1
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Wang Y, Ruan L, Zhu J, Zhang X, Chang ACC, Tomaszewski A, Li R. Metabolic regulation of misfolded protein import into mitochondria. eLife 2024; 12:RP87518. [PMID: 38900507 PMCID: PMC11189628 DOI: 10.7554/elife.87518] [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] [Indexed: 06/21/2024] Open
Abstract
Mitochondria are the cellular energy hub and central target of metabolic regulation. Mitochondria also facilitate proteostasis through pathways such as the 'mitochondria as guardian in cytosol' (MAGIC) whereby cytosolic misfolded proteins (MPs) are imported into and degraded inside mitochondria. In this study, a genome-wide screen in Saccharomyces cerevisiae uncovered that Snf1, the yeast AMP-activated protein kinase (AMPK), inhibits the import of MPs into mitochondria while promoting mitochondrial biogenesis under glucose starvation. We show that this inhibition requires a downstream transcription factor regulating mitochondrial gene expression and is likely to be conferred through substrate competition and mitochondrial import channel selectivity. We further show that Snf1/AMPK activation protects mitochondrial fitness in yeast and human cells under stress induced by MPs such as those associated with neurodegenerative diseases.
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Affiliation(s)
- Yuhao Wang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Linhao Ruan
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Jin Zhu
- Mechanobiology Institute and Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Xi Zhang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Alexander Chih-Chieh Chang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins UniversityBaltimoreUnited States
| | - Alexis Tomaszewski
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Mechanobiology Institute and Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins UniversityBaltimoreUnited States
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2
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Barbosa AD, Siniossoglou S. Membranes that make fat: roles of membrane lipids as acyl donors for triglyceride synthesis and organelle function. FEBS Lett 2024; 598:1226-1234. [PMID: 38140812 DOI: 10.1002/1873-3468.14793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Triglycerides constitute an inert storage form for fatty acids deposited in lipid droplets and are mobilized to provide metabolic energy or membrane building blocks. The biosynthesis of triglycerides is highly conserved within eukaryotes and normally involves the sequential esterification of activated fatty acids with a glycerol backbone. Some eukaryotes, however, can also use cellular membrane lipids as direct fatty acid donors for triglyceride synthesis. The biological significance of a pathway that generates triglycerides at the expense of organelle membranes has remained elusive. Here we review current knowledge on how cells use membrane lipids as fatty acid donors for triglyceride synthesis and discuss the hypothesis that a primary function of this pathway is to regulate membrane lipid remodeling and organelle function.
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Affiliation(s)
- Antonio D Barbosa
- Cambridge Institute for Medical Research, University of Cambridge, UK
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3
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Gunn AL, Yashchenko AI, Dubrulle J, Johnson J, Hatch EM. A high-content screen reveals new regulators of nuclear membrane stability. Sci Rep 2024; 14:6013. [PMID: 38472343 PMCID: PMC10933478 DOI: 10.1038/s41598-024-56613-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 03/08/2024] [Indexed: 03/14/2024] Open
Abstract
Nuclear membrane rupture is a physiological response to multiple in vivo processes, such as cell migration, that can cause extensive genome instability and upregulate invasive and inflammatory pathways. However, the underlying molecular mechanisms of rupture are unclear and few regulators have been identified. In this study, we developed a reporter that is size excluded from re-compartmentalization following nuclear rupture events. This allows for robust detection of factors influencing nuclear integrity in fixed cells. We combined this with an automated image analysis pipeline in a high-content siRNA screen to identify new proteins that both increase and decrease nuclear rupture frequency in cancer cells. Pathway analysis identified an enrichment of nuclear membrane and ER factors in our hits and we demonstrate that one of these, the protein phosphatase CTDNEP1, is required for nuclear stability. Analysis of known rupture determinants, including an automated quantitative analysis of nuclear lamina gaps, are consistent with CTDNEP1 acting independently of actin and nuclear lamina organization. Our findings provide new insights into the molecular mechanism of nuclear rupture and define a highly adaptable program for rupture analysis that removes a substantial barrier to new discoveries in the field.
