle progression to allow time for the implementation of corrective measures. Prominent among these is the DNA damage checkpoint which operates at G2/M transition to ensure that cells with damaged chromosomes do not enter the mitotic phase. The execution and maintenance of cell cycle arrest are essential aspects of G2/M checkpoint and have been studied in detail. Equally critical is cells’ ability to switch-off the checkpoint controls after a successful completion of corrective actions and to recommence cell cycle progression. Interestingly, when corrective measures fail, cells can mount an unusual cellular response, termed adaptation, where they escape checkpoint arrest and resume cell cycle progression with damaged chromosomes at the cost of genome instability or even death. Here, we discuss the DNA damage checkpoint, the mitotic networks it inhibits to prevent segregation of damaged chromosomes and the strategies cells employ to quench the checkpoint controls to override the G2/M arrest.
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Affiliation(s)
| | - Hong Hwa Lim
- A*STAR Singapore Immunology Network, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Uttam Surana
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Pharmacology, National University of Singapore, Singapore, Singapore
- *Correspondence: Uttam Surana,
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6
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Regulation of ATR-CHK1 signaling by ubiquitination of CLASPIN. Biochem Soc Trans 2022; 50:1471-1480. [PMID: 36196914 DOI: 10.1042/bst20220729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/14/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022]
Abstract
DNA replication forks are frequently forced into stalling by persistent DNA aberrations generated from endogenous or exogenous insults. Stalled replication forks are catastrophic for genome integrity and cell survival if not immediately stabilized. The ataxia-telangiectasia and RAD3-related kinase (ATR)-CLASPIN-checkpoint kinase 1 (CHK1) signaling cascade is a pivotal mechanism that initiates cell-cycle checkpoints and stabilizes stalled replication forks, assuring the faithful duplication of genomic information before entry into mitosis. The timely recovery of checkpoints after stressors are resolved is also crucial for normal cell proliferation. The precise activation and inactivation of ATR-CHK1 signaling are usually efficiently regulated by turnover and the cellular re-localization of the adaptor protein CLASPIN. The ubiquitination-proteasome-mediated degradation of CLASPIN, driven by APC/CCDH1 and SCFβTrCP, results in a cell-cycle-dependent fluctuation pattern of CLASPIN levels, with peak levels seen in S/G2 phase when it functions in the DNA replisome or as an adaptor protein in ATR-CHK1 signaling under replication stress. Deubiquitination mediated by a series of ubiquitin-specific protease family proteins releases CLASPIN from proteasome-dependent destruction and activates the ATR-CHK1 checkpoint to overcome replication stress. Moreover, the non-proteolytic ubiquitination of CLASPIN also affects CHK1 activation by regulating CLASPIN localization. In this review, we discuss the functions of CLASPIN ubiquitination with specific linkage types in the regulation of the ATR-CHK1 signaling pathway. Research in this area is progressing at pace and provides promising chemotherapeutic targets.
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7
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Wavelet-Vermuse C, Odnokoz O, Xue Y, Lu X, Cristofanilli M, Wan Y. CDC20-Mediated hnRNPU Ubiquitination Regulates Chromatin Condensation and Anti-Cancer Drug Response. Cancers (Basel) 2022; 14:3732. [PMID: 35954396 PMCID: PMC9367339 DOI: 10.3390/cancers14153732] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 02/08/2023] Open
Abstract
Cell division cycle 20 (CDC20) functions as a critical cell cycle regulator. It plays an important role in cancer development and drug resistance. However, the molecular mechanisms by which CDC20 regulates cellular drug response remain poorly understood. Chromatin-associated CDC20 interactome in breast cancer cells was analyzed by using affinity purification coupled with mass spectrometry. hnRNPU as a CDC20 binding partner was validated by co-immunoprecipitation and immunostaining. The molecular domain, comprising amino acid residues 461-653, on hnRNPU required for its interaction with CDC20 was identified by mapping of interactions. Co-immunoprecipitation showed that CDC20-mediated hnRNPU ubiquitination promotes its interaction with the CTCF and cohesin complex. The effects of CDC20-hnRNPU on nuclear size and chromatin condensation were investigated by analyzing DAPI and H2B-mCherry staining, respectively. The role of CDC20-hnRNPU in tumor progression and drug resistance was examined by CCK-8 cell survival and clonogenic assays. Our study indicates that CDC20-mediated ubiquitination of hnRNPU modulates chromatin condensation by regulating the interaction between hnRNPU and the CTCF-cohesin complex. Dysregulation of the CDC20-hnRNPU axis contributes to tumor progression and drug resistance.
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Affiliation(s)
- Cindy Wavelet-Vermuse
- Department of Pharmacology and Chemical Biology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA; (C.W.-V.); (O.O.)
| | - Olena Odnokoz
- Department of Pharmacology and Chemical Biology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA; (C.W.-V.); (O.O.)
| | - Yifan Xue
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15206, USA; (Y.X.); (X.L.)
| | - Xinghua Lu
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15206, USA; (Y.X.); (X.L.)
| | | | - Yong Wan
- Department of Pharmacology and Chemical Biology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA; (C.W.-V.); (O.O.)
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
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8
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Raina VB, Schoot Uiterkamp M, Vader G. Checkpoint control in meiotic prophase: Idiosyncratic demands require unique characteristics. Curr Top Dev Biol 2022; 151:281-315. [PMID: 36681474 DOI: 10.1016/bs.ctdb.2022.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chromosomal transactions such as replication, recombination and segregation are monitored by cell cycle checkpoint cascades. These checkpoints ensure the proper execution of processes that are needed for faithful genome inheritance from one cell to the next, and across generations. In meiotic prophase, a specialized checkpoint monitors defining events of meiosis: programmed DNA break formation, followed by dedicated repair through recombination based on interhomolog (IH) crossovers. This checkpoint shares molecular characteristics with canonical DNA damage checkpoints active during somatic cell cycles. However, idiosyncratic requirements of meiotic prophase have introduced unique features in this signaling cascade. In this review, we discuss the unique features of the meiotic prophase checkpoint. While being related to canonical DNA damage checkpoint cascades, the meiotic prophase checkpoint also shows similarities with the spindle assembly checkpoint (SAC) that guards chromosome segregation. We highlight these emerging similarities in the signaling logic of the checkpoints that govern meiotic prophase and chromosome segregation, and how thinking of these similarities can help us better understand meiotic prophase control. We also discuss work showing that, when aberrantly expressed, components of the meiotic prophase checkpoint might alter DNA repair fidelity and chromosome segregation in cancer cells. Considering checkpoint function in light of demands imposed by the special characteristics of meiotic prophase helps us understand checkpoint integration into the meiotic cell cycle machinery.
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Affiliation(s)
- Vivek B Raina
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York City, NY, United States
| | - Maud Schoot Uiterkamp
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands; Section of Oncogenetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Gerben Vader
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands; Section of Oncogenetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands.
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9
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Adler SO, Spiesser TW, Uschner F, Münzner U, Hahn J, Krantz M, Klipp E. A yeast cell cycle model integrating stress, signaling, and physiology. FEMS Yeast Res 2022; 22:6592118. [PMID: 35617157 PMCID: PMC9246278 DOI: 10.1093/femsyr/foac026] [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] [Received: 01/14/2022] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/25/2022] Open
Abstract
The cell division cycle in eukaryotic cells is a series of highly coordinated molecular interactions that ensure that cell growth, duplication of genetic material, and actual cell division are precisely orchestrated to give rise to two viable progeny cells. Moreover, the cell cycle machinery is responsible for incorporating information about external cues or internal processes that the cell must keep track of to ensure a coordinated, timely progression of all related processes. This is most pronounced in multicellular organisms, but also a cardinal feature in model organisms such as baker's yeast. The complex and integrative behavior is difficult to grasp and requires mathematical modeling to fully understand the quantitative interplay of the single components within the entire system. Here, we present a self-oscillating mathematical model of the yeast cell cycle that comprises all major cyclins and their main regulators. Furthermore, it accounts for the regulation of the cell cycle machinery by a series of external stimuli such as mating pheromones and changes in osmotic pressure or nutrient quality. We demonstrate how the external perturbations modify the dynamics of cell cycle components and how the cell cycle resumes after adaptation to or relief from stress.
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Affiliation(s)
- Stephan O Adler
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Thomas W Spiesser
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Friedemann Uschner
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany.,Institute for Medical Informatics and Biometry, Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Sachsen, Germany
| | - Ulrike Münzner
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany.,Laboratory of Cell Systems, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, 565-0871, Suita, Osaka, Japan
| | - Jens Hahn
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Marcus Krantz
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
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10
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Mitotic kinase oscillation governs the latching of cell cycle switches. Curr Biol 2022; 32:2780-2785.e2. [PMID: 35504285 PMCID: PMC9616797 DOI: 10.1016/j.cub.2022.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 11/20/2022]
Abstract
In 1996, Kim Nasmyth1 proposed that the eukaryotic cell cycle is an alternating sequence of transitions from G1 to S-G2-M and back again. These two phases correlate to high activity of cyclin-dependent kinases (CDKs) that trigger S-G2-M events and CDK antagonists that stabilize G1 phase. We associated these “alternative phases” with the coexistence of two stable steady states of the biochemical reactions among CDKs and their antagonists.2,3 Transitions between these steady states (G1-to-S and M-to-G1) are driven by “helper” proteins. The fact that the transitions are irreversible is guaranteed by a “latching” property of the molecular switches, as we have argued in previous publications.4,5 Here, we show that if the latch is broken, then the biochemical reactions can swing back-and-forth across the transitions; either G1-S-G1-S … (periodic DNA replication without mitosis or cell division) or M-(G1)-M-(G1) … (periodic Cdc14 release, without fully exiting mitosis). Using mathematical modeling of the molecular control circuit in budding yeast, we provide a fresh account of aberrant cell cycles in mutant strains: endoreplication in the clb1-5Δ strain6 and periodic release and resequestration of Cdc14 (an “exit” phosphatase) in the CLB2kdΔ strain.7,8 In our opinion, these “endocycles” are not autonomous oscillatory modules that must be entrained by the CDK oscillator6,7 but rather inadvertent and deleterious oscillations that are normally suppressed by the CDK latching-gate mechanism.8 Mitotic kinases enforce once-per-cycle occurrence of cell cycle events Many cell cycle events can occur periodically in the absence of mitosis Are they autonomous oscillators or accidental consequences of faulty regulation? Regulatory mutations allow negative feedback loops to sustain oscillations
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11
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Bruno S, Ghelli Luserna di Rorà A, Napolitano R, Soverini S, Martinelli G, Simonetti G. CDC20 in and out of mitosis: a prognostic factor and therapeutic target in hematological malignancies. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:159. [PMID: 35490245 PMCID: PMC9055704 DOI: 10.1186/s13046-022-02363-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/11/2022] [Indexed: 12/31/2022]
Abstract
Cell division cycle 20 homologue (CDC20) is a well-known regulator of cell cycle, as it controls the correct segregation of chromosomes during mitosis. Many studies have focused on the biological role of CDC20 in cancer development, as alterations of its functionality have been linked to genomic instability and evidence demonstrated that high CDC20 expression levels are associated with poor overall survival in solid cancers. More recently, novel CDC20 functions have been demonstrated or suggested, including the regulation of apoptosis and stemness properties and a correlation with immune cell infiltration. Here, we here summarize and discuss the role of CDC20 inside and outside mitosis, starting from its network of interacting proteins. In the last years, CDC20 has also attracted more interest in the blood cancer field, being overexpressed and showing an association with prognosis both in myeloid and lymphoid malignancies. Preclinical findings showed that selective CDC20 and APC/CCDC20/APC/CCDH1 inhibitors, namely Apcin and proTAME, are effective against lymphoma and multiple myeloma cells, resulting in mitotic arrest and apoptosis and synergizing with clinically-relevant drugs. The evidence and hypothesis presented in this review provide the input for further biological and chemical studies aiming to dissect novel potential CDC20 roles and targeting strategies in hematological malignancies.
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Affiliation(s)
- Samantha Bruno
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna and Institute of Hematology "L. e A. Seràgnoli", Bologna, Italy
| | - Andrea Ghelli Luserna di Rorà
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", via Piero Maroncelli 40, 47014, Meldola, FC, Italy.
| | - Roberta Napolitano
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna and Institute of Hematology "L. e A. Seràgnoli", Bologna, Italy
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Giorgia Simonetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", via Piero Maroncelli 40, 47014, Meldola, FC, Italy
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12
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Yamada C, Morooka A, Miyazaki S, Nagai M, Mase S, Iemura K, Tasnin MN, Takuma T, Nakamura S, Morshed S, Koike N, Mostofa MG, Rahman MA, Sharmin T, Katsuta H, Ohara K, Tanaka K, Ushimaru T. TORC1 inactivation promotes APC/C-dependent mitotic slippage in yeast and human cells. iScience 2022; 25:103675. [PMID: 35141499 PMCID: PMC8814761 DOI: 10.1016/j.isci.2021.103675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 10/20/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
Unsatisfied kinetochore-microtubule attachment activates the spindle assembly checkpoint to inhibit the metaphase-anaphase transition. However, some cells eventually override mitotic arrest by mitotic slippage. Here, we show that inactivation of TORC1 kinase elicits mitotic slippage in budding yeast and human cells. Yeast mitotic slippage was accompanied with aberrant aspects, such as degradation of the nucleolar protein Net1, release of phosphatase Cdc14, and anaphase-promoting complex/cyclosome (APC/C)-Cdh1-dependent degradation of securin and cyclin B in metaphase. This mitotic slippage caused chromosome instability. In human cells, mammalian TORC1 (mTORC1) inactivation also invoked mitotic slippage, indicating that TORC1 inactivation-induced mitotic slippage is conserved from yeast to mammalian cells. However, the invoked mitotic slippage in human cells was not dependent on APC/C-Cdh1. This study revealed an unexpected involvement of TORC1 in mitosis and provides information on undesirable side effects of the use of TORC1 inhibitors as immunosuppressants and anti-tumor drugs. Yeast TORC1 inhibition promotes Net1 degradation and Cdc14 release Yeast TORC1 inhibition invokes mitotic slippage in an APC/C-Cdh1-dependent manner Human mTORC1 inhibition also elicits mitotic slippage
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Affiliation(s)
- Chihiro Yamada
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan
| | - Aya Morooka
- Department of Biological Science, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Seira Miyazaki
- Department of Biological Science, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Masayoshi Nagai
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan.,Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Satoru Mase
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan
| | - Kenji Iemura
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Most Naoshia Tasnin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tsuneyuki Takuma
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan
| | - Shotaro Nakamura
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan
| | - Shamsul Morshed
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Naoki Koike
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Md Golam Mostofa
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Muhammad Arifur Rahman
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tasnuva Sharmin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Haruko Katsuta
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan
| | - Kotaro Ohara
- Department of Biological Science, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Kozo Tanaka
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Takashi Ushimaru
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8021, Japan.,Department of Biological Science, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.,Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
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13
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Greenwood BL, Stuart DT. Synchronization of Saccharomyces cerevisiae Cells for Analysis of Progression Through the Cell Cycle. Methods Mol Biol 2022; 2579:145-168. [PMID: 36045205 DOI: 10.1007/978-1-0716-2736-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The cell division cycle is a fundamental process required for proliferation of all living organisms. The eukaryotic cell cycle follows a basic template with an ordered series of events beginning with G1 (Gap1) phase, followed successively by S (Synthesis) phase, G2 (Gap 2) phase, and M-phase (Mitosis). The process is tightly regulated in response to signals from both the internal and external milieu. The budding yeast S. cerevisiae is an outstanding model for the study of the cell cycle and its regulatory process. The basic events and regulatory processes of the S. cerevisiae cell cycle are highly conserved with other eukaryotes. The organism grows rapidly in simple medium, has a sequenced annotated genome, well-established genetics, and is amenable to analysis by proteomics and microscopy. Additionally, a range of tools and techniques are available to generate cultures of S. cerevisiae that are homogenously arrested or captured at specific phases of the cell cycle and upon release from that arrest these can be used to monitor cell cycle events as the cells synchronously proceed through a division cycle. In this chapter, we describe a series of commonly used techniques that are used to generate synchronized populations of S. cerevisiae and provide an overview of methods that can be used to monitor the progression of the cells through the cell division cycle.
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Affiliation(s)
| | - David T Stuart
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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14
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Vannini M, Mingione VR, Meyer A, Sniffen C, Whalen J, Seshan A. A Novel Hyperactive Nud1 Mitotic Exit Network Scaffold Causes Spindle Position Checkpoint Bypass in Budding Yeast. Cells 2021; 11:46. [PMID: 35011608 PMCID: PMC8750578 DOI: 10.3390/cells11010046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 11/20/2022] Open
Abstract
Mitotic exit is a critical cell cycle transition that requires the careful coordination of nuclear positioning and cyclin B destruction in budding yeast for the maintenance of genome integrity. The mitotic exit network (MEN) is a Ras-like signal transduction pathway that promotes this process during anaphase. A crucial step in MEN activation occurs when the Dbf2-Mob1 protein kinase complex associates with the Nud1 scaffold protein at the yeast spindle pole bodies (SPBs; centrosome equivalents) and thereby becomes activated. This requires prior priming phosphorylation of Nud1 by Cdc15 at SPBs. Cdc15 activation, in turn, requires both the Tem1 GTPase and the Polo kinase Cdc5, but how Cdc15 associates with SPBs is not well understood. We have identified a hyperactive allele of NUD1, nud1-A308T, that recruits Cdc15 to SPBs in all stages of the cell cycle in a CDC5-independent manner. This allele leads to early recruitment of Dbf2-Mob1 during metaphase and requires known Cdc15 phospho-sites on Nud1. The presence of nud1-A308T leads to loss of coupling between nuclear position and mitotic exit in cells with mispositioned spindles. Our findings highlight the importance of scaffold regulation in signaling pathways to prevent improper activation.
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Affiliation(s)
- Michael Vannini
- Boston University School of Medicine, Boston, MA 02118, USA;
| | - Victoria R. Mingione
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA;
| | | | - Courtney Sniffen
- Renaissance School of Medicine, Stony Brook University Hospital, Stony Brook, NY 11794, USA;
| | - Jenna Whalen
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA;
| | - Anupama Seshan
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
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15
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Arsenault HE, Ghizzoni JM, Leech CM, Diers AR, Gesta S, Vishnudas VK, Narain NR, Sarangarajan R, Benanti JA. Ubc1 turnover contributes to the spindle assembly checkpoint in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2021; 11:jkab346. [PMID: 34586382 PMCID: PMC8664427 DOI: 10.1093/g3journal/jkab346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/20/2021] [Indexed: 11/21/2022]
Abstract
The spindle assembly checkpoint protects the integrity of the genome by ensuring that chromosomes are properly attached to the mitotic spindle before they are segregated during anaphase. Activation of the spindle checkpoint results in inhibition of the Anaphase-Promoting Complex (APC), an E3 ubiquitin ligase that triggers the metaphase-anaphase transition. Here, we show that levels of Ubc1, an E2 enzyme that functions in complex with the APC, modulate the response to spindle checkpoint activation in Saccharomyces cerevisiae. Overexpression of Ubc1 increased resistance to microtubule poisons, whereas Ubc1 shut-off sensitized cells. We also found that Ubc1 levels are regulated by the spindle checkpoint. Checkpoint activation or direct APC inhibition led to a decrease in Ubc1 levels, charging, and half-life. Additionally, stabilization of Ubc1 prevented its down-regulation by the spindle checkpoint and increased resistance to checkpoint-activating drugs. These results suggest that down-regulation of Ubc1 in response to spindle checkpoint signaling is necessary for a robust cell cycle arrest.
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Affiliation(s)
- Heather E Arsenault
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Julie M Ghizzoni
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Cassandra M Leech
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | | | | | | | | | - Jennifer A Benanti
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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16
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Meng Z, Wu J, Liu X, Zhou W, Ni M, Liu S, Guo S, Jia S, Zhang J. Identification of potential hub genes associated with the pathogenesis and prognosis of hepatocellular carcinoma via integrated bioinformatics analysis. J Int Med Res 2021; 48:300060520910019. [PMID: 32722976 PMCID: PMC7391448 DOI: 10.1177/0300060520910019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Objective The objective was to identify potential hub genes associated with the pathogenesis and prognosis of hepatocellular carcinoma (HCC). Methods Gene expression profile datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between HCC and normal samples were identified via an integrated analysis. A protein–protein interaction network was constructed and analyzed using the STRING database and Cytoscape software, and enrichment analyses were carried out through DAVID. Gene Expression Profiling Interactive Analysis and Kaplan–Meier plotter were used to determine expression and prognostic values of hub genes. Results We identified 11 hub genes (CDK1, CCNB2, CDC20, CCNB1, TOP2A, CCNA2, MELK, PBK, TPX2, KIF20A, and AURKA) that might be closely related to the pathogenesis and prognosis of HCC. Enrichment analyses indicated that the DEGs were significantly enriched in metabolism-associated pathways, and hub genes and module 1 were highly associated with cell cycle pathway. Conclusions In this study, we identified key genes of HCC, which indicated directions for further research into diagnostic and prognostic biomarkers that could facilitate targeted molecular therapy for HCC.
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Affiliation(s)
- Ziqi Meng
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jiarui Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xinkui Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Wei Zhou
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Mengwei Ni
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shuyu Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Siyu Guo
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shanshan Jia
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jingyuan Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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17
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Higgins R, Kabbaj MH, Sherwin D, Howell LA, Hatcher A, Tomko RJ, Wang Y. The Cdc48 Complex Alleviates the Cytotoxicity of Misfolded Proteins by Regulating Ubiquitin Homeostasis. Cell Rep 2021; 32:107898. [PMID: 32668237 DOI: 10.1016/j.celrep.2020.107898] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 05/04/2020] [Accepted: 06/22/2020] [Indexed: 10/23/2022] Open
Abstract
The accumulation of misfolded proteins is associated with multiple neurodegenerative disorders, but it remains poorly defined how this accumulation causes cytotoxicity. Here, we demonstrate that the Cdc48/p97 segregase machinery drives the clearance of ubiquitinated model misfolded protein Huntingtin (Htt103QP) and limits its aggregation. Nuclear ubiquitin ligase San1 acts upstream of Cdc48 to ubiquitinate Htt103QP. Unexpectedly, deletion of SAN1 and/or its cytosolic counterpart UBR1 rescues the toxicity associated with Cdc48 deficiency, suggesting that ubiquitin depletion, rather than compromised proteolysis of misfolded proteins, causes the growth defect in cells with Cdc48 deficiency. Indeed, Cdc48 deficiency leads to elevated protein ubiquitination levels and decreased free ubiquitin, which depends on San1/Ubr1. Furthermore, enhancing free ubiquitin levels rescues the toxicity in various Cdc48 pathway mutants and restores normal turnover of a known Cdc48-independent substrate. Our work highlights a previously unappreciated function for Cdc48 in ensuring the regeneration of monoubiquitin that is critical for normal cellular function.
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Affiliation(s)
- Ryan Higgins
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Marie-Helene Kabbaj
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Delaney Sherwin
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Lauren A Howell
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Alexa Hatcher
- College of Nursing, Florida State University, 600 West College Avenue, Tallahassee, FL 32306, USA
| | - Robert J Tomko
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Yanchang Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA.
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18
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Emanuele MJ, Enrico TP, Mouery RD, Wasserman D, Nachum S, Tzur A. Complex Cartography: Regulation of E2F Transcription Factors by Cyclin F and Ubiquitin. Trends Cell Biol 2020; 30:640-652. [PMID: 32513610 PMCID: PMC7859860 DOI: 10.1016/j.tcb.2020.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
The E2F family of transcriptional regulators sits at the center of cell cycle gene expression and plays vital roles in normal and cancer cell cycles. Whereas control of E2Fs by the retinoblastoma family of proteins is well established, much less is known about their regulation by ubiquitin pathways. Recent studies placed the Skp1-Cul1-F-box-protein (SCF) family of E3 ubiquitin ligases with the F-box protein Cyclin F at the center of E2F regulation, demonstrating temporal proteolysis of both activator and atypical repressor E2Fs. Importantly, these E2F members, in particular activator E2F1 and repressors E2F7 and E2F8, form a feedback circuit at the crossroads of cell cycle and cell death. Moreover, Cyclin F functions in a reciprocal circuit with the cell cycle E3 ligase anaphase-promoting complex/cyclosome (APC/C), which also controls E2F7 and E2F8. This review focuses on the complex contours of feedback within this circuit, highlighting the deep crosstalk between E2F, SCF-Cyclin F, and APC/C in regulating the oscillator underlying human cell cycles.
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Affiliation(s)
- Michael J Emanuele
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Taylor P Enrico
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan D Mouery
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Genetics and Molecular Biology Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Danit Wasserman
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sapir Nachum
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Amit Tzur
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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19
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Du LL. Resurrection from lethal knockouts: Bypass of gene essentiality. Biochem Biophys Res Commun 2020; 528:405-412. [PMID: 32507598 DOI: 10.1016/j.bbrc.2020.05.207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 01/03/2023]
Abstract
Understanding genotype-phenotype relationships is a central pursuit in biology. Gene knockout generates a complete loss-of-function genotype and is a commonly used approach for probing gene functions. The most severe phenotypic consequence of gene knockout is lethality. Genes with a lethal knockout phenotype are called essential genes. Based on genome-wide knockout analyses in yeasts, up to approximately a quarter of genes in a genome can be essential. Like other genotype-phenotype relationships, gene essentiality is subject to background effects and can vary due to gene-gene interactions. In particular, for some essential genes, lethality caused by knockout can be rescued by extragenic suppressors. Such "bypass of essentiality" (BOE) gene-gene interactions have been an understudied type of genetic suppression. A recent systematic analysis revealed that, remarkably, the essentiality of nearly 30% of essential genes in the fission yeast Schizosaccharomyces pombe can be bypassed by BOE interactions. Here, I review the history and recent progress on uncovering and understanding the bypass of gene essentiality.
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Affiliation(s)
- Li-Lin Du
- National Institute of Biological Sciences, Beijing, 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
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20
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CDK Regulation of Meiosis: Lessons from S. cerevisiae and S. pombe. Genes (Basel) 2020; 11:genes11070723. [PMID: 32610611 PMCID: PMC7397238 DOI: 10.3390/genes11070723] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022] Open
Abstract
Meiotic progression requires precise orchestration, such that one round of DNA replication is followed by two meiotic divisions. The order and timing of meiotic events is controlled through the modulation of the phosphorylation state of proteins. Key components of this phospho-regulatory system include cyclin-dependent kinase (CDK) and its cyclin regulatory subunits. Over the past two decades, studies in budding and fission yeast have greatly informed our understanding of the role of CDK in meiotic regulation. In this review, we provide an overview of how CDK controls meiotic events in both budding and fission yeast. We discuss mechanisms of CDK regulation through post-translational modifications and changes in the levels of cyclins. Finally, we highlight the similarities and differences in CDK regulation between the two yeast species. Since CDK and many meiotic regulators are highly conserved, the findings in budding and fission yeasts have revealed conserved mechanisms of meiotic regulation among eukaryotes.
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21
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Katebi A, Kohar V, Lu M. Random Parametric Perturbations of Gene Regulatory Circuit Uncover State Transitions in Cell Cycle. iScience 2020; 23:101150. [PMID: 32450514 PMCID: PMC7251928 DOI: 10.1016/j.isci.2020.101150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/05/2020] [Accepted: 05/05/2020] [Indexed: 02/03/2023] Open
Abstract
Many biological processes involve precise cellular state transitions controlled by complex gene regulation. Here, we use budding yeast cell cycle as a model system and explore how a gene regulatory circuit encodes essential information of state transitions. We present a generalized random circuit perturbation method for circuits containing heterogeneous regulation types and its usage to analyze both steady and oscillatory states from an ensemble of circuit models with random kinetic parameters. The stable steady states form robust clusters with a circular structure that are associated with cell cycle phases. This circular structure in the clusters is consistent with single-cell RNA sequencing data. The oscillatory states specify the irreversible state transitions along cell cycle progression. Furthermore, we identify possible mechanisms to understand the irreversible state transitions from the steady states. We expect this approach to be robust and generally applicable to unbiasedly predict dynamical transitions of a gene regulatory circuit.
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Affiliation(s)
- Ataur Katebi
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Vivek Kohar
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Mingyang Lu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA.
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22
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Abstract
Cells confront DNA damage in every cell cycle. Among the most deleterious types of DNA damage are DNA double-strand breaks (DSBs), which can cause cell lethality if unrepaired or cancers if improperly repaired. In response to DNA DSBs, cells activate a complex DNA damage checkpoint (DDC) response that arrests the cell cycle, reprograms gene expression, and mobilizes DNA repair factors to prevent the inheritance of unrepaired and broken chromosomes. Here we examine the DDC, induced by DNA DSBs, in the budding yeast model system and in mammals.
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Affiliation(s)
- David P Waterman
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA;
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA;
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA;
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23
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Yam CQX, Chia DB, Shi I, Lim HH, Surana U. Dun1, a Chk2-related kinase, is the central regulator of securin-separase dynamics during DNA damage signaling. Nucleic Acids Res 2020; 48:6092-6107. [PMID: 32402080 PMCID: PMC7293041 DOI: 10.1093/nar/gkaa355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 01/26/2023] Open
Abstract
The DNA damage checkpoint halts cell cycle progression in G2 in response to genotoxic insults. Central to the execution of cell cycle arrest is the checkpoint-induced stabilization of securin-separase complex (yeast Pds1-Esp1). The checkpoint kinases Chk1 and Chk2 (yeast Chk1 and Rad53) are thought to critically contribute to the stability of securin-separase complex by phosphorylation of securin, rendering it resistant to proteolytic destruction by the anaphase promoting complex (APC). Dun1, a Rad53 paralog related to Chk2, is also essential for checkpoint-imposed arrest. Dun1 is required for the DNA damage-induced transcription of DNA repair genes; however, its role in the execution of cell cycle arrest remains unknown. Here, we show that Dun1′s role in checkpoint arrest is independent of its involvement in the transcription of repair genes. Instead, Dun1 is necessary to prevent Pds1 destruction during DNA damage in that the Dun1-deficient cells degrade Pds1, escape G2 arrest and undergo mitosis despite the presence of checkpoint-active Chk1 and Rad53. Interestingly, proteolytic degradation of Pds1 in the absence of Dun1 is mediated not by APC but by the HECT domain-containing E3 ligase Rsp5. Our results suggest a regulatory scheme in which Dun1 prevents chromosome segregation during DNA damage by inhibiting Rsp5-mediated proteolytic degradation of securin Pds1.
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Affiliation(s)
- Candice Qiu Xia Yam
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, 61 Biopolis Drive, Singapore.,Bioprocessing Technology Institute, A*STAR, Singapore
| | - David Boy Chia
- Biotransformation Innovation Platform, A*STAR, Singapore
| | - Idina Shi
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, 61 Biopolis Drive, Singapore
| | - Hong Hwa Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, 61 Biopolis Drive, Singapore.,Bioprocessing Technology Institute, A*STAR, Singapore
| | - Uttam Surana
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, 61 Biopolis Drive, Singapore.,Bioprocessing Technology Institute, A*STAR, Singapore.,Biotransformation Innovation Platform, A*STAR, Singapore.,Department of Pharmacology, National University of Singapore, Singapore
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24
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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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25
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Machín F, Ayra-Plasencia J. Are Anaphase Events Really Irreversible? The Endmost Stages of Cell Division and the Paradox of the DNA Double-Strand Break Repair. Bioessays 2020; 42:e2000021. [PMID: 32363600 DOI: 10.1002/bies.202000021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/16/2020] [Indexed: 12/25/2022]
Abstract
It has been recently demonstrated that yeast cells are able to partially regress chromosome segregation in telophase as a response to DNA double-strand breaks (DSBs), likely to find a donor sequence for homology-directed repair (HDR). This regression challenges the traditional concept that establishes anaphase events as irreversible, hence opening a new field of research in cell biology. Here, the nature of this new behavior in yeast is summarized and the underlying mechanisms are speculated about. It is also discussed whether it can be reproduced in other eukaryotes. Overall, this work brings forwards the need of understanding how cells attempt to repair DSBs when transiting the latest stages of mitosis, i.e., anaphase and telophase.
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Affiliation(s)
- Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, 38010, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, 38200, Spain.,Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, 35450, Spain
| | - Jessel Ayra-Plasencia
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, 38010, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, 38200, Spain
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26
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Simmons AJ, Park R, Sterling NA, Jang MH, van Deursen JMA, Yen TJ, Cho SH, Kim S. Nearly complete deletion of BubR1 causes microcephaly through shortened mitosis and massive cell death. Hum Mol Genet 2020; 28:1822-1836. [PMID: 30668728 DOI: 10.1093/hmg/ddz022] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/14/2018] [Accepted: 01/15/2019] [Indexed: 02/06/2023] Open
Abstract
BUB-related 1 (BubR1) encoded by Budding Uninhibited by Benzimidazole 1B (BUB1B) is a crucial mitotic checkpoint protein ensuring proper segregation of chromosomes during mitosis. Mutations of BUB1B are responsible for mosaic variegated aneuploidy (MVA), a human congenital disorder characterized by extensive abnormalities in chromosome number. Although microcephaly is a prominent feature of MVA carrying the BUB1B mutation, how BubR1 deficiency disturbs neural progenitor proliferation and neuronal output and leads to microcephaly is unknown. Here we show that conditional loss of BubR1 in mouse cerebral cortex recapitulates microcephaly. BubR1-deficient cortex includes a strikingly reduced number of late-born, but not of early-born, neurons, although BubR1 expression is substantially reduced from an early stage. Importantly, absence of BubR1 decreases the proportion of neural progenitors in mitosis, specifically in metaphase, suggesting shortened mitosis owing to premature chromosome segregation. In the BubR1 mutant, massive apoptotic cell death, which is likely due to the compromised genomic integrity that results from aberrant mitosis, depletes progenitors and neurons during neurogenesis. There is no apparent alteration in centrosome number, spindle formation or primary cilia, suggesting that the major effect of BubR1 deficiency on neural progenitors is to impair the mitotic checkpoint. This finding highlights the importance of the mitotic checkpoint in the pathogenesis of microcephaly. Furthermore, the ependymal cell layer does not form in the conditional knockout, revealing an unrecognized role of BubR1 in assuring the integrity of the ventricular system, which may account for the presence of hydrocephalus in some patients.
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Affiliation(s)
- Ambrosia J Simmons
- Shriners Hospitals Pediatric Research Center, Department of Anatomy and Cell Biology, Lewis Katz School of Medicine Temple University, Philadelphia, PA, USA.,MD/Ph.D. program, Lewis Katz School of Medicine Temple University, Philadelphia, PA, USA
| | - Raehee Park
- Shriners Hospitals Pediatric Research Center, Department of Anatomy and Cell Biology, Lewis Katz School of Medicine Temple University, Philadelphia, PA, USA
| | - Noelle A Sterling
- Shriners Hospitals Pediatric Research Center, Department of Anatomy and Cell Biology, Lewis Katz School of Medicine Temple University, Philadelphia, PA, USA
| | - Mi-Hyeon Jang
- Department of Neurologic Surgery, Mayo Clinic College of Medicine, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jan M A van Deursen
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | | | - Seo-Hee Cho
- Shriners Hospitals Pediatric Research Center, Department of Anatomy and Cell Biology, Lewis Katz School of Medicine Temple University, Philadelphia, PA, USA
| | - Seonhee Kim
- Shriners Hospitals Pediatric Research Center, Department of Anatomy and Cell Biology, Lewis Katz School of Medicine Temple University, Philadelphia, PA, USA
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27
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Mizrak A, Morgan DO. Polyanions provide selective control of APC/C interactions with the activator subunit. Nat Commun 2019; 10:5807. [PMID: 31862931 PMCID: PMC6925294 DOI: 10.1038/s41467-019-13864-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/04/2019] [Indexed: 01/18/2023] Open
Abstract
Transient interactions between the anaphase-promoting complex/cyclosome (APC/C) and its activator subunit Cdc20 or Cdh1 generate oscillations in ubiquitylation activity necessary to maintain the order of cell cycle events. Activator binds the APC/C with high affinity and exhibits negligible dissociation kinetics in vitro, and it is not clear how the rapid turnover of APC/C-activator complexes is achieved in vivo. Here, we describe a mechanism that controls APC/C-activator interactions based on the availability of substrates. We find that APC/C-activator dissociation is stimulated by abundant cellular polyanions such as nucleic acids and polyphosphate. Polyanions also interfere with substrate ubiquitylation. However, engagement with high-affinity substrate blocks the inhibitory effects of polyanions on activator binding and APC/C activity. We propose that this mechanism amplifies the effects of substrate affinity on APC/C function, stimulating processive ubiquitylation of high-affinity substrates and suppressing ubiquitylation of low-affinity substrates.
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Affiliation(s)
- Arda Mizrak
- Department of Physiology, University of California, San Francisco, CA, 94143, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, CA, 94143, USA.
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28
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Melloy PG. The anaphase-promoting complex: A key mitotic regulator associated with somatic mutations occurring in cancer. Genes Chromosomes Cancer 2019; 59:189-202. [PMID: 31652364 DOI: 10.1002/gcc.22820] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that helps control chromosome separation and exit from mitosis in many different kinds of organisms, including yeast, flies, worms, and humans. This review represents a new perspective on the connection between APC/C subunit mutations and cancer. The complex nature of APC/C and limited mutation analysis of its subunits has made it difficult to determine the relationship of each subunit to cancer. In this work, cancer genomic data were examined to identify APC/C subunits with a greater than 5% alteration frequency in 11 representative cancers using the cBioPortal database. Using the Genetic Determinants of Cancer Patient Survival database, APC/C subunits were also studied and found to be significantly associated with poor patient prognosis in several cases. In comparing these two kinds of cancer genomics data to published large-scale genomic analyses looking for cancer driver genes, ANAPC1 and ANAPC3/CDC27 stood out as being represented in all three types of analyses. Seven other subunits were found to be associated both with >5% alteration frequency in certain cancers and being associated with an effect on cancer patient prognosis. The aim of this review is to provide new approaches for investigators conducting in vivo studies of APC/C subunits and cancer progression. In turn, a better understanding of these APC/C subunits and their role in different cancers will help scientists design drugs that are more precisely targeted to certain cancers, using APC/C mutation status as a biomarker.
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Affiliation(s)
- Patricia G Melloy
- Department of Biological and Allied Health Sciences, Fairleigh Dickinson University, Madison, New Jersey
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29
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Özsezen S, Papagiannakis A, Chen H, Niebel B, Milias-Argeitis A, Heinemann M. Inference of the High-Level Interaction Topology between the Metabolic and Cell-Cycle Oscillators from Single-Cell Dynamics. Cell Syst 2019; 9:354-365.e6. [DOI: 10.1016/j.cels.2019.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 02/06/2023]
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30
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Zhou Q, Pham KTM, Hu H, Kurasawa Y, Li Z. A kinetochore-based ATM/ATR-independent DNA damage checkpoint maintains genomic integrity in trypanosomes. Nucleic Acids Res 2019; 47:7973-7988. [PMID: 31147720 PMCID: PMC6736141 DOI: 10.1093/nar/gkz476] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/23/2019] [Accepted: 05/17/2019] [Indexed: 02/02/2023] Open
Abstract
DNA damage-induced cell cycle checkpoints serve as surveillance mechanisms to maintain genomic stability, and are regulated by ATM/ATR-mediated signaling pathways that are conserved from yeast to humans. Trypanosoma brucei, an early divergent microbial eukaryote, lacks key components of the conventional DNA damage-induced G2/M cell cycle checkpoint and the spindle assembly checkpoint, and nothing is known about how T. brucei controls its cell cycle checkpoints. Here we discover a kinetochore-based, DNA damage-induced metaphase checkpoint in T. brucei. MMS-induced DNA damage triggers a metaphase arrest by modulating the abundance of the outer kinetochore protein KKIP5 in an Aurora B kinase- and kinetochore-dependent, but ATM/ATR-independent manner. Overexpression of KKIP5 arrests cells at metaphase through stabilizing the mitotic cyclin CYC6 and the cohesin subunit SCC1, mimicking DNA damage-induced metaphase arrest, whereas depletion of KKIP5 alleviates the DNA damage-induced metaphase arrest and causes chromosome mis-segregation and aneuploidy. These findings suggest that trypanosomes employ a novel DNA damage-induced metaphase checkpoint to maintain genomic integrity.
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Affiliation(s)
- Qing Zhou
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, TX 77030, USA
| | - Kieu T M Pham
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, TX 77030, USA
| | - Huiqing Hu
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, TX 77030, USA
| | - Yasuhiro Kurasawa
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, TX 77030, USA
| | - Ziyin Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, TX 77030, USA
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31
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CDC20 and its downstream genes: potential prognosis factors of osteosarcoma. Int J Clin Oncol 2019; 24:1479-1489. [PMID: 31278532 DOI: 10.1007/s10147-019-01500-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 06/23/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND We investigated the microarray data GSE42352 to identify genes that can be used as prognosis factors in osteosarcoma. METHODS Gene Ontology (GO) biological process analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of Cytoscape ClueGo were used in verifying the function of different genes. Realtime-PCR were used to confirm the microarray results. 83 patient samples were collected and underwent Kaplan-Meier survival analysis and multivariate analysis to predict the prospect of genes using as prognosis factors. RESULTS After analyzing the microarray data GSE42352, mitosis metaphase to anaphase-related genes CDC20, securin, cyclin A2 and cyclin B2 were found to be overexpressed in osteosarcoma cell lines. Kaplan-Meier survival analysis showed that overexpression of these genes can predict poor prognosis outcomes in osteosarcoma patients. Furthermore, any combination of the four genes seems to be more effective in predicting osteosarcoma outcomes than any of these genes alone. CONCLUSIONS CDC20 and its downstream substracts securin, cyclin A2 and cyclin B2 are good factors that can predict prognosis outcomes in osteosarcoma. Any two combination of these four genes are more effective to be used as osteosarcoma prognosis factors.
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32
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Addis Jones O, Tiwari A, Olukoga T, Herbert A, Chan KL. PLK1 facilitates chromosome biorientation by suppressing centromere disintegration driven by BLM-mediated unwinding and spindle pulling. Nat Commun 2019; 10:2861. [PMID: 31253795 PMCID: PMC6599003 DOI: 10.1038/s41467-019-10938-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/07/2019] [Indexed: 12/16/2022] Open
Abstract
Centromeres provide a pivotal function for faithful chromosome segregation. They serve as a foundation for the assembly of the kinetochore complex and spindle connection, which is essential for chromosome biorientation. Cells lacking Polo-like kinase 1 (PLK1) activity suffer severe chromosome alignment defects, which is believed primarily due to unstable kinetochore-microtubule attachment. Here, we reveal a previously undescribed mechanism named 'centromere disintegration' that drives chromosome misalignment in PLK1-inactivated cells. We find that PLK1 inhibition does not necessarily compromise metaphase establishment, but instead its maintenance. We demonstrate that this is caused by unlawful unwinding of DNA by BLM helicase at a specific centromere domain underneath kinetochores. Under bipolar spindle pulling, the distorted centromeres are promptly decompacted into DNA threadlike molecules, leading to centromere rupture and whole-chromosome arm splitting. Consequently, chromosome alignment collapses. Our study unveils an unexpected role of PLK1 as a chromosome guardian to maintain centromere integrity for chromosome biorientation.
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Affiliation(s)
- Owen Addis Jones
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 7BG, UK
| | - Ankana Tiwari
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 7BG, UK
| | - Tomisin Olukoga
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 7BG, UK
| | - Alex Herbert
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 7BG, UK
| | - Kok-Lung Chan
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 7BG, UK.
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33
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Kudriaeva AA, Belogurov AA. Proteasome: a Nanomachinery of Creative Destruction. BIOCHEMISTRY (MOSCOW) 2019; 84:S159-S192. [PMID: 31213201 DOI: 10.1134/s0006297919140104] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the middle of the 20th century, it was postulated that degradation of intracellular proteins is a stochastic process. More than fifty years of intense studies have finally proven that protein degradation is a very complex and tightly regulated in time and space process that plays an incredibly important role in the vast majority of metabolic pathways. Degradation of more than a half of intracellular proteins is controlled by a hierarchically aligned and evolutionarily perfect system consisting of many components, the main ones being ubiquitin ligases and proteasomes, together referred to as the ubiquitin-proteasome system (UPS). The UPS includes more than 1000 individual components, and most of them are critical for the cell functioning and survival. In addition to the well-known signaling functions of ubiquitination, such as modification of substrates for proteasomal degradation and DNA repair, polyubiquitin (polyUb) chains are involved in other important cellular processes, e.g., cell cycle regulation, immunity, protein degradation in mitochondria, and even mRNA stability. This incredible variety of ubiquitination functions is related to the ubiquitin ability to form branching chains through the ε-amino group of any of seven lysine residues in its sequence. Deubiquitination is accomplished by proteins of the deubiquitinating enzyme family. The second main component of the UPS is proteasome, a multisubunit proteinase complex that, in addition to the degradation of functionally exhausted and damaged proteins, regulates many important cellular processes through controlled degradation of substrates, for example, transcription factors and cyclins. In addition to the ubiquitin-dependent-mediated degradation, there is also ubiquitin-independent degradation, when the proteolytic signal is either an intrinsic protein sequence or shuttle molecule. Protein hydrolysis is a critically important cellular function; therefore, any abnormalities in this process lead to systemic impairments further transforming into serious diseases, such as diabetes, malignant transformation, and neurodegenerative disorders (multiple sclerosis, Alzheimer's disease, Parkinson's disease, Creutzfeldt-Jakob disease and Huntington's disease). In this review, we discuss the mechanisms that orchestrate all components of the UPS, as well as the plurality of the fine-tuning pathways of proteasomal degradation.
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Affiliation(s)
- A A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - A A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia. .,Lomonosov Moscow State University, Moscow, 119991, Russia
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34
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Herrera MC, Chymkowitch P, Robertson JM, Eriksson J, Bøe SO, Alseth I, Enserink JM. Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity. Nucleic Acids Res 2019; 46:11698-11711. [PMID: 30247619 PMCID: PMC6294503 DOI: 10.1093/nar/gky846] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/10/2018] [Indexed: 01/14/2023] Open
Abstract
tRNA genes are transcribed by RNA polymerase III (RNAPIII). During recent years it has become clear that RNAPIII activity is strictly regulated by the cell in response to environmental cues and the homeostatic status of the cell. However, the molecular mechanisms that control RNAPIII activity to regulate the amplitude of tDNA transcription in normally cycling cells are not well understood. Here, we show that tRNA levels fluctuate during the cell cycle and reveal an underlying molecular mechanism. The cyclin Clb5 recruits the cyclin dependent kinase Cdk1 to tRNA genes to boost tDNA transcription during late S phase. At tDNA genes, Cdk1 promotes the recruitment of TFIIIC, stimulates the interaction between TFIIIB and TFIIIC, and increases the dynamics of RNA polymerase III in vivo. Furthermore, we identified Bdp1 as a putative Cdk1 substrate in this process. Preventing Bdp1 phosphorylation prevented cell cycle-dependent recruitment of TFIIIC and abolished the cell cycle-dependent increase in tDNA transcription. Our findings demonstrate that under optimal growth conditions Cdk1 gates tRNA synthesis in S phase by regulating the RNAPIII machinery, revealing a direct link between the cell cycle and RNAPIII activity.
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Affiliation(s)
- Maria C Herrera
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,The Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371, Norway
| | - Pierre Chymkowitch
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway
| | - Joseph M Robertson
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jens Eriksson
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Stig Ove Bøe
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,The Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371, Norway
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35
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Haliki E, Alpagut Keskin N, Masalci O. Boolean gene regulatory network model of centromere function in Saccharomyces cerevisiae. J Biol Phys 2019; 45:235-251. [PMID: 31175490 DOI: 10.1007/s10867-019-09526-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/09/2019] [Indexed: 10/26/2022] Open
Abstract
Centromeres, a highly conserved locus of eukaryotic chromosomes, have critical function for genome stability and integrity. Because their centromeric DNA sequences are necessary and sufficient for kinetochore recruitment and DNA segregation, point centromeres of Saccharomyces cerevisiae chromosomes provide an attractive system for the study of the regulation of centromere function. Using the mathematical model of Boolean gene regulatory networks, the gene regulatory dynamics of centromere region of S. cerevisiae (budding yeast), which is actively involved in the cell-cycle, has been examined. A gene regulatory network containing the relevant centromere genes of the model organism from biological databases was established and all possible cellular phenotypes subjected to a synchronous gene regulation and attracted to several basins. Gene expression in the largest attractor was compared with the biological data by obtaining changes in the cell-cycle. We show that the model for centromere function recovers a single cyclic attractor. The trajectory flow diagram plotted over all initial conditions of the system also shows good correspondence with the cell-cycle phases. Although other upstream signals are possibly involved in the regulation of centromere genes, proposed interactions with selected cell-cycle genes were sufficient to recover whole cell-cycle process. To truly clarify these proposed regulatory interactions of candidate genes for centromere function, profiling and analyzing their expression levels over time with expanded nodes/edges are required. Moreover, a previously modeled gene knock-down mechanism applied to the network and robustness versus knock-down was interpreted based on the obtained consequences.
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36
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Gay S, Piccini D, Bruhn C, Ricciardi S, Soffientini P, Carotenuto W, Biffo S, Foiani M. A Mad2-Mediated Translational Regulatory Mechanism Promoting S-Phase Cyclin Synthesis Controls Origin Firing and Survival to Replication Stress. Mol Cell 2019; 70:628-638.e5. [PMID: 29775579 PMCID: PMC5972228 DOI: 10.1016/j.molcel.2018.04.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/26/2018] [Accepted: 04/23/2018] [Indexed: 11/03/2022]
Abstract
Cell survival to replication stress depends on the activation of the Mec1ATR-Rad53 checkpoint response that protects the integrity of stalled forks and controls the origin firing program. Here we found that Mad2, a member of the spindle assembly checkpoint (SAC), contributes to efficient origin firing and to cell survival in response to replication stress. We show that Rad53 and Mad2 promote S-phase cyclin expression through different mechanisms: while Rad53 influences Clb5,6 degradation, Mad2 promotes their protein synthesis. We found that Mad2 co-sediments with polysomes and modulates the association of the translation inhibitor Caf204E-BP with the translation machinery and the initiation factor eIF4E. This Mad2-dependent translational regulatory process does not depend on other SAC proteins. Altogether our observations indicate that Mad2 has an additional function outside of mitosis to control DNA synthesis and collaborates with the Mec1-Rad53 regulatory axis to allow cell survival in response to replication stress.
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Affiliation(s)
- Sophie Gay
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy.
| | - Daniele Piccini
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Christopher Bruhn
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Sara Ricciardi
- Fondazione Istituto Nazionale Genetica Molecolare, Via Francesco Sforza, 32, 20122 Milan, Italy; Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Paolo Soffientini
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Walter Carotenuto
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Stefano Biffo
- Fondazione Istituto Nazionale Genetica Molecolare, Via Francesco Sforza, 32, 20122 Milan, Italy; Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Marco Foiani
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.
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37
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Campbell IW, Zhou X, Amon A. The Mitotic Exit Network integrates temporal and spatial signals by distributing regulation across multiple components. eLife 2019; 8:41139. [PMID: 30672733 PMCID: PMC6363386 DOI: 10.7554/elife.41139] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/10/2019] [Indexed: 12/30/2022] Open
Abstract
GTPase signal transduction pathways control cellular decision making by integrating multiple cellular events into a single signal. The Mitotic Exit Network (MEN), a Ras-like GTPase signaling pathway, integrates spatial and temporal cues to ensure that cytokinesis only occurs after the genome has partitioned between mother and daughter cells during anaphase. Here we show that signal integration does not occur at a single step of the pathway. Rather, sequential components of the pathway are controlled in series by different signals. The spatial signal, nuclear position, regulates the MEN GTPase Tem1. The temporal signal, commencement of anaphase, is mediated by mitotic cyclin-dependent kinase (CDK) phosphorylation of the GTPase's downstream kinases. We propose that integrating multiple signals through sequential steps in the GTPase pathway represents a generalizable principle in GTPase signaling and explains why intracellular signal transmission is a multi-step process. Serial signal integration rather than signal amplification makes multi-step signal transduction necessary.
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Affiliation(s)
- Ian Winsten Campbell
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Xiaoxue Zhou
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
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38
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Meza Gutierrez F, Simsek D, Mizrak A, Deutschbauer A, Braberg H, Johnson J, Xu J, Shales M, Nguyen M, Tamse-Kuehn R, Palm C, Steinmetz LM, Krogan NJ, Toczyski DP. Genetic analysis reveals functions of atypical polyubiquitin chains. eLife 2018; 7:42955. [PMID: 30547882 PMCID: PMC6305200 DOI: 10.7554/elife.42955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/30/2018] [Indexed: 12/27/2022] Open
Abstract
Although polyubiquitin chains linked through all lysines of ubiquitin exist, specific functions are well-established only for lysine-48 and lysine-63 linkages in Saccharomyces cerevisiae. To uncover pathways regulated by distinct linkages, genetic interactions between a gene deletion library and a panel of lysine-to-arginine ubiquitin mutants were systematically identified. The K11R mutant had strong genetic interactions with threonine biosynthetic genes. Consistently, we found that K11R mutants import threonine poorly. The K11R mutant also exhibited a strong genetic interaction with a subunit of the anaphase-promoting complex (APC), suggesting a role in cell cycle regulation. K11-linkages are important for vertebrate APC function, but this was not previously described in yeast. We show that the yeast APC also modifies substrates with K11-linkages in vitro, and that those chains contribute to normal APC-substrate turnover in vivo. This study reveals comprehensive genetic interactomes of polyubiquitin chains and characterizes the role of K11-chains in two biological pathways.
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Affiliation(s)
- Fernando Meza Gutierrez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Arda Mizrak
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jeffrey Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michelle Nguyen
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Raquel Tamse-Kuehn
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Curt Palm
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - David P Toczyski
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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39
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Regulation of Mammalian DNA Replication via the Ubiquitin-Proteasome System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:421-454. [PMID: 29357069 DOI: 10.1007/978-981-10-6955-0_19] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Proper regulation of DNA replication ensures the faithful transmission of genetic material essential for optimal cellular and organismal physiology. Central to this regulation is the activity of a set of enzymes that induce or reverse posttranslational modifications of various proteins critical for the initiation, progression, and termination of DNA replication. This is particularly important when DNA replication proceeds in cancer cells with elevated rates of genomic instability and increased proliferative capacities. Here, we describe how DNA replication in mammalian cells is regulated via the activity of the ubiquitin-proteasome system as well as the consequence of derailed ubiquitylation signaling involved in this important cellular activity.
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40
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Transcriptional timing and noise of yeast cell cycle regulators-a single cell and single molecule approach. NPJ Syst Biol Appl 2018; 4:17. [PMID: 29844922 PMCID: PMC5962571 DOI: 10.1038/s41540-018-0053-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/05/2018] [Accepted: 04/19/2018] [Indexed: 12/12/2022] Open
Abstract
Gene expression is a stochastic process and its appropriate regulation is critical for cell cycle progression. Cellular stress response necessitates expression reprogramming and cell cycle arrest. While previous studies are mostly based on bulk experiments influenced by synchronization effects or lack temporal distribution, time-resolved methods on single cells are needed to understand eukaryotic cell cycle in context of noisy gene expression and external perturbations. Using smFISH, microscopy and morphological markers, we monitored mRNA abundances over cell cycle phases and calculated transcriptional noise for SIC1, CLN2, and CLB5, the main G1/S transition regulators in budding yeast. We employed mathematical modeling for in silico synchronization and for derivation of time-courses from single cell data. This approach disclosed detailed quantitative insights into transcriptional regulation with and without stress, not available from bulk experiments before. First, besides the main peak in G1 we found an upshift of CLN2 and CLB5 expression in late mitosis. Second, all three genes showed basal expression throughout cell cycle enlightening that transcription is not divided in on and off but rather in high and low phases. Finally, exposing cells to osmotic stress revealed different periods of transcriptional inhibition for CLN2 and CLB5 and the impact of stress on cell cycle phase duration. Combining experimental and computational approaches allowed us to precisely assess cell cycle progression timing, as well as gene expression dynamics.
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41
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Phizicky DV, Berchowitz LE, Bell SP. Multiple kinases inhibit origin licensing and helicase activation to ensure reductive cell division during meiosis. eLife 2018; 7:33309. [PMID: 29388912 PMCID: PMC5805409 DOI: 10.7554/elife.33309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/31/2018] [Indexed: 12/26/2022] Open
Abstract
Meiotic cells undergo a single round of DNA replication followed by two rounds of chromosome segregation (the meiotic divisions) to produce haploid gametes. Both DNA replication and chromosome segregation are similarly regulated by CDK oscillations in mitotic cells. Yet how these two events are uncoupled between the meiotic divisions is unclear. Using Saccharomyces cerevisiae, we show that meiotic cells inhibit both helicase loading and helicase activation to prevent DNA replication between the meiotic divisions. CDK and the meiosis–specific kinase Ime2 cooperatively inhibit helicase loading, and their simultaneous inhibition allows inappropriate helicase reloading. Further analysis uncovered two previously unknown mechanisms by which Ime2 inhibits helicase loading. Finally, we show that CDK and the polo–like kinase Cdc5 trigger degradation of Sld2, an essential helicase–activation protein. Together, our data demonstrate that multiple kinases inhibit both helicase loading and activation between the meiotic divisions, thereby ensuring reductive cell division.
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Affiliation(s)
- David V Phizicky
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Maryland, United States
| | - Luke E Berchowitz
- Department of Genetics and Development, Columbia University Medical Center, New York, United States
| | - Stephen P Bell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Maryland, United States
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42
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Multiple signaling kinases target Mrc1 to prevent genomic instability triggered by transcription-replication conflicts. Nat Commun 2018; 9:379. [PMID: 29371596 PMCID: PMC5785523 DOI: 10.1038/s41467-017-02756-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 12/21/2017] [Indexed: 02/05/2023] Open
Abstract
Conflicts between replication and transcription machineries represent a major source of genomic instability and cells have evolved strategies to prevent such conflicts. However, little is known regarding how cells cope with sudden increases of transcription while replicating. Here, we report the existence of a general mechanism for the protection of genomic integrity upon transcriptional outbursts in S phase that is mediated by Mrc1. The N-terminal phosphorylation of Mrc1 blocked replication and prevented transcription-associated recombination (TAR) and genomic instability during stress-induced gene expression in S phase. An unbiased kinome screening identified several kinases that phosphorylate Mrc1 at the N terminus upon different environmental stresses. Mrc1 function was not restricted to environmental cues but was also required when unscheduled transcription was triggered by low fitness states such as genomic instability or slow growth. Our data indicate that Mrc1 integrates multiple signals, thereby defining a general safeguard mechanism to protect genomic integrity upon transcriptional outbursts. During S phase of the cell cycle, transcription and replication need to be coordinated in order to avoid conflicts leading to potential genomic instability. Here, the authors find that Mrc1 integrates signals from different kinases to regulate replication during unscheduled transcription events.
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43
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Zhao L, He X, Grevelding CG, Ye Q, Li Y, Gasser RB, Dissous C, Mughal MN, Zhou YQ, Zhao JL, Hu M. The RIO protein kinase-encoding gene Sj-riok-2 is involved in key reproductive processes in Schistosoma japonicum. Parasit Vectors 2017; 10:604. [PMID: 29233188 PMCID: PMC5727939 DOI: 10.1186/s13071-017-2524-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 11/05/2017] [Indexed: 11/24/2022] Open
Abstract
Background Schistosomiasis is one of the most prevalent parasitic diseases worldwide and is caused by parasitic trematodes of the genus Schistosoma. The pathogenesis of schistosomiasis is caused by eggs whose production is the consequence of the pairing of schistosomes and the subsequent sexual maturation of the female. Previous studies have demonstrated that protein kinases are involved in processes leading to the male-induced differentiation of the female gonads, ovary and vitellarium. Right open reading frame protein kinase 2 (RIOK-2) is a member of the atypical kinase family and shown in other organisms to be responsible for ribosomal RNA biogenesis and cell-cycle progression, as well as involves in nematode development. However, nothing is known about its functions in any trematode including schistosome. Methods We isolated and characterized the riok-2 gene from S. japonicum, and detected the transcriptional profiles of Sj-riok-2 by using real-time PCR and in situ hybridization. RNAi-mediated knockdown of Sj-riok-2 was performed, mitotic activities were detected by EdU incorporation assay and morphological changes on organs were observed by confocal laser scanning microscope (CLSM). Results In silico analyses of the amino acid sequence of Sj-RIOK-2 revealed typical features of this class of kinases including a winged helix (wHTH) domain and a RIO kinase domain. Sj-riok-2 is transcribed in different developmental stages of S. japonicum, with a higher abundance in adult females and eggs. Localization studies showed that Sj-riok-2 was mainly transcribed in female reproductive organs. Experiments with adult schistosomes in vitro demonstrated that the transcriptional level of Sj-riok-2 was affected by pairing. Knocking down Sj-riok-2 by RNAi reduced cell proliferation in the vitellarium and caused the increased amount of mature oocytes in ovary and an accumulation of eggs within the uterus. Conclusions Sj-riok-2 is involved in the reproductive development and maturation of female S. japonicum. Our findings provide first evidence for a pairing-dependent role of Sj-riok-2 in the reproductive development and maturation of female S. japonicum. Thus this study contributes to the understanding of molecular processes controlling reproduction in schistosomes. Electronic supplementary material The online version of this article (10.1186/s13071-017-2524-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lu Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xin He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | | | - Qing Ye
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Ying Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, Australia
| | - Colette Dissous
- CIIL - Center for Infection and Immunity of Lille Inserm, University Lille, Lille, France
| | - Mudassar N Mughal
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yan-Qin Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jun-Long Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.
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44
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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: 97] [Impact Index Per Article: 13.9] [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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45
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Cho CY, Motta FC, Kelliher CM, Deckard A, Haase SB. Reconciling conflicting models for global control of cell-cycle transcription. Cell Cycle 2017; 16:1965-1978. [PMID: 28934013 PMCID: PMC5638368 DOI: 10.1080/15384101.2017.1367073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 08/07/2017] [Indexed: 10/18/2022] Open
Abstract
Models for the control of global cell-cycle transcription have advanced from a CDK-APC/C oscillator, a transcription factor (TF) network, to coupled CDK-APC/C and TF networks. Nonetheless, current models were challenged by a recent study that concluded that the cell-cycle transcriptional program is primarily controlled by a CDK-APC/C oscillator in budding yeast. Here we report an analysis of the transcriptome dynamics in cyclin mutant cells that were not queried in the previous study. We find that B-cyclin oscillation is not essential for control of phase-specific transcription. Using a mathematical model, we demonstrate that the function of network TFs can be retained in the face of significant reductions in transcript levels. Finally, we show that cells arrested at mitotic exit with non-oscillating levels of B-cyclins continue to cycle transcriptionally. Taken together, these findings support a critical role of a TF network and a requirement for CDK activities that need not be periodic.
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Affiliation(s)
- Chun-Yi Cho
- Department of Biology, Duke University, Durham, NC, USA
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46
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Visconti R, Grieco D. Fighting tubulin-targeting anticancer drug toxicity and resistance. Endocr Relat Cancer 2017; 24:T107-T117. [PMID: 28808045 DOI: 10.1530/erc-17-0120] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/10/2017] [Indexed: 01/27/2023]
Abstract
Tubulin-targeting drugs, like taxanes and vinca alkaloids, are among the most effective anticancer therapeutics used in the clinic today. Specifically, anti-microtubule cancer drugs (AMCDs) have proven to be effective in the treatment of castration-resistant prostate cancer and triple-negative breast cancer. AMCDs, however, have limiting toxicities that include neutropenia and neurotoxicity, and, in addition, tumor cells can become resistant to the drugs after long-term use. Co-targeting mitotic progression/slippage with inhibition of the protein kinases WEE1 and MYT1 that regulate CDK1 kinase activity may improve AMCD efficacy, reducing the acquisition of resistance by the tumor and side effects from the drug and/or its vehicle. Other possible treatments that improve outcomes in the clinic for these two drug-resistant cancers, including new formulations of the AMCDs and pursuing different molecular targets, will be discussed.
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Affiliation(s)
- Roberta Visconti
- Institute for the Experimental Endocrinology and Oncology 'G. Salvatore'Italian National Council of Research, Napoli, Italy
| | - Domenico Grieco
- Ceinge-Biotecnologie AvanzateNapoli, Italy
- Department of Molecular Medicine and Medical BiotechnologiesUniversity of Napoli 'Federico II', Napoli, Italy
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47
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Oguz C, Watson LT, Baumann WT, Tyson JJ. Predicting network modules of cell cycle regulators using relative protein abundance statistics. BMC SYSTEMS BIOLOGY 2017; 11:30. [PMID: 28241833 PMCID: PMC5329933 DOI: 10.1186/s12918-017-0409-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/17/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Parameter estimation in systems biology is typically done by enforcing experimental observations through an objective function as the parameter space of a model is explored by numerical simulations. Past studies have shown that one usually finds a set of "feasible" parameter vectors that fit the available experimental data equally well, and that these alternative vectors can make different predictions under novel experimental conditions. In this study, we characterize the feasible region of a complex model of the budding yeast cell cycle under a large set of discrete experimental constraints in order to test whether the statistical features of relative protein abundance predictions are influenced by the topology of the cell cycle regulatory network. RESULTS Using differential evolution, we generate an ensemble of feasible parameter vectors that reproduce the phenotypes (viable or inviable) of wild-type yeast cells and 110 mutant strains. We use this ensemble to predict the phenotypes of 129 mutant strains for which experimental data is not available. We identify 86 novel mutants that are predicted to be viable and then rank the cell cycle proteins in terms of their contributions to cumulative variability of relative protein abundance predictions. Proteins involved in "regulation of cell size" and "regulation of G1/S transition" contribute most to predictive variability, whereas proteins involved in "positive regulation of transcription involved in exit from mitosis," "mitotic spindle assembly checkpoint" and "negative regulation of cyclin-dependent protein kinase by cyclin degradation" contribute the least. These results suggest that the statistics of these predictions may be generating patterns specific to individual network modules (START, S/G2/M, and EXIT). To test this hypothesis, we develop random forest models for predicting the network modules of cell cycle regulators using relative abundance statistics as model inputs. Predictive performance is assessed by the areas under receiver operating characteristics curves (AUC). Our models generate an AUC range of 0.83-0.87 as opposed to randomized models with AUC values around 0.50. CONCLUSIONS By using differential evolution and random forest modeling, we show that the model prediction statistics generate distinct network module-specific patterns within the cell cycle network.
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Affiliation(s)
- Cihan Oguz
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061, USA.
| | - Layne T Watson
- Department of Computer Science, Virginia Tech, Blacksburg VA, 24061, USA.,Department of Mathematics, Virginia Tech, Blacksburg VA, 24061, USA.,Department of Aerospace and Ocean Engineering, Virginia Tech, Blacksburg VA, 24061, USA
| | - William T Baumann
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg VA, 24061, USA
| | - John J Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061, USA
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48
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Wang R, Burton JL, Solomon MJ. Transcriptional and post-transcriptional regulation of Cdc20 during the spindle assembly checkpoint in S. cerevisiae. Cell Signal 2017; 33:41-48. [PMID: 28189585 DOI: 10.1016/j.cellsig.2017.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/21/2017] [Accepted: 02/06/2017] [Indexed: 01/26/2023]
Abstract
The anaphase-promoting complex (APC) is a ubiquitin ligase responsible for promoting the degradation of many cell cycle regulators. One of the activators and substrate-binding proteins for the APC is Cdc20. It has been shown previously that Cdc20 can promote its own degradation by the APC in normal cycling cells mainly through a cis-degradation mode (i.e. via an intramolecular mechanism). However, how Cdc20 is degraded during the spindle assembly checkpoint (SAC) is still not fully clear. In this study, we used a dual-Cdc20 system to investigate this issue and found that the cis-degradation mode is also the major pathway responsible for Cdc20 degradation during the SAC. In addition, we found that there is an inverse relationship between APCCdc20 activity and the transcriptional activity of the CDC20 promoter, which likely occurs through feedback regulation by APCCdc20 substrates, such as the cyclins Clb2 and Clb5. These findings contribute to our understanding of how the inhibition of APCCdc20 activity and enhanced Cdc20 degradation are required for proper spindle checkpoint arrest.
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Affiliation(s)
- Ruiwen Wang
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province 350108, China.
| | - Janet L Burton
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Mark J Solomon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
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49
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Caydasi AK, Pereira G. Evaluation of the Dynamicity of Mitotic Exit Network and Spindle Position Checkpoint Components on Spindle Pole Bodies by Fluorescence Recovery After Photobleaching (FRAP). Methods Mol Biol 2017; 1505:167-182. [PMID: 27826864 DOI: 10.1007/978-1-4939-6502-1_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Fluorescence recovery after photobleaching (FRAP) is a powerful technique to study in vivo binding and diffusion dynamics of fluorescently labeled proteins. In this chapter, we describe how to determine spindle pole body (SPB) binding dynamics of mitotic exit network (MEN) and spindle position checkpoint (SPOC) proteins using FRAP microscopy. Procedures presented here include the growth of the yeast cultures, sample preparation, image acquisition and analysis.
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Affiliation(s)
- Ayse Koca Caydasi
- DKFZ-ZMBH Alliance, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze/Kocaeli, 41400, Turkey
| | - Gislene Pereira
- DKFZ-ZMBH Alliance, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany.
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50
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Corbett KD. Molecular Mechanisms of Spindle Assembly Checkpoint Activation and Silencing. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:429-455. [PMID: 28840248 DOI: 10.1007/978-3-319-58592-5_18] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In eukaryotic cell division, the Spindle Assembly Checkpoint (SAC) plays a key regulatory role by monitoring the status of chromosome-microtubule attachments and allowing chromosome segregation only after all chromosomes are properly attached to spindle microtubules. While the identities of SAC components have been known, in some cases, for over two decades, the molecular mechanisms of the SAC have remained mostly mysterious until very recently. In the past few years, advances in biochemical reconstitution, structural biology, and bioinformatics have fueled an explosion in the molecular understanding of the SAC. This chapter seeks to synthesize these recent advances and place them in a biological context, in order to explain the mechanisms of SAC activation and silencing at a molecular level.
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Affiliation(s)
- Kevin D Corbett
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA, USA.
- Departments of Cellular & Molecular Medicine and Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
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