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Sychla A, Stach CS, Roach SN, Hayward AN, Langlois RA, Smanski MJ. High-throughput investigation of genetic design constraints in domesticated Influenza A Virus for transient gene delivery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580300. [PMID: 38405907 PMCID: PMC10888799 DOI: 10.1101/2024.02.14.580300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Replication-incompetent single cycle infectious Influenza A Virus (sciIAV) has demonstrated utility as a research and vaccination platform. Protein-based therapeutics are increasingly attractive due to their high selectivity and potent efficacy but still suffer from low bioavailability and high manufacturing cost. Transient RNA-mediated delivery is a safe alternative that allows for expression of protein-based therapeutics within the target cells or tissues but is limited by delivery efficiency. Here, we develop recombinant sciIAV as a platform for transient gene delivery in vivo and in vitro for therapeutic, research, and manufacturing applications (in vivo antimicrobial production, cell culture contamination clearance, and production of antiviral proteins in vitro). While adapting the system to deliver new protein cargo we discovered expression differences presumably resulting from genetic context effects. We applied a high-throughput screen to map these within the 3'-untranslated and coding regions of the hemagglutinin-encoding segment 4. This screen revealed permissible mutations in the 3'-UTR and depletion of RNA level motifs in the N-terminal coding region.
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Affiliation(s)
- Adam Sychla
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN 55108
- Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108
| | - Christopher S Stach
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN 55108
- Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108
| | - Shanley N Roach
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN 55108
- Department of Microbiology and Immunology, University of Minnesota, Saint Paul, MN 55108
| | - Amanda N Hayward
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN 55108
- Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108
| | - Ryan A Langlois
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN 55108
- Department of Microbiology and Immunology, University of Minnesota, Saint Paul, MN 55108
| | - Michael J Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN 55108
- Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108
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2
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Stevens TA, Tomaleri GP, Hazu M, Wei S, Nguyen VN, DeKalb C, Voorhees RM, Pleiner T. A nanobody-based strategy for rapid and scalable purification of human protein complexes. Nat Protoc 2024; 19:127-158. [PMID: 37974029 DOI: 10.1038/s41596-023-00904-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/18/2023] [Indexed: 11/19/2023]
Abstract
The isolation of proteins in high yield and purity is a major bottleneck for the analysis of their three-dimensional structure, function and interactome. Here, we present a streamlined workflow for the rapid production of proteins or protein complexes using lentiviral transduction of human suspension cells, combined with highly specific nanobody-mediated purification and proteolytic elution. Application of the method requires prior generation of a plasmid coding for a protein of interest (POI) fused to an N- or C-terminal GFP or ALFA peptide tag using a lentiviral plasmid toolkit we have designed. The plasmid is then used to generate human suspension cell lines stably expressing the tagged fusion protein by lentiviral transduction. By leveraging the picomolar affinity of the GFP and ALFA nanobodies for their respective tags, the POI can be specifically captured from the resulting cell lysate even when expressed at low levels and under a variety of conditions, including detergents and mild denaturants. Finally, rapid and specific elution of the POI (in its tagged or untagged form) under native conditions is achieved within minutes at 4 °C, using the engineered SUMO protease SENPEuB. We demonstrate the wide applicability of the method by purifying multiple challenging soluble and membrane protein complexes to high purity from human cells. Our strategy is also directly compatible with many widely used GFP-expression plasmids, cell lines and transgenic model organisms. Finally, our method is faster than alternative approaches, requiring only 8 d from plasmid to purified protein, and results in substantially improved yields and purity.
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Affiliation(s)
- Taylor Anthony Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Giovani Pinton Tomaleri
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Masami Hazu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sophia Wei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Vy N Nguyen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Charlene DeKalb
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Tino Pleiner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Nakamura A, Goto Y, Sugiyama H, Tsukiji S, Aoki K. Chemogenetic Manipulation of Endogenous Proteins in Fission Yeast Using a Self-Localizing Ligand-Induced Protein Translocation System. ACS Chem Biol 2023; 18:2506-2515. [PMID: 37990966 DOI: 10.1021/acschembio.3c00478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Cells sense extracellular stimuli through membrane receptors and process information through an intracellular signaling network. Protein translocation triggers intracellular signaling, and techniques such as chemically induced dimerization (CID) have been used to manipulate signaling pathways by altering the subcellular localization of signaling molecules. However, in the fission yeast Schizosaccharomyces pombe, the commonly used FKBP-FRB system has technical limitations, and therefore, perturbation tools with low cytotoxicity and high temporal resolution are needed. We here applied our recently developed self-localizing ligand-induced protein translocation (SLIPT) system to S. pombe and successfully perturbed several cell cycle-related proteins. The SLIPT system utilizes self-localizing ligands to recruit binding partners to specific subcellular compartments such as the plasma membrane or nucleus. We optimized the self-localizing ligands to maintain the long-term recruitment of target molecules to the plasma membrane. By knocking in genes encoding the binding partners for self-localizing ligands, we observed changes in the localization of several endogenous molecules and found perturbations in the cell cycle and associated phenotypes. This study demonstrates the effectiveness of the SLIPT system as a chemogenetic tool for rapid perturbation of endogenous molecules in S. pombe, providing a valuable approach for studying intracellular signaling and cell cycle regulation with an improved temporal resolution.
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Affiliation(s)
- Akinobu Nakamura
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Hironori Sugiyama
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
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4
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Pyrih J, Hammond M, Alves A, Dean S, Sunter JD, Wheeler RJ, Gull K, Lukeš J. Comprehensive sub-mitochondrial protein map of the parasitic protist Trypanosoma brucei defines critical features of organellar biology. Cell Rep 2023; 42:113083. [PMID: 37669165 DOI: 10.1016/j.celrep.2023.113083] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/30/2023] [Accepted: 08/17/2023] [Indexed: 09/07/2023] Open
Abstract
We have generated a high-confidence mitochondrial proteome (MitoTag) of the Trypanosoma brucei procyclic stage containing 1,239 proteins. For 337 of these, a mitochondrial localization had not been described before. We use the TrypTag dataset as a foundation and take advantage of the properties of the fluorescent protein tag that causes aberrant but fortuitous accumulation of tagged matrix and inner membrane proteins near the kinetoplast (mitochondrial DNA). Combined with transmembrane domain predictions, this characteristic allowed categorization of 1,053 proteins into mitochondrial sub-compartments, the detection of unique matrix-localized fucose and methionine synthesis, and the identification of new kinetoplast proteins, which showed kinetoplast-linked pyrimidine synthesis. Moreover, disruption of targeting signals by tagging allowed mapping of the mode of protein targeting to these sub-compartments, identifying a set of C-tail anchored outer mitochondrial membrane proteins and mitochondrial carriers likely employing multiple target peptides. This dataset represents a comprehensive, updated mapping of the mitochondrion.
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Affiliation(s)
- Jan Pyrih
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Department of Biochemistry, University of Cambridge, Cambridge, UK; Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
| | - Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | | | - Samuel Dean
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | | | - Richard John Wheeler
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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5
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Sunter JD, Dean S, Wheeler RJ. TrypTag.org: from images to discoveries using genome-wide protein localisation in Trypanosoma brucei. Trends Parasitol 2023; 39:328-331. [PMID: 36925446 DOI: 10.1016/j.pt.2023.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/19/2023] [Accepted: 02/19/2023] [Indexed: 03/18/2023]
Abstract
TrypTag was a 4-year project to tag the N- and C-termini of almost all Trypanosoma brucei proteins with a fluorescent protein and record the subcellular localisation through images and manual annotation. We highlight the new routes to cell biological discovery this transformative resource is enabling for parasitologists and cell biologists.
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Affiliation(s)
- Jack D Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
| | - Samuel Dean
- Warwick Medical School, University of Warwick, Coventry, UK.
| | - Richard John Wheeler
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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6
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Yang HJ, Asakawa H, Li FA, Haraguchi T, Shih HM, Hiraoka Y. A nuclear pore complex-associated regulation of SUMOylation in meiosis. Genes Cells 2023; 28:188-201. [PMID: 36562208 DOI: 10.1111/gtc.13003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The nuclear pore complex (NPC) provides a permeable barrier between the nucleoplasm and cytoplasm. In a subset of NPC constituents that regulate meiosis in the fission yeast Schizosaccharomyces pombe, we found that nucleoporin Nup132 (homolog of human Nup133) deficiency resulted in transient leakage of nuclear proteins during meiosis I, as observed in the nup132 gene-deleted mutant. The nuclear protein leakage accompanied the liberation of the small ubiquitin-like modifier (SUMO)-specific ubiquitin-like protease 1 (Ulp1) from the NPC. Ulp1 retention at the nuclear pore prevented nuclear protein leakage and restored normal meiosis in a mutant lacking Nup132. Furthermore, using mass spectrometry analysis, we identified DNA topoisomerase 2 (Top2) and RCC1-related protein (Pim1) as the target proteins for SUMOylation. SUMOylation levels of Top2 and Pim1 were altered in meiotic cells lacking Nup132. HyperSUMOylated Top2 increased the binding affinity at the centromeres of nup132 gene-deleted meiotic cells. The Top2-12KR sumoylation mutant was less localized to the centromeric regions. Our results suggest that SUMOylation of chromatin-binding proteins is regulated by the NPC-bound SUMO-specific protease and is important for the progression of meiosis.
