1
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Walsh ME, King GA, Ünal E. Not just binary: embracing the complexity of nuclear division dynamics. Nucleus 2024; 15:2360601. [PMID: 38842147 PMCID: PMC11164224 DOI: 10.1080/19491034.2024.2360601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024] Open
Abstract
Cell division presents a challenge for eukaryotic cells: how can chromosomes effectively segregate within the confines of a membranous nuclear compartment? Different organisms have evolved diverse solutions by modulating the degree of nuclear compartmentalization, ranging from complete nuclear envelope breakdown to complete maintenance of nuclear compartmentalization via nuclear envelope expansion. Many intermediate forms exist between these extremes, suggesting that nuclear dynamics during cell division are surprisingly plastic. In this review, we highlight the evolutionary diversity of nuclear divisions, focusing on two defining characteristics: (1) chromosome compartmentalization and (2) nucleocytoplasmic transport. Further, we highlight recent evidence that nuclear behavior during division can vary within different cellular contexts in the same organism. The variation observed within and between organisms underscores the dynamic evolution of nuclear divisions tailored to specific contexts and cellular requirements. In-depth investigation of diverse nuclear divisions will enhance our understanding of the nucleus, both in physiological and pathological states.
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Affiliation(s)
- Madison E. Walsh
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA
| | - Grant A. King
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA
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2
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Marešová A, Oravcová M, Rodríguez-López M, Hradilová M, Zemlianski V, Häsler R, Hernández P, Bähler J, Převorovský M. Critical importance of DNA binding for CSL protein functions in fission yeast. J Cell Sci 2024; 137:jcs261568. [PMID: 38482739 DOI: 10.1242/jcs.261568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/07/2024] [Indexed: 05/01/2024] Open
Abstract
CSL proteins [named after the homologs CBF1 (RBP-Jκ in mice), Suppressor of Hairless and LAG-1] are conserved transcription factors found in animals and fungi. In the fission yeast Schizosaccharomyces pombe, they regulate various cellular processes, including cell cycle progression, lipid metabolism and cell adhesion. CSL proteins bind to DNA through their N-terminal Rel-like domain and central β-trefoil domain. Here, we investigated the importance of DNA binding for CSL protein functions in fission yeast. We created CSL protein mutants with disrupted DNA binding and found that the vast majority of CSL protein functions depend on intact DNA binding. Specifically, DNA binding is crucial for the regulation of cell adhesion, lipid metabolism, cell cycle progression, long non-coding RNA expression and genome integrity maintenance. Interestingly, perturbed lipid metabolism leads to chromatin structure changes, potentially linking lipid metabolism to the diverse phenotypes associated with CSL protein functions. Our study highlights the critical role of DNA binding for CSL protein functions in fission yeast.
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Affiliation(s)
- Anna Marešová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Martina Oravcová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - María Rodríguez-López
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Miluše Hradilová
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czechia
| | - Viacheslav Zemlianski
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Robert Häsler
- Center for Inflammatory Skin Diseases, Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Rosalind-Franklin-Straße 9, 24105 Kiel, Germany
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution and Environment , University College London, Gower Street, London WC1E 6BT, UK
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
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3
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Etherington GJ, Wu PS, Oliferenko S, Uhlmann F, Nieduszynski CA. Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features. Yeast 2024; 41:73-86. [PMID: 38451028 DOI: 10.1002/yea.3912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 03/08/2024] Open
Abstract
Schizosaccharomyces japonicus belongs to the single-genus class Schizosaccharomycetes, otherwise known as "fission yeasts." As part of a composite model system with its widely studied S. pombe sister species, S. japonicus has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes S. japonicus a valuable model organism in its own right. However, the currently available genome assembly contains gaps and has been unable to resolve centromeres and other repeat-rich chromosomal regions. Here we present a telomere-to-telomere long-read genome assembly of the S. japonicus genome. This includes the three megabase-length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNA genes, transfer RNA genes, long terminal repeats, and short repeats. We identify a gene-sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size of S. japonicus to at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growing S. japonicus research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics.
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Affiliation(s)
| | | | - Snezhana Oliferenko
- The Francis Crick Institute, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Frank Uhlmann
- The Francis Crick Institute, London, UK
- Cell Biology Centre, Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, Japan
| | - Conrad A Nieduszynski
- The Earlham Institute, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
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4
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Etherington GJ, Gil EG, Haerty W, Oliferenko S, Nieduszynski CA. Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast. Yeast 2024; 41:95-107. [PMID: 38146786 DOI: 10.1002/yea.3919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023] Open
Abstract
The fission yeast species Schizosaccharomyces japonicus is currently divided into two varieties-S. japonicus var. japonicus and S. japonicus var. versatilis. Here we examine the var. versatilis isolate CBS5679. The CBS5679 genome shows 88% identity to the reference genome of S. japonicus var. japonicus at the coding sequence level, with phylogenetic analyses suggesting that it has split from the S. japonicus lineage 25 million years ago. The CBS5679 genome contains a reciprocal translocation between chromosomes 1 and 2, together with several large inversions. The products of genes linked to the major translocation are associated with 'metabolism' and 'cellular assembly' ontology terms. We further show that CBS5679 does not generate viable progeny with the reference strain of S. japonicus. Although CBS5679 shares closer similarity to the 'type' strain of var. versatilis as compared to S. japonicus, it is not identical to the type strain, suggesting population structure within var. versatilis. We recommend that the taxonomic status of S. japonicus var. versatilis is raised, with it being treated as a separate species, Schizosaccharomyces versatilis.
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Affiliation(s)
| | - Elisa Gomez Gil
- Oliferenko Lab, The Francis Crick Institute, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Wilfried Haerty
- Research Faculty, The Earlham Institute, Norwich Research Park, Norwich, UK
| | - Snezhana Oliferenko
- Oliferenko Lab, The Francis Crick Institute, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Conrad A Nieduszynski
- Research Faculty, The Earlham Institute, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
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5
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Siniossoglou S. Oiling the wheels of nuclear division: SUMOylation regulates the expansion of the mitotic nuclear membrane. J Cell Biol 2023; 222:e202306126. [PMID: 37440179 PMCID: PMC10345213 DOI: 10.1083/jcb.202306126] [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] [Indexed: 07/14/2023] Open
Abstract
Eukaryotic cell division involves the segregation of chromosomes between two daughter cells and must be coordinated with extensive rearrangement of their nuclear envelopes. In this issue, Saik et al. (2023 J. Cell Biol. https://doi.org/10.1083/jcb.202208137) show that a SUMOylation cascade at the inner nuclear membrane elevates the levels of phosphatidic acid, a key phospholipid precursor, to support the need for nuclear membrane expansion during mitosis.
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Affiliation(s)
- Symeon Siniossoglou
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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6
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Santana-Sosa S, Matos-Perdomo E, Ayra-Plasencia J, Machín F. A Yeast Mitotic Tale for the Nucleus and the Vacuoles to Embrace. Int J Mol Sci 2023; 24:9829. [PMID: 37372977 DOI: 10.3390/ijms24129829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The morphology of the nucleus is roughly spherical in most eukaryotic cells. However, this organelle shape needs to change as the cell travels through narrow intercellular spaces during cell migration and during cell division in organisms that undergo closed mitosis, i.e., without dismantling the nuclear envelope, such as yeast. In addition, the nuclear morphology is often modified under stress and in pathological conditions, being a hallmark of cancer and senescent cells. Thus, understanding nuclear morphological dynamics is of uttermost importance, as pathways and proteins involved in nuclear shaping can be targeted in anticancer, antiaging, and antifungal therapies. Here, we review how and why the nuclear shape changes during mitotic blocks in yeast, introducing novel data that associate these changes with both the nucleolus and the vacuole. Altogether, these findings suggest a close relationship between the nucleolar domain of the nucleus and the autophagic organelle, which we also discuss here. Encouragingly, recent evidence in tumor cell lines has linked aberrant nuclear morphology to defects in lysosomal function.
