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Chica N, Portantier M, Nyquist-Andersen M, Espada-Burriel S, Lopez-Aviles S. Uncoupling of Mitosis and Cytokinesis Upon a Prolonged Arrest in Metaphase Is Influenced by Protein Phosphatases and Mitotic Transcription in Fission Yeast. Front Cell Dev Biol 2022; 10:876810. [PMID: 35923846 PMCID: PMC9340479 DOI: 10.3389/fcell.2022.876810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/11/2022] [Indexed: 11/22/2022] Open
Abstract
Depletion of the Anaphase-Promoting Complex/Cyclosome (APC/C) activator Cdc20 arrests cells in metaphase with high levels of the mitotic cyclin (Cyclin B) and the Separase inhibitor Securin. In mammalian cells this arrest has been exploited for the treatment of cancer with drugs that engage the spindle assembly checkpoint and, recently, with chemical inhibitors of the APC/C. While most cells arrested in mitosis for prolonged periods undergo apoptosis, others skip cytokinesis and enter G1 with unsegregated chromosomes. This process, known as mitotic slippage, generates aneuploidy and increases genomic instability in the cancer cell. Here, we analyze the behavior of fission yeast cells arrested in mitosis through the transcriptional silencing of the Cdc20 homolog slp1. While depletion of slp1 readily halts cells in metaphase, this arrest is only transient and a majority of cells eventually undergo cytokinesis and show steady mitotic dephosphorylation. Notably, this occurs in the absence of Cyclin B (Cdc13) degradation. We investigate the involvement of phosphatase activity in these events and demonstrate that PP2A-B55Pab1 is required to prevent septation and, during the arrest, its CDK-mediated inhibition facilitates the induction of cytokinesis. In contrast, deletion of PP2A-B56Par1 completely abrogates septation. We show that this effect is partly due to this mutant entering mitosis with reduced CDK activity. Interestingly, both PP2A-B55Pab1 and PP2A-B56Par1, as well as Clp1 (the homolog of the budding yeast mitotic phosphatase Cdc14) are required for the dephosphorylation of mitotic substrates during the escape. Finally, we show that the mitotic transcriptional wave controlled by the RFX transcription factor Sak1 facilitates the induction of cytokinesis and also requires the activity of PP2A-B56Par1 in a mechanism independent of CDK.
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Affiliation(s)
- Nathalia Chica
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- *Correspondence: Sandra Lopez-Aviles, ; Nathalia Chica,
| | - Marina Portantier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mari Nyquist-Andersen
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Silvia Espada-Burriel
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sandra Lopez-Aviles
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- Institute of Biosciences (IBV), Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- *Correspondence: Sandra Lopez-Aviles, ; Nathalia Chica,
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2
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Gopalan S, Gibbon DM, Banks CA, Zhang Y, Florens LA, Washburn MP, Dabas P, Sharma N, Seidel CW, Conaway RC, Conaway JW. Schizosaccharomyces pombe Pol II transcription elongation factor ELL functions as part of a rudimentary super elongation complex. Nucleic Acids Res 2019; 46:10095-10105. [PMID: 30102332 PMCID: PMC6212713 DOI: 10.1093/nar/gky713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
ELL family transcription factors activate the overall rate of RNA polymerase II (Pol II) transcription elongation by binding directly to Pol II and suppressing its tendency to pause. In metazoa, ELL regulates Pol II transcription elongation as part of a large multisubunit complex referred to as the Super Elongation Complex (SEC), which includes P-TEFb and EAF, AF9 or ENL, and an AFF family protein. Although orthologs of ELL and EAF have been identified in lower eukaryotes including Schizosaccharomyces pombe, it has been unclear whether SEC-like complexes function in lower eukaryotes. In this report, we describe isolation from S. pombe of an ELL-containing complex with features of a rudimentary SEC. This complex includes S. pombe Ell1, Eaf1, and a previously uncharacterized protein we designate Ell1 binding protein 1 (Ebp1), which is distantly related to metazoan AFF family members. Like the metazoan SEC, this S. pombe ELL complex appears to function broadly in Pol II transcription. Interestingly, it appears to have a particularly important role in regulating genes involved in cell separation.
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Affiliation(s)
- Sneha Gopalan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,The Open University, Milton Keynes, UK
| | - Dana M Gibbon
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Charles As Banks
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Pathology and Laboratory Med icine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Preeti Dabas
- University School of Biotechnology, G.G.S.Indraprastha University, New Delhi 110078, India
| | - Nimisha Sharma
- University School of Biotechnology, G.G.S.Indraprastha University, New Delhi 110078, India
| | | | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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3
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Larriba Y, Rueda C, Fernández MA, Peddada SD. Microarray Data Normalization and Robust Detection of Rhythmic Features. Methods Mol Biol 2019; 1986:207-225. [PMID: 31115890 DOI: 10.1007/978-1-4939-9442-7_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Data derived from microarray technologies are generally subject to various sources of noise and accordingly the raw data are pre-processed before formally analysed. Data normalization is a key pre-processing step when dealing with microarray experiments, such as circadian gene-expressions, since it removes systematic variations across arrays. A wide variety of normalization methods are available in the literature. However, from our experience in the study of rhythmic expression patterns in oscillatory systems (e.g. cell-cycle, circadian clock), the choice of the normalization method may substantially impair the identification of rhythmic genes. Hence, the identification of a gene as rhythmic could be just as an artefact of how the data were normalized. Yet, gene rhythmicity detection is crucial in modern toxicological and pharmacological studies, thus a procedure to truly identify rhythmic genes that are robust to the choice of a normalization method is required.To perform the task of detecting rhythmic features, we propose a rhythmicity measure based on bootstrap methodology to robustly identify rhythmic genes in oscillatory systems. Although our methodology can be extended to any high-throughput experiment, in this chapter, we illustrate how to apply it to a publicly available circadian clock microarray gene-expression data and give full details (both statistical and computational) so that the methodology can be used in an easy way. We will show that the choice of normalization method has very little effect on the proposed methodology since the results derived from the bootstrap-based rhythmicity measure are highly rank correlated for any pair of normalization methods considered. This suggests, on the one hand, that the rhythmicity measure proposed is robust to the choice of the normalization method, and on the other hand, that gene rhythmicity detected using this measure is potentially not a mere artefact of the normalization method used. In this way the researcher using this methodology will be protected against the possible effect of different normalizations, as the conclusions obtained will not depend so strongly on them. Additionally, the described bootstrap methodology can also be employed as a tool to simulate gene-expression participating in an oscillatory system from a reference data set.
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Affiliation(s)
- Yolanda Larriba
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Valladolid, Spain.
| | - Cristina Rueda
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Valladolid, Spain
| | - Miguel A Fernández
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Valladolid, Spain
| | - Shyamal D Peddada
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
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Nuñez I, Rodriguez Pino M, Wiley DJ, Das ME, Chen C, Goshima T, Kume K, Hirata D, Toda T, Verde F. Spatial control of translation repression and polarized growth by conserved NDR kinase Orb6 and RNA-binding protein Sts5. eLife 2016; 5. [PMID: 27474797 PMCID: PMC5011436 DOI: 10.7554/elife.14216] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 07/28/2016] [Indexed: 12/18/2022] Open
Abstract
RNA-binding proteins contribute to the formation of ribonucleoprotein (RNP) granules by phase transition, but regulatory mechanisms are not fully understood. Conserved fission yeast NDR (Nuclear Dbf2-Related) kinase Orb6 governs cell morphogenesis in part by spatially controlling Cdc42 GTPase. Here we describe a novel, independent function for Orb6 kinase in negatively regulating the recruitment of RNA-binding protein Sts5 into RNPs to promote polarized cell growth. We find that Orb6 kinase inhibits Sts5 recruitment into granules, its association with processing (P) bodies, and degradation of Sts5-bound mRNAs by promoting Sts5 interaction with 14-3-3 protein Rad24. Many Sts5-bound mRNAs encode essential factors for polarized cell growth, and Orb6 kinase spatially and temporally controls the extent of Sts5 granule formation. Disruption of this control system affects cell morphology and alters the pattern of polarized cell growth, revealing a role for Orb6 kinase in the spatial control of translational repression that enables normal cell morphogenesis.
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Affiliation(s)
- Illyce Nuñez
- Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, United States
| | - Marbelys Rodriguez Pino
- Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, United States
| | - David J Wiley
- Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, United States
| | - Maitreyi E Das
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, United States
| | - Chuan Chen
- Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, United States
| | - Tetsuya Goshima
- National Research Institute of Brewing, Higashi-Hiroshima, Japan
| | - Kazunori Kume
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Dai Hirata
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takashi Toda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan.,The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, United Kingdom
| | - Fulvia Verde
- Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, United States.,Marine Biological Laboratory, Woods Hole, United States
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Abstract
Recent studies have revealed exciting new functions for forkhead transcription factors in cell proliferation and development. Cell proliferation is a fundamental process controlled by multiple overlapping mechanisms, and the control of gene expression plays a major role in the orderly and timely division of cells. This occurs through transcription factors regulating the expression of groups of genes at particular phases of the cell division cycle. In this way, the encoded gene products are present when they are required. This review outlines recent advances in our understanding of this process in yeast model systems and describes how this knowledge has informed analysis in more developmentally complex eukaryotes, particularly where it is relevant to human disease.
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6
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Martín-García R, Santos B. The price of independence: cell separation in fission yeast. World J Microbiol Biotechnol 2016; 32:65. [PMID: 26931605 DOI: 10.1007/s11274-016-2021-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/29/2016] [Indexed: 12/28/2022]
Abstract
The ultimate goal of cell division is to give rise to two viable independent daughter cells. A tight spatial and temporal regulation between chromosome segregation and cytokinesis ensures the viability of the daughter cells. Schizosaccharomyces pombe, commonly known as fission yeast, has become a leading model organism for studying essential and conserved mechanisms of the eukaryotic cell division process. Like many other eukaryotic cells it divides by binary fission and the cleavage furrow undergoes ingression due to the contraction of an actomyosin ring. In contrast to mammalian cells, yeasts as cell-walled organisms, also need to form a division septum made of cell wall material to complete the process of cytokinesis. The division septum is deposited behind the constricting ring and it will constitute the new ends of the daughter cells. Cell separation also involves cell wall degradation and this process should be precisely regulated to avoid cell lysis. In this review, we will give a brief overview of the whole cytokinesis process in fission yeast, from the positioning and assembly of the contractile ring to the final step of cell separation, and the problems generated when these processes are not precise.
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Affiliation(s)
- Rebeca Martín-García
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas, University of Salamanca, 37007, Salamanca, Spain
| | - Beatriz Santos
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas, University of Salamanca, 37007, Salamanca, Spain.
- Departamento de Microbiología y Genética, University of Salamanca, 37007, Salamanca, Spain.
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Rodríguez-López M, Bähler J. Ace2 receives helping hand for cell-cycle transcription. Cell Cycle 2015; 14:3351-2. [PMID: 26399486 PMCID: PMC4825591 DOI: 10.1080/15384101.2015.1093444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 08/31/2015] [Indexed: 01/15/2023] Open
Affiliation(s)
- María Rodríguez-López
- Research Department of Genetics; Evolution & Environment; University College London; London, UK
| | - Jürg Bähler
- Research Department of Genetics; Evolution & Environment; University College London; London, UK
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