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Affiliation(s)
- Hui-Ju Yang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Fu-An Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Hsiu-Ming Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
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7
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Virant D, Vojnovic I, Winkelmeier J, Endesfelder M, Turkowyd B, Lando D, Endesfelder U. Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color SMLM imaging. J Cell Biol 2023; 222:213836. [PMID: 36705602 PMCID: PMC9930162 DOI: 10.1083/jcb.202209096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/28/2023] Open
Abstract
The key to ensuring proper chromosome segregation during mitosis is the kinetochore (KT), a tightly regulated multiprotein complex that links the centromeric chromatin to the spindle microtubules and as such leads the segregation process. Understanding its architecture, function, and regulation is therefore essential. However, due to its complexity and dynamics, only its individual subcomplexes could be studied in structural detail so far. In this study, we construct a nanometer-precise in situ map of the human-like regional KT of Schizosaccharomyces pombe using multi-color single-molecule localization microscopy. We measure each protein of interest (POI) in conjunction with two references, cnp1CENP-A at the centromere and sad1 at the spindle pole. This allows us to determine cell cycle and mitotic plane, and to visualize individual centromere regions separately. We determine protein distances within the complex using Bayesian inference, establish the stoichiometry of each POI and, consequently, build an in situ KT model with unprecedented precision, providing new insights into the architecture.
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Affiliation(s)
- David Virant
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Ilijana Vojnovic
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Jannik Winkelmeier
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Marc Endesfelder
- https://ror.org/05591te55Institute for Assyriology and Hittitology, Ludwig-Maximilians-Universität München, München, Germany
| | - Bartosz Turkowyd
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - David Lando
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Ulrike Endesfelder
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany,Correspondence to Ulrike Endesfelder:
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8
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Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei. Nat Microbiol 2023; 8:533-547. [PMID: 36804636 PMCID: PMC9981465 DOI: 10.1038/s41564-022-01295-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/21/2022] [Indexed: 02/22/2023]
Abstract
Trypanosoma brucei is a model trypanosomatid, an important group of human, animal and plant unicellular parasites. Understanding their complex cell architecture and life cycle is challenging because, as with most eukaryotic microbes, ~50% of genome-encoded proteins have completely unknown functions. Here, using fluorescence microscopy and cell lines expressing endogenously tagged proteins, we mapped the subcellular localization of 89% of the T. brucei proteome, a resource we call TrypTag. We provide clues to function and define lineage-specific organelle adaptations for parasitism, mapping the ultraconserved cellular architecture of eukaryotes, including the first comprehensive 'cartographic' analysis of the eukaryotic flagellum, which is vital for morphogenesis and pathology. To demonstrate the power of this resource, we identify novel organelle subdomains and changes in molecular composition through the cell cycle. TrypTag is a transformative resource, important for hypothesis generation for both eukaryotic evolutionary molecular cell biology and fundamental parasite cell biology.
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9
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Asakawa H, Hirano Y, Shindo T, Haraguchi T, Hiraoka Y. Fission yeast Ish1 and Les1 interact with each other in the lumen of the nuclear envelope. Genes Cells 2022; 27:643-656. [PMID: 36043331 DOI: 10.1111/gtc.12981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/09/2022] [Accepted: 08/24/2022] [Indexed: 11/28/2022]
Abstract
Nuclear envelope (NE) provides a permeable barrier that separates the eukaryotic genome from the cytoplasm. NE is a double membrane composed of inner and outer nuclear membranes. Ish1 is a stress-responsive NE protein in the fission yeast, Schizosaccharomyces pombe. Les1 is another NE protein that shares several similar domains with Ish1, but the relationship between them remains unknown. In this study, using fluorescence and electron microscopy, we found that most regions of these proteins were localized within the NE lumen. We also found that Ish1 interacted with Les1 via its C-terminal region in the NE lumen and that the NE localization of Ish1 depended on the C-terminal region of Les1. Ish1 and Les1 were co-localized at the NE in interphase cells, but when the nucleus divided at the end of mitosis (closed mitosis), they showed distinguishable localization at the midzone membrane domain. These results suggest the regulated interaction between Ish1 and Les1 in the NE lumen, although this interaction does not appear to be essential for cell survival. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Japan
| | - Yasuhiro Hirano
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Japan
| | - Tomoko Shindo
- Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Japan
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10
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Holič R, Šťastný D, Griač P. Sec14 family of lipid transfer proteins in yeasts. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158990. [PMID: 34118432 DOI: 10.1016/j.bbalip.2021.158990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022]
Abstract
The hydrophobicity of lipids prevents their free movement across the cytoplasm. To achieve highly heterogeneous and precisely regulated lipid distribution in different cellular membranes, lipids are transported by lipid transfer proteins (LTPs) in addition to their transport by vesicles. Sec14 family is one of the most extensively studied groups of LTPs. Here we provide an overview of Sec14 family of LTPs in the most studied yeast Saccharomyces cerevisiae as well as in other selected non-Saccharomyces yeasts-Schizosaccharomyces pombe, Kluyveromyces lactis, Candida albicans, Candida glabrata, Cryptococcus neoformans, and Yarrowia lipolytica. Discussed are specificities of Sec14-domain LTPs in various yeasts, their mode of action, subcellular localization, and physiological function. In addition, quite few Sec14 family LTPs are target of antifungal drugs, serve as modifiers of drug resistance or influence virulence of pathologic yeasts. Thus, they represent an important object of study from the perspective of human health.
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Affiliation(s)
- Roman Holič
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Dominik Šťastný
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Griač
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia.
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11
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Hirano Y, Kinugasa Y, Osakada H, Shindo T, Kubota Y, Shibata S, Haraguchi T, Hiraoka Y. Lem2 and Lnp1 maintain the membrane boundary between the nuclear envelope and endoplasmic reticulum. Commun Biol 2020; 3:276. [PMID: 32483293 PMCID: PMC7264229 DOI: 10.1038/s42003-020-0999-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 05/11/2020] [Indexed: 01/09/2023] Open
Abstract
The nuclear envelope (NE) continues to the endoplasmic reticulum (ER). Proper partitioning of NE and ER is crucial for cellular activity, but the key factors maintaining the boundary between NE and ER remain to be elucidated. Here we show that the conserved membrane proteins Lem2 and Lnp1 cooperatively play a crucial role in maintaining the NE-ER membrane boundary in fission yeast Schizosaccharomyces pombe. Cells lacking both Lem2 and Lnp1 caused severe growth defects associated with aberrant expansion of the NE/ER membranes, abnormal leakage of nuclear proteins, and abnormal formation of vacuolar-like structures in the nucleus. Overexpression of the ER membrane protein Apq12 rescued the growth defect associated with membrane disorder caused by the loss of Lem2 and Lnp1. Genetic analysis showed that Apq12 had overlapping functions with Lnp1. We propose that a membrane protein network with Lem2 and Lnp1 acts as a critical factor to maintain the NE-ER boundary.
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Affiliation(s)
- Yasuhiro Hirano
- Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan.
| | - Yasuha Kinugasa
- Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan
| | - Tomoko Shindo
- Electron Microscope Laboratory, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yoshino Kubota
- Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan
| | - Shinsuke Shibata
- Electron Microscope Laboratory, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan.
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan.
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12
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Fission Yeast Puf2, a Pumilio and FBF Family RNA-Binding Protein, Links Stress Granules to Processing Bodies. Mol Cell Biol 2020; 40:MCB.00589-19. [PMID: 32071154 DOI: 10.1128/mcb.00589-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/12/2020] [Indexed: 11/20/2022] Open
Abstract
Stress granules (SGs) are cytoplasmic aggregates formed upon stress when untranslated messenger ribonucleoproteins accumulate in the cells. In a green fluorescent protein library screening of the fission yeast SG proteins, Puf2 of the PUF family of RNA-binding proteins was identified that is required for SG formation after deprivation of glucose. Accordingly, the puf2 mutant is defective in recovery from glucose starvation with a much longer lag to reenter the cell cycle. In keeping with these results, Puf2 contains several low-complexity and intrinsically disordered protein regions with a tendency to form aggregates and, when overexpressed, it represses translation to induce aggregation of poly(A) binding protein Pabp, the signature constituent of SGs. Intriguingly, overexpression of Puf2 also enhances the structure of processing bodies (PBs), another type of cytoplasmic RNA granule, a complex of factors involved in mRNA degradation. In this study, we demonstrate a function of the fission yeast PB in SG formation and show Puf2 may provide a link between these two structures.
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13
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Ding DQ, Okamasa K, Katou Y, Oya E, Nakayama JI, Chikashige Y, Shirahige K, Haraguchi T, Hiraoka Y. Chromosome-associated RNA-protein complexes promote pairing of homologous chromosomes during meiosis in Schizosaccharomyces pombe. Nat Commun 2019; 10:5598. [PMID: 31811152 PMCID: PMC6898681 DOI: 10.1038/s41467-019-13609-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 11/18/2019] [Indexed: 01/07/2023] Open
Abstract
Pairing of homologous chromosomes in meiosis is essential for sexual reproduction. We have previously demonstrated that the fission yeast sme2 RNA, a meiosis-specific long noncoding RNA (lncRNA), accumulates at the sme2 chromosomal loci and mediates their robust pairing in meiosis. However, the mechanisms underlying lncRNA-mediated homologous pairing have remained elusive. In this study, we identify conserved RNA-binding proteins that are required for robust pairing of homologous chromosomes. These proteins accumulate mainly at the sme2 and two other chromosomal loci together with meiosis-specific lncRNAs transcribed from these loci. Remarkably, the chromosomal accumulation of these lncRNA–protein complexes is required for robust pairing. Moreover, the lncRNA–protein complexes exhibit phase separation properties, since 1,6-hexanediol treatment reversibly disassembled these complexes and disrupted the pairing of associated loci. We propose that lncRNA–protein complexes assembled at specific chromosomal loci mediate recognition and subsequent pairing of homologous chromosomes. During meiosis, pairing of homologous chromosomes is critical for sexual reproduction. Here the authors reveal in S. pombe the role of lncRNA–protein complexes during the pairing of homologues chromosomes that assemble at specific chromosomal loci to mediate recognition of the pairs.