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Affiliation(s)
- Silvia Santana-Sosa
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Emiliano Matos-Perdomo
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Jessel Ayra-Plasencia
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Félix Machín
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
- Faculty of Health Sciences, Fernando Pessoa Canarias University, 35450 Santa María de Guía, Spain
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7
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Alam S, Gu Y, Reichert P, Bähler J, Oliferenko S. Optimization of energy production and central carbon metabolism in a non-respiring eukaryote. Curr Biol 2023; 33:2175-2186.e5. [PMID: 37164017 PMCID: PMC7615655 DOI: 10.1016/j.cub.2023.04.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
Most eukaryotes respire oxygen, using it to generate biomass and energy. However, a few organisms have lost the capacity to respire. Understanding how they manage biomass and energy production may illuminate the critical points at which respiration feeds into central carbon metabolism and explain possible routes to its optimization. Here, we use two related fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces japonicus, as a comparative model system. We show that although S. japonicus does not respire oxygen, unlike S. pombe, it is capable of efficient NADH oxidation, amino acid synthesis, and ATP generation. We probe possible optimization strategies through the use of stable isotope tracing metabolomics, mass isotopologue distribution analysis, genetics, and physiological experiments. S. japonicus appears to have optimized cytosolic NADH oxidation via glycerol-3-phosphate synthesis. It runs a fully bifurcated TCA pathway, sustaining amino acid production. Finally, we propose that it has optimized glycolysis to maintain high ATP/ADP ratio, in part by using the pentose phosphate pathway as a glycolytic shunt, reducing allosteric inhibition of glycolysis and supporting biomass generation. By comparing two related organisms with vastly different metabolic strategies, our work highlights the versatility and plasticity of central carbon metabolism in eukaryotes, illuminating critical adaptations supporting the preferential use of glycolysis over oxidative phosphorylation.
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Affiliation(s)
- Sara Alam
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Ying Gu
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Polina Reichert
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK; School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Jürg Bähler
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK.
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8
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Foo S, Cazenave-Gassiot A, Wenk MR, Oliferenko S. Diacylglycerol at the inner nuclear membrane fuels nuclear envelope expansion in closed mitosis. J Cell Sci 2023; 136:286881. [PMID: 36695178 DOI: 10.1242/jcs.260568] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/22/2022] [Indexed: 01/26/2023] Open
Abstract
Nuclear envelope (NE) expansion must be controlled to maintain nuclear shape and function. The nuclear membrane expands massively during closed mitosis, enabling chromosome segregation within an intact NE. Phosphatidic acid (PA) and diacylglycerol (DG) can both serve as biosynthetic precursors for membrane lipid synthesis. How they are regulated in time and space and what the implications are of changes in their flux for mitotic fidelity are largely unknown. Using genetically encoded PA and DG probes, we show that DG is depleted from the inner nuclear membrane during mitosis in the fission yeast Schizosaccharomyces pombe, but PA does not accumulate, indicating that it is rerouted to membrane synthesis. We demonstrate that DG-to-PA conversion catalyzed by the diacylglycerol kinase Dgk1 (also known as Ptp4) and direct glycerophospholipid synthesis from DG by diacylglycerol cholinephosphotransferase/ethanolaminephosphotransferase Ept1 reinforce NE expansion. We conclude that DG consumption through both the de novo pathway and the Kennedy pathway fuels a spike in glycerophospholipid biosynthesis, controlling NE expansion and, ultimately, mitotic fidelity.
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Affiliation(s)
- Sherman Foo
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Amaury Cazenave-Gassiot
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, 117596 Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, 117596 Singapore
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
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9
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Varberg JM, Unruh JR, Bestul AJ, Khan AA, Jaspersen SL. Quantitative analysis of nuclear pore complex organization in Schizosaccharomyces pombe. Life Sci Alliance 2022; 5:5/7/e202201423. [PMID: 35354597 PMCID: PMC8967992 DOI: 10.26508/lsa.202201423] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 01/06/2023] Open
Abstract
Characterization of nuclear pores in Schizosaccharomyces pombe identifies regions of heterogeneous NPC density and composition and shows that NPCs are excluded near the spindle pole body by Lem2-mediated centromere tethering. The number, distribution, and composition of nuclear pore complexes (NPCs) in the nuclear envelope varies between cell types and changes during cellular differentiation and in disease. To understand how NPC density and organization are controlled, we analyzed the NPC number and distribution in the fission yeast Schizosaccharomyces pombe using structured illumination microscopy. The small size of yeast nuclei, genetic features of fungi, and our robust image analysis pipeline allowed us to study NPCs in intact nuclei under multiple conditions. Our data revealed that NPC density is maintained across a wide range of nuclear sizes. Regions of reduced NPC density are observed over the nucleolus and surrounding the spindle pole body (SPB). Lem2-mediated tethering of the centromeres to the SPB is required to maintain NPC exclusion near SPBs. These findings provide a quantitative understanding of NPC number and distribution in S. pombe and show that interactions between the centromere and the nuclear envelope influences local NPC distribution.
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Affiliation(s)
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Andrew J Bestul
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Azqa A Khan
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO, USA .,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
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10
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Coupling lipid synthesis with nuclear envelope remodeling. Trends Biochem Sci 2022; 47:52-65. [PMID: 34556392 PMCID: PMC9943564 DOI: 10.1016/j.tibs.2021.08.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/12/2021] [Accepted: 08/25/2021] [Indexed: 01/10/2023]
Abstract
The nuclear envelope (NE) is a protective barrier to the genome, yet its membranes undergo highly dynamic remodeling processes that are necessary for cell growth and maintenance. While mechanisms by which proteins promote NE remodeling are emerging, the types of bilayer lipids and the lipid-protein interactions that define and sculpt nuclear membranes remain elusive. The NE is continuous with the endoplasmic reticulum (ER) and recent evidence suggests that lipids produced in the ER are harnessed to remodel nuclear membranes. In this review, we examine new roles for lipid species made proximally within the ER and locally at the NE to control NE dynamics. We further explore how the biosynthesis of lipids coordinates NE remodeling to ensure genome protection.
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11
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Rutherford KM, Harris MA, Oliferenko S, Wood V. JaponicusDB: rapid deployment of a model organism database for an emerging model species. Genetics 2021; 220:6481558. [PMID: 35380656 PMCID: PMC9209809 DOI: 10.1093/genetics/iyab223] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023] Open
Abstract
The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.
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Affiliation(s)
- Kim M Rutherford
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Midori A Harris
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, London NW1 1AT, UK,Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London SE1 1UL, UK,Corresponding author: (S.O.); (V.W.)
| | - Valerie Wood
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK,Corresponding author: (S.O.); (V.W.)
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12
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Merta H, Carrasquillo Rodríguez JW, Anjur-Dietrich MI, Vitale T, Granade ME, Harris TE, Needleman DJ, Bahmanyar S. Cell cycle regulation of ER membrane biogenesis protects against chromosome missegregation. Dev Cell 2021; 56:3364-3379.e10. [PMID: 34852214 PMCID: PMC8692360 DOI: 10.1016/j.devcel.2021.11.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/15/2021] [Accepted: 11/05/2021] [Indexed: 01/05/2023]
Abstract
Failure to reorganize the endoplasmic reticulum (ER) in mitosis results in chromosome missegregation. Here, we show that accurate chromosome segregation in human cells requires cell cycle-regulated ER membrane production. Excess ER membranes increase the viscosity of the mitotic cytoplasm to physically restrict chromosome movements, which impedes the correction of mitotic errors leading to the formation of micronuclei. Mechanistically, we demonstrate that the protein phosphatase CTDNEP1 counteracts mTOR kinase to establish a dephosphorylated pool of the phosphatidic acid phosphatase lipin 1 in interphase. CTDNEP1 control of lipin 1 limits the synthesis of fatty acids for ER membrane biogenesis in interphase that then protects against chromosome missegregation in mitosis. Thus, regulation of ER size can dictate the biophysical properties of mitotic cells, providing an explanation for why ER reorganization is necessary for mitotic fidelity. Our data further suggest that dysregulated lipid metabolism is a potential source of aneuploidy in cancer cells.
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Affiliation(s)
- Holly Merta
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | | | - Maya I Anjur-Dietrich
- Department of Applied Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Tevis Vitale
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Mitchell E Granade
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Daniel J Needleman
- Department of Applied Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Shirin Bahmanyar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.
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13
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Cantwell H, Dey G. Nuclear size and shape control. Semin Cell Dev Biol 2021; 130:90-97. [PMID: 34776332 DOI: 10.1016/j.semcdb.2021.10.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 11/27/2022]
Abstract
The nucleus displays a wide range of sizes and shapes in different species and cell types, yet its size scaling and many of the key structural constituents that determine its shape are highly conserved. In this review, we discuss the cellular properties and processes that contribute to nuclear size and shape control, drawing examples from across eukaryotes and highlighting conserved themes and pathways. We then outline physiological roles that have been uncovered for specific nuclear morphologies and disease pathologies associated with aberrant nuclear morphology. We argue that a comparative approach, assessing and integrating observations from different systems, will be a powerful way to help us address the open questions surrounding functional roles of nuclear size and shape in cell physiology.
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Affiliation(s)
- Helena Cantwell
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory, Meyerhofstr.1, 69117 Heidelberg, Germany.
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14
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Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection. J Fungi (Basel) 2021; 7:jof7100864. [PMID: 34682285 PMCID: PMC8537764 DOI: 10.3390/jof7100864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
Fission yeasts have a unique life history and exhibit distinct evolutionary patterns from other yeasts. Besides, the species demonstrate stable genome structures despite the relatively fast evolution of their genomic sequences. To reveal what could be the reason for that, comparative genomic analyses were carried out. Our results provided evidence that the structural and sequence evolution of the fission yeasts were correlated. Moreover, we revealed ancestral locally collinear blocks (aLCBs), which could have been inherited from their last common ancestor. These aLCBs proved to be the most conserved regions of the genomes as the aLCBs contain almost eight genes/blocks on average in the same orientation and order across the species. Gene order of the aLCBs is mainly fission-yeast-specific but supports the idea of filamentous ancestors. Nevertheless, the sequences and gene structures within the aLCBs are as mutable as any sequences in other parts of the genomes. Although genes of certain Gene Ontology (GO) categories tend to cluster at the aLCBs, those GO enrichments are not related to biological functions or high co-expression rates, they are, rather, determined by the density of essential genes and Rec12 cleavage sites. These data and our simulations indicated that aLCBs might not only be remnants of ancestral gene order but are also maintained by natural selection.
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15
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Abstract
Nuclear shape and size depend on nuclear membrane availability through an unknown process. A new study of asymmetric cell division reveals that nuclear membrane is derived from the endoplasmic reticulum and that limiting nuclear membrane expansion can affect cell fate.
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Affiliation(s)
- Orna Cohen-Fix
- The Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bethesda, MD 20892, USA.
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16
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Kutay U, Jühlen R, Antonin W. Mitotic disassembly and reassembly of nuclear pore complexes. Trends Cell Biol 2021; 31:1019-1033. [PMID: 34294532 DOI: 10.1016/j.tcb.2021.06.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 12/19/2022]
Abstract
Nuclear pore complexes (NPCs) are huge protein assemblies within the nuclear envelope (NE) that serve as selective gates for macromolecular transport between nucleus and cytoplasm. When higher eukaryotic cells prepare for division, they rapidly disintegrate NPCs during NE breakdown such that nuclear and cytoplasmic components mix to enable the formation of a cytoplasmic mitotic spindle. At the end of mitosis, reassembly of NPCs is coordinated with the establishment of the NE around decondensing chromatin. We review recent progress on mitotic NPC disassembly and reassembly, focusing on vertebrate cells. We highlight novel mechanistic insights into how NPCs are rapidly disintegrated into conveniently reusable building blocks, and put divergent models of (post-)mitotic NPC assembly into a spatial and temporal context.
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Affiliation(s)
- Ulrike Kutay
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland.
| | - Ramona Jühlen
- Institute of Biochemistry and Molecular Cell Biology, Medical School, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany.
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17
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Abstract
Membrane-bound organelles provide physical and functional compartmentalization of biological processes in eukaryotic cells. The characteristic shape and internal organization of these organelles is determined by a combination of multiple internal and external factors. The maintenance of the shape of nucleus, which houses the genetic material within a double membrane bilayer, is crucial for a seamless spatio-temporal control over nuclear and cellular functions. Dynamic morphological changes in the shape of nucleus facilitate various biological processes. Chromatin packaging, nuclear and cytosolic protein organization, and nuclear membrane lipid homeostasis are critical determinants of overall nuclear morphology. As such, a multitude of molecular players and pathways act together to regulate the nuclear shape. Here, we review the known mechanisms governing nuclear shape in various unicellular and multicellular organisms, including the non-spherical nuclei and non-lamin-related structural determinants. The review also touches upon cellular consequences of aberrant nuclear morphologies.
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Affiliation(s)
- Pallavi Deolal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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18
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Smith P, Owen DM, Lorenz CD, Makarova M. Asymmetric glycerophospholipids impart distinctive biophysical properties to lipid bilayers. Biophys J 2021; 120:1746-1754. [PMID: 33705758 DOI: 10.1016/j.bpj.2021.02.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 01/25/2023] Open
Abstract
Phospholipids are a diverse group of biomolecules consisting of a hydrophilic headgroup and two hydrophobic acyl tails. The nature of the head and length and saturation of the acyl tails are important for defining the biophysical properties of lipid bilayers. It has recently been shown that the membranes of certain yeast species contain high levels of unusual asymmetric phospholipids consisting of one long and one medium-chain acyl moiety, a configuration not common in mammalian cells or other well-studied model yeast species. This raises the possibility that structurally asymmetric glycerophospholipids impart distinctive biophysical properties to the yeast membranes. Previously, it has been shown that lipids with asymmetric length tails form a mixed interdigitated gel phase and exhibit unusual endotherm behavior upon heating and cooling. Here, however, we address physiologically relevant temperature conditions and, using atomistic molecular dynamics simulations and environmentally sensitive fluorescent membrane probes, characterize key biophysical parameters (such as lipid packing, diffusion coefficient, membrane thickness, and area per lipid) in membranes composed of both length-asymmetric glycerophospholipids and ergosterol. Interestingly, we show that saturated but asymmetric glycerophospholipids maintain membrane lipid order across a wide range of temperatures. We also show that these asymmetric lipids can substiture of unsaturated symmetric lipids in the phase behaviour of ternary lipid bilayers. This may allow cells to maintain membrane fluidity, even in environments that lack oxygen, which is required for the synthesis of unsaturated lipids and sterols.
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Affiliation(s)
- Paul Smith
- Department of Physics, King's College London, London, United Kingdom
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences and School of Mathematics, College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | | | - Maria Makarova
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.
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19
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Penfield L, Shankar R, Szentgyörgyi E, Laffitte A, Mauro MS, Audhya A, Müller-Reichert T, Bahmanyar S. Regulated lipid synthesis and LEM2/CHMP7 jointly control nuclear envelope closure. J Cell Biol 2021; 219:151636. [PMID: 32271860 PMCID: PMC7199858 DOI: 10.1083/jcb.201908179] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 01/22/2020] [Accepted: 03/03/2020] [Indexed: 11/22/2022] Open
Abstract
The nuclear permeability barrier depends on closure of nuclear envelope (NE) holes. Here, we investigate closure of the NE opening surrounding the meiotic spindle in C. elegans oocytes. ESCRT-III components accumulate at the opening but are not required for nuclear closure on their own. 3D analysis revealed cytoplasmic membranes directly adjacent to NE holes containing meiotic spindle microtubules. We demonstrate that the NE protein phosphatase, CNEP-1/CTDNEP1, controls de novo glycerolipid synthesis through lipin to prevent invasion of excess ER membranes into NE holes and a defective NE permeability barrier. Loss of NE adaptors for ESCRT-III exacerbates ER invasion and nuclear permeability defects in cnep-1 mutants, suggesting that ESCRTs restrict excess ER membranes during NE closure. Restoring glycerolipid synthesis in embryos deleted for CNEP-1 and ESCRT components rescued NE permeability defects. Thus, regulating the production and feeding of ER membranes into NE holes together with ESCRT-mediated remodeling is required for nuclear closure.
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Affiliation(s)
- Lauren Penfield
- Department of Molecular, Cellular and Developmental Biology, New Haven, CT
| | - Raakhee Shankar
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI
| | - Erik Szentgyörgyi
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Alyssa Laffitte
- Department of Molecular, Cellular and Developmental Biology, New Haven, CT
| | - Michael Sean Mauro
- Department of Molecular, Cellular and Developmental Biology, New Haven, CT
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Shirin Bahmanyar
- Department of Molecular, Cellular and Developmental Biology, New Haven, CT
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20
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Scotchman E, Kume K, Navarro FJ, Nurse P. Identification of mutants with increased variation in cell size at onset of mitosis in fission yeast. J Cell Sci 2021; 134:jcs251769. [PMID: 33419777 PMCID: PMC7888708 DOI: 10.1242/jcs.251769] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/10/2020] [Indexed: 12/19/2022] Open
Abstract
Fission yeast cells divide at a similar cell length with little variation about the mean. This is thought to be the result of a control mechanism that senses size and corrects for any deviations by advancing or delaying onset of mitosis. Gene deletions that advance cells into mitosis at a smaller size or delay cells entering mitosis have led to the identification of genes potentially involved in this mechanism. However, the molecular basis of this control is still not understood. In this work, we have screened for genes that when deleted increase the variability in size of dividing cells. The strongest candidate identified in this screen was mga2 The mga2 deletion strain shows a greater variation in cell length at division, with a coefficient of variation (CV) of 15-24%, while the wild-type strain has a CV of 5-8%. Furthermore, unlike wild-type cells, the mga2 deletion cells are unable to correct cell size deviations within one cell cycle. We show that the mga2 gene genetically interacts with nem1 and influences the nuclear membrane and the nuclear-cytoplasmic transport of CDK regulators.
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Affiliation(s)
| | - Kazunori Kume
- Cell Cycle Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University,Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | | | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, New York, NY 10065, USA
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21
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Dey G, Baum B. Nuclear envelope remodelling during mitosis. Curr Opin Cell Biol 2021; 70:67-74. [PMID: 33421755 PMCID: PMC8129912 DOI: 10.1016/j.ceb.2020.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/20/2022]
Abstract
The defining feature of the eukaryotic cell, the nucleus, is bounded by a double envelope. This envelope and the nuclear pores within it play a critical role in separating the genome from the cytoplasm. It also presents cells with a challenge. How are cells to remodel the nuclear compartment boundary during mitosis without compromising nuclear function? In the two billion years since the emergence of the first cells with a nucleus, eukaryotes have evolved a range of strategies to do this. At one extreme, the nucleus is disassembled upon entry into mitosis and then reassembled anew in the two daughter cells. At the other, cells maintain an intact nuclear compartment boundary throughout the division process. In this review, we discuss common features of the division process that underpin remodelling mechanisms, the topological challenges involved and speculate on the selective pressures that may drive the evolution of distinct modes of division.
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Affiliation(s)
- Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Buzz Baum
- Lab of Molecular Biology, Cambridge, CB2 0QH, United Kingdom; Lab for Molecular Cell Biology, UCL, London, WC1E 6BT, United Kingdom.
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22
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High-Throughput Identification of Nuclear Envelope Protein Interactions in Schizosaccharomyces pombe Using an Arrayed Membrane Yeast-Two Hybrid Library. G3-GENES GENOMES GENETICS 2020; 10:4649-4663. [PMID: 33109728 PMCID: PMC7718735 DOI: 10.1534/g3.120.401880] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The nuclear envelope (NE) contains a specialized set of integral membrane proteins that maintain nuclear shape and integrity and influence chromatin organization and gene expression. Advances in proteomics techniques and studies in model organisms have identified hundreds of proteins that localize to the NE. However, the function of many of these proteins at the NE remains unclear, in part due to a lack of understanding of the interactions that these proteins participate in at the NE membrane. To assist in the characterization of NE transmembrane protein interactions we developed an arrayed library of integral and peripheral membrane proteins from the fission yeast Schizosaccharomyces pombe for high-throughput screening using the split-ubiquitin based membrane yeast two -hybrid system. We used this approach to characterize protein interactions for three conserved proteins that localize to the inner nuclear membrane: Cut11/Ndc1, Lem2 and Ima1/Samp1/Net5. Additionally, we determined how the interaction network for Cut11 is altered in canonical temperature-sensitive cut11-ts mutants. This library and screening approach is readily applicable to characterizing the interactomes of integral membrane proteins localizing to various subcellular compartments.
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23
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Schutt KL, Moseley JB. The phosphatase inhibitor Sds23 promotes symmetric spindle positioning in fission yeast. Cytoskeleton (Hoboken) 2020; 77:544-557. [PMID: 33280247 PMCID: PMC8195570 DOI: 10.1002/cm.21648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/05/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022]
Abstract
A hallmark of cell division in eukaryotic cells is the formation and elongation of a microtubule (MT)-based mitotic spindle. Proper positioning of the spindle is critical to ensure equal segregation of the genetic material to the resulting daughter cells. Both the timing of spindle elongation and constriction of the actomyosin contractile ring must be precisely coordinated to prevent missegregation or damage to the genetic material during cellular division. Here, we show that Sds23, an inhibitor of protein phosphatases, contributes to proper positioning of elongating spindles in fission yeast cells. We found that sds23∆ mutant cells exhibit asymmetric spindles that initially elongate asymmetrically toward one end of the dividing cell. Spindle asymmetry in sds23∆ cells results from a defect that is distinct from previously identified mechanisms, including MT protrusions and enlarged vacuoles. Combined with our previous work, this study demonstrates that Sds23, an inhibitor of PP2A-family protein phosphatases, promotes proper positioning of both the bipolar spindle and cytokinetic ring during fission yeast cell division. These two steps ensure the overall symmetry and fidelity of the cell division process.
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Affiliation(s)
- Katherine L. Schutt
- Department of Biochemistry and Cell Biology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - James B. Moseley
- Department of Biochemistry and Cell Biology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755
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24
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Expósito-Serrano M, Sánchez-Molina A, Gallardo P, Salas-Pino S, Daga RR. Selective Nuclear Pore Complex Removal Drives Nuclear Envelope Division in Fission Yeast. Curr Biol 2020; 30:3212-3222.e2. [DOI: 10.1016/j.cub.2020.05.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/24/2020] [Accepted: 05/20/2020] [Indexed: 01/09/2023]
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25
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Makarova M, Peter M, Balogh G, Glatz A, MacRae JI, Lopez Mora N, Booth P, Makeyev E, Vigh L, Oliferenko S. Delineating the Rules for Structural Adaptation of Membrane-Associated Proteins to Evolutionary Changes in Membrane Lipidome. Curr Biol 2020; 30:367-380.e8. [PMID: 31956022 PMCID: PMC6997885 DOI: 10.1016/j.cub.2019.11.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/31/2019] [Accepted: 11/13/2019] [Indexed: 01/01/2023]
Abstract
Membrane function is fundamental to life. Each species explores membrane lipid diversity within a genetically predefined range of possibilities. How membrane lipid composition in turn defines the functional space available for evolution of membrane-centered processes remains largely unknown. We address this fundamental question using related fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus. We show that, unlike S. pombe that generates membranes where both glycerophospholipid acyl tails are predominantly 16-18 carbons long, S. japonicus synthesizes unusual "asymmetrical" glycerophospholipids where the tails differ in length by 6-8 carbons. This results in stiffer bilayers with distinct lipid packing properties. Retroengineered S. pombe synthesizing the S.-japonicus-type phospholipids exhibits unfolded protein response and downregulates secretion. Importantly, our protein sequence comparisons and domain swap experiments support the hypothesis that transmembrane helices co-evolve with membranes, suggesting that, on the evolutionary scale, changes in membrane lipid composition may necessitate extensive adaptation of the membrane-associated proteome.
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Affiliation(s)
- Maria Makarova
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Maria Peter
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Gabor Balogh
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Attila Glatz
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - James I MacRae
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nestor Lopez Mora
- Department of Chemistry, King's College London, Britannia House, London SE1 1DB, UK
| | - Paula Booth
- Department of Chemistry, King's College London, Britannia House, London SE1 1DB, UK
| | - Eugene Makeyev
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Laszlo Vigh
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, Guy's Campus, London SE1 1UL, UK.
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26
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Abstract
A new study compares two sister species of fission yeast that use very different fatty acids to make membrane lipids and reveals an adaptation in transmembrane helix lengths that maintains membrane protein functions.
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Affiliation(s)
- Takeshi Harayama
- Department of Biochemistry and National Centre of Competence in Research in Chemical Biology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva, Switzerland.
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27
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Holič R, Pokorná L, Griač P. Metabolism of phospholipids in the yeast
Schizosaccharomyces pombe. Yeast 2019; 37:73-92. [DOI: 10.1002/yea.3451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/28/2022] Open
Affiliation(s)
- Roman Holič
- Centre of Biosciences, Slovak Academy of Sciences Institute of Animal Biochemistry and Genetics Dúbravská cesta 9 Bratislava Slovakia
| | - Lucia Pokorná
- Centre of Biosciences, Slovak Academy of Sciences Institute of Animal Biochemistry and Genetics Dúbravská cesta 9 Bratislava Slovakia
| | - Peter Griač
- Centre of Biosciences, Slovak Academy of Sciences Institute of Animal Biochemistry and Genetics Dúbravská cesta 9 Bratislava Slovakia
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28
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Salas-Pino S, Daga RR. Spatiotemporal control of spindle disassembly in fission yeast. Cell Mol Life Sci 2019; 76:3543-3551. [PMID: 31129857 PMCID: PMC11105212 DOI: 10.1007/s00018-019-03139-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/29/2019] [Accepted: 05/07/2019] [Indexed: 12/20/2022]
Abstract
Maintenance of genomic stability during cell division is one of the most important cellular tasks, and it critically depends on the faithful replication of the genetic material and its equal partitioning into daughter cells, gametes, or spores in the case of yeasts. Defective mitotic spindle assembly and disassembly both result in changes in cellular ploidy that ultimately impinge proliferation fitness and might increase tumor malignancy. Although a great progress has been made in understanding how spindles are assembled to orchestrate chromosome segregation, much less is known about how they are disassembled once completed their function. Here, we review two recently uncovered mechanisms of spindle disassembly that operate at different stages of the fission yeast life cycle.
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Affiliation(s)
- Silvia Salas-Pino
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucia, Carretera de Utrera, km1, 41013, Seville, Spain.
| | - Rafael R Daga
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucia, Carretera de Utrera, km1, 41013, Seville, Spain.
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29
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Jackson CL. Lipid droplet biogenesis. Curr Opin Cell Biol 2019; 59:88-96. [PMID: 31075519 DOI: 10.1016/j.ceb.2019.03.018] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/24/2019] [Accepted: 03/29/2019] [Indexed: 11/18/2022]
Abstract
Lipid droplets (LDs) store neutral lipids in their core as an energy source when nutrients are scarce. The center of an LD is hydrophobic, and hence it is surrounded by a phospholipid monolayer, unlike other organelles that have an aqueous interior and are bounded by a phospholipid bilayer. LDs arise from the ER, where neutral lipid synthesis enzymes are localized. A combination of biophysical analysis and modeling, in vitro reconstitution and cell biological analyses has provided a great deal of information over the past few years on the process of LD biogenesis from the ER. In addition to lipid composition, four protein families (seipin proteins, perilipins, FIT proteins and ER shaping proteins) are crucial for LD biogenesis. Recent studies have shown that LDs preferentially arise, along with peroxisomes, at special ER sites marked by the reticulon-like Pex30/MCTP2 protein. New functions for perilipins and FIT family proteins have been uncovered, and the cryo-electron microscopy structure of seipin coupled with high resolution imaging in cells has provided a more comprehensive picture of its function in LD biogenesis. Seipin, along with other proteins such as Rab18 and its effector NRZ, have been shown to carry out their functions at least in part through regulation of ER-LD contact sites, whose establishment and maintenance have emerged as an essential component of LD biogenesis and maturation.
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Affiliation(s)
- Catherine L Jackson
- Institut Jacques Monod, UMR7592 CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.
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30
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Chemudupati M, Johns M, Osmani SA. The mode of mitosis is dramatically modified by deletion of a single nuclear pore complex gene in Aspergillus nidulans. Fungal Genet Biol 2019; 130:72-81. [PMID: 31026588 DOI: 10.1016/j.fgb.2019.04.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 02/06/2023]
Abstract
Nuclear pore complex (NPC) proteins (Nups) play multiple roles during mitosis. In this study we expand these roles and reveal that in Aspergillus nidulans, compromising the core Nup84-120 subcomplex of the NPC modifies the mitotic behavior of the nuclear envelope (NE). In wildtype cells, the NE undergoes simultaneous double pinching events to separate daughter nuclei during mitotic exit, whereas in Nup84-120 complex mutants, only one restriction of the NE is observed. Investigating the basis for this modified behavior of the NE in Nup deleted cells uncovered previously unrealized roles for core Nups in mitotic exit. During wildtype anaphase, the NE surrounds the two separating daughter DNA masses which typically flank the central nucleolus, to form three distinct nuclear compartments. In contrast, deletion of core Nups frequently results in early nucleolar eviction from the mitotic nucleus, in turn causing an uncharacteristic dumbbell-shaped NE morphology of anaphase nuclei with a nuclear membrane bridge connecting the two forming G1 nuclei. Importantly, the absence of the nucleolus between the separating daughter nuclei during anaphase delays chromosome segregation and progression into G1 as nuclei remain connected by chromatin bridges. Proteins localizing to late segregating chromosome arms are observed between forming daughter nuclei, and the mitotic spindle fails to resolve in a timely manner. These chromatin bridges are occupied by the Aurora kinase until nuclei have fully separated, suggesting involvement of Aurora in monitoring mitotic spindle and nuclear membrane resolution during mitotic exit. Our findings thus reveal a novel requirement for core Nups in mediating nucleolar positioning during mitosis, which dictates the pattern of NE fissions during karyokinesis and facilitates normal chromosome segregation. The findings additionally demonstrate that the mode of mitosis can be dramatically modified by deletion of a single NPC gene and reveals surprising fluidity in mitotic mechanisms.
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Affiliation(s)
- Mahesh Chemudupati
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, United States; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, United States
| | - Matthew Johns
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, United States
| | - Stephen A Osmani
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, United States; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, United States.
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31
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Nuclear membrane protein Lem2 regulates nuclear size through membrane flow. Nat Commun 2019; 10:1871. [PMID: 31015410 PMCID: PMC6478680 DOI: 10.1038/s41467-019-09623-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 03/18/2019] [Indexed: 11/08/2022] Open
Abstract
The size of the membrane-bound nucleus scales with cell size in a wide range of cell types but the mechanisms determining overall nuclear size remain largely unknown. Here we investigate the role of fission yeast inner nuclear membrane proteins in determining nuclear size, and propose that the Lap2-Emerin-Man1 domain protein Lem2 acts as a barrier to membrane flow between the nucleus and other parts of the cellular membrane system. Lem2 deletion increases membrane flow into and out of the nuclear envelope in response to changes in membrane synthesis and nucleocytoplasmic transport, altering nuclear size. The endoplasmic reticulum protein Lnp1 acts as a secondary barrier to membrane flow, functionally compensating for lack of Lem2. We propose that this is part of the mechanism that maintains nuclear size proportional to cellular membrane content and thus to cell size. Similar regulatory principles may apply to other organelles in the eukaryotic subcellular membrane network.
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Zach R, Převorovský M. The phenomenon of lipid metabolism "cut" mutants. Yeast 2018; 35:631-637. [PMID: 30278108 DOI: 10.1002/yea.3358] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/06/2018] [Accepted: 09/24/2018] [Indexed: 02/05/2023] Open
Abstract
Every cell cycle iteration culminates with the resolution of a mitotic nucleus into a pair of daughter nuclei, which are distributed between the two daughter cells. In the fission yeast Schizosaccharomyces pombe, the faithful division of a mitotic nucleus depends on unperturbed lipogenesis. Upon genetically or chemically induced perturbation of lipid anabolism, S. pombe cells fail to separate the two daughter nuclei and subsequently initiate lethal cytokinesis resulting in the so-called "cut" terminal phenotype. Evidence supporting a critical role of lipid biogenesis in successful mitosis in S. pombe has been accumulating for almost two decades, but the exact mechanism explaining the reported observations had been elusive. Recently, several studies established a functional link between biosynthesis of structural phospholipids, nuclear membrane growth, and the fidelity of "closed" mitosis in S. pombe. These novel insights suggest a mechanistic explanation for the mitotic defects characteristic for some S. pombe mutants deficient in lipid anabolism and extend our knowledge of metabolic modulation within the context of the cell cycle. In this review, we cover the essential role of lipogenesis in "closed" mitosis, focusing mainly on S. pombe as a model system.
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Affiliation(s)
- Róbert Zach
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic.,Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
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Zach R, Tvarůžková J, Schätz M, Ťupa O, Grallert B, Převorovský M. Mitotic defects in fission yeast lipid metabolism 'cut' mutants are suppressed by ammonium chloride. FEMS Yeast Res 2018; 18:5040229. [PMID: 29931271 PMCID: PMC6037054 DOI: 10.1093/femsyr/foy064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/15/2018] [Indexed: 01/01/2023] Open
Abstract
Fission yeast 'cut' mutants show defects in temporal coordination of nuclear division with cytokinesis, resulting in aberrant mitosis and lethality. Among other causes, the 'cut' phenotype can be triggered by genetic or chemical perturbation of lipid metabolism, supposedly resulting in shortage of membrane phospholipids and insufficient nuclear envelope expansion during anaphase. Interestingly, penetrance of the 'cut' phenotype in mutants of the transcription factor cbf11 and acetyl-coenzyme A carboxylase cut6, both related to lipid metabolism, is highly dependent on growth media, although the specific nutrient(s) affecting 'cut' occurrence is not known. In this study, we set out to identify the growth media component(s) responsible for 'cut' phenotype suppression in Δcbf11 and cut6-621 cells. We show that mitotic defects occur rapidly in Δcbf11 cells upon shift from the minimal EMM medium ('cut' suppressing) to the complex YES medium ('cut' promoting). By growing cells in YES medium supplemented with individual EMM components, we identified ammonium chloride, an efficiently utilized nitrogen source, as a specific and potent suppressor of the 'cut' phenotype in both Δcbf11 and cut6-621. Furthermore, we found that ammonium chloride boosts lipid droplet formation in wild-type cells. Our findings suggest a possible involvement of nutrient-responsive signaling in 'cut' suppression.
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Affiliation(s)
- Róbert Zach
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jarmila Tvarůžková
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Schätz
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Computing and Control Engineering, University of Chemistry and Technology, Prague, Czech Republic
| | - Ondřej Ťupa
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Computing and Control Engineering, University of Chemistry and Technology, Prague, Czech Republic
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
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Sajiki K, Tahara Y, Uehara L, Sasaki T, Pluskal T, Yanagida M. Genetic regulation of mitotic competence in G 0 quiescent cells. SCIENCE ADVANCES 2018; 4:eaat5685. [PMID: 30116786 PMCID: PMC6093628 DOI: 10.1126/sciadv.aat5685] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/04/2018] [Indexed: 05/03/2023]
Abstract
Quiescent (G0 phase) cells must maintain mitotic competence (MC) to restart the cell cycle. This is essential for reproduction in unicellular organisms and also for development and cell replacement in higher organisms. Recently, suppression of MC has gained attention as a possible therapeutic strategy for cancer. Using a Schizosaccharomyces pombe deletion-mutant library, we identified 85 genes required to maintain MC during the G0 phase induced by nitrogen deprivation. G0 cells must recycle proteins and RNA, governed by anabolism, catabolism, transport, and availability of small molecules such as antioxidants. Protein phosphatases are also essential to maintain MC. In particular, Nem1-Spo7 protects the nucleus from autophagy by regulating Ned1, a lipin. These genes, designated GZE (G-Zero Essential) genes, reveal the landscape of genetic regulation of MC.
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Affiliation(s)
- Kenichi Sajiki
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna, Okinawa, Japan
- Corresponding author. (K.S.); (M.Y.)
| | - Yuria Tahara
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna, Okinawa, Japan
| | - Lisa Uehara
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna, Okinawa, Japan
| | - Toshio Sasaki
- Research Support Imaging Section, OIST, Onna, Okinawa, Japan
| | - Tomáš Pluskal
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna, Okinawa, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna, Okinawa, Japan
- Corresponding author. (K.S.); (M.Y.)
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35
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Oliferenko S. Understanding eukaryotic chromosome segregation from a comparative biology perspective. J Cell Sci 2018; 131:131/14/jcs203653. [PMID: 30030298 DOI: 10.1242/jcs.203653] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A long-appreciated variation in fundamental cell biological processes between different species is becoming increasingly tractable due to recent breakthroughs in whole-genome analyses and genome editing techniques. However, the bulk of our mechanistic understanding in cell biology continues to come from just a few well-established models. In this Review, I use the highly diverse strategies of chromosome segregation in eukaryotes as an instrument for a more general discussion on phenotypic variation, possible rules underlying its emergence and its utility in understanding conserved functional relationships underlying this process. Such a comparative approach, supported by modern molecular biology tools, might provide a wider, holistic view of biology that is difficult to achieve when concentrating on a single experimental system.
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Affiliation(s)
- Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK .,Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
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36
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Flor-Parra I, Iglesias-Romero AB, Salas-Pino S, Lucena R, Jimenez J, Daga RR. Importin α and vNEBD Control Meiotic Spindle Disassembly in Fission Yeast. Cell Rep 2018; 23:933-941. [DOI: 10.1016/j.celrep.2018.03.073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/13/2018] [Accepted: 03/16/2018] [Indexed: 11/15/2022] Open
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38
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Abstract
Cells depend on hugely diverse lipidomes for many functions. The actions and structural integrity of the plasma membrane and most organelles also critically depend on membranes and their lipid components. Despite the biological importance of lipids, our understanding of lipid engagement, especially the roles of lipid hydrophobic alkyl side chains, in key cellular processes is still developing. Emerging research has begun to dissect the importance of lipids in intricate events such as cell division. This review discusses how these structurally diverse biomolecules are spatially and temporally regulated during cell division, with a focus on cytokinesis. We analyze how lipids facilitate changes in cellular morphology during division and how they participate in key signaling events. We identify which cytokinesis proteins are associated with membranes, suggesting lipid interactions. More broadly, we highlight key unaddressed questions in lipid cell biology and techniques, including mass spectrometry, advanced imaging, and chemical biology, which will help us gain insights into the functional roles of lipids.
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Affiliation(s)
- Elisabeth M Storck
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom;
| | - Cagakan Özbalci
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom;
| | - Ulrike S Eggert
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom; .,Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
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39
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Jacquemyn J, Cascalho A, Goodchild RE. The ins and outs of endoplasmic reticulum-controlled lipid biosynthesis. EMBO Rep 2017; 18:1905-1921. [PMID: 29074503 DOI: 10.15252/embr.201643426] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 08/18/2017] [Accepted: 09/18/2017] [Indexed: 12/21/2022] Open
Abstract
Endoplasmic reticulum (ER)-localized enzymes synthesize the vast majority of cellular lipids. The ER therefore has a major influence on cellular lipid biomass and balances the production of different lipid categories, classes, and species. Signals from outside and inside the cell are directed to ER-localized enzymes, and lipid enzyme activities are defined by the integration of internal, homeostatic, and external information. This allows ER-localized lipid synthesis to provide the cell with membrane lipids for growth, proliferation, and differentiation-based changes in morphology and structure, and to maintain membrane homeostasis across the cell. ER enzymes also respond to physiological signals to drive carbohydrates and nutritionally derived lipids into energy-storing triglycerides. In this review, we highlight some key regulatory mechanisms that control ER-localized enzyme activities in animal cells. We also discuss how they act in concert to maintain cellular lipid homeostasis, as well as how their dysregulation contributes to human disease.
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Affiliation(s)
- Julie Jacquemyn
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Ana Cascalho
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Rose E Goodchild
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium .,Department of Neurosciences, KU Leuven, Leuven, Belgium
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40
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Yang HJ, Iwamoto M, Hiraoka Y, Haraguchi T. Function of nuclear membrane proteins in shaping the nuclear envelope integrity during closed mitosis. J Biochem 2017; 161:471-477. [PMID: 28398483 DOI: 10.1093/jb/mvx020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/28/2017] [Indexed: 11/13/2022] Open
Abstract
The nuclear envelope (NE) not only protects the genome from being directly accessed by detrimental agents but also regulates genome organization. Breaches in NE integrity threaten genome stability and impede cellular function. Nonetheless, the NE constantly remodels, and NE integrity is endangered in dividing or differentiating cells. Specifically, in unicellular eukaryotes undergoing closed mitosis, the NE expands instead of breaking down during chromosome segregation. The newly assembling nuclear pore complexes (NPCs) penetrate the existing NE in interphase. A peculiar example of NE remodelling during nuclear differentiation in Tetrahymena involves formation of the redundant NE and clustered NPCs. Even under these conditions, the NE remains intact. Many recent studies on unicellular organisms have revealed that nuclear membrane proteins, such as LEM-domain proteins, play a role in maintaining NE integrity. This review summarizes and discusses how nuclear membrane proteins participate in NE integrity.
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Affiliation(s)
- Hui-Ju Yang
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Masaaki Iwamoto
- Advance ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advance ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advance ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan
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41
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Russell JJ, Theriot JA, Sood P, Marshall WF, Landweber LF, Fritz-Laylin L, Polka JK, Oliferenko S, Gerbich T, Gladfelter A, Umen J, Bezanilla M, Lancaster MA, He S, Gibson MC, Goldstein B, Tanaka EM, Hu CK, Brunet A. Non-model model organisms. BMC Biol 2017; 15:55. [PMID: 28662661 PMCID: PMC5492503 DOI: 10.1186/s12915-017-0391-5] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.
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Affiliation(s)
- James J Russell
- Department of Biology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA
| | - Julie A Theriot
- Departments of Biochemistry and of Microbiology & Immunology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA.
| | - Pranidhi Sood
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA
| | - Wallace F Marshall
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA.
| | - Laura F Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY, 10032, USA
| | | | - Jessica K Polka
- Visiting Scholar, Whitehead Institute, 9 Cambridge Center, Cambridge, MA, 02142, USA
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Therese Gerbich
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Amy Gladfelter
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - James Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO, 63132, USA
| | | | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, CB2 0QH, Cambridge, UK
| | - Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Bob Goldstein
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, CA, 94305, USA
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42
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Kume K, Cantwell H, Neumann FR, Jones AW, Snijders AP, Nurse P. A systematic genomic screen implicates nucleocytoplasmic transport and membrane growth in nuclear size control. PLoS Genet 2017; 13:e1006767. [PMID: 28545058 PMCID: PMC5436639 DOI: 10.1371/journal.pgen.1006767] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/19/2017] [Indexed: 01/14/2023] Open
Abstract
How cells control the overall size and growth of membrane-bound organelles is an important unanswered question of cell biology. Fission yeast cells maintain a nuclear size proportional to cellular size, resulting in a constant ratio between nuclear and cellular volumes (N/C ratio). We have conducted a genome-wide visual screen of a fission yeast gene deletion collection for viable mutants altered in their N/C ratio, and have found that defects in both nucleocytoplasmic mRNA transport and lipid synthesis alter the N/C ratio. Perturbing nuclear mRNA export results in accumulation of both mRNA and protein within the nucleus, and leads to an increase in the N/C ratio which is dependent on new membrane synthesis. Disruption of lipid synthesis dysregulates nuclear membrane growth and results in an enlarged N/C ratio. We propose that both properly regulated nucleocytoplasmic transport and nuclear membrane growth are central to the control of nuclear growth and size.
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Affiliation(s)
- Kazunori Kume
- Hiroshima Research Center for Healthy Aging, Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Cell Cycle Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Helena Cantwell
- Cell Cycle Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Frank R. Neumann
- Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, New York, New York, United States of America
| | - Andrew W. Jones
- Cell Cycle Laboratory, The Francis Crick Institute, London, United Kingdom
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, London, United Kingdom
| | - Ambrosius P. Snijders
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, London, United Kingdom
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, London, United Kingdom
- Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, New York, New York, United States of America
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43
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Péter M, Glatz A, Gudmann P, Gombos I, Török Z, Horváth I, Vígh L, Balogh G. Metabolic crosstalk between membrane and storage lipids facilitates heat stress management in Schizosaccharomyces pombe. PLoS One 2017; 12:e0173739. [PMID: 28282432 PMCID: PMC5345867 DOI: 10.1371/journal.pone.0173739] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 02/24/2017] [Indexed: 12/28/2022] Open
Abstract
Cell membranes actively participate in stress sensing and signalling. Here we present the first in-depth lipidomic analysis to characterize alterations in the fission yeast Schizosaccharomyces pombe in response to mild heat stress (HS). The lipidome was assessed by a simple one-step methanolic extraction. Genetic manipulations that altered triglyceride (TG) content in the absence or presence of HS gave rise to distinct lipidomic fingerprints for S. pombe. Cells unable to produce TG demonstrated long-lasting growth arrest and enhanced signalling lipid generation. Our results reveal that metabolic crosstalk between membrane and storage lipids facilitates homeostatic maintenance of the membrane physical/chemical state that resists negative effects on cell growth and viability in response to HS. We propose a novel stress adaptation mechanism in which heat-induced TG synthesis contributes to membrane rigidization by accommodating unsaturated fatty acids of structural lipids, enabling their replacement by newly synthesized saturated fatty acids.
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Affiliation(s)
- Mária Péter
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Attila Glatz
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Péter Gudmann
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Imre Gombos
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Zsolt Török
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ibolya Horváth
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - László Vígh
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Gábor Balogh
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail:
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44
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Abstract
As a compartment border, the nuclear envelope (NE) needs to serve as both a protective membrane shell for the genome and a versatile communication interface between the nucleus and the cytoplasm. Despite its important structural role in sheltering the genome, the NE is a dynamic and highly adaptable boundary that changes composition during differentiation, deforms in response to mechanical challenges, can be repaired upon rupture and even rapidly disassembles and reforms during open mitosis. NE remodelling is fundamentally involved in cell growth, division and differentiation, and if perturbed can lead to devastating diseases such as muscular dystrophies or premature ageing.
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45
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Craddock CP, Adams N, Kroon JT, Bryant FM, Hussey PJ, Kurup S, Eastmond PJ. Cyclin-dependent kinase activity enhances phosphatidylcholine biosynthesis in Arabidopsis by repressing phosphatidic acid phosphohydrolase activity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:3-14. [PMID: 27595588 PMCID: PMC5299491 DOI: 10.1111/tpj.13321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 05/21/2023]
Abstract
Coordination of endomembrane biogenesis with cell cycle progression is considered to be important in maintaining cell function during growth and development. We previously showed that the disruption of PHOSPHATIDIC ACID PHOSPHOHYDROLASE (PAH) activity in Arabidopsis thaliana stimulates biosynthesis of the major phospholipid phosphatidylcholine (PC) and causes expansion of the endoplasmic reticulum. Here we show that PC biosynthesis is repressed by disruption of the core cell cycle regulator CYCLIN-DEPENDENT KINASE A;1 (CDKA;1) and that this repression is reliant on PAH. Furthermore, we show that cyclin-dependent kinases (CDKs) phosphorylate PAH1 at serine 162, which reduces both its activity and membrane association. Expression of a CDK-insensitive version of PAH1 with a serine 162 to alanine substitution represses PC biosynthesis and also reduces the rate of cell division in early leaf development. Together our findings reveal a physiologically important mechanism that couples the rate of phospholipid biosynthesis and endomembrane biogenesis to cell cycle progression in Arabidopsis.
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Affiliation(s)
- Christian P. Craddock
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUK
- Present address: Center for Plant Cell BiologyDepartment of Botany and Plant SciencesUniversity of CaliforniaRiverside92521USA
| | - Nicolette Adams
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUK
- Present address: Centre for Proteomic and Genomic ResearchUpper LevelSt Peter's MallCorner Anzio and Main Road ObservatoryCape Town7925South Africa
| | - Johan T.M. Kroon
- School of Biological and Biomedical SciencesDurham UniversityDurhamDH1 3LEUK
| | - Fiona M. Bryant
- Department of Plant Biology and Crop ScienceRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
- Present address: School of Biological and Biomedical SciencesDurham UniversityDurhamDH1 3LEUK
| | - Patrick J. Hussey
- School of Biological and Biomedical SciencesDurham UniversityDurhamDH1 3LEUK
| | - Smita Kurup
- Department of Plant Biology and Crop ScienceRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
| | - Peter J. Eastmond
- Department of Plant Biology and Crop ScienceRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
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46
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Cellular Reorganization during Mitotic Entry. Trends Cell Biol 2017; 27:26-41. [DOI: 10.1016/j.tcb.2016.07.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/14/2016] [Accepted: 07/18/2016] [Indexed: 12/27/2022]
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47
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Makarova M, Oliferenko S. Mixing and matching nuclear envelope remodeling and spindle assembly strategies in the evolution of mitosis. Curr Opin Cell Biol 2016; 41:43-50. [PMID: 27062548 PMCID: PMC7100904 DOI: 10.1016/j.ceb.2016.03.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/20/2016] [Accepted: 03/23/2016] [Indexed: 12/11/2022]
Abstract
In eukaryotes, cellular genome is enclosed inside a membrane-bound organelle called the nucleus. The nucleus compartmentalizes genome replication, repair and expression, keeping these activities separated from protein synthesis and other metabolic processes. Each proliferative division, the duplicated chromosomes must be equipartitioned between the daughter cells and this requires precise coordination between assembly of the microtubule-based mitotic spindle and nuclear remodeling. Here we review a surprising variety of strategies used by modern eukaryotes to manage these processes and discuss possible mechanisms that might have led to the emergence of this diversity in evolution.
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Affiliation(s)
- Maria Makarova
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Snezhana Oliferenko
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK.
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Meseroll RA, Cohen-Fix O. The Malleable Nature of the Budding Yeast Nuclear Envelope: Flares, Fusion, and Fenestrations. J Cell Physiol 2016; 231:2353-60. [PMID: 26909870 DOI: 10.1002/jcp.25355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 02/19/2016] [Indexed: 11/10/2022]
Abstract
In eukaryotes, the nuclear envelope (NE) physically separates nuclear components and activities from rest of the cell. The NE also provides rigidity to the nucleus and contributes to chromosome organization. At the same time, the NE is highly dynamic; it must change shape and rearrange its components during development and throughout the cell cycle, and its morphology can be altered in response to mutation and disease. Here we focus on the NE of budding yeast, Saccharomyces cerevisiae, which has several unique features: it remains intact throughout the cell cycle, expands symmetrically during interphase, elongates during mitosis and, expands asymmetrically during mitotic delay. Moreover, its NE is safely breached during mating and when large structures, such as nuclear pore complexes and the spindle pole body, are embedded into its double membrane. The budding yeast NE lacks lamins and yet the nucleus is capable of maintaining a spherical shape throughout interphase. Despite these eccentricities, studies of the budding yeast NE have uncovered interesting, and likely conserved, processes that contribute to NE dynamics. In particular, we discuss the processes that drive and enable NE expansion and the dramatic changes in the NE that lead to extensions and fenestrations. J. Cell. Physiol. 231: 2353-2360, 2016. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Rebecca A Meseroll
- The Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Orna Cohen-Fix
- The Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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Prasad R, Barral Y. Posttranslational Regulation: A Way to Evolve. Curr Biol 2016; 26:R119-21. [PMID: 26859269 DOI: 10.1016/j.cub.2015.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A new study shows that differences in the regulation of lipin can account for the different strategies of nuclear division in two closely related fission yeast species.
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Affiliation(s)
- Rupali Prasad
- Institute of Biochemistry, Department of Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, Department of Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
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