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Affiliation(s)
- Amanda L Gunn
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Artem I Yashchenko
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Julien Dubrulle
- Cellular Imaging Shared Resource, The Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jodiene Johnson
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Emily M Hatch
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, Seattle, WA, USA.
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4
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Gunn AL, Yashchenko AI, Dubrulle J, Johnson J, Hatch EM. A high-content screen reveals new regulators of nuclear membrane stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542944. [PMID: 37398267 PMCID: PMC10312541 DOI: 10.1101/2023.05.30.542944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Nuclear membrane rupture is a physiological response to multiple in vivo processes, such as cell migration, that can cause extensive genome instability and upregulate invasive and inflammatory pathways. However, the underlying molecular mechanisms of rupture are unclear and few regulators have been identified. In this study, we developed a reporter that is size excluded from re-compartmentalization following nuclear rupture events. This allows for robust detection of factors influencing nuclear integrity in fixed cells. We combined this with an automated image analysis pipeline in a high-content siRNA screen to identify new proteins that both increase and decrease nuclear rupture frequency in cancer cells. Pathway analysis identified an enrichment of nuclear membrane and ER factors in our hits and we demonstrate that one of these, the protein phosphatase CTDNEP1, is required for nuclear stability. Further analysis of known rupture contributors, including a newly developed automated quantitative analysis of nuclear lamina gaps, strongly suggests that CTDNEP1 acts in a new pathway. Our findings provide new insights into the molecular mechanism of nuclear rupture and define a highly adaptable program for rupture analysis that removes a substantial barrier to new discoveries in the field.
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Affiliation(s)
- Amanda L. Gunn
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, 1100 Fairview Ave, Seattle, Washington 98109, USA
| | - Artem I. Yashchenko
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, 1100 Fairview Ave, Seattle, Washington 98109, USA
| | - Julien Dubrulle
- Cellular Imaging Shared Resource, The Fred Hutchinson Cancer Center, 1100 Fairview Ave, Seattle, Washington 98109, USA
| | - Jodiene Johnson
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, 1100 Fairview Ave, Seattle, Washington 98109, USA
| | - Emily M. Hatch
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, 1100 Fairview Ave, Seattle, Washington 98109, USA
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5
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Wang Y, Ruan L, Zhu J, Zhang X, Chih-Chieh Chang A, Tomaszewski A, Li R. Metabolic regulation of misfolded protein import into mitochondria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534670. [PMID: 37034811 PMCID: PMC10081186 DOI: 10.1101/2023.03.29.534670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Mitochondria are the cellular energy hub and central target of metabolic regulation. Mitochondria also facilitate proteostasis through pathways such as the 'mitochondria as guardian in cytosol' (MAGIC) whereby cytosolic misfolded proteins (MPs) are imported into and degraded inside mitochondria. In this study, a genome-wide screen in yeast uncovered that Snf1, the yeast AMP-activated protein kinase (AMPK), inhibits the import of MPs into mitochondria while promoting mitochondrial biogenesis under glucose starvation. We show that this inhibition requires a downstream transcription factor regulating mitochondrial gene expression and is likely to be conferred through substrate competition and mitochondrial import channel selectivity. We further show that Snf1/AMPK activation protects mitochondrial fitness in yeast and human cells under stress induced by MPs such as those associated with neurodegenerative diseases.
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Affiliation(s)
- Yuhao Wang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine; Baltimore, MD 21287, USA
| | - Linhao Ruan
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
| | - Jin Zhu
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore; Singapore 117411, Singapore
| | - Xi Zhang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
| | - Alexander Chih-Chieh Chang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University; Baltimore, MD 21218, USA
| | - Alexis Tomaszewski
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine; Baltimore, MD 21287, USA
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore; Singapore 117411, Singapore
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University; Baltimore, MD 21218, USA
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6
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Saik NO, Ptak C, Rehman S, Aitchison JD, Montpetit B, Wozniak RW. SUMOylation at the inner nuclear membrane facilitates nuclear envelope biogenesis during mitosis. J Cell Biol 2023; 222:e202208137. [PMID: 37398994 PMCID: PMC10318406 DOI: 10.1083/jcb.202208137] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/24/2023] [Accepted: 05/15/2023] [Indexed: 07/04/2023] Open
Abstract
As eukaryotic cells progress through cell division, the nuclear envelope (NE) membrane must expand to accommodate the formation of progeny nuclei. In Saccharomyces cerevisiae, closed mitosis allows visualization of NE biogenesis during mitosis. During this period, the SUMO E3 ligase Siz2 binds the inner nuclear membrane (INM) and initiates a wave of INM protein SUMOylation. Here, we show these events increase INM levels of phosphatidic acid (PA), an intermediate of phospholipid biogenesis, and are necessary for normal mitotic NE membrane expansion. The increase in INM PA is driven by the Siz2-mediated inhibition of the PA phosphatase Pah1. During mitosis, this results from the binding of Siz2 to the INM and dissociation of Spo7 and Nem1, a complex required for the activation of Pah1. As cells enter interphase, the process is then reversed by the deSUMOylase Ulp1. This work further establishes a central role for temporally controlled INM SUMOylation in coordinating processes, including membrane expansion, that regulate NE biogenesis during mitosis.
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Affiliation(s)
- Natasha O. Saik
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Saif Rehman
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - John D. Aitchison
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
- Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics and Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Richard W. Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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7
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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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8
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Bâcle J, Groizard L, Kumanski S, Moriel-Carretero M. Nuclear envelope-remodeling events as models to assess the potential role of membranes on genome stability. FEBS Lett 2023; 597:1946-1956. [PMID: 37339935 DOI: 10.1002/1873-3468.14688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 06/22/2023]
Abstract
The nuclear envelope (NE) encloses the genetic material and functions in chromatin organization and stability. In Saccharomyces cerevisiae, the NE is bound to the ribosomal DNA (rDNA), highly repeated and transcribed, thus prone to genetic instability. While tethering limits instability, it simultaneously triggers notable NE remodeling. We posit here that NE remodeling may contribute to genome integrity maintenance. The NE importance in genome expression, structure, and integrity is well recognized, yet studies mostly focus on peripheral proteins and nuclear pores, not on the membrane itself. We recently characterized a NE invagination drastically obliterating the rDNA, which we propose here as a model to probe if and how membranes play an active role in genome stability preservation.
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Affiliation(s)
- Janélie Bâcle
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
| | - Léa Groizard
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
| | - Sylvain Kumanski
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
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9
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Sosa Ponce ML, Remedios MH, Moradi-Fard S, Cobb JA, Zaremberg V. SIR telomere silencing depends on nuclear envelope lipids and modulates sensitivity to a lysolipid. J Cell Biol 2023; 222:e202206061. [PMID: 37042812 PMCID: PMC10103788 DOI: 10.1083/jcb.202206061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/29/2022] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
The nuclear envelope (NE) is important in maintaining genome organization. The role of lipids in communication between the NE and telomere regulation was investigated, including how changes in lipid composition impact gene expression and overall nuclear architecture. Yeast was treated with the non-metabolizable lysophosphatidylcholine analog edelfosine, known to accumulate at the perinuclear ER. Edelfosine induced NE deformation and disrupted telomere clustering but not anchoring. Additionally, the association of Sir4 at telomeres decreased. RNA-seq analysis showed altered expression of Sir-dependent genes located at sub-telomeric (0-10 kb) regions, consistent with Sir4 dispersion. Transcriptomic analysis revealed that two lipid metabolic circuits were activated in response to edelfosine, one mediated by the membrane sensing transcription factors, Spt23/Mga2, and the other by a transcriptional repressor, Opi1. Activation of these transcriptional programs resulted in higher levels of unsaturated fatty acids and the formation of nuclear lipid droplets. Interestingly, cells lacking Sir proteins displayed resistance to unsaturated-fatty acids and edelfosine, and this phenotype was connected to Rap1.
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Affiliation(s)
| | | | - Sarah Moradi-Fard
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Calgary, Canada
| | - Jennifer A. Cobb
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Calgary, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary, Calgary, Canada
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10
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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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11
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Amm I, Weberruss M, Hellwig A, Schwarz J, Tatarek-Nossol M, Lüchtenborg C, Kallas M, Brügger B, Hurt E, Antonin W. Distinct domains in Ndc1 mediate its interaction with the Nup84 complex and the nuclear membrane. J Cell Biol 2023; 222:e202210059. [PMID: 37154843 PMCID: PMC10165475 DOI: 10.1083/jcb.202210059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/31/2023] [Accepted: 03/17/2023] [Indexed: 05/10/2023] Open
Abstract
Nuclear pore complexes (NPCs) are embedded in the nuclear envelope and built from ∼30 different nucleoporins (Nups) in multiple copies, few are integral membrane proteins. One of these transmembrane nucleoporins, Ndc1, is thought to function in NPC assembly at the fused inner and outer nuclear membranes. Here, we show a direct interaction of Ndc1's transmembrane domain with Nup120 and Nup133, members of the pore membrane coating Y-complex. We identify an amphipathic helix in Ndc1's C-terminal domain binding highly curved liposomes. Upon overexpression, this amphipathic motif is toxic and dramatically alters the intracellular membrane organization in yeast. Ndc1's amphipathic motif functionally interacts with related motifs in the C-terminus of the nucleoporins Nup53 and Nup59, important for pore membrane binding and interconnecting NPC modules. The essential function of Ndc1 can be suppressed by deleting the amphipathic helix from Nup53. Our data indicate that nuclear membrane and presumably NPC biogenesis depends on a balanced ratio between amphipathic motifs in diverse nucleoporins.
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Affiliation(s)
- Ingo Amm
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Marion Weberruss
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Andrea Hellwig
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), University of Heidelberg, Heidelberg, Germany
| | - Johannes Schwarz
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Christian Lüchtenborg
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Martina Kallas
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
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12
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Hammer SE, Polymenis M. One-carbon metabolic enzymes are regulated during cell division and make distinct contributions to the metabolome and cell cycle progression in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2023; 13:6983127. [PMID: 36627750 PMCID: PMC9997564 DOI: 10.1093/g3journal/jkad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
Enzymes of one-carbon (1C) metabolism play pivotal roles in proliferating cells. They are involved in the metabolism of amino acids, nucleotides, and lipids and the supply of all cellular methylations. However, there is limited information about how these enzymes are regulated during cell division and how cell cycle kinetics are affected in several loss-of-function mutants of 1C metabolism. Here, we report that the levels of the S. cerevisiae enzymes Ade17p and Cho2p, involved in the de novo synthesis of purines and phosphatidylcholine (PC), respectively, are cell cycle-regulated. Cells lacking Ade17p, Cho2p, or Shm2p (an enzyme that supplies 1C units from serine) have distinct alterations in size homeostasis and cell cycle kinetics. Loss of Ade17p leads to a specific delay at START, when cells commit to a new round of cell division, while loss of Shm2p has broader effects, reducing growth rate. Furthermore, the inability to synthesize PC de novo in cho2Δ cells delays START and reduces the coherence of nuclear elongation late in the cell cycle. Loss of Cho2p also leads to profound metabolite changes. Besides the expected changes in the lipidome, cho2Δ cells have reduced levels of amino acids, resembling cells shifted to poorer media. These results reveal the different ways that 1C metabolism allocates resources to affect cell proliferation at multiple cell cycle transitions.
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Affiliation(s)
- Staci E Hammer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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13
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Tuning between Nuclear Organization and Functionality in Health and Disease. Cells 2023; 12:cells12050706. [PMID: 36899842 PMCID: PMC10000962 DOI: 10.3390/cells12050706] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/08/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
The organization of eukaryotic genome in the nucleus, a double-membraned organelle separated from the cytoplasm, is highly complex and dynamic. The functional architecture of the nucleus is confined by the layers of internal and cytoplasmic elements, including chromatin organization, nuclear envelope associated proteome and transport, nuclear-cytoskeletal contacts, and the mechano-regulatory signaling cascades. The size and morphology of the nucleus could impose a significant impact on nuclear mechanics, chromatin organization, gene expression, cell functionality and disease development. The maintenance of nuclear organization during genetic or physical perturbation is crucial for the viability and lifespan of the cell. Abnormal nuclear envelope morphologies, such as invagination and blebbing, have functional implications in several human disorders, including cancer, accelerated aging, thyroid disorders, and different types of neuro-muscular diseases. Despite the evident interplay between nuclear structure and nuclear function, our knowledge about the underlying molecular mechanisms for regulation of nuclear morphology and cell functionality during health and illness is rather poor. This review highlights the essential nuclear, cellular, and extracellular components that govern the organization of nuclei and functional consequences associated with nuclear morphometric aberrations. Finally, we discuss the recent developments with diagnostic and therapeutic implications targeting nuclear morphology in health and disease.
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14
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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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15
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Lara-Barba E, Torán-Vilarrubias A, Moriel-Carretero M. An Expansion of the Endoplasmic Reticulum that Halts Autophagy is Permissive to Genome Instability. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231157706. [PMID: 37366415 PMCID: PMC10243512 DOI: 10.1177/25152564231157706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 06/28/2023]
Abstract
The links between autophagy and genome stability, and whether they are important for lifespan and health, are not fully understood. We undertook a study to explore this notion at the molecular level using Saccharomyces cerevisiae. On the one hand, we triggered autophagy using rapamycin, to which we exposed mutants defective in preserving genome integrity, then assessed their viability, their ability to induce autophagy and the link between these two parameters. On the other hand, we searched for molecules derived from plant extracts known to have powerful benefits on human health to try to rescue the negative effects rapamycin had against some of these mutants. We uncover that autophagy execution is lethal for mutants unable to repair DNA double strand breaks, while the extract from Silybum marianum seeds induces an expansion of the endoplasmic reticulum (ER) that blocks autophagy and protects them. Our data uncover a connection between genome integrity and homeostasis of the ER whereby ER stress-like scenarios render cells tolerant to sub-optimal genome integrity conditions.
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Affiliation(s)
- Eliana Lara-Barba
- Institut de Génétique Humaine (IGH), Université de Montpellier-Centre National de la Recherche Scientifique,
Montpellier, France
| | - Alba Torán-Vilarrubias
- Institut de Génétique Humaine (IGH), Université de Montpellier-Centre National de la Recherche Scientifique,
Montpellier, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de
Montpellier (CRBM), Université de Montpellier-Centre National de la Recherche Scientifique,
Montpellier, France
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16
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Matos-Perdomo E, Santana-Sosa S, Ayra-Plasencia J, Medina-Suárez S, Machín F. The vacuole shapes the nucleus and the ribosomal DNA loop during mitotic delays. Life Sci Alliance 2022; 5:5/10/e202101161. [PMID: 35961781 PMCID: PMC9375157 DOI: 10.26508/lsa.202101161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022] Open
Abstract
Chromosome structuring and condensation is one of the main features of mitosis. Here, Matos-Perdomo et al show how the nuclear envelope reshapes around the vacuole to give rise to the outstanding ribosomal DNA loop in budding yeast. The ribosomal DNA (rDNA) array of Saccharomyces cerevisiae has served as a model to address chromosome organization. In cells arrested before anaphase (mid-M), the rDNA acquires a highly structured chromosomal organization referred to as the rDNA loop, whose length can double the cell diameter. Previous works established that complexes such as condensin and cohesin are essential to attain this structure. Here, we report that the rDNA loop adopts distinct presentations that arise as spatial adaptations to changes in the nuclear morphology triggered during mid-M arrests. Interestingly, the formation of the rDNA loop results in the appearance of a space under the loop (SUL) which is devoid of nuclear components yet colocalizes with the vacuole. We show that the rDNA-associated nuclear envelope (NE) often reshapes into a ladle to accommodate the vacuole in the SUL, with the nucleus becoming bilobed and doughnut-shaped. Finally, we demonstrate that the formation of the rDNA loop and the SUL require TORC1, membrane synthesis and functional vacuoles, yet is independent of nucleus–vacuole junctions and rDNA-NE tethering.
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Affiliation(s)
- Emiliano Matos-Perdomo
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Silvia Santana-Sosa
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jessel Ayra-Plasencia
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Sara Medina-Suárez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain .,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Santa María de Guía, Spain
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17
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Garcia M, Kumanski S, Elías-Villalobos A, Cazevieille C, Soulet C, Moriel-Carretero M. Nuclear ingression of cytoplasmic bodies accompanies a boost in autophagy. Life Sci Alliance 2022; 5:5/9/e202101160. [PMID: 35568434 PMCID: PMC9107791 DOI: 10.26508/lsa.202101160] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 05/02/2022] [Accepted: 05/02/2022] [Indexed: 12/28/2022] Open
Abstract
We describe a fully new remodeling event of the nuclear envelope surrounding the nucleolus: it partitions into its regular contact with the vacuole and a dramatic internalization of globular cytoplasmic portions within the nucleus. Membrane contact sites are functional nodes at which organelles reorganize metabolic pathways and adapt to changing cues. In Saccharomyces cerevisiae, the nuclear envelope subdomain surrounding the nucleolus, very plastic and prone to expansion, can establish contacts with the vacuole and be remodeled in response to various metabolic stresses. While using genotoxins with unrelated purposes, we serendipitously discovered a fully new remodeling event at this nuclear subdomain: the nuclear envelope partitions into its regular contact with the vacuole and a dramatic internalization within the nucleus. This leads to the nuclear engulfment of a globular, cytoplasmic portion. In spite of how we discovered it, the phenomenon is likely DNA damage-independent. We define lipids supporting negative curvature, such as phosphatidic acid and sterols, as bona fide drivers of this event. Mechanistically, we suggest that the engulfment of the cytoplasm triggers a suction phenomenon that enhances the docking of proton pump-containing vesicles with the vacuolar membrane, which we show matches a boost in autophagy. Thus, our findings unveil an unprecedented remodeling of the nucleolus-surrounding membranes with impact on metabolic adaptation.
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Affiliation(s)
- Manon Garcia
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - Sylvain Kumanski
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - Alberto Elías-Villalobos
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Sevilla, Spain.,Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - Chantal Cazevieille
- Institut de Neurosciences de Montpellier (INM), Université de Montpellier, INSERM, Montpellier, France
| | - Caroline Soulet
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
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18
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Phenomics approaches to understand genetic networks and gene function in yeast. Biochem Soc Trans 2022; 50:713-721. [PMID: 35285506 PMCID: PMC9162466 DOI: 10.1042/bst20210285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 01/03/2023]
Abstract
Over the past decade, major efforts have been made to systematically survey the characteristics or phenotypes associated with genetic variation in a variety of model systems. These so-called phenomics projects involve the measurement of 'phenomes', or the set of phenotypic information that describes an organism or cell, in various genetic contexts or states, and in response to external factors, such as environmental signals. Our understanding of the phenome of an organism depends on the availability of reagents that enable systematic evaluation of the spectrum of possible phenotypic variation and the types of measurements that can be taken. Here, we highlight phenomics studies that use the budding yeast, a pioneer model organism for functional genomics research. We focus on genetic perturbation screens designed to explore genetic interactions, using a variety of phenotypic read-outs, from cell growth to subcellular morphology.
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19
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Maitra N, Hammer S, Kjerfve C, Bankaitis VA, Polymenis M. Translational control of lipogenesis links protein synthesis and phosphoinositide signaling with nuclear division in Saccharomyces cerevisiae. Genetics 2022; 220:iyab171. [PMID: 34849864 PMCID: PMC8733439 DOI: 10.1093/genetics/iyab171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Continuously dividing cells coordinate their growth and division. How fast cells grow in mass determines how fast they will multiply. Yet, there are few, if any, examples of a metabolic pathway that actively drives a cell cycle event instead of just being required for it. Here, we show that translational upregulation of lipogenic enzymes in Saccharomyces cerevisiae increased the abundance of lipids and promoted nuclear elongation and division. Derepressing translation of acetyl-CoA carboxylase and fatty acid synthase also suppressed cell cycle-related phenotypes, including delayed nuclear division, associated with Sec14p phosphatidylinositol transfer protein deficiencies, and the irregular nuclear morphologies of mutants defective in phosphatidylinositol 4-OH kinase activities. Our results show that increased lipogenesis drives a critical cell cycle landmark and report a phosphoinositide signaling axis in control of nuclear division. The broad conservation of these lipid metabolic and signaling pathways raises the possibility these activities similarly govern nuclear division in other eukaryotes.
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Affiliation(s)
- Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Staci Hammer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Clara Kjerfve
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Vytas A Bankaitis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular & Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX 77843, USA
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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20
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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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21
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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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22
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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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23
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Torán-Vilarrubias A, Moriel-Carretero M. Oxidative agents elicit endoplasmic reticulum morphological changes suggestive of alterations in lipid metabolism. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 34557658 PMCID: PMC8453305 DOI: 10.17912/micropub.biology.000462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/03/2021] [Accepted: 09/10/2021] [Indexed: 11/06/2022]
Abstract
The endoplasmic reticulum (ER) is a central organelle in charge of correct protein folding; lipids synthesis, modification, and sorting; as well as of maintenance of calcium homeostasis. To accomplish these functions, the ER lumen possesses an oxidative potential. Challenging cells with reductive agents therefore provokes an ER stress that immediately affects protein folding, and which morphologically manifests by an expansion of the cytoplasmic ER network. Yet less is known about the impact on the ER of exposing cells to oxidative agents, which risk to exacerbate the basal, physiologically oxidative environment. We have monitored the morphology of the ER of Saccharomyces cerevisiae in response to this type of treatment. We bring the notion that oxidative agents give rise to diverse alterations in the perinuclear ER subdomain that are suggestive of lipid metabolism perturbations.
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Affiliation(s)
- Alba Torán-Vilarrubias
- Institut de Génétique Humaine (IGH), Université de Montpellier, Centre National de la Recherche Scientifique, 34396 Montpellier CEDEX 05, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France
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24
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Wang R, Huang A, Wang Y, Mei P, Zhu H, Chen Q, Xu S. High-Resolution Microscopy to Learn the Nuclear Organization of the Living Yeast Cells. Stem Cells Int 2021; 2021:9951114. [PMID: 34497652 PMCID: PMC8421178 DOI: 10.1155/2021/9951114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/07/2021] [Indexed: 11/18/2022] Open
Abstract
The spatial organization of the nucleus is a key determinant in all genome activities. However, the accurate measurement of the nuclear organization is still technically challenging. Here, the technology NucQuant we created previously was utilized to detect the variation of the nuclear organization, including the heterogeneity of the nuclear geometry, the change of the NPC distribution along different cell cycle stages during interphase, and the organization of the nucleolus. The results confirmed that not only the growth rate and the NPC distribution are influenced by the carbon source; the nuclear shape is also impacted by the carbon source. The nuclei lost their spherical geometry gradually when the cell was cultured from the most to a less favorable carbon source. We also discovered that the nucleolus prefers to locate at the nuclear periphery, which was called the "genes poor region," especially when the cells entered quiescence. Furthermore, the distribution of the NPC along the different stages during the interphase was analyzed. We proposed that with the growth of the cell, the nucleus would grow from the surface of the NE flanking the nucleolus firstly.
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Affiliation(s)
- Renjie Wang
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - Aiwen Huang
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - Yan Wang
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - Pengxin Mei
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - He Zhu
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - Qianqian Chen
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - Sankui Xu
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
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25
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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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26
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Kumar K, Gibbs HC, Yeh AT, Griffing LR. The Sterol Trafficking Pathway in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:616631. [PMID: 34122463 PMCID: PMC8187924 DOI: 10.3389/fpls.2021.616631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
In plants, the trafficking mechanisms by which sterols move through the plant and into target cells are unknown. Earlier studies identified endosomes as primary candidates for internalization of sterols in plants, but these results have come into question. Here, we show that in elongating root cells, the internalization of sterol occurs primarily by a non-endocytic mechanism. Added fluorescent sterols [dehydroergosterol (DHE) and BODIPY-cholesterol (BCh)] do not initially label endosomes identified by fluorescent protein markers or by internalized FM4-64. Instead, the nuclear envelope, an organelle not associated with the endocytic pathway but part of the endoplasmic reticulum (ER), becomes labeled. This result is supported by experiments with the inducible overexpression of auxilin-2-like protein (AUX2 line), which blocks most endocytosis upon induction. Internalization and nuclear envelope labeling still occur in induced AUX2 cells. Longer-term incubation labels the oil body, a site involved in sterol storage. Although the first site of localization, the nuclear envelope, is part of the ER, other domains of the ER do not accumulate the label. The trafficking pathway differs from vesicular endocytosis and points toward a different pathway of sterol transport possibly involving other mechanisms, such as ER-plasma membrane contact sites and cytoplasmic transport.
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Affiliation(s)
- Krishna Kumar
- Molecular and Environmental Plant Sciences Interdisciplinary Program, Texas A&M University, College Station, TX, United States
| | - Holly C. Gibbs
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
- Microscopy and Imaging Center, Texas A&M University, College Station, TX, United States
| | - Alvin T. Yeh
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Lawrence R. Griffing
- Molecular and Environmental Plant Sciences Interdisciplinary Program, Texas A&M University, College Station, TX, United States
- Department of Biology, Texas A&M University, College Station, TX, United States
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27
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Deolal P, Male G, Mishra K. The challenge of staying in shape: nuclear size matters. Curr Genet 2021; 67:605-612. [PMID: 33779777 DOI: 10.1007/s00294-021-01176-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
Cellular organelles have unique morphology and the organelle size to cell size ratio is regulated. Nucleus is one of the most prominent, usually round in shape, organelle of a eukaryotic cell that occupies 8-10% of cellular volume. The shape and size of nucleus is known to undergo remodeling during processes such as cell growth, division and certain stresses. Regulation of protein and lipid distribution at the nuclear envelope is crucial for preserving the nuclear morphology and size. As size and morphology are interlinked, altering one influences the other. In this perspective, we discuss the relationship between size and shape regulation of the nucleus.
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Affiliation(s)
- Pallavi Deolal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Gurranna Male
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
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28
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Male G, Deolal P, Manda NK, Yagnik S, Mazumder A, Mishra K. Nucleolar size regulates nuclear envelope shape in Saccharomyces cerevisiae. J Cell Sci 2020; 133:jcs242172. [PMID: 32973112 DOI: 10.1242/jcs.242172] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Nuclear shape and size are cell-type specific. Change in nuclear shape is seen during cell division, development and pathology. The nucleus of Saccharomycescerevisiae is spherical in interphase and becomes dumbbell shaped during mitotic division to facilitate the transfer of one nucleus to the daughter cell. Because yeast cells undergo closed mitosis, the nuclear envelope remains intact throughout the cell cycle. The pathways that regulate nuclear shape are not well characterized. The nucleus is organized into various subcompartments, with the nucleolus being the most prominent. We have conducted a candidate-based genetic screen for nuclear shape abnormalities in S. cerevisiae to ask whether the nucleolus influences nuclear shape. We find that increasing nucleolar volume triggers a non-isometric nuclear envelope expansion resulting in an abnormal nuclear envelope shape. We further show that the tethering of rDNA to the nuclear envelope is required for the appearance of these extensions.
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Affiliation(s)
- Gurranna Male
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Pallavi Deolal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Naresh Kumar Manda
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Shantam Yagnik
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serilingampally Manda 500046l, Hyderabