1
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Zhang H, Zhang D, Li L, Willard B, Runge KW. In Vivo Proximity Labeling Identifies a New Function for the Lifespan and Autophagy-regulating Kinase Pef1, an Ortholog of Human Cdk5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598664. [PMID: 38915521 PMCID: PMC11195251 DOI: 10.1101/2024.06.12.598664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cdk5 is a highly-conserved, noncanonical cell division kinase important to the terminal differentiation of mammalian cells in multiple organ systems. We previously identified Pef1, the Schizosaccharomyces pombe ortholog of cdk5, as regulator of chronological lifespan. To reveal the processes impacted by Pef1, we developed APEX2-biotin phenol-mediated proximity labeling in S. pombe. Efficient labeling required a short period of cell wall digestion and eliminating glucose and nitrogen sources from the medium. We identified 255 high-confidence Pef1 neighbors in growing cells and a novel Pef1-interacting partner, the DNA damage response protein Rad24. The Pef1-Rad24 interaction was validated by reciprocal proximity labeling and co-immunoprecipitation. Eliminating Pef1 partially rescued the DNA damage sensitivity of cells lacking Rad24. To monitor how Pef1 neighbors change under different conditions, cells induced for autophagy were labeled and 177 high-confidence Pef1 neighbors were identified. Gene ontology (GO) analysis of the Pef1 neighbors identified proteins participating in processes required for autophagosome expansion including regulation of actin dynamics and vesicle-mediated transport. Some of these proteins were identified in both exponentially growing and autophagic cells. Pef1-APEX2 proximity labeling therefore identified a new Pef1 function in modulating the DNA damage response and candidate processes that Pef1 and other cdk5 orthologs may regulate.
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Affiliation(s)
- Haitao Zhang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at CWRU
| | - Dongmei Zhang
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Ling Li
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Belinda Willard
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Kurt W. Runge
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at CWRU
- Department of Genomics and Genome Sciences, Case Western Reserve University School of Medicine
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2
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Takado M, Komamura T, Nishimura T, Ohkubo I, Ohuchi K, Matsumoto T, Takeda K. Phosphate uptake restriction, phosphate export, and polyphosphate synthesis contribute synergistically to cellular proliferation and survival. J Biol Chem 2023; 299:105454. [PMID: 37949217 PMCID: PMC10704438 DOI: 10.1016/j.jbc.2023.105454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
Phosphate (Pi) is a macronutrient, and Pi homeostasis is essential for life. Pi homeostasis has been intensively studied; however, many questions remain, even at the cellular level. Using Schizosaccharomyces pombe, we sought to better understand cellular Pi homeostasis and showed that three Pi regulators with SPX domains, Xpr1/Spx2, Pqr1, and the VTC complex synergistically contribute to Pi homeostasis to support cell proliferation and survival. SPX domains bind to inositol pyrophosphate and modulate activities of Pi-related proteins. Xpr1 is a plasma membrane protein and its Pi-exporting activity has been demonstrated in metazoan orthologs, but not in fungi. We first found that S. pombe Xpr1 is a Pi exporter, activity of which is regulated and accelerated in the mutants of Pqr1 and the VTC complex. Pqr1 is the ubiquitin ligase downregulating the Pi importers, Pho84 and Pho842. The VTC complex synthesizes polyphosphate in vacuoles. Triple deletion of Xpr1, Pqr1, and Vtc4, the catalytic core of the VTC complex, was nearly lethal in normal medium but survivable at lower [Pi]. All double-deletion mutants of the three genes were viable at normal Pi, but Δpqr1Δxpr1 showed severe viability loss at high [Pi], accompanied by hyper-elevation of cellular total Pi and free Pi. This study suggests that the three cellular processes, restriction of Pi uptake, Pi export, and polyP synthesis, contribute synergistically to cell proliferation through maintenance of Pi homeostasis, leading to the hypothesis that cooperation between Pqr1, Xpr1, and the VTC complex protects the cytoplasm and/or the nucleus from lethal elevation of free Pi.
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Affiliation(s)
- Masahiro Takado
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Tochi Komamura
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Tomoki Nishimura
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Ikkei Ohkubo
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Keita Ohuchi
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Tomohiro Matsumoto
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kojiro Takeda
- Graduate School of Natural Science, Konan University, Kobe, Japan; Institute of Integrative Neurobiology, Konan University, Kobe, Japan.
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3
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Pluta AJ, Studniarek C, Murphy S, Norbury CJ. Cyclin-dependent kinases: Masters of the eukaryotic universe. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1816. [PMID: 37718413 PMCID: PMC10909489 DOI: 10.1002/wrna.1816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A family of structurally related cyclin-dependent protein kinases (CDKs) drives many aspects of eukaryotic cell function. Much of the literature in this area has considered individual members of this family to act primarily either as regulators of the cell cycle, the context in which CDKs were first discovered, or as regulators of transcription. Until recently, CDK7 was the only clear example of a CDK that functions in both processes. However, new data points to several "cell-cycle" CDKs having important roles in transcription and some "transcriptional" CDKs having cell cycle-related targets. For example, novel functions in transcription have been demonstrated for the archetypal cell cycle regulator CDK1. The increasing evidence of the overlap between these two CDK types suggests that they might play a critical role in coordinating the two processes. Here we review the canonical functions of cell-cycle and transcriptional CDKs, and provide an update on how these kinases collaborate to perform important cellular functions. We also provide a brief overview of how dysregulation of CDKs contributes to carcinogenesis, and possible treatment avenues. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | | | - Shona Murphy
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Chris J. Norbury
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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4
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Obando-Montoya EJ, Zapata-Ocampo PA, Cuesta-Astroz Y, Atehortua L. Impact of light wavelength on the transcriptome of Porphyridium cruentum and culture yield. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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5
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Chatfield-Reed K, Marno Jones K, Shah F, Chua G. Genetic-interaction screens uncover novel biological roles and regulators of transcription factors in fission yeast. G3 GENES|GENOMES|GENETICS 2022; 12:6655692. [PMID: 35924983 PMCID: PMC9434175 DOI: 10.1093/g3journal/jkac194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022]
Abstract
In Schizosaccharomyces pombe, systematic analyses of single transcription factor deletion or overexpression strains have made substantial advances in determining the biological roles and target genes of transcription factors, yet these characteristics are still relatively unknown for over a quarter of them. Moreover, the comprehensive list of proteins that regulate transcription factors remains incomplete. To further characterize Schizosaccharomyces pombe transcription factors, we performed synthetic sick/lethality and synthetic dosage lethality screens by synthetic genetic array. Examination of 2,672 transcription factor double deletion strains revealed a sick/lethality interaction frequency of 1.72%. Phenotypic analysis of these sick/lethality strains revealed potential cell cycle roles for several poorly characterized transcription factors, including SPBC56F2.05, SPCC320.03, and SPAC3C7.04. In addition, we examined synthetic dosage lethality interactions between 14 transcription factors and a miniarray of 279 deletion strains, observing a synthetic dosage lethality frequency of 4.99%, which consisted of known and novel transcription factor regulators. The miniarray contained deletions of genes that encode primarily posttranslational-modifying enzymes to identify putative upstream regulators of the transcription factor query strains. We discovered that ubiquitin ligase Ubr1 and its E2/E3-interacting protein, Mub1, degrade the glucose-responsive transcriptional repressor Scr1. Loss of ubr1+ or mub1+ increased Scr1 protein expression, which resulted in enhanced repression of flocculation through Scr1. The synthetic dosage lethality screen also captured interactions between Scr1 and 2 of its known repressors, Sds23 and Amk2, each affecting flocculation through Scr1 by influencing its nuclear localization. Our study demonstrates that sick/lethality and synthetic dosage lethality screens can be effective in uncovering novel functions and regulators of Schizosaccharomyces pombe transcription factors.
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Affiliation(s)
- Kate Chatfield-Reed
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Kurtis Marno Jones
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Farah Shah
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
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6
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The S. pombe CDK5 Orthologue Pef1 Cooperates with Three Cyclins, Clg1, Pas1 and Psl1, to Promote Pre-Meiotic DNA Replication. Biomolecules 2021; 11:biom11010089. [PMID: 33445784 PMCID: PMC7828282 DOI: 10.3390/biom11010089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 12/11/2022] Open
Abstract
Meiosis is a specialized cell division process that mediates genetic information transfer to the next generation. Meiotic chromosomal segregation occurs when DNA replication is completed during the pre-meiotic S phase. Here, we show that Schizosaccharomyces pombe Pef1, an orthologue of mammalian cyclin-dependent kinase 5 (CDK5), is required to promote pre-meiotic DNA replication. We examined the efficiency of meiotic initiation using pat1-114 mutants and found that, meiotic nuclear divisions did not occur in the pef1Δ pat1-114 strain. Deletion of pef1 also suppressed the expression of DNA replication factors and the phosphorylation of Cdc2 Tyr-15. The double deletion of clg1 and psl1 arrested meiotic initiation in pat1-114 mutant cells, similar to that of pef1-deficient cells. Meiotic progression was also slightly delayed in the pas1-deficient strain. Our results reveal that Pef1 regulates cyclin-coordinated meiotic progression.
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7
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Matsuda S, Kikkawa U, Uda H, Nakashima A. The S. pombe CDK5 ortholog Pef1 regulates sexual differentiation through control of the TORC1 pathway and autophagy. J Cell Sci 2020; 133:jcs247817. [PMID: 32788233 DOI: 10.1242/jcs.247817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022] Open
Abstract
In Schizosaccharomyces pombe, a general strategy for survival in response to environmental changes is sexual differentiation, which is triggered by TORC1 inactivation. However, mechanisms of TORC1 regulation in fission yeast remain poorly understood. In this study, we found that Pef1, which is an ortholog of mammalian CDK5, regulates the initiation of sexual differentiation through positive regulation of TORC1 activity. Conversely, deletion of pef1 leads to activation of autophagy and subsequent excessive TORC1 reactivation during the early phases of the nitrogen starvation response. This excessive TORC1 reactivation results in the silencing of the Ste11-Mei2 pathway and mating defects. Additionally, we found that pef1 genetically interacts with tsc1 and tsc2 for TORC1 regulation, and physically interacts with three cyclins, Clg1, Pas1 and Psl1. The double deletion of clg1 and pas1 promotes activation of autophagy and TORC1 during nitrogen starvation, similar to what is seen in pef1Δ cells. Overall, our work suggests that Pef1-Clg1 and Pef1-Pas1 complexes regulate initiation of sexual differentiation through control of the TSC-TORC1 pathway and autophagy.
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Affiliation(s)
- Shinya Matsuda
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Ushio Kikkawa
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Haruka Uda
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Akio Nakashima
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
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8
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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: 17] [Impact Index Per Article: 4.3] [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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9
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Xiong F, Wang Y, Lu Q, Hao X, Fang W, Yang Y, Zhu X, Wang X. Lifestyle Characteristics and Gene Expression Analysis of Colletotrichum camelliae Isolated from Tea Plant [ Camellia sinensis (L.) O. Kuntze] Based on Transcriptome. Biomolecules 2020; 10:biom10050782. [PMID: 32443615 PMCID: PMC7278179 DOI: 10.3390/biom10050782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 11/16/2022] Open
Abstract
Colletotrichum camelliae is one of the most serious pathogens causing anthracnose in tea plants, but the interactive relationship between C. camelliae and tea plants has not been fully elucidated. This study investigated the gene expression changes in five different growth stages of C. camelliae based on transcriptome analysis to explain the lifestyle characteristics during the infection. On the basis of gene ontology (GO) enrichment analyses of differentially expressed genes (DEGs) in comparisons of germ tube (GT)/conidium (Con), appressoria (App)/Con, and cellophane infectious hyphae (CIH)/Con groups, the cellular process in the biological process category and intracellular, intracellular part, cell, and cell part in the cellular component category were significantly enriched. Hydrolase activity, catalytic activity, and molecular_function in the molecular function category were particularly enriched in the infection leaves (IL)/Con group. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the DEGs were enriched in the genetic information processing pathway (ribosome) at the GT stage and the metabolism pathway (metabolic pathways and biosynthesis of secondary metabolism) in the rest of the stages. Interestingly, the genes associated with melanin biosynthesis and carbohydrate-active enzymes (CAZys), which are vital for penetration and cell wall degradation, were significantly upregulated at the App, CIH and IL stages. Subcellular localization results further showed that the selected non-annotated secreted proteins based on transcriptome data were majorly located in the cytoplasm and nucleus, predicted as new candidate effectors. The results of this study may establish a foundation and provide innovative ideas for subsequent research on C. camelliae.
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Affiliation(s)
- Fei Xiong
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (F.X.); (W.F.)
- Tea Research Institute, Chinese Academy of Agricultural Sciences; National Center for Tea Improvement; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Hangzhou, 310008, China; (Y.W.); (Q.L.); (X.H.); (Y.Y.)
| | - Yuchun Wang
- Tea Research Institute, Chinese Academy of Agricultural Sciences; National Center for Tea Improvement; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Hangzhou, 310008, China; (Y.W.); (Q.L.); (X.H.); (Y.Y.)
- College of Agriculture and Food Sciences, Zhejiang A&F University, Lin’an, Hangzhou 311300, China
| | - Qinhua Lu
- Tea Research Institute, Chinese Academy of Agricultural Sciences; National Center for Tea Improvement; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Hangzhou, 310008, China; (Y.W.); (Q.L.); (X.H.); (Y.Y.)
| | - Xinyuan Hao
- Tea Research Institute, Chinese Academy of Agricultural Sciences; National Center for Tea Improvement; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Hangzhou, 310008, China; (Y.W.); (Q.L.); (X.H.); (Y.Y.)
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (F.X.); (W.F.)
| | - Yajun Yang
- Tea Research Institute, Chinese Academy of Agricultural Sciences; National Center for Tea Improvement; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Hangzhou, 310008, China; (Y.W.); (Q.L.); (X.H.); (Y.Y.)
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (F.X.); (W.F.)
- Correspondence: (X.Z.); (X.W.); Tel.: +86-25-84395182 (X.Z.); Fax: +86-25-84395182 (X.Z.)
| | - Xinchao Wang
- Tea Research Institute, Chinese Academy of Agricultural Sciences; National Center for Tea Improvement; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Hangzhou, 310008, China; (Y.W.); (Q.L.); (X.H.); (Y.Y.)
- Correspondence: (X.Z.); (X.W.); Tel.: +86-25-84395182 (X.Z.); Fax: +86-25-84395182 (X.Z.)
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10
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Birot A, Tormos-Pérez M, Vaur S, Feytout A, Jaegy J, Alonso Gil D, Vazquez S, Ekwall K, Javerzat JP. The CDK Pef1 and protein phosphatase 4 oppose each other for regulating cohesin binding to fission yeast chromosomes. eLife 2020; 9:e50556. [PMID: 31895039 PMCID: PMC6954021 DOI: 10.7554/elife.50556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/02/2020] [Indexed: 12/19/2022] Open
Abstract
Cohesin has essential roles in chromosome structure, segregation and repair. Cohesin binding to chromosomes is catalyzed by the cohesin loader, Mis4 in fission yeast. How cells fine tune cohesin deposition is largely unknown. Here, we provide evidence that Mis4 activity is regulated by phosphorylation of its cohesin substrate. A genetic screen for negative regulators of Mis4 yielded a CDK called Pef1, whose closest human homologue is CDK5. Inhibition of Pef1 kinase activity rescued cohesin loader deficiencies. In an otherwise wild-type background, Pef1 ablation stimulated cohesin binding to its regular sites along chromosomes while ablating Protein Phosphatase 4 had the opposite effect. Pef1 and PP4 control the phosphorylation state of the cohesin kleisin Rad21. The CDK phosphorylates Rad21 on Threonine 262. Pef1 ablation, non-phosphorylatable Rad21-T262 or mutations within a Rad21 binding domain of Mis4 alleviated the effect of PP4 deficiency. Such a CDK/PP4-based regulation of cohesin loader activity could provide an efficient mechanism for translating cellular cues into a fast and accurate cohesin response.
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Affiliation(s)
- Adrien Birot
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Marta Tormos-Pérez
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Sabine Vaur
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Amélie Feytout
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Julien Jaegy
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Dácil Alonso Gil
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Stéphanie Vazquez
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Karl Ekwall
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
| | - Jean-Paul Javerzat
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
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11
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Humaidan D, Breinig F, Helms V. Adding phosphorylation events to the core oscillator driving the cell cycle of fission yeast. PLoS One 2018; 13:e0208515. [PMID: 30513113 PMCID: PMC6279014 DOI: 10.1371/journal.pone.0208515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/19/2018] [Indexed: 11/19/2022] Open
Abstract
Much is known about the regulatory elements controlling the cell cycle in fission yeast (Schizosaccharomyces pombe). This regulation is mainly done by the (cyclin-dependent kinase/cyclin) complex (Cdc2/Cdc13) that activates specific target genes and proteins via phosphorylation events during the cell cycle in a time-dependent manner. However, more work is still needed to complement the existing gaps in the current fission yeast gene regulatory network to be able to overcome abnormalities in its growth, repair and development, i.e. explain many phenomena including mitotic catastrophe. In this work we complement the previously presented core oscillator of the cell cycle of fission yeast by selected phosphorylation events and study their effects on the temporal evolution of the core oscillator based Boolean network. Thereby, we attempt to establish a regulatory link between the autonomous cell cycle oscillator and the remainder of the cell. We suggest the unclear yet regulatory effect of phosphorylation on the added components, and discuss many unreported points regarding the temporal evolution of the cell cycle and its components. To better visualize the results regardless of the programming background we developed an Android application that can be used to run the core and extended model of the fission yeast cell cycle step by step.
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Affiliation(s)
- Dania Humaidan
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany
- * E-mail:
| | - Frank Breinig
- Molecular and Cell Biology and Center of Human and Molecular Biology, Saarland University, Saarbruecken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany
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12
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Alkan N, Friedlander G, Ment D, Prusky D, Fluhr R. Simultaneous transcriptome analysis of Colletotrichum gloeosporioides and tomato fruit pathosystem reveals novel fungal pathogenicity and fruit defense strategies. THE NEW PHYTOLOGIST 2015; 205:801-15. [PMID: 25377514 DOI: 10.1111/nph.13087] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 08/22/2014] [Indexed: 05/20/2023]
Abstract
The fungus Colletotrichum gloeosporioides breaches the fruit cuticle but remains quiescent until fruit ripening signals a switch to necrotrophy, culminating in devastating anthracnose disease. There is a need to understand the distinct fungal arms strategy and the simultaneous fruit response. Transcriptome analysis of fungal-fruit interactions was carried out concurrently in the appressoria, quiescent and necrotrophic stages. Conidia germinating on unripe fruit cuticle showed stage-specific transcription that was accompanied by massive fruit defense responses. The subsequent quiescent stage showed the development of dendritic-like structures and swollen hyphae within the fruit epidermis. The quiescent fungal transcriptome was characterized by activation of chromatin remodeling genes and unsuspected environmental alkalization. Fruit response was portrayed by continued highly integrated massive up-regulation of defense genes. During cuticle infection of green or ripe fruit, fungi recapitulate the same developmental stages but with differing quiescent time spans. The necrotrophic stage showed a dramatic shift in fungal metabolism and up-regulation of pathogenicity factors. Fruit response to necrotrophy showed activation of the salicylic acid pathway, climaxing in cell death. Transcriptome analysis of C. gloeosporioides infection of fruit reveals its distinct stage-specific lifestyle and the concurrent changing fruit response, deepening our perception of the unfolding fungal-fruit arms and defenses race.
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Affiliation(s)
- Noam Alkan
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel
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13
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Dissection of the PHO pathway in Schizosaccharomyces pombe using epistasis and the alternate repressor adenine. Curr Genet 2014; 61:175-83. [DOI: 10.1007/s00294-014-0466-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 12/11/2014] [Accepted: 12/15/2014] [Indexed: 12/27/2022]
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14
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Chen BR, Li Y, Eisenstatt JR, Runge KW. Identification of a lifespan extending mutation in the Schizosaccharomyces pombe cyclin gene clg1+ by direct selection of long-lived mutants. PLoS One 2013; 8:e69084. [PMID: 23874875 PMCID: PMC3711543 DOI: 10.1371/journal.pone.0069084] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 06/12/2013] [Indexed: 11/30/2022] Open
Abstract
Model organisms such as budding yeast, worms and flies have proven instrumental
in the discovery of genetic determinants of aging, and the fission yeast
Schizosaccharomyces
pombe is a promising new system for these
studies. We devised an approach to directly select for long-lived
S.
pombe mutants from a random DNA insertion
library. Each insertion mutation bears a unique sequence tag called a bar code
that allows one to determine the proportion of an individual mutant in a culture
containing thousands of different mutants. Aging these mutants in culture
allowed identification of a long-lived mutant bearing an insertion mutation in
the cyclin gene clg1+. Clg1p, like
Pas1p, physically associates with the cyclin-dependent kinase Pef1p. We
identified a third Pef1p cyclin, Psl1p, and found that only loss of Clg1p or
Pef1p extended lifespan. Genetic and co-immunoprecipitation results indicate
that Pef1p controls lifespan through the downstream protein kinase Cek1p. While
Pef1p is conserved as Pho85p in Saccharomyces
cerevisiae, and as cdk5 in humans, genome-wide
searches for lifespan regulators in S. cerevisiae have
never identified Pho85p. Thus, the S. pombe system
can be used to identify novel, evolutionarily conserved lifespan extending
mutations, and our results suggest a potential role for mammalian cdk5 as a
lifespan regulator.
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Affiliation(s)
- Bo-Ruei Chen
- Department of Molecular Genetics, Cleveland Clinic Lerner College of
Medicine at Case Western Reserve University, Cleveland, Ohio,
USA
- Department of Genetics and Genome Sciences, Case Western Reserve
University School of Medicine, Cleveland, Ohio, United States of
America
- Department of Biochemistry, Case Western Reserve University School of
Medicine, Cleveland, Ohio, United States of America
| | - Yanhui Li
- Department of Molecular Genetics, Cleveland Clinic Lerner College of
Medicine at Case Western Reserve University, Cleveland, Ohio,
USA
- Department of Genetics and Genome Sciences, Case Western Reserve
University School of Medicine, Cleveland, Ohio, United States of
America
| | - Jessica R. Eisenstatt
- Department of Molecular Genetics, Cleveland Clinic Lerner College of
Medicine at Case Western Reserve University, Cleveland, Ohio,
USA
- Department of Biochemistry, Case Western Reserve University School of
Medicine, Cleveland, Ohio, United States of America
| | - Kurt W. Runge
- Department of Molecular Genetics, Cleveland Clinic Lerner College of
Medicine at Case Western Reserve University, Cleveland, Ohio,
USA
- Department of Genetics and Genome Sciences, Case Western Reserve
University School of Medicine, Cleveland, Ohio, United States of
America
- * E-mail:
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15
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Carter-O'Connell I, Peel MT, Wykoff DD, O'Shea EK. Genome-wide characterization of the phosphate starvation response in Schizosaccharomyces pombe. BMC Genomics 2012; 13:697. [PMID: 23231582 PMCID: PMC3556104 DOI: 10.1186/1471-2164-13-697] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 12/06/2012] [Indexed: 11/18/2022] Open
Abstract
Background Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway, leading to expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway involving genetically identified positive (pho7+) and negative (csk1+) regulators. The genes induced by phosphate limitation and the molecular mechanism by which pho7+ and csk1+ function are unknown. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response. Results We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response that contains the ScPHO5 (pho1+), ScPHO84 (SPBC8E4.01c), and ScGIT1 (SPBC1271.09) orthologs. We identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction. Conclusions We provide a global analysis of the transcriptional response to phosphate limitation in S. pombe. Our results elucidate the conserved core regulon induced in response to phosphate starvation in this ascomycete distantly related to S. cerevisiae and provide a better understanding of flexibility in environmental stress response networks.
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Affiliation(s)
- Ian Carter-O'Connell
- Howard Hughes Medical Institute, Faculty of Arts and Sciences, Center for Systems Biology, Northwest Labs, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
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16
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Saiardi A. How inositol pyrophosphates control cellular phosphate homeostasis? Adv Biol Regul 2012; 52:351-9. [PMID: 22781748 DOI: 10.1016/j.jbior.2012.03.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 03/20/2012] [Indexed: 10/28/2022]
Abstract
Phosphorus in his phosphate PO(4)(3-) configuration is an essential constituent of all life forms. Phosphate diesters are at the core of nucleic acid structure, while phosphate monoester transmits information under the control of protein kinases and phosphatases. Due to these fundamental roles in biology it is not a surprise that phosphate cellular homeostasis is under tight control. Inositol pyrophosphates are organic molecules with the highest proportion of phosphate groups, and they are capable of regulating many biological processes, possibly by controlling energetic metabolism and adenosine triphosphate (ATP) production. Furthermore, inositol pyrophosphates influence inorganic polyphosphates (polyP) synthesis. The polymer polyP is solely constituted by phosphate groups and beside other known functions, it also plays a role in buffering cellular free phosphate [Pi] levels, an event that is ultimately necessary to generate ATP and inositol pyrophosphate. Although it is not yet clear how inositol pyrophosphates regulate cellular metabolism, understanding how inositol pyrophosphates influence phosphates homeostasis will help to clarify this important link. In this review I will describe the recent literature on this topic, with in the hope of inspiring further research in this fascinating area of biology.
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Affiliation(s)
- Adolfo Saiardi
- Cell Biology Unit, Medical Research Council Laboratory for Molecular Cell Biology, Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
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17
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Okayama H. Functional cDNA expression cloning: pushing it to the limit. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2012; 88:102-119. [PMID: 22450538 PMCID: PMC3365248 DOI: 10.2183/pjab.88.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 01/05/2012] [Indexed: 05/31/2023]
Abstract
The 1970s and the following decade are the era of the birth and early development of recombinant DNA technologies, which have entirely revolutionized the modern life science by providing tools that enable us to know the structures of genes and genomes and to dissect their components and understand their functions at the molecular and submolecular levels. One major objective of the life sciences is to achieve molecular and chemical understandings of the functions of genes and their encoded proteins, which are responsible for the manifestation of all biological phenomena in organisms. In the early 1980s, I developed, together with Paul Berg, a new technique that enables the cloning of full-length complementary DNAs (cDNAs) on the basis of their functional expression in a given cell of interest. I review the development, application and future implications in the life sciences of this gene-cloning technique.
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Affiliation(s)
- Hiroto Okayama
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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18
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Nakano K, Toya M, Yoneda A, Asami Y, Yamashita A, Kamasawa N, Osumi M, Yamamoto M. Pob1 ensures cylindrical cell shape by coupling two distinct rho signaling events during secretory vesicle targeting. Traffic 2011; 12:726-39. [PMID: 21401840 DOI: 10.1111/j.1600-0854.2011.01190.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Proper cell morphogenesis requires the co-ordination of cell polarity, cytoskeletal organization and vesicle trafficking. The Schizosaccharomyces pombe mutant pob1-664 has a curious lemon-like shape, the basis of which is not understood. Here, we found abundant vesicle accumulation in these cells, suggesting that Pob1 plays a role in vesicle trafficking. We identified Rho3 as a multicopy suppressor of this phenotype. Because Rho3 function is related to For3, an actin-polymerizing protein, and Sec8, a component of the exocyst complex, we analyzed their functional relationship with Pob1. Pob1 was essential for the formation of actin cables (by interacting with For3) and for the polarized localization of Sec8. Although neither For3 nor Sec8 is essential for polarized growth, their simultaneous disruption prevented tip growth and yielded a lemon-like cell morphology similar to pob1-664. Thus, Pob1 may ensure cylindrical cell shape of S. pombe by coupling actin-mediated vesicle transport and exocyst-mediated vesicle tethering during secretory vesicle targeting.
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Affiliation(s)
- Kentaro Nakano
- Department of Structural Biosciences, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan.
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19
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20
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Coudreuse D, Nurse P. Driving the cell cycle with a minimal CDK control network. Nature 2010; 468:1074-9. [DOI: 10.1038/nature09543] [Citation(s) in RCA: 300] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 09/28/2010] [Indexed: 01/18/2023]
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21
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Systematic screen of Schizosaccharomyces pombe deletion collection uncovers parallel evolution of the phosphate signal transduction pathway in yeasts. EUKARYOTIC CELL 2010; 10:198-206. [PMID: 21169418 DOI: 10.1128/ec.00216-10] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The phosphate signal transduction (PHO) pathway, which regulates genes in response to phosphate starvation, is well defined in Saccharomyces cerevisiae. We asked whether the PHO pathway was the same in the distantly related fission yeast Schizosaccharomyces pombe. We screened a deletion collection for mutants aberrant in phosphatase activity, which is primarily a consequence of pho1(+) transcription. We identified a novel zinc finger-containing protein (encoded by spbc27b12.11c(+)), which we have named pho7(+), that is essential for pho1(+) transcriptional induction during phosphate starvation. Few of the S. cerevisiae genes involved in the PHO pathway appear to be involved in the regulation of the phosphate starvation response in S. pombe. Only the most upstream genes in the PHO pathway in S. cerevisiae (ADO1, DDP1, and PPN1) share a similar role in both yeasts. Because ADO1 and DDP1 regulate ATP and IP(7) levels, we hypothesize that the ancestor of these yeasts must have sensed similar metabolites in response to phosphate starvation but have evolved distinct mechanisms in parallel to sense these metabolites and induce phosphate starvation genes.
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22
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Deconvolution of chromatin immunoprecipitation-microarray (ChIP-chip) analysis of MBF occupancies reveals the temporal recruitment of Rep2 at the MBF target genes. EUKARYOTIC CELL 2010; 10:130-41. [PMID: 21076007 DOI: 10.1128/ec.00218-10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
MBF (or DSC1) is known to regulate transcription of a set of G(1)/S-phase genes encoding proteins involved in regulation of DNA replication. Previous studies have shown that MBF binds not only the promoter of G(1)/S-phase genes, but also the constitutive genes; however, it was unclear if the MBF bindings at the G(1)/S-phase and constitutive genes were mechanistically distinguishable. Here, we report a chromatin immunoprecipitation-microarray (ChIP-chip) analysis of MBF binding in the Schizosaccharomyces pombe genome using high-resolution genome tiling microarrays. ChIP-chip analysis indicates that the majority of the MBF occupancies are located at the intragenic regions. Deconvolution analysis using Rpb1 ChIP-chip results distinguishes the Cdc10 bindings at the Rpb1-poor loci (promoters) from those at the Rpb1-rich loci (intragenic sequences). Importantly, Res1 binding at the Rpb1-poor loci, but not at the Rpb1-rich loci, is dependent on the Cdc10 function, suggesting a distinct binding mechanism. Most Cdc10 promoter bindings at the Rpb1-poor loci are associated with the G(1)/S-phase genes. While Res1 or Res2 is found at both the Cdc10 promoter and intragenic binding sites, Rep2 appears to be absent at the Cdc10 promoter binding sites but present at the intragenic sites. Time course ChIP-chip analysis demonstrates that Rep2 is temporally accumulated at the coding region of the MBF target genes, resembling the RNAP-II occupancies. Taken together, our results show that deconvolution analysis of Cdc10 occupancies refines the functional subset of genomic binding sites. We propose that the MBF activator Rep2 plays a role in mediating the cell cycle-specific transcription through the recruitment of RNAP-II to the MBF-bound G(1)/S-phase genes.
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23
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A Cds1-mediated checkpoint protects the MBF activator Rep2 from ubiquitination by anaphase-promoting complex/cyclosome-Ste9 at S-phase arrest in fission yeast. Mol Cell Biol 2009; 29:4959-70. [PMID: 19596787 DOI: 10.1128/mcb.00562-09] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription of the MluI cell cycle box (MCB) motif-containing genes at G(1) phase is regulated by the MCB-binding factors (MBF) (also called DSC1) in Schizosaccharomyces pombe. Upon S-phase arrest, the MBF transcriptional activity is induced through the accumulation of the MBF activator Rep2. In this study, we show that the turnover of Rep2 is attributable to ubiquitin-mediated proteolysis. Levels of Rep2 oscillate during the cell cycle, with a peak at G(1) phase, coincident with the MBF activity. Furthermore, we show that Rep2 ubiquitination requires the function of the E3 ligase anaphase-promoting complex/cyclosome (APC/C). Ste9 can be phosphorylated by the checkpoint kinase Cds1 in vitro, and its inhibition/phosphorylation at S-phase arrest is dependent on the function of Cds1. Our data indicate that the Cds1-dependent stabilization of Rep2 is achieved through the inhibition/phosphorylation of APC/C-Ste9 at the onset of S-phase arrest. Stabilization of Rep2 is important for stimulating transcription of the MBF-dependent genes to ensure a sufficient supply of proteins essential for cell recovery from S-phase arrest. We propose that oscillation of Rep2 plays a role in regulation of periodic transcription of the MBF-dependent genes during cell cycle progression.
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24
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Abstract
We discuss the mechanisms regulating entry into and progression through S phase in eukaryotic cells. Methods to study the G1/S transition are briefly reviewed and an overview of G1/S-checkpoints is given, with particular emphasis on fission yeast. Thereafter we discuss different aspects of the intra-S checkpoint and introduce the main molecular players and mechanisms.
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Affiliation(s)
- Erik Boye
- Department of Cell Biology, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Centre, Oslo, Norway
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25
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Liang J, Fantes P. The Schizosaccharomyces pombe Cdc7 protein kinase required for septum formation is a client protein of Cdc37. EUKARYOTIC CELL 2007; 6:1089-96. [PMID: 17496123 PMCID: PMC1951107 DOI: 10.1128/ec.00080-07] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Cdc37 is an essential molecular chaperone found in fungi and metazoa whose main specificity is for certain protein kinases. Cdc37 can act as an Hsp90 cochaperone or alone; in yeasts, the interaction with Hsp90 is weak and appears not to be essential for Cdc37 function. Numerous genetic interactions between Cdc37 and likely client proteins have been observed in yeasts, but biochemical confirmation has been reported in only a few cases. We and others have generated and characterized temperature-sensitive cdc37 alleles in S. pombe and have used them to investigate the cellular roles of Cdc37: previous work has shown that mitotic Cdc2 is a major client. In this paper, we describe a screen for mutations synthetically lethal with a cdc37ts mutant with the aim of identifying genes encoding further client proteins of Cdc37. Ten such strains were isolated, and genomic libraries were screened for rescuing plasmids. In one case, a truncated cdc7 gene was identified. Further experiments showed that the mutation in this strain was indeed in cdc7. Cdc7 is a protein kinase required for septum initiation, and we show that its kinase activity is greatly reduced when Cdc37 function is impaired. Cdc7 normally locates to the spindle pole body during mitosis, and this appears to be unaffected in the cdc37ts mutant. Other evidence suggests that, in addition to mitosis and septum initiation, Cdc37 may also be required for septum cleavage.
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Affiliation(s)
- Jun Liang
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
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26
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Jackson WT, Martin GS. Transcription of the Schizosaccharomyces pombe gene cdc18+: roles of MCB elements and the DSC1 complex. Gene 2006; 369:100-8. [PMID: 16460890 DOI: 10.1016/j.gene.2005.10.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 10/19/2005] [Accepted: 10/25/2005] [Indexed: 11/22/2022]
Abstract
In Schizosaccharomyces pombe, commitment to a round of DNA synthesis and entry into the cell cycle are dependent on the function of genes that are transcribed periodically during the cell cycle. Activation of these genes prior to S phase is primarily controlled through cis-acting elements known as MluI Cell-cycle Boxes, or MCBs, and by a family of transcription factors, including Cdc10, Res1, Res2 and Rep2. These transcription factors are also known to be present in a complex, DSC1, that binds to the promoters of pre-S genes. We have demonstrated that within the promoter of cdc18+, a representative pre-S gene, the orientation and spacing of MCBs are crucial for activation and cell-cycle dependence. To our surprise, electrophoretic mobility shift assays showed a highly active mutant form of the promoter, which alters the spacing of the MCB elements, does not bind DSC1 but does bind a higher mobility complex. The binding of this second complex is not dependent on Cdc10 or the Res/Rep proteins. We conclude that, DSC1 binding does not correlate with cell-cycle dependent transcriptional activation, and the higher mobility species may represent a novel transcriptional activation complex that is also likely to function in pre-S transcription.
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Affiliation(s)
- William T Jackson
- Department of Microbiology and Immunology, Stanford University Medical Center, Fairchild D315, 299 Campus Drive, Stanford, CA 94305, United States.
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27
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Abstract
Cell-cycle control of transcription seems to be a universal feature of proliferating cells, although relatively little is known about its biological significance and conservation between organisms. The two distantly related yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have provided valuable complementary insight into the regulation of periodic transcription as a function of the cell cycle. More recently, genome-wide studies of proliferating cells have identified hundreds of periodically expressed genes and underlying mechanisms of transcriptional control. This review discusses the regulation of three major transcriptional waves, which roughly coincide with three main cell-cycle transitions (initiation of DNA replication, entry into mitosis, and exit from mitosis). I also compare and contrast the transcriptional regulatory networks between the two yeasts and discuss the evolutionary conservation and possible roles for cell cycle-regulated transcription.
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Affiliation(s)
- Jürg Bähler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.
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28
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Bimbó A, Jia Y, Poh SL, Karuturi RKM, den Elzen N, Peng X, Zheng L, O'Connell M, Liu ET, Balasubramanian MK, Liu J. Systematic deletion analysis of fission yeast protein kinases. EUKARYOTIC CELL 2005; 4:799-813. [PMID: 15821139 PMCID: PMC1087820 DOI: 10.1128/ec.4.4.799-813.2005] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Eukaryotic protein kinases are key molecules mediating signal transduction that play a pivotal role in the regulation of various biological processes, including cell cycle progression, cellular morphogenesis, development, and cellular response to environmental changes. A total of 106 eukaryotic protein kinase catalytic-domain-containing proteins have been found in the entire fission yeast genome, 44% (or 64%) of which possess orthologues (or nearest homologues) in humans, based on sequence similarity within catalytic domains. Systematic deletion analysis of all putative protein kinase-encoding genes have revealed that 17 out of 106 were essential for viability, including three previously uncharacterized putative protein kinases. Although the remaining 89 protein kinase mutants were able to form colonies under optimal growth conditions, 46% of the mutants exhibited hypersensitivity to at least 1 of the 17 different stress factors tested. Phenotypic assessment of these mutants allowed us to arrange kinases into functional groups. Based on the results of this assay, we propose also the existence of four major signaling pathways that are involved in the response to 17 stresses tested. Microarray analysis demonstrated a significant correlation between the expression signature and growth phenotype of kinase mutants tested. Our complete microarray data sets are available at http://giscompute.gis.a-star.edu.sg/~gisljh/kinome.
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Affiliation(s)
- Andrea Bimbó
- Temasek Life Sciences Laboratory, 1 Research Link, NUS, Singapore 117604
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29
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van Slegtenhorst M, Mustafa A, Henske EP. Pas1, a G1 cyclin, regulates amino acid uptake and rescues a delay in G1 arrest in Tsc1 and Tsc2 mutants in Schizosaccharomyces pombe. Hum Mol Genet 2005; 14:2851-8. [PMID: 16115814 DOI: 10.1093/hmg/ddi317] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Tuberous sclerosis complex is a tumor suppressor syndrome caused by mutations in either the TSC1 or the TSC2 gene. Previous studies have shown that deletion of the TSC1 or TSC2 ortholog in Schizosaccharomyces pombe results in an amino acid uptake defect, with conditional lethality. We identified a G1 cyclin, pas1+, as a high-copy suppressor of this defect in Deltatsc1. Disruption of pas1+ causes defects in arginine and leucine uptake that are remarkably similar to Deltatsc1 and Deltatsc2, whereas Deltapas1Deltatsc1 and Deltapas1Deltatsc2 double mutants have more severe amino acid uptake defects. In a second screen, we identified a novel G63D/S165 N mutant of the small GTPase Rhb1, the target of the Tsc1/Tsc2 protein complex. The Rhb1 mutant suppresses amino acid uptake in Deltatsc1 yeast, but not in Deltapas1 yeast. Hence, Pas1 does not regulate amino acid uptake through Rhb1. To determine whether Pas1 links nutrient availability to cell cycle progression downstream of the Tsc1/Tsc2 complex, we examined the kinetics of G1 arrest in single and double mutant strains. After nitrogen starvation, Deltatsc1 and Deltatsc2 yeast had a delay in G1 arrest when compared with wild-type, which was rescued by deletion of pas1+. In summary, we identified the G1 cyclin, Pas1, as a novel regulator of amino acid uptake. Our data support a model in which Pas1 inhibits G1 arrest downstream of Tsc1 and Tsc2, linking nutrient uptake and cell cycle progression in yeast.
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30
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Moro T, Ogasawara T, Chikuda H, Ikeda T, Ogata N, Maruyama Z, Komori T, Hoshi K, Chung UI, Nakamura K, Okayama H, Kawaguchi H. Inhibition of Cdk6 expression through p38 MAP kinase is involved in differentiation of mouse prechondrocyte ATDC5. J Cell Physiol 2005; 204:927-33. [PMID: 15795936 DOI: 10.1002/jcp.20350] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Because a temporal arrest in the G1-phase of the cell cycle is a prerequisite for cell differentiation, this study investigated the involvement of cell cycle factors in the differentiation of cultured mouse prechondrocyte cell line ATDC5. Among the G1 cell cycle factors examined, both protein and mRNA levels of cyclin-dependent kinase (Cdk6) were downregulated during the culture in a differentiation medium. The protein degradation of Cdk6 was not involved in this downregulation because proteasome inhibitors did not reverse the protein level. When inhibitors of p38 MAPK, ERK-1/2, and PI3K/Akt were added to the culture, only a p38 MAPK inhibitor SB203580 blocked the decrease in the Cdk6 protein level by the differentiation medium, indicating that the Cdk6 inhibition was mediated by p38 MAPK pathway. In fact, p38 MAPK was confirmed to be phosphorylated during differentiation of ATDC5 cells. Enforced expression of Cdk6 in ATDC5 cells blocked the chondrocyte differentiation and inhibited Sox5 and Sox6 expressions. However, the Cdk6 overexpression did not affect the proliferation or the cell cycle progression, suggesting that the inhibitory effect of Cdk6 on the differentiation was exerted by a mechanism largely independent of its cell cycle regulation. These results indicate that Cdk6 may be a regulator of chondrocyte differentiation and that its p38-mediated downregulation is involved in the efficient differentiation.
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Affiliation(s)
- Toru Moro
- Department of Sensory and Motor System Medicine, Faculty of Medicine, University of Tokyo, Japan
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31
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Abstract
A fundamental process in biology is the mechanism by which cells duplicate and divide to produce two identical daughter cells. The fission yeast, Schizosaccharomyces pombe, has proved to be an excellent model organism to study the role that gene expression plays in this process. The basic paradigm emerging is that a number of groups of genes are expressed in successive waves at different cell cycle times. Transcription of a particular group is controlled by a common DNA motif present in each gene's promoter, bound by a transcription factor complex. Each motif and transcription factor complex is specific to the time in the cell cycle when the group of genes is expressed. Examples of this are the MBF (MCB-binding factor)/MCB (MluI cell cycle box) system controlling gene expression at the start of S-phase, and PBF (PCB-binding factor)/PCB (Pombe cell cycle box) regulation of transcription at the end of mitosis. In some cases, these transcription control systems also operate during the alternative form of cell division, meiosis.
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Uzawa S, Li F, Jin Y, McDonald KL, Braunfeld MB, Agard DA, Cande WZ. Spindle pole body duplication in fission yeast occurs at the G1/S boundary but maturation is blocked until exit from S by an event downstream of cdc10+. Mol Biol Cell 2004; 15:5219-30. [PMID: 15385623 PMCID: PMC532005 DOI: 10.1091/mbc.e04-03-0255] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The regulation and timing of spindle pole body (SPB) duplication and maturation in fission yeast was examined by transmission electron microscopy. When cells are arrested at G1 by nitrogen starvation, the SPB is unduplicated. On release from G1, the SPBs were duplicated after 1-2 h. In cells arrested at S by hydroxyurea, SPBs are duplicated but not mature. In G1 arrest/release experiments with cdc2.33 cells at the restrictive temperature, SPBs remained single, whereas in cells at the permissive temperature, SPBs were duplicated. In cdc10 mutant cells, the SPBs seem not only to be duplicated but also to undergo partial maturation, including invagination of the nuclear envelope underneath the SPB. There may be an S-phase-specific inhibitor of SPB maturation whose expression is under control of cdc10(+). This model was examined by induction of overreplication of the genome by overexpression of rum1p or cdc18p. In cdc18p-overexpressing cells, the SPBs are duplicated but not mature, suggesting that cdc18p is one component of this feedback mechanism. In contrast, cells overexpressing rum1p have large, deformed SPBs accompanied by other features of maturation and duplication. We propose a feedback mechanism for maturation of the SPB that is coupled with exit from S to trigger morphological changes.
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Affiliation(s)
- Satoru Uzawa
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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33
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Ogasawara T, Kawaguchi H, Jinno S, Hoshi K, Itaka K, Takato T, Nakamura K, Okayama H. Bone morphogenetic protein 2-induced osteoblast differentiation requires Smad-mediated down-regulation of Cdk6. Mol Cell Biol 2004; 24:6560-8. [PMID: 15254224 PMCID: PMC444857 DOI: 10.1128/mcb.24.15.6560-6568.2004] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Because a temporal arrest in the G(1) phase of the cell cycle is thought to be a prerequisite for cell differentiation, we investigated cell cycle factors that critically influence the differentiation of mouse osteoblastic MC3T3-E1 cells induced by bone morphogenetic protein 2 (BMP-2), a potent inducer of osteoblast differentiation. Of the G(1) cell cycle factors examined, the expression of cyclin-dependent kinase 6 (Cdk6) was found to be strongly down-regulated by BMP-2/Smads signaling, mainly via transcriptional repression. The enforced expression of Cdk6 blocked BMP-2-induced osteoblast differentiation to various degrees, depending on the level of its overexpression. However, neither BMP-2 treatment nor Cdk6 overexpression significantly affected cell proliferation, suggesting that the inhibitory effect of Cdk6 on cell differentiation was exerted by a mechanism that is largely independent of its cell cycle regulation. These results indicate that Cdk6 is a critical regulator of BMP-2-induced osteoblast differentiation and that its Smads-mediated down-regulation is essential for efficient osteoblast differentiation.
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Affiliation(s)
- Toru Ogasawara
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
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Takeo K, Ogura Y, Virtudazo E, Raclavsky V, Kawamoto S. Isolation of a CDC28 homologue from Cryptococcus neoformans that is able to complement cdc28 temperature-sensitive mutants of Saccharomyces cerevisiae. FEMS Yeast Res 2004; 4:737-44. [PMID: 15093777 DOI: 10.1016/j.femsyr.2004.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Revised: 01/19/2004] [Accepted: 01/25/2004] [Indexed: 11/30/2022] Open
Abstract
A partial cDNA fragment of the Cryptococcus neoformans homologue of the main cell cycle control gene CDC28/cdc2 was isolated using degenerate primer RT-PCR. A subsequent search in the C. neoformans genome database identified several sequences similar to CDC28/cdc2. A part of the sequence which showed the highest similarity to CDC28/cdc2 turned out to be identical to the partial cyclin-dependent kinase (Cdk) cDNA fragment isolated by degenerate RT-PCR. The full-length coding region of this Cdk homologue was amplified by RT-PCR using primers designed to target regions around start and stop codons, and the gene was named CnCdk1. To determine its function, an analysis of deduced amino acid sequence of the CnCdk1 was performed and its ability to rescue Saccharomyces cerevisiae cdc28-temperature sensitive mutants was tested. S. cerevisiae cdc28-4 and cdc28-1N strains transformed with the pYES2- CnCdk1 construct exhibited growth at 36.5 degrees C in galactose-raffinose medium, but not in glucose medium. Results of the sequence analysis and the fact that CnCdk1 is able to complement the S. cerevisiae cdc28-ts mutation support its assumed role as the CDC28/cdc2 homologue in C. neoformans.
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Affiliation(s)
- Kanji Takeo
- Research Center for Pathogenic Fungi and Microbial Toxicoses, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan.
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Ogasawara T, Katagiri M, Yamamoto A, Hoshi K, Takato T, Nakamura K, Tanaka S, Okayama H, Kawaguchi H. Osteoclast differentiation by RANKL requires NF-kappaB-mediated downregulation of cyclin-dependent kinase 6 (Cdk6). J Bone Miner Res 2004; 19:1128-36. [PMID: 15176996 DOI: 10.1359/jbmr.2004.19.7.1128] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2003] [Revised: 02/05/2004] [Accepted: 03/11/2004] [Indexed: 11/18/2022]
Abstract
UNLABELLED This study investigated the involvement of cell cycle factors in RANKL-induced osteoclast differentiation. Among the G1 cell cycle factors, Cdk6 was found to be a key molecule in determining the differentiation rate of osteoclasts as a downstream effector of the NF-kappaB signaling. INTRODUCTION A temporal arrest in the G1 phase of the cell cycle is a prerequisite for cell differentiation, making it possible that cell cycle factors regulate not only the proliferation but also the differentiation of cells. This study investigated cell cycle factors that critically influence differentiation of the murine monocytic RAW264.7 cells to osteoclasts induced by RANKL. MATERIALS AND METHODS Growth-arrested RAW cells were stimulated with serum in the presence or absence of soluble RANKL (100 ng/ml). Expressions of the G1 cell cycle factors cyclin D1, D2, D3, E, cyclin-dependent kinase (Cdk) 2, 4, 6, and Cdk inhibitors (p18 and p27) were determined by Western blot analysis. Involvement of NF-kappaB and c-jun N-terminal kinase (JNK) pathways was examined by overexpressing dominant negative mutants of the IkappaB kinase 2 (IKK(DN)) gene and mitogen-activated protein kinase kinase 7 (MKK7(DN)) gene, respectively, using the adenovirus vectors. To determine the direct effect of Cdk6 on osteoclast differentiation, stable clones of RAW cells transfected with Cdk6 cDNA were established. Osteoclast differentiation was determined by TRACP staining, and cell cycle regulation was determined by BrdU uptake and flow cytometric analysis. RESULTS AND CONCLUSION Among the cell cycle factors examined, the Cdk6 level was downregulated by RANKL synchronously with the appearance of multinucleated osteoclasts. Inhibition of the NF-kappaB pathway by IKK(DN) overexpression, but not that of the JNK pathway by MKK7(DN) overexpression, caused the decreases in both Cdk6 downregulation and osteoclastogenesis by RANKL. RAW cells overexpressing Cdk6 resist RANKL-induced osteoclastogenesis; however, cell cycle regulation was not affected by the levels of Cdk6 overexpression, suggesting that the inhibitory effect of Cdk6 on osteoclast differentiation was not exerted through cell cycle regulation. These results indicate that Cdk6 is a critical regulator of RANKL-induced osteoclast differentiation and that its NF-kappaB-mediated downregulation is essential for efficient osteoclast differentiation.
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Affiliation(s)
- Toru Ogasawara
- Department of Sensory and Motor System Medicine, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
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Kita A, Sugiura R, Shoji H, He Y, Deng L, Lu Y, Sio SO, Takegawa K, Sakaue M, Shuntoh H, Kuno T. Loss of Apm1, the micro1 subunit of the clathrin-associated adaptor-protein-1 complex, causes distinct phenotypes and synthetic lethality with calcineurin deletion in fission yeast. Mol Biol Cell 2004; 15:2920-31. [PMID: 15047861 PMCID: PMC420114 DOI: 10.1091/mbc.e03-09-0659] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Calcineurin is a highly conserved regulator of Ca(2+) signaling in eukaryotes. In fission yeast, calcineurin is not essential for viability but is required for cytokinesis and Cl(-) homeostasis. In a genetic screen for mutations that are synthetically lethal with calcineurin deletion, we isolated a mutant, cis1-1/apm1-1, an allele of the apm1(+) gene that encodes a homolog of the mammalian micro1A subunit of the clathrin-associated adaptor protein-1 (AP-1) complex. The cis1-1/apm1-1 mutant as well as the apm1-deleted (Deltaapm1) cells showed distinct phenotypes: temperature sensitivity; tacrolimus (FK506) sensitivity; and pleiotropic defects in cytokinesis, cell integrity, and vacuole fusion. Electron micrographs revealed that Deltaapm1 cells showed large vesicular structures associated with Golgi stacks and accumulated post-Golgi secretory vesicles. Deltaapm1 cells also showed the massive accumulation of the exocytic v-SNARE Syb1 in the Golgi/endosomes and a reduced secretion of acid phosphatase. These phenotypes observed in apm1 mutations were accentuated upon temperature up-shift and FK506 treatment. Notably, Apm1-GFP localized to the Golgi/endosomes, the spindle pole bodies, and the medial region. These findings suggest a role for Apm1 associated with the Golgi/endosome function, thereby affecting various cellular processes, including secretion, cytokinesis, vacuole fusion, and cell integrity and also suggest that calcineurin is involved in these events.
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Affiliation(s)
- Ayako Kita
- Division of Molecular Pharmacology and Pharmacogenomics, Department of Genome Sciences, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
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Dou X, Wu D, An W, Davies J, Hashmi SB, Ukil L, Osmani SA. The PHOA and PHOB Cyclin-Dependent Kinases Perform an Essential Function in Aspergillus nidulans. Genetics 2003; 165:1105-15. [PMID: 14668368 PMCID: PMC1462817 DOI: 10.1093/genetics/165.3.1105] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Unlike Pho85 of Saccharomyces cerevisiae, the highly related PHOA cyclin-dependent kinase (CDK) of Aspergillus nidulans plays no role in regulation of enzymes involved in phosphorous acquisition but instead modulates differentiation in response to environmental conditions, including limited phosphorous. Like PHO85, Aspergillus phoA is a nonessential gene. However, we find that expression of dominant-negative PHOA inhibits growth, suggesting it may have an essential but redundant function. Supporting this we have identified another cyclin-dependent kinase, PHOB, which is 77% identical to PHOA. Deletion of phoB causes no phenotype, even under phosphorous-limited growth conditions. To investigate the function of phoA/phoB, double mutants were selected from a cross of strains containing null alleles and by generating a temperature-sensitive allele of phoA in a ΔphoB background. Double-deleted ascospores were able to germinate but had a limited capacity for nuclear division, suggesting a cell cycle defect. Longer germination revealed morphological defects. The temperature-sensitive phoA allele caused both nuclear division and polarity defects at restrictive temperature, which could be complemented by expression of mammalian CDK5. Therefore, an essential function exists in A. nidulans for the Pho85-like kinase pair PHOA and PHOB, which may involve cell cycle control and morphogenesis.
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Affiliation(s)
- Xiaowei Dou
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
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Nilssen EA, Synnes M, Kleckner N, Grallert B, Boye E. Intra-G1 arrest in response to UV irradiation in fission yeast. Proc Natl Acad Sci U S A 2003; 100:10758-63. [PMID: 12960401 PMCID: PMC196876 DOI: 10.1073/pnas.1833769100] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
G1 is a crucial phase of cell growth because the decision to begin another mitotic cycle is made during this period. Occurrence of DNA damage in G1 poses a particular challenge, because replication of damaged DNA can be deleterious and because no sister chromatid is present to provide a template for recombinational repair. We therefore have studied the response of Schizosaccharomyces pombe cells to UV irradiation in early G1 phase. We find that irradiation results in delayed progression through G1, as manifested most critically in the delayed formation of the pre-replication complex. This delay does not have the molecular hallmarks of known checkpoint responses: it is independent of the checkpoint proteins Rad3, Cds1, and Chk1 and does not elicit inhibitory phosphorylation of Cdc2. Irradiated cells eventually progress into S phase and arrest in early S by a rad3- and cds1-dependent mechanism, most likely the intra-S checkpoint. Caffeine alleviates both the intra-G1- and intra-S-phase delays. We suggest that intra-G1 delay may be widely conserved and discuss significance and possible mechanisms.
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Affiliation(s)
- Esben A Nilssen
- Department of Cell Biology, Institute for Cancer Research, Montebello, 0310 Oslo, Norway
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Hiroi N, Ito T, Yamamoto H, Ochiya T, Jinno S, Okayama H. Mammalian Rcd1 is a novel transcriptional cofactor that mediates retinoic acid-induced cell differentiation. EMBO J 2002; 21:5235-44. [PMID: 12356739 PMCID: PMC129043 DOI: 10.1093/emboj/cdf521] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rcd1, initially identified as a factor essential for the commitment to nitrogen starvation-invoked differentiation in fission yeast, is one of the most conserved proteins found across eukaryotes, and its mammalian homolog is expressed in a variety of differentiating tissues. Here we show that mammalian Rcd1 is a novel transcriptional cofactor and is critically involved in the commitment step in the retinoic acid-induced differentiation of F9 mouse teratocarcinoma cells, at least in part, via forming complexes with retinoic acid receptor and activation transcription factor-2 (ATF-2). In addition, antisense oligonucleotide treatment of embryonic mouse lung explants suggests that Rcd1 also plays a role in retinoic acid-controlled lung development.
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Affiliation(s)
| | - Takaaki Ito
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033,
Department of Pathology, Yokohama City University, School of Medicine, Kanazawa-ku, Yokohama 236-0004 and Section for Studies on Metastasis, National Cancer Center Institute, Chuo-ku, Tokyo 104-0045, Japan Corresponding author e-mail: o
| | - Hanako Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033,
Department of Pathology, Yokohama City University, School of Medicine, Kanazawa-ku, Yokohama 236-0004 and Section for Studies on Metastasis, National Cancer Center Institute, Chuo-ku, Tokyo 104-0045, Japan Corresponding author e-mail: o
| | - Takahiro Ochiya
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033,
Department of Pathology, Yokohama City University, School of Medicine, Kanazawa-ku, Yokohama 236-0004 and Section for Studies on Metastasis, National Cancer Center Institute, Chuo-ku, Tokyo 104-0045, Japan Corresponding author e-mail: o
| | | | - Hiroto Okayama
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033,
Department of Pathology, Yokohama City University, School of Medicine, Kanazawa-ku, Yokohama 236-0004 and Section for Studies on Metastasis, National Cancer Center Institute, Chuo-ku, Tokyo 104-0045, Japan Corresponding author e-mail: o
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de Jesús-Berríos M, Rodríguez-del Valle N. Expression of a Pho85 cyclin-dependent kinase is repressed during the dimorphic transition in Sporothrix schenckii. Fungal Genet Biol 2002; 37:39-48. [PMID: 12223188 DOI: 10.1016/s1087-1845(02)00031-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sporothrix schenckii is a pathogenic fungus that undergoes a dimorphic transition from yeast to mycelium in response to environmental conditions such as cell density, temperature, and calcium. We identified a homolog of the Pho85 cyclin-dependent kinase (Cdk) that mediates cellular responses to environmental conditions in other organisms. By Western blot, three proteins containing the PSTAIRE motif, which characterize the cyclin-dependent protein kinases, were identified in S. schenckii. The gene encoding a Pho85 homolog, PhoSs, was identified and sequenced. The phoSs gene consists of 990bp, contains one intron, and encodes a protein of 306 amino acids. The S. schenckii Pho85 homolog shares features with Cdks, including the PSTAIRE motif, an ATP binding domain, and a serine-threonine kinase domain. By quantitative competitive RT-PCR, expression of the phoSs gene was found to decrease 30-fold during the yeast to mycelium transition. The addition of extracellular calcium accelerated the dimorphic transition and restored phoSs expression. These findings suggest PhoSs may participate in the control of the yeast to mycelium transition in S. schenckii.
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Affiliation(s)
- Marisol de Jesús-Berríos
- Department of Microbiology and Medical Zoology, Medical Sciences Campus, University of Puerto Rico, San Juan 00936, USA.
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41
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Wang H, Tang X, Liu J, Trautmann S, Balasundaram D, McCollum D, Balasubramanian MK. The multiprotein exocyst complex is essential for cell separation in Schizosaccharomyces pombe. Mol Biol Cell 2002; 13:515-29. [PMID: 11854409 PMCID: PMC65646 DOI: 10.1091/mbc.01-11-0542] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2001] [Revised: 10/27/2001] [Accepted: 11/14/2001] [Indexed: 11/11/2022] Open
Abstract
Schizosaccharomyces pombe cells divide by medial fission through the use of an actomyosin-based contractile ring. A mulitlayered division septum is assembled in concert with ring constriction. Finally, cleavage of the inner layer of the division septum results in the liberation of daughter cells. Although numerous studies have focused on actomyosin ring and division septum assembly, little information is available on the mechanism of cell separation. Here we describe a mutant, sec8-1, that is defective in cell separation but not in other aspects of cytokinesis. sec8-1 mutants accumulate about 100-nm vesicles and have reduced secretion of acid phosphatase, suggesting that they are defective in exocytosis. Sec8p is a component of the exocyst complex. Using biochemical methods, we show that Sec8p physically interacts with other members of the exocyst complex, including Sec6p, Sec10p, and Exo70p. These exocyst proteins localize to regions of active exocytosis-at the growing ends of interphase cells and in the medial region of cells undergoing cytokinesis-in an F-actin-dependent and exocytosis-independent manner. Analysis of a number of mutations in various exocyst components has established that these components are essential for cell viability. Interestingly, all exocyst mutants analyzed appear to be able to elongate and to assemble division septa but are defective for cell separation. We therefore propose that the fission yeast exocyst is involved in targeting of enzymes responsible for septum cleavage. We further propose that cell elongation and division septum assembly can continue with minimal levels of exocyst function.
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Affiliation(s)
- Hongyan Wang
- The Institute of Molecular Agrobiology, The National University of Singapore, Singapore 117604, Republic of Singapore
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42
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Kim SM, Huberman JA. Regulation of replication timing in fission yeast. EMBO J 2001; 20:6115-26. [PMID: 11689451 PMCID: PMC125695 DOI: 10.1093/emboj/20.21.6115] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2001] [Revised: 09/06/2001] [Accepted: 09/06/2001] [Indexed: 11/12/2022] Open
Abstract
Here we report the first characterization of replication timing and its regulation in the fission yeast Schizosaccharomyces pombe. We used three different synchronization methods: centrifugal elutriation, cdc10 temperature-shift and release, and starvation for deoxyribonucleoside triphosphates (dNTPs) by treatment with hydroxyurea (HU) followed by removal of HU, to study the times when specific autonomously replicating sequence elements (ARS elements; potential replication origins) replicate during S phase. We found that individual ARS elements replicate at characteristic times, some early and some late, independently of synchronization method. In wild-type cells treated with HU, early ARS elements replicated but late ones did not. However, in HU-treated mutant cells lacking the Rad3 (similar to human ATR and ATM) or Cds1 (similar to human CHK2) checkpoint kinase, both early and late ARS elements were able to replicate. Thus under conditions of dNTP starvation the Rad3 and Cds1 kinases are needed to suppress the replication of normally late-replicating regions.
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Affiliation(s)
- Soo-Mi Kim
- Department of Cancer Genetics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA Present address: Department of Biology, California Institute of Technology, Pasadena, CA 91125, USA Corresponding author e-mail:
| | - Joel A. Huberman
- Department of Cancer Genetics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA Present address: Department of Biology, California Institute of Technology, Pasadena, CA 91125, USA Corresponding author e-mail:
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Tanaka K, Hao Z, Kai M, Okayama H. Establishment and maintenance of sister chromatid cohesion in fission yeast by a unique mechanism. EMBO J 2001; 20:5779-90. [PMID: 11598020 PMCID: PMC125673 DOI: 10.1093/emboj/20.20.5779] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2001] [Revised: 08/29/2001] [Accepted: 08/29/2001] [Indexed: 11/13/2022] Open
Abstract
During S phase, chromatid cohesion is established only between nascent sisters and with faithful pairing along their entire region, but how this is ensured is unknown. Here we report that sister chromatid cohesion is formed and maintained by a unique mechanism. In fission yeast, Eso1p, functioning in close coupling to DNA replication, establishes sister chromatid cohesion whereas the newly identified Cohesin-associated protein Pds5p hinders the establishment of cohesion until counteracted by Eso1p, yet stabilizes cohesion once it is established. Eso1p interacts physically with Pds5p via its Ctf7p/Eco1p-homologous domain.
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Affiliation(s)
- Koichi Tanaka
- Department of Biochemistry and Molecular Biology, The University of Tokyo, Graduate School of Medicine, Bunkyo-ku, Tokyo 113-0033, Japan Present address: Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA Present address: Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305-5324, USA Corresponding author e-mail:
| | - Zhonglin Hao
- Department of Biochemistry and Molecular Biology, The University of Tokyo, Graduate School of Medicine, Bunkyo-ku, Tokyo 113-0033, Japan Present address: Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA Present address: Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305-5324, USA Corresponding author e-mail:
| | - Mihoko Kai
- Department of Biochemistry and Molecular Biology, The University of Tokyo, Graduate School of Medicine, Bunkyo-ku, Tokyo 113-0033, Japan Present address: Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA Present address: Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305-5324, USA Corresponding author e-mail:
| | - Hiroto Okayama
- Department of Biochemistry and Molecular Biology, The University of Tokyo, Graduate School of Medicine, Bunkyo-ku, Tokyo 113-0033, Japan Present address: Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA Present address: Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305-5324, USA Corresponding author e-mail:
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Chang L, Morrell JL, Feoktistova A, Gould KL. Study of cyclin proteolysis in anaphase-promoting complex (APC) mutant cells reveals the requirement for APC function in the final steps of the fission yeast septation initiation network. Mol Cell Biol 2001; 21:6681-94. [PMID: 11533255 PMCID: PMC99813 DOI: 10.1128/mcb.21.19.6681-6694.2001] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cytokinesis in eukaryotic cells requires the inactivation of mitotic cyclin-dependent kinase complexes. An apparent exception to this relationship is found in Schizosaccharomyces pombe mutants with mutations of the anaphase-promoting complex (APC). These conditional lethal mutants arrest with unsegregated chromosomes because they cannot degrade the securin, Cut2p. Although failing at nuclear division, these mutants septate and divide. Since septation requires Cdc2p inactivation in wild-type S. pombe, it has been suggested that Cdc2p inactivation occurs in these mutants by a mechanism independent of cyclin degradation. In contrast to this prediction, we show that Cdc2p kinase activity fluctuates in APC cut mutants due to Cdc13/cyclin B destruction. In APC-null mutants, however, septation and cutting do not occur and Cdc13p is stable. We conclude that APC cut mutants are hypomorphic with respect to Cdc13p degradation. Indeed, overproduction of nondestructible Cdc13p prevents septation in APC cut mutants and the normal reorganization of septation initiation network components during anaphase.
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Affiliation(s)
- L Chang
- Howard Hughes Medical Institute and Department of Cell Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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45
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Sveiczer A, Tyson JJ, Novak B. A stochastic, molecular model of the fission yeast cell cycle: role of the nucleocytoplasmic ratio in cycle time regulation. Biophys Chem 2001; 92:1-15. [PMID: 11527575 DOI: 10.1016/s0301-4622(01)00183-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We propose a stochastic version of a recently published, deterministic model of the molecular mechanism regulating the mitotic cell cycle of fission yeast, Schizosaccharomyces pombe. Stochasticity is introduced in two ways: (i) by considering the known asymmetry of cell division, which produces daughter cells of slightly different sizes; and (ii) by assuming that the nuclear volumes of the two newborn cells may also differ. In this model, the accumulation of cyclins in the nucleus is proportional to the ratio of cytoplasmic to nuclear volumes. We have simulated the cell-cycle statistics of populations of wild-type cells and of wee1(-) mutant cells. Our results are consistent with well known experimental observations.
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Affiliation(s)
- A Sveiczer
- Department of Agricultural Chemical Technology, Budapest University of Technology and Economics, 1521 Budapest, Szt. Gellert ter 4, Hungary.
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46
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Schier N, Liese R, Fischer R. A Pcl-like cyclin of Aspergillus nidulans is transcriptionally activated by developmental regulators and is involved in sporulation. Mol Cell Biol 2001; 21:4075-88. [PMID: 11359914 PMCID: PMC87069 DOI: 10.1128/mcb.21.12.4075-4088.2001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The filamentous fungus Aspergillus nidulans reproduces asexually through the formation of spores on a multicellular aerial structure, called a conidiophore. A key regulator of asexual development is the TFIIIA-type zinc finger containing transcriptional activator Bristle (BRLA). Besides BRLA, the transcription factor ABAA, which is located downstream of BRLA in the developmental regulation cascade, is necessary to direct later gene expression during sporulation. We isolated a new developmental mutant and identified a leaky brlA mutation and the mutated Saccharomyces cerevisiae cyclin homologue pclA, both contributing to the developmental phenotype of the mutant. pclA was found to be 10-fold transcriptionally upregulated during conidiation, and a pclA deletion strain was reduced three- to fivefold in production of conidia. Expression of pclA was strongly induced by ectopic expression of brlA or abaA under conidiation-suppressing conditions, indicating a direct role for brlA and abaA in pclA regulation. PCLA is homologous to yeast Pcl cyclins, which interact with the Pho85 cyclin-dependent kinase. Although interaction with a PSTAIRE kinase was shown in vivo, PCLA function during sporulation was independent of the A. nidulans Pho85 homologue PHOA. Besides the developmental regulation, pclA expression was cell cycle dependent with peak transcript levels in S phase. Our findings suggest a role for PCLA in mediating cell cycle events during late stages of sporulation.
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Affiliation(s)
- N Schier
- Laboratorium für Mikrobiologie, Philipps-Universität Marburg and Max-Planck-Institut für Terrestrische Mikrobiologie, D-35043 Marburg, Germany
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Toh-E A, Nishizawa M. Structure and function of cyclin-dependent Pho85 kinase of Saccharomyces cerevisiae. J GEN APPL MICROBIOL 2001; 47:107-117. [PMID: 12483553 DOI: 10.2323/jgam.47.107] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Yeast Saccharomyces cerevisiae has five cyclin-dependent protein kinases (Cdks), Cdc28, Srb10, Kin28, Ctk1, and Pho85. Any of these Cdks requires a cyclin partner for its kinase activity and a Cdk/cyclin complex, thus produced, phosphorylates a set of specific substrate proteins to exert its function. The cyclin partners of Srb10, Kin28, and Ctk1 are Srb11, Ccl1, and Ctk2, respectively. In contrast to the fact that each of Srb10, Kin28, and Ctk1 has a single cyclin partner, Cdc28 and Pho85 are polygamous; Cdc28 has 9 cyclins and Pho85 has 10 cyclins. Among these Cdks, Kin28 and Cdc28 are essential Cdks and it is well known that Cdc28 kinase plays a major role in regulating cell cycle progression. Pho85 is a non-essential Cdk but its absence causes a broad spectrum of phenotypes such as constitutive expression of PHO5, inability to utilize non-fermentable carbon sources, defects in cell cycle progression, and so on. Pho85 homologues are expanding to higher eukaryotes. Pho85 is most closely related with Cdk5 in terms of the amino acid sequence. The functional analysis of the domains of Pho85 also supports the close relationship between Pho85 and Cdk5, in which it was shown that the method of regulation of these two kinases is similar. Furthermore, forced expression of the mammalian CDK5 gene in a pho85Delta strain canceled a part of the pho85 defects. In this review, we summarize the functions of both Pho85/cyclin kinase and emphasize yeast Pho85 as valuable model systems to elucidate the functions of their homologues in other organisms.
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Affiliation(s)
- Akio Toh-E
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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