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Affiliation(s)
- Da-Qiao Ding
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan.
| | - Kasumi Okamasa
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan
| | - Yuki Katou
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Eriko Oya
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, 467-8501, Japan.,Faculty of Science and Engineering, Chuo University, Tokyo, 112-8551, Japan
| | - Jun-Ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, 467-8501, Japan.,Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Yuji Chikashige
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan
| | - Katsuhiko Shirahige
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan. .,Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan.
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14
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Kashiwazaki J, Yoneda Y, Mutoh T, Arai R, Yoshida M, Mabuchi I. A unique kinesin-like protein, Klp8, is involved in mitosis and cell morphology through microtubule stabilization. Cytoskeleton (Hoboken) 2019; 76:355-367. [PMID: 31276301 DOI: 10.1002/cm.21551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/23/2019] [Accepted: 07/01/2019] [Indexed: 11/10/2022]
Abstract
Kinesins are microtubule (MT)-based motors involved in various cellular functions including intracellular transport of vesicles and organelles, and dynamics of chromosomes during cell division. The fission yeast Schizosaccharomyces pombe expresses nine kinesin-like proteins (klps). Klp8 is one of them and has not been characterized yet though it has been reported to localize at the division site. Here, we studied function and localization of Klp8 in S. pombe cells. The gene klp8+ was not essential for both viability and cytoskeletal organization. Klp8-YFP was concentrated as medial cortical dots during interphase, and organized into a ring at the division site during mitosis. The Klp8 ring seemed to be localized in the space between the actomyosin contractile ring and the plasma membrane. The Klp8 ring shrank as cytokinesis proceeded. In klp8-deleted (Δ) cells, the speed of spindle elongation during anaphase B was slowed down. Overproduction of Klp8 caused bent or elongated cells, in which MTs were abnormally elongated and less dynamic than those in normal cells. Deletion of klp8+ gene suppressed the delay in mitotic entry in blt1Δ cells. These results suggest that Klp8 is involved in mitosis and cell morphology through MT stabilization.
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Affiliation(s)
- Jun Kashiwazaki
- Department of Life Science, Gakushuin University, Tokyo, Japan
| | - Yumi Yoneda
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Tadashi Mutoh
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Ritsuko Arai
- Chemical Genetics Laboratory, RIKEN, Wako, Japan
| | - Minoru Yoshida
- Chemical Genetics Laboratory, RIKEN, Wako, Japan.,CREST Research Project, Japan Science and Technology Corporation, Wako, Japan
| | - Issei Mabuchi
- Department of Life Science, Gakushuin University, Tokyo, Japan.,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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15
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Prole DL, Taylor CW. A genetically encoded toolkit of functionalized nanobodies against fluorescent proteins for visualizing and manipulating intracellular signalling. BMC Biol 2019; 17:41. [PMID: 31122229 PMCID: PMC6533734 DOI: 10.1186/s12915-019-0662-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Intrabodies enable targeting of proteins in live cells, but generating specific intrabodies against the thousands of proteins in a proteome poses a challenge. We leverage the widespread availability of fluorescently labelled proteins to visualize and manipulate intracellular signalling pathways in live cells by using nanobodies targeting fluorescent protein tags. RESULTS We generated a toolkit of plasmids encoding nanobodies against red and green fluorescent proteins (RFP and GFP variants), fused to functional modules. These include fluorescent sensors for visualization of Ca2+, H+ and ATP/ADP dynamics; oligomerising or heterodimerising modules that allow recruitment or sequestration of proteins and identification of membrane contact sites between organelles; SNAP tags that allow labelling with fluorescent dyes and targeted chromophore-assisted light inactivation; and nanobodies targeted to lumenal sub-compartments of the secretory pathway. We also developed two methods for crosslinking tagged proteins: a dimeric nanobody, and RFP-targeting and GFP-targeting nanobodies fused to complementary hetero-dimerizing domains. We show various applications of the toolkit and demonstrate, for example, that IP3 receptors deliver Ca2+ to the outer membrane of only a subset of mitochondria and that only one or two sites on a mitochondrion form membrane contacts with the plasma membrane. CONCLUSIONS This toolkit greatly expands the utility of intrabodies and will enable a range of approaches for studying and manipulating cell signalling in live cells.
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Affiliation(s)
- David L Prole
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
| | - Colin W Taylor
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
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16
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Short-Homology-Mediated CRISPR/Cas9-Based Method for Genome Editing in Fission Yeast. G3-GENES GENOMES GENETICS 2019; 9:1153-1163. [PMID: 30755408 PMCID: PMC6469419 DOI: 10.1534/g3.118.200976] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CRISPR/Cas9 system enables the editing of genomes of numerous organisms through the induction of the double-strand breaks (DSB) at specific chromosomal targets. We improved the CRISPR/Cas9 system to ease the direct introduction of a point mutation or a tagging sequence into the chromosome by combining it with the noncanonical homology-directed DNA repair (HDR) based genome editing in fission yeast. We constructed convenient cloning vectors, which possessed a guide RNA (gRNA) expression module, or the humanized Streptococcus pyogenes Cas9 gene that is expressed under the control of an inducible promoter to avoid the needless expression, or both a gRNA and Cas9 gene. Using this system, we attempted the short-homology-mediated genome editing and found that the HDR pathway provides high-frequency genome editing at target loci without the need of a long donor DNA. Using short oligonucleotides, we successfully introduced point mutations into two target genes at high frequency. We also precisely integrated the sequences for epitope and GFP tagging using donor DNA possessing short homology into the target loci, which enabled us to obtain cells expressing N-terminally tagged fusion proteins. This system could expedite genome editing in fission yeast, and could be applicable to other organisms.
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17
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Asakawa H, Hiraoka Y, Haraguchi T. Estimation of GFP-Nucleoporin Amount Based on Fluorescence Microscopy. Methods Mol Biol 2018; 1721:105-115. [PMID: 29423851 DOI: 10.1007/978-1-4939-7546-4_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Cellular structures and biomolecular complexes are not simply assemblies of proteins, but are organized with defined numbers of protein molecules in precise locations. Thus, evaluating the spatial localization and numbers of protein molecules is of fundamental importance in understanding cellular structures and functions. The amounts of proteins of interest have conventionally been determined by biochemical methods. However, biochemical measurements based on the population average have limitations: it is sometimes difficult to determine the amounts of insoluble proteins or low expression proteins localized in small portions of the cell. In contrast, microphotometric measurements using fluorescence microscopes enable us to detect the amounts of such proteins in situ in a particular subcellular region. Here, we describe a method to measure the amounts of fluorescently tagged proteins by fluorescence microscopy, and present an example of an application to nuclear pore proteins in the fission yeast Schizosaccharomyces pombe.
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Affiliation(s)
- Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan. .,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.
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18
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Parua PK, Booth GT, Sansó M, Benjamin B, Tanny JC, Lis JT, Fisher RP. A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II. Nature 2018; 558:460-464. [PMID: 29899453 PMCID: PMC6021199 DOI: 10.1038/s41586-018-0214-z] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 04/17/2018] [Indexed: 11/09/2022]
Abstract
The end of the RNA polymerase II (Pol II) transcription cycle is strictly regulated to prevent interference between neighbouring genes and to safeguard transcriptome integrity 1 . The accumulation of Pol II downstream of the cleavage and polyadenylation signal can facilitate the recruitment of factors involved in mRNA 3'-end formation and termination 2 , but how this sequence is initiated remains unclear. In a chemical-genetic screen, human protein phosphatase 1 (PP1) isoforms were identified as substrates of positive transcription elongation factor b (P-TEFb), also known as the cyclin-dependent kinase 9 (Cdk9)-cyclin T1 (CycT1) complex 3 . Here we show that Cdk9 and PP1 govern phosphorylation of the conserved elongation factor Spt5 in the fission yeast Schizosaccharomyces pombe. Cdk9 phosphorylates both Spt5 and a negative regulatory site on the PP1 isoform Dis2 4 . Sites targeted by Cdk9 in the Spt5 carboxy-terminal domain can be dephosphorylated by Dis2 in vitro, and dis2 mutations retard Spt5 dephosphorylation after inhibition of Cdk9 in vivo. Chromatin immunoprecipitation and sequencing analysis indicates that Spt5 is dephosphorylated as transcription complexes traverse the cleavage and polyadenylation signal, concomitant with the accumulation of Pol II phosphorylated at residue Ser2 of the carboxy-terminal domain consensus heptad repeat 5 . A conditionally lethal Dis2-inactivating mutation attenuates the drop in Spt5 phosphorylation on chromatin, promotes transcription beyond the normal termination zone (as detected by precision run-on transcription and sequencing 6 ) and is genetically suppressed by the ablation of Cdk9 target sites in Spt5. These results suggest that the transition of Pol II from elongation to termination coincides with a Dis2-dependent reversal of Cdk9 signalling-a switch that is analogous to a Cdk1-PP1 circuit that controls mitotic progression 4 .
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Affiliation(s)
- Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Bradley Benjamin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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19
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A peptide tag-specific nanobody enables high-quality labeling for dSTORM imaging. Nat Commun 2018; 9:930. [PMID: 29500346 PMCID: PMC5834503 DOI: 10.1038/s41467-018-03191-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/26/2018] [Indexed: 11/08/2022] Open
Abstract
Dense fluorophore labeling without compromising the biological target is crucial for genuine super-resolution microscopy. Here we introduce a broadly applicable labeling strategy for fixed and living cells utilizing a short peptide tag-specific nanobody (BC2-tag/bivBC2-Nb). BC2-tagging of ectopically introduced or endogenous proteins does not interfere with the examined structures and bivBC2-Nb staining results in a close-grained fluorophore labeling with minimal linkage errors. This allowed us to perform high-quality dSTORM imaging of various targets in mammalian and yeast cells. We expect that this versatile strategy will render many more demanding cellular targets amenable to dSTORM imaging.
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20
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Yang HJ, Osakada H, Kojidani T, Haraguchi T, Hiraoka Y. Lipid droplet dynamics during Schizosaccharomyces pombe sporulation and their role in spore survival. Biol Open 2017; 6:217-222. [PMID: 28011631 PMCID: PMC5312105 DOI: 10.1242/bio.022384] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Upon nitrogen starvation, the fission yeast Schizosaccharomyces pombe forms dormant spores; however, the mechanisms by which a spore sustains life without access to exogenous nutrients remain unclear. Lipid droplets are reservoirs of neutral lipids that act as important cellular energy resources. Using live-cell imaging analysis, we found that the lipid droplets of mother cells redistribute to their nascent spores. Notably, this process was actin polymerization-dependent and facilitated by the leading edge proteins of the forespore membrane. Spores lacking triacylglycerol synthesis, which is essential for lipid droplet formation, failed to germinate. Our results suggest that the lipid droplets are important for the sustenance of life in spores. Summary: Lipid droplets of yeast mother cells are shown to redistribute to their nascent spores by live-cell imaging analysis, suggesting that the lipid droplets are important for yeast spore survival.
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Affiliation(s)
- Hui-Ju Yang
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Hiroko Osakada
- Advance ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Tomoko Kojidani
- Advance ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.,Japan Women's University, Tokyo, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advance ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan .,Advance ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
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21
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Landgraf D, Huh D, Hallacli E, Lindquist S. Scarless Gene Tagging with One-Step Transformation and Two-Step Selection in Saccharomyces cerevisiae and Schizosaccharomyces pombe. PLoS One 2016; 11:e0163950. [PMID: 27736907 PMCID: PMC5063382 DOI: 10.1371/journal.pone.0163950] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 09/16/2016] [Indexed: 11/24/2022] Open
Abstract
Gene tagging with fluorescent proteins is commonly applied to investigate the localization and dynamics of proteins in their cellular environment. Ideally, a fluorescent tag is genetically inserted at the endogenous locus at the N- or C- terminus of the gene of interest without disrupting regulatory sequences including the 5’ and 3’ untranslated region (UTR) and without introducing any extraneous unwanted “scar” sequences, which may create unpredictable transcriptional or translational effects. We present a reliable, low-cost, and highly efficient method for the construction of such scarless C-terminal and N-terminal fusions with fluorescent proteins in yeast. The method relies on sequential positive and negative selection and uses an integration cassette with long flanking regions, which is assembled by two-step PCR, to increase the homologous recombination frequency. The method also enables scarless tagging of essential genes with no need for a complementing plasmid. To further ease high-throughput strain construction, we have computationally automated design of the primers, applied the primer design code to all open reading frames (ORFs) of the budding yeast Saccharomyces cerevisiae (S. cerevisiae) and the fission yeast Schizosaccharomyces pombe (S. pombe), and provide here the computed sequences. To illustrate the scarless N- and C-terminal gene tagging methods in S. cerevisiae, we tagged various genes including the E3 ubiquitin ligase RSP5, the proteasome subunit PRE1, and the eleven Rab GTPases with yeast codon-optimized mNeonGreen or mCherry; several of these represent essential genes. We also implemented the scarless C-terminal gene tagging method in the distantly related organism S. pombe using kanMX6 and HSV1tk as positive and negative selection markers, respectively, as well as ura4. The scarless gene tagging methods presented here are widely applicable to visualize and investigate the functional roles of proteins in living cells.
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Affiliation(s)
- Dirk Landgraf
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Dann Huh
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Erinc Hallacli
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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22
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Schuchmann K, Vonck J, Müller V. A bacterial hydrogen-dependent CO2 reductase forms filamentous structures. FEBS J 2016; 283:1311-22. [PMID: 26833643 DOI: 10.1111/febs.13670] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/16/2016] [Accepted: 01/25/2016] [Indexed: 12/01/2022]
Abstract
Interconversion of CO2 and formic acid is an important reaction in bacteria. A novel enzyme complex that directly utilizes molecular hydrogen as electron donor for the reversible reduction of CO2 has recently been identified in the Wood-Ljungdahl pathway of an acetogenic bacterium. This pathway is utilized for carbon fixation as well as energy conservation. Here we describe the further characterization of the quaternary structure of this enzyme complex and the unexpected behavior of this enzyme in polymerizing into filamentous structures. Polymerization of metabolic enzymes into similar structures has been observed only in rare cases but the increasing number of examples point towards a more general characteristic of enzyme functioning. Polymerization of the purified enzyme into ordered filaments of more than 0.1 μm in length was only dependent on the presence of divalent cations. Polymerization was a reversible process and connected to the enzymatic activity of the oxygen-sensitive enzyme with the filamentous form being the most active state.
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Affiliation(s)
- Kai Schuchmann
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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23
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Yang HJ, Asakawa H, Haraguchi T, Hiraoka Y. Nup132 modulates meiotic spindle attachment in fission yeast by regulating kinetochore assembly. J Cell Biol 2015; 211:295-308. [PMID: 26483559 PMCID: PMC4621824 DOI: 10.1083/jcb.201501035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 09/11/2015] [Indexed: 02/06/2023] Open
Abstract
The fission yeast nucleoporin Nup132 is required for timely assembly of outer kinetochore proteins during meiotic prophase and its depletion activates the spindle assembly checkpoint in meiosis I, suggesting a role in establishing monopolar spindle attachment through outer kinetochore reorganization at meiotic prophase. During meiosis, the kinetochore undergoes substantial reorganization to establish monopolar spindle attachment. In the fission yeast Schizosaccharomyces pombe, the KNL1–Spc7-Mis12-Nuf2 (KMN) complex, which constitutes the outer kinetochore, is disassembled during meiotic prophase and is reassembled before meiosis I. Here, we show that the nucleoporin Nup132 is required for timely assembly of the KMN proteins: In the absence of Nup132, Mis12 and Spc7 are precociously assembled at the centromeres during meiotic prophase. In contrast, Nuf2 shows timely dissociation and reappearance at the meiotic centromeres. We further demonstrate that depletion of Nup132 activates the spindle assembly checkpoint in meiosis I, possibly because of the increased incidence of erroneous spindle attachment at sister chromatids. These results suggest that precocious assembly of the kinetochores leads to the meiosis I defects observed in the nup132-disrupted mutant. Thus, we propose that Nup132 plays an important role in establishing monopolar spindle attachment at meiosis I through outer kinetochore reorganization at meiotic prophase.
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Affiliation(s)
- Hui-Ju Yang
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan
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24
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Lorenz A. New cassettes for single-step drug resistance and prototrophic marker switching in fission yeast. Yeast 2015; 32:703-10. [PMID: 26305038 DOI: 10.1002/yea.3097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/10/2015] [Accepted: 08/10/2015] [Indexed: 11/05/2022] Open
Abstract
Construction of multiply mutated strains for genetic interaction analysis and of strains carrying different epitope tags at multiple open reading frames for testing protein localization, abundance and protein-protein interactions is hampered by the availability of a sufficient number of different selectable markers. Moreover, strains with single gene deletions or tags often already exist in strain collections; for historical reasons these will mostly carry the ura4(+) gene or the G418-resistance kanMX as marker. Because it is rather cumbersome to produce multiply deleted or tagged strains using the same marker, or to completely reconstruct a particular strain with a different marker, single-step exchange protocols of markers are a time-saving alternative. In recent years, dominant drug resistance markers (DDRMs) against clonNAT, hygromycin B and bleomycin have been adapted and successfully used in Schizosaccharomyces pombe. The corresponding DDRM cassettes, natMX, hphMX and bleMX, carry the TEF promotor and terminator sequences from Ashbya gossypii as kanMX; this provides flanking homologies to enable single-step marker swapping by homologous gene targeting. To expand this very useful toolset for single-step marker exchange, I constructed MX cassettes containing the nutritional markers arg3(+), his3(+), leu1(+) and ura4(+). Furthermore, a set of constructs was created to enable single-step exchange of ura4(+) to kanMX6, natMX4 and hphMX4. The functionality of the cassettes is demonstrated by successful single-step marker swapping at several loci. These constructs allow straightforward and rapid remarking of existing ura4(+) - and MX-deleted and -tagged strains.
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25
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Abstract
Faithful DNA replication is a prerequisite for cell proliferation. Several cytological studies have shown that chromosome structures alter in the S-phase of the cell cycle. However, the molecular mechanisms behind the alteration of chromosome structures associated with DNA replication have not been elucidated. Here, we investigated chromatin structures and acetylation of specific histone residues during DNA replication using the meiotic nucleus of the fission yeast Schizosaccharomyces pombe. The S. pombe meiotic nucleus provides a unique opportunity for measuring the levels of compaction of chromatin along the chromosome in a defined orientation. By direct measurement of chromatin compaction in living cells, we demonstrated that decompaction of chromatin occurs during meiotic DNA replication. This chromatin decompaction was suppressed by depletion of histone acetyltransferase Mst1 or by arginine substitution of specific lysine residues (K8 and K12) of histone H4. These results suggest that acetylation of histone H4 residues K8 and K12 plays a critical role in loosening chromatin structures during DNA replication.
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26
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Asakawa H, Yang HJ, Yamamoto TG, Ohtsuki C, Chikashige Y, Sakata-Sogawa K, Tokunaga M, Iwamoto M, Hiraoka Y, Haraguchi T. Characterization of nuclear pore complex components in fission yeast Schizosaccharomyces pombe. Nucleus 2014; 5:149-62. [PMID: 24637836 PMCID: PMC4049921 DOI: 10.4161/nucl.28487] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The nuclear pore complex (NPC) is an enormous proteinaceous complex composed of multiple copies of about 30 different proteins called nucleoporins. In this study, we analyzed the composition of the NPC in the model organism Schizosaccharomyces pombe using strains in which individual nucleoporins were tagged with GFP. We identified 31 proteins as nucleoporins by their localization to the nuclear periphery. Gene disruption analysis in previous studies coupled with gene disruption analysis in the present study indicates that 15 of these nucleoporins are essential for vegetative cell growth and the other 16 nucleoporins are non-essential. Among the 16 non-essential nucleoporins, 11 are required for normal progression through meiosis and their disruption caused abnormal spore formation or poor spore viability. Based on fluorescence measurements of GFP-fused nucleoporins, we estimated the composition of the NPC in S. pombe and found that the organization of the S. pombe NPC is largely similar to that of other organisms; a single NPC was estimated as being 45.8–47.8 MDa in size. We also used fluorescence measurements of single NPCs and quantitative western blotting to analyze the composition of the Nup107-Nup160 subcomplex, which plays an indispensable role in NPC organization and function. Our analysis revealed low amounts of Nup107 and Nup131 and high amounts of Nup132 in the Nup107-Nup160 subcomplex, suggesting that the composition of this complex in S. pombe may differ from that in S. cerevisiae and humans. Comparative analysis of NPCs in various organisms will lead to a comprehensive understanding of the functional architecture of the NPC.
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Affiliation(s)
- Haruhiko Asakawa
- Graduate School of Frontier Biosciences; Osaka University; Suita, Japan
| | - Hui-Ju Yang
- Graduate School of Frontier Biosciences; Osaka University; Suita, Japan
| | - Takaharu G Yamamoto
- Advanced ICT Research Institute Kobe; National Institute of Information and Communications Technology; Kobe, Japan
| | - Chizuru Ohtsuki
- Graduate School of Frontier Biosciences; Osaka University; Suita, Japan
| | - Yuji Chikashige
- Advanced ICT Research Institute Kobe; National Institute of Information and Communications Technology; Kobe, Japan; Graduate School of Science; Osaka University; Toyonaka, Japan
| | - Kumiko Sakata-Sogawa
- Department of Biological Information; Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology; Yokohama, Japan; RIKEN Center for Integrative Medical Sciences (IMS-RCAI); Yokohama, Japan
| | - Makio Tokunaga
- Department of Biological Information; Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology; Yokohama, Japan; RIKEN Center for Integrative Medical Sciences (IMS-RCAI); Yokohama, Japan
| | - Masaaki Iwamoto
- Advanced ICT Research Institute Kobe; National Institute of Information and Communications Technology; Kobe, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences; Osaka University; Suita, Japan; Advanced ICT Research Institute Kobe; National Institute of Information and Communications Technology; Kobe, Japan; Graduate School of Science; Osaka University; Toyonaka, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences; Osaka University; Suita, Japan; Advanced ICT Research Institute Kobe; National Institute of Information and Communications Technology; Kobe, Japan; Graduate School of Science; Osaka University; Toyonaka, Japan
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27
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Spivey EC, Finkelstein IJ. From cradle to grave: high-throughput studies of aging in model organisms. MOLECULAR BIOSYSTEMS 2014; 10:1658-67. [PMID: 24535099 DOI: 10.1039/c3mb70604d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aging-the progressive decline of biological functions-is a universal fact of life. Decades of intense research in unicellular and metazoan model organisms have highlighted that aging manifests at all levels of biological organization - from the decline of individual cells, to tissue and organism degeneration. To better understand the aging process, we must first aim to integrate quantitative biological understanding on the systems and cellular levels. A second key challenge is to then understand the many heterogeneous outcomes that may result in aging cells, and to connect cellular aging to organism-wide degeneration. Addressing these challenges requires the development of high-throughput aging and longevity assays. In this review, we highlight the emergence of high-throughput aging approaches in the most commonly used model organisms. We conclude with a discussion of the critical questions that can be addressed with these new methods.
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Affiliation(s)
- Eric C Spivey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
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28
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Endesfelder U, Finan K, Holden SJ, Cook PR, Kapanidis AN, Heilemann M. Multiscale spatial organization of RNA polymerase in Escherichia coli. Biophys J 2014; 105:172-81. [PMID: 23823236 DOI: 10.1016/j.bpj.2013.05.048] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 05/10/2013] [Accepted: 05/29/2013] [Indexed: 12/26/2022] Open
Abstract
Nucleic acid synthesis is spatially organized in many organisms. In bacteria, however, the spatial distribution of transcription remains obscure, owing largely to the diffraction limit of conventional light microscopy (200-300 nm). Here, we use photoactivated localization microscopy to localize individual molecules of RNA polymerase (RNAP) in Escherichia coli with a spatial resolution of ∼40 nm. In cells growing rapidly in nutrient-rich media, we find that RNAP is organized in 2-8 bands. The band number scaled directly with cell size (and so with the chromosome number), and bands often contained clusters of >70 tightly packed RNAPs (possibly engaged on one long ribosomal RNA operon of 6000 bp) and clusters of such clusters (perhaps reflecting a structure like the eukaryotic nucleolus where many different ribosomal RNA operons are transcribed). In nutrient-poor media, RNAPs were located in only 1-2 bands; within these bands, a disproportionate number of RNAPs were found in clusters containing ∼20-50 RNAPs. Apart from their importance for bacterial transcription, our studies pave the way for molecular-level analysis of several cellular processes at the nanometer scale.
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Affiliation(s)
- Ulrike Endesfelder
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt, Germany
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29
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Smialowska A, Djupedal I, Wang J, Kylsten P, Swoboda P, Ekwall K. RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe. Biochem Biophys Res Commun 2014; 444:254-9. [PMID: 24462781 DOI: 10.1016/j.bbrc.2014.01.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 01/15/2014] [Indexed: 11/25/2022]
Abstract
RNA interference (RNAi) is a gene silencing mechanism conserved from fungi to mammals. Small interfering RNAs are products and mediators of the RNAi pathway and act as specificity factors in recruiting effector complexes. The Schizosaccharomyces pombe genome encodes one of each of the core RNAi proteins, Dicer, Argonaute and RNA-dependent RNA polymerase (dcr1, ago1, rdp1). Even though the function of RNAi in heterochromatin assembly in S. pombe is established, its role in controlling gene expression is elusive. Here, we report the identification of small RNAs mapped anti-sense to protein coding genes in fission yeast. We demonstrate that these genes are up-regulated at the protein level in RNAi mutants, while their mRNA levels are not significantly changed. We show that the repression by RNAi is not a result of heterochromatin formation. Thus, we conclude that RNAi is involved in post-transcriptional gene silencing in S. pombe.
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Affiliation(s)
- Agata Smialowska
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83, Sweden; School of Life Sciences, Södertörn Högskola, Huddinge 141-89, Sweden.
| | - Ingela Djupedal
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83, Sweden
| | - Jingwen Wang
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83, Sweden
| | - Per Kylsten
- School of Life Sciences, Södertörn Högskola, Huddinge 141-89, Sweden
| | - Peter Swoboda
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83, Sweden
| | - Karl Ekwall
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83, Sweden; School of Life Sciences, Södertörn Högskola, Huddinge 141-89, Sweden.
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30
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O'Connell JD, Zhao A, Ellington AD, Marcotte EM. Dynamic reorganization of metabolic enzymes into intracellular bodies. Annu Rev Cell Dev Biol 2013; 28:89-111. [PMID: 23057741 DOI: 10.1146/annurev-cellbio-101011-155841] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Both focused and large-scale cell biological and biochemical studies have revealed that hundreds of metabolic enzymes across diverse organisms form large intracellular bodies. These proteinaceous bodies range in form from fibers and intracellular foci--such as those formed by enzymes of nitrogen and carbon utilization and of nucleotide biosynthesis--to high-density packings inside bacterial microcompartments and eukaryotic microbodies. Although many enzymes clearly form functional mega-assemblies, it is not yet clear for many recently discovered cases whether they represent functional entities, storage bodies, or aggregates. In this article, we survey intracellular protein bodies formed by metabolic enzymes, asking when and why such bodies form and what their formation implies for the functionality--and dysfunctionality--of the enzymes that comprise them. The panoply of intracellular protein bodies also raises interesting questions regarding their evolution and maintenance within cells. We speculate on models for how such structures form in the first place and why they may be inevitable.
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Affiliation(s)
- Jeremy D O'Connell
- Center for Systems and Synthetic Biology, University of Texas, Austin, Texas 78712, USA
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31
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Schuldiner M, Weissman JS. The contribution of systematic approaches to characterizing the proteins and functions of the endoplasmic reticulum. Cold Spring Harb Perspect Biol 2013; 5:a013284. [PMID: 23359093 DOI: 10.1101/cshperspect.a013284] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The endoplasmic reticulum (ER) is a complex organelle responsible for a range of functions including protein folding and secretion, lipid biosynthesis, and ion homeostasis. Despite its central and essential roles in eukaryotic cells during development, growth, and disease, many ER proteins are poorly characterized. Moreover, the range of biochemical reactions that occur within the ER membranes, let alone how these different activities are coordinated, is not yet defined. In recent years, focused studies on specific ER functions have been complemented by systematic approaches and innovative technologies for high-throughput analysis of the location, levels, and biological impact of given components. This article focuses on the recent progress of these efforts, largely pioneered in the budding yeast Saccharomyces cerevisiae, and also addresses how future systematic studies can be geared to uncover the "dark matter" of uncharted ER functions.
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Affiliation(s)
- Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 76100.
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32
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Krzyzanowski MK, Kozlowska E, Kozlowski P. Identification and functional analysis of the erh1(+) gene encoding enhancer of rudimentary homolog from the fission yeast Schizosaccharomyces pombe. PLoS One 2012; 7:e49059. [PMID: 23145069 PMCID: PMC3492181 DOI: 10.1371/journal.pone.0049059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 10/07/2012] [Indexed: 11/19/2022] Open
Abstract
The ERH gene encodes a highly conserved small nuclear protein with a unique amino acid sequence and three-dimensional structure but unknown function. The gene is present in animals, plants, and protists but to date has only been found in few fungi. Here we report that ERH homologs are also present in all four species from the genus Schizosaccharomyces, S. pombe, S. octosporus, S. cryophilus, and S. japonicus, which, however, are an exception in this respect among Ascomycota and Basidiomycota. The ERH protein sequence is moderately conserved within the genus (58% identity between S. pombe and S.japonicus), but the intron-rich genes have almost identical intron-exon organizations in all four species. In S. pombe, erh1(+) is expressed at a roughly constant level during vegetative growth and adaptation to unfavorable conditions such as nutrient limitation and hyperosmotic stress caused by sorbitol. Erh1p localizes preferentially to the nucleus with the exception of the nucleolus, but is also present in the cytoplasm. Cells lacking erh1(+) have an aberrant cell morphology and a comma-like shape when cultured to the stationary phase, and exhibit a delayed recovery from this phase followed by slower growth. Loss of erh1(+) in an auxotrophic background results in enhanced arrest in the G1 phase following nutritional stress, and also leads to hypersensitivity to agents inducing hyperosmotic stress (sorbitol), inhibiting DNA replication (hydroxyurea), and destabilizing the plasma membrane (SDS); this hypersensitivity can be abolished by expression of S. pombe erh1(+) and, to a lesser extent, S. japonicus erh1(+) or human ERH. Erh1p fails to interact with the human Ciz1 and PDIP46/SKAR proteins, known molecular partners of human ERH. Our data suggest that in Schizosaccharomyces sp. erh1(+) is non-essential for normal growth and Erh1p could play a role in response to adverse environmental conditions and in cell cycle regulation.
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Affiliation(s)
- Marek K. Krzyzanowski
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Ewa Kozlowska
- Department of Immunology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Piotr Kozlowski
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail:
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Abstract
RNA interference (RNAi) is a conserved eukaryotic gene regulatory mechanism that uses small noncoding RNAs to mediate posttranscriptional/transcriptional gene silencing. The fission yeast Schizosaccharomyces pombe and the filamentous fungus Neurospora crassa have served as important model systems for RNAi research. Studies on these two organisms and other fungi have contributed significantly to our understanding of the mechanisms and functions of RNAi in eukaryotes. In addition, surprisingly diverse RNAi-mediated processes and small RNA biogenesis pathways have been discovered in fungi. In this review, we give an overview of different fungal RNAi pathways with a focus on their mechanisms and functions.
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Affiliation(s)
- Shwu-Shin Chang
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, 75390, USA
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Pancaldi V, Saraç ÖS, Rallis C, McLean JR, Převorovský M, Gould K, Beyer A, Bähler J. Predicting the fission yeast protein interaction network. G3 (BETHESDA, MD.) 2012; 2:453-67. [PMID: 22540037 PMCID: PMC3337474 DOI: 10.1534/g3.111.001560] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 01/31/2012] [Indexed: 12/03/2022]
Abstract
A systems-level understanding of biological processes and information flow requires the mapping of cellular component interactions, among which protein-protein interactions are particularly important. Fission yeast (Schizosaccharomyces pombe) is a valuable model organism for which no systematic protein-interaction data are available. We exploited gene and protein properties, global genome regulation datasets, and conservation of interactions between budding and fission yeast to predict fission yeast protein interactions in silico. We have extensively tested our method in three ways: first, by predicting with 70-80% accuracy a selected high-confidence test set; second, by recapitulating interactions between members of the well-characterized SAGA co-activator complex; and third, by verifying predicted interactions of the Cbf11 transcription factor using mass spectrometry of TAP-purified protein complexes. Given the importance of the pathway in cell physiology and human disease, we explore the predicted sub-networks centered on the Tor1/2 kinases. Moreover, we predict the histidine kinases Mak1/2/3 to be vital hubs in the fission yeast stress response network, and we suggest interactors of argonaute 1, the principal component of the siRNA-mediated gene silencing pathway, lost in budding yeast but preserved in S. pombe. Of the new high-quality interactions that were discovered after we started this work, 73% were found in our predictions. Even though any predicted interactome is imperfect, the protein network presented here can provide a valuable basis to explore biological processes and to guide wet-lab experiments in fission yeast and beyond. Our predicted protein interactions are freely available through PInt, an online resource on our website (www.bahlerlab.info/PInt).
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Affiliation(s)
- Vera Pancaldi
- Department of Genetics, Evolution, and Environment and
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Ömer S. Saraç
- Cellular Networks and Systems Biology, Biotechnology Center, Dresden University of Technology (TU Dresden), Dresden 01307, Germany, and
| | - Charalampos Rallis
- Department of Genetics, Evolution, and Environment and
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Janel R. McLean
- Howard Hughes Medical Institute
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Martin Převorovský
- Department of Genetics, Evolution, and Environment and
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Kathleen Gould
- Howard Hughes Medical Institute
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Andreas Beyer
- Cellular Networks and Systems Biology, Biotechnology Center, Dresden University of Technology (TU Dresden), Dresden 01307, Germany, and
| | - Jürg Bähler
- Department of Genetics, Evolution, and Environment and
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
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35
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Gonzalez Y, Saito A, Sazer S. Fission yeast Lem2 and Man1 perform fundamental functions of the animal cell nuclear lamina. Nucleus 2012; 3:60-76. [PMID: 22540024 PMCID: PMC3337167 DOI: 10.4161/nucl.18824] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In animal cells the nuclear lamina, which consists of lamins and lamin-associated proteins, serves several functions: it provides a structural scaffold for the nuclear envelope and tethers proteins and heterochromatin to the nuclear periphery. In yeast, proteins and large heterochromatic domains including telomeres are also peripherally localized, but there is no evidence that yeast have lamins or a fibrous nuclear envelope scaffold. Nonetheless, we found that the Lem2 and Man1 proteins of the fission yeast Schizosaccharomyces pombe, evolutionarily distant relatives of the Lap2/Emerin/Man1 (LEM) sub-family of animal cell lamin-associated proteins, perform fundamental functions of the animal cell lamina. These integral inner nuclear membrane localized proteins, with nuclear localized DNA binding Helix-Extension-Helix (HEH) domains, impact nuclear envelope structure and integrity, are essential for the enrichment of telomeres at the nuclear periphery and by means of their HEH domains anchor chromatin, most likely transcriptionally repressed heterochromatin, to the nuclear periphery. These data indicate that the core functions of the nuclear lamina are conserved between fungi and animal cells and can be performed in fission yeast, without lamins or other intermediate filament proteins.
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Affiliation(s)
- Yanira Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology; Baylor College of Medicine; Houston, TX USA
| | - Akira Saito
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology; Baylor College of Medicine; Houston, TX USA
| | - Shelley Sazer
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology; Baylor College of Medicine; Houston, TX USA
- Department of Molecular and Cellular Biology; Baylor College of Medicine; Houston, TX USA
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36
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Systematic localization study on novel proteins encoded by meiotically up-regulated ORFs in fission yeast. Biosci Biotechnol Biochem 2011; 75:2364-70. [PMID: 22146723 DOI: 10.1271/bbb.110558] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We conducted a mitotic localization study on gene products encoded by 56 uncharacterized fission yeast ORFs that were transcriptionally up-regulated during meiotic division. Despite meiotic gene induction, these genes were expressed during mitosis as well. Seven gene products were localized in the nucleus and/or chromatin; another one was a mitosis-specific spindle pole body component and, intriguingly, its human homologue was also localized in the centrosome of cultured HeLa cells. Two products appeared to be localized in cytoplasmic microtubules, whereas four were mitochondrial proteins. Three other proteins were found in the medial ring upon cytokinesis and another was localized on the entire cell periphery. The remaining 38 proteins were detected in the cytoplasm and showed varied spatial patterns. This systematic study helps our integrated understanding of all the protein functions in the fission yeast as a eukaryotic model.
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37
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Diversity in requirement of genetic and epigenetic factors for centromere function in fungi. EUKARYOTIC CELL 2011; 10:1384-95. [PMID: 21908596 DOI: 10.1128/ec.05165-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A centromere is a chromosomal region on which several proteins assemble to form the kinetochore. The centromere-kinetochore complex helps in the attachment of chromosomes to spindle microtubules to mediate segregation of chromosomes to daughter cells during mitosis and meiosis. In several budding yeast species, the centromere forms in a DNA sequence-dependent manner, whereas in most other fungi, factors other than the DNA sequence also determine the centromere location, as centromeres were able to form on nonnative sequences (neocentromeres) when native centromeres were deleted in engineered strains. Thus, in the absence of a common DNA sequence, the cues that have facilitated centromere formation on a specific DNA sequence for millions of years remain a mystery. Kinetochore formation is facilitated by binding of a centromere-specific histone protein member of the centromeric protein A (CENP-A) family that replaces a canonical histone H3 to form a specialized centromeric chromatin structure. However, the process of kinetochore formation on the rapidly evolving and seemingly diverse centromere DNAs in different fungal species is largely unknown. More interestingly, studies in various yeasts suggest that the factors required for de novo centromere formation (establishment) may be different from those required for maintenance (propagation) of an already established centromere. Apart from the DNA sequence and CENP-A, many other factors, such as posttranslational modification (PTM) of histones at centric and pericentric chromatin, RNA interference, and DNA methylation, are also involved in centromere formation, albeit in a species-specific manner. In this review, we discuss how several genetic and epigenetic factors influence the evolution of structure and function of centromeres in fungal species.
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38
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Kashiwazaki J, Yamasaki Y, Itadani A, Teraguchi E, Maeda Y, Shimoda C, Nakamura T. Endocytosis is essential for dynamic translocation of a syntaxin 1 orthologue during fission yeast meiosis. Mol Biol Cell 2011; 22:3658-70. [PMID: 21832151 PMCID: PMC3183020 DOI: 10.1091/mbc.e11-03-0255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fission yeast sporulation seems to accompany a dynamic alteration of membrane traffic pathways in which the destination of secretory vesicles changes from the plasma membrane to the developing spore membrane. Evidence shows that endocytosis is responsible for this alteration in traffic pathways via the relocalization of syntaxin 1. Syntaxin is a component of the target soluble N-ethylmaleimide–sensitive factor attachment protein receptor complex, which is responsible for fusion of membrane vesicles at the target membrane. The fission yeast syntaxin 1 orthologue Psy1 is essential for both vegetative growth and spore formation. During meiosis, Psy1 disappears from the plasma membrane (PM) and dramatically relocalizes on the nascent forespore membrane, which becomes the PM of the spore. Here we report the molecular details and biological significance of Psy1 relocalization. We find that, immediately after meiosis I, Psy1 is selectively internalized by endocytosis. In addition, a meiosis-specific signal induced by the transcription factor Mei4 seems to trigger this internalization. The internalization of many PM proteins is facilitated coincident with the initiation of meiosis, whereas Pma1, a P-type ATPase, persists on the PM even during the progression of meiosis II. Ergosterol on the PM is also important for the internalization of PM proteins in general during meiosis. We consider that during meiosis in Schizosaccharomyces pombe cells, the characteristics of endocytosis change, thereby facilitating internalization of Psy1 and accomplishing sporulation.
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Affiliation(s)
- Jun Kashiwazaki
- Department of Biology, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan
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39
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Nakazawa N, Mehrotra R, Ebe M, Yanagida M. Condensin phosphorylated by the Aurora-B-like kinase Ark1 is continuously required until telophase in a mode distinct from Top2. J Cell Sci 2011; 124:1795-807. [PMID: 21540296 DOI: 10.1242/jcs.078733] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Condensin is a conserved protein complex that functions in chromosome condensation and segregation. It has not been previously unequivocally determined whether condensin is required throughout mitosis. Here, we examined whether Schizosaccharomyces pombe condensin continuously acts on chromosomes during mitosis and compared its role with that of DNA topoisomerase II (Top2). Using double mutants containing a temperature-sensitive allele of the condensin SMC2 subunit cut14 (cut14-208) or of top2, together with the cold-sensitive nda3-KM311 mutation (in β-tubulin), temperature-shift experiments were performed. These experiments allowed inactivation of condensin or Top2 at various stages throughout mitosis, even after late anaphase. The results established that mitotic chromosomes require condensin and Top2 throughout mitosis, even in telophase. We then showed that the Cnd2 subunit of condensin (also known as Barren) is the target subunit of Aurora-B-like kinase Ark1 and that Ark1-mediated phosphorylation of Cnd2 occurred throughout mitosis. The phosphorylation sites in Cnd2 were determined by mass spectrometry, and alanine and glutamate residue replacement mutant constructs for these sites were constructed. Alanine substitution mutants of Cnd2, which mimic the unphosphorylated protein, exhibited broad mitotic defects, including at telophase, and overexpression of these constructs caused a severe dominant-negative effect. By contrast, glutamate substitution mutants, which mimic the phosphorylated protein, alleviated the segregation defect in Ark1-inhibited cells. In telophase, the condensin subunits in cut14-208 mutant accumulated in lumps that contained telomeric DNA and proteins that failed to segregate. Condensin might thus serve to keep the segregated chromosomes apart during telophase.
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Affiliation(s)
- Norihiko Nakazawa
- Okinawa Institute and Science Technology Promotion Corporation, 1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0412, Japan
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40
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Kitano E, Hayashi A, Kanai D, Shinmyozu K, Nakayama JI. Roles of fission yeast Grc3 protein in ribosomal RNA processing and heterochromatic gene silencing. J Biol Chem 2011; 286:15391-402. [PMID: 21385875 PMCID: PMC3083176 DOI: 10.1074/jbc.m110.201343] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Revised: 03/01/2011] [Indexed: 01/26/2023] Open
Abstract
Grc3 is an evolutionarily conserved protein. Genome-wide budding yeast studies suggest that Grc3 is involved in rRNA processing. In the fission yeast Schizosaccharomyces pombe, Grc3 was identified as a factor exhibiting distinct nuclear dot localization, yet its exact physiological function remains unknown. Here, we show that S. pombe Grc3 is required for both rRNA processing and heterochromatic gene silencing. Cytological analysis revealed that Grc3 nuclear dots correspond to heterochromatic regions and that some Grc3 is also present in the nucleolar peripheral region. Depleting the heterochromatic proteins Swi6 or Clr4 abolished heterochromatic localization of Grc3 and resulted in its preferential accumulation in the perinucleolar region, suggesting its dynamic association with these nuclear compartments. Cells expressing mutant grc3 showed defects in 25 S rRNA maturation and in heterochromatic gene silencing. Protein analysis of Grc3-containing complexes led to the identification of Las1 and components of the IPI complex (Rix1, Ipi1, and Crb3). All of these Grc3-interacting proteins showed a dynamic nuclear localization similar to that observed for Grc3, and those conditional mutants showed defects in both rRNA processing and silencing of centromeric transcripts. Our data suggest that Grc3 functions cooperatively with Las1 and the IPI complex in both ribosome biogenesis and heterochromatin assembly.
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Affiliation(s)
- Erina Kitano
- From the Laboratory for Chromatin Dynamics and
- the Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan, and
| | - Aki Hayashi
- From the Laboratory for Chromatin Dynamics and
| | - Daigo Kanai
- From the Laboratory for Chromatin Dynamics and
- the Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda 669-1337, Japan
| | - Kaori Shinmyozu
- Proteomics Support Unit, RIKEN Center for Developmental Biology, Kobe Hyogo 650-0047, Japan
| | - Jun-ichi Nakayama
- From the Laboratory for Chromatin Dynamics and
- the Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda 669-1337, Japan
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41
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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: 28] [Impact Index Per Article: 2.2] [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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Lejeune E, Allshire RC. Common ground: small RNA programming and chromatin modifications. Curr Opin Cell Biol 2011; 23:258-65. [PMID: 21478005 DOI: 10.1016/j.ceb.2011.03.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 03/07/2011] [Accepted: 03/13/2011] [Indexed: 11/27/2022]
Abstract
Epigenetic mechanisms regulate genome structure and expression profiles in eukaryotes. RNA interference (RNAi) and other small RNA-based chromatin-modifying activities can act to reset the epigenetic landscape at defined chromatin domains. Centromeric heterochromatin assembly is a RNAi-dependent process in the fission yeast Schizosaccharomyces pombe, and provides a paradigm for detailed examination of such epigenetic processes. Here we review recent progress in understanding the mechanisms that underpin RNAi-mediated heterochromatin formation in S. pombe. We discuss recent analyses of the events that trigger RNAi and manipulations which uncouple RNAi and chromatin modification. Finally we provide an overview of similar molecular machineries across species where related small RNA pathways appear to drive the epigenetic reprogramming in germ cells and/or during early development in metazoans.
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Affiliation(s)
- Erwan Lejeune
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK.
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Hansen KR, Hazan I, Shanker S, Watt S, Verhein-Hansen J, Bähler J, Martienssen RA, Partridge JF, Cohen A, Thon G. H3K9me-independent gene silencing in fission yeast heterochromatin by Clr5 and histone deacetylases. PLoS Genet 2011; 7:e1001268. [PMID: 21253571 PMCID: PMC3017117 DOI: 10.1371/journal.pgen.1001268] [Citation(s) in RCA: 24] [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: 03/31/2010] [Accepted: 12/03/2010] [Indexed: 01/01/2023] Open
Abstract
Nucleosomes in heterochromatic regions bear histone modifications that distinguish them from euchromatic nucleosomes. Among those, histone H3 lysine 9 methylation (H3K9me) and hypoacetylation have been evolutionarily conserved and are found in both multicellular eukaryotes and single-cell model organisms such as fission yeast. In spite of numerous studies, the relative contributions of the various heterochromatic histone marks to the properties of heterochromatin remain largely undefined. Here, we report that silencing of the fission yeast mating-type cassettes, which are located in a well-characterized heterochromatic region, is hardly affected in cells lacking the H3K9 methyltransferase Clr4. We document the existence of a pathway parallel to H3K9me ensuring gene repression in the absence of Clr4 and identify a silencing factor central to this pathway, Clr5. We find that Clr5 controls gene expression at multiple chromosomal locations in addition to affecting the mating-type region. The histone deacetylase Clr6 acts in the same pathway as Clr5, at least for its effects in the mating-type region, and on a subset of other targets, notably a region recently found to be prone to neo-centromere formation. The genomic targets of Clr5 also include Ste11, a master regulator of sexual differentiation. Hence Clr5, like the multi-functional Atf1 transcription factor which also modulates chromatin structure in the mating-type region, controls sexual differentiation and genome integrity at several levels. Globally, our results point to histone deacetylases as prominent repressors of gene expression in fission yeast heterochromatin. These deacetylases can act in concert with, or independently of, the widely studied H3K9me mark to influence gene silencing at heterochromatic loci. In eukaryotes some histone modifications are preponderantly associated with silent chromosomal domains, however the extent to which distinct modifications contribute to the silencing of gene expression is often not known. A well-studied chromosomal domain in which histone modifications have been extensively characterized is the fission yeast mating-type region. There, histone hypo-acetylation and histone H3 lysine 9 methylation (H3K9me) are associated with a domain refractory to gene expression. Contrary to a general assumption, we found that genes naturally present in the mating-type region of wild-type strains remain repressed in the absence of the H3K9 methyltransferase Clr4. Their repression depends on histone deacetylases and on a hitherto uncharacterized factor, Clr5. Our results reveal an unsuspected robustness in the silencing mechanism, where H3K9me and deacetylation cooperate to ensure that the genes naturally present in the mating-type region remain silent in conditions where their expression would otherwise kill the cells.
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Affiliation(s)
- Klavs R. Hansen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Plant Genetics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Idit Hazan
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University – Hadassah Medical School, Jerusalem, Israel
| | - Sreenath Shanker
- Department of Biochemistry, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Stephen Watt
- Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
- University College London Cancer Institute, London, United Kingdom
| | | | - Jürg Bähler
- Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
- University College London Cancer Institute, London, United Kingdom
| | - Robert A. Martienssen
- Department of Plant Genetics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Janet F. Partridge
- Department of Biochemistry, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Amikam Cohen
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University – Hadassah Medical School, Jerusalem, Israel
| | - Geneviève Thon
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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Asakawa H, Kojidani T, Mori C, Osakada H, Sato M, Ding DQ, Hiraoka Y, Haraguchi T. Virtual breakdown of the nuclear envelope in fission yeast meiosis. Curr Biol 2010; 20:1919-25. [PMID: 20970342 DOI: 10.1016/j.cub.2010.09.070] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 09/01/2010] [Accepted: 09/30/2010] [Indexed: 10/18/2022]
Abstract
Asymmetric localization of Ran regulators (RanGAP1 and RanGEF/RCC1) produces a gradient of RanGTP across the nuclear envelope. In higher eukaryotes, the nuclear envelope breaks down as the cell enters mitosis (designated "open" mitosis). This nuclear envelope breakdown (NEBD) leads to collapse of the RanGTP gradient and the diffusion of nuclear and cytoplasmic macromolecules in the cell, resulting in irreversible progression of the cell cycle. On the other hand, in many fungi, chromosome segregation takes place without NEBD (designated "closed" mitosis). Here we report that in the fission yeast Schizosaccharomyces pombe, despite the nuclear envelope and the nuclear pore complex remaining intact throughout both the meiotic and mitotic cell cycles, nuclear proteins diffuse into the cytoplasm transiently for a few minutes at the onset of anaphase of meiosis II. We also found that nuclear protein diffusion into the cytoplasm occurred coincidently with nuclear localization of Rna1, an S. pombe RanGAP1 homolog that is usually localized in the cytoplasm. These results suggest that nuclear localization of RanGAP1 and depression of RanGTP activity in the nucleus may be mechanistically tied to meiosis-specific diffusion of nuclear proteins into the cytoplasm. This nucleocytoplasmic shuffling of RanGAP1 and nuclear proteins represents virtual breakdown of the nuclear envelope.
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Affiliation(s)
- Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
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45
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Shiku H, Okazaki D, Suzuki J, Takahashi Y, Murata T, Akita H, Harashima H, Ino K, Matsue T. Reporter gene expression at single-cell level characterized with real-time RT-PCR, chemiluminescence, fluorescence, and electrochemical imaging. FEBS Lett 2010; 584:4000-8. [DOI: 10.1016/j.febslet.2010.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 07/31/2010] [Accepted: 08/05/2010] [Indexed: 11/28/2022]
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Wen WL, Stevenson AL, Wang CY, Chen HJ, Kearsey SE, Norbury CJ, Watt S, Bähler J, Wang SW. Vgl1, a multi-KH domain protein, is a novel component of the fission yeast stress granules required for cell survival under thermal stress. Nucleic Acids Res 2010; 38:6555-66. [PMID: 20547592 PMCID: PMC2965253 DOI: 10.1093/nar/gkq555] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Multiple KH-domain proteins, collectively known as vigilins, are evolutionarily highly conserved proteins that are present in eukaryotic organisms from yeast to metazoa. Proposed roles for vigilins include chromosome segregation, messenger RNA (mRNA) metabolism, translation and tRNA transport. As a step toward understanding its biological function, we have identified the fission yeast vigilin, designated Vgl1, and have investigated its role in cellular response to environmental stress. Unlike its counterpart in Saccharomyces cerevisiae, we found no indication that Vgl1 is required for the maintenance of cell ploidy in Schizosaccharomyces pombe. Instead, Vgl1 is required for cell survival under thermal stress, and vgl1Δ mutants lose their viability more rapidly than wild-type cells when incubated at high temperature. As for Scp160 in S. cerevisiae, Vgl1 bound polysomes accumulated at endoplasmic reticulum (ER) but in a microtubule-independent manner. Under thermal stress, Vgl1 is rapidly relocalized from the ER to cytoplasmic foci that are distinct from P-bodies but contain stress granule markers such as poly(A)-binding protein and components of the translation initiation factor eIF3. Together, these observations demonstrated in S. pombe the presence of RNA granules with similar composition as mammalian stress granules and identified Vgl1 as a novel component that required for cell survival under thermal stress.
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Affiliation(s)
- Wei-Ling Wen
- Division of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan
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47
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Huh S, Lee D, Murphy RF. Efficient framework for automated classification of subcellular patterns in budding yeast. Cytometry A 2010; 75:934-40. [PMID: 19753630 DOI: 10.1002/cyto.a.20793] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Fluorescent-tagging and digital imaging are widely used to determine the subcellular location of proteins. An extensive publicly available collection of images for most proteins expressed in the yeast S. cerevisae has provided both an important source of information on protein location but also a testbed for methods designed to automate the assignment of locations to unknown proteins. The first system for automated classification of subcellular patterns in these yeast images utilized a computationally expensive method for segmentation of images into individual cells and achieved an overall accuracy of 81%. The goal of the present study was to improve on both the computational efficiency and accuracy of this task. Numerical features derived from applying Gabor filters to small image patches were implemented so that patterns could be classified without segmentation into single cells. When tested on 20 classes of images visually classified as showing a single subcellular pattern, an overall accuracy of 87.8% was achieved, with 2330 images out of 2655 images in the UCSF dataset being correctly classified. On the 4 largest classes of these images, 95.3% accuracy was achieved. The improvement over the previous approach is not only in classification accuracy but also in computational efficiency, with the new approach taking about 1 h on a desktop computer to complete all steps required to perform a 6-fold cross validation on all images.
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Affiliation(s)
- Seungil Huh
- Robotics Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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48
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Simpson JC. Screening the secretion machinery: High throughput imaging approaches to elucidate the secretory pathway. Semin Cell Dev Biol 2009; 20:903-9. [DOI: 10.1016/j.semcdb.2009.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 07/08/2009] [Accepted: 07/28/2009] [Indexed: 10/20/2022]
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49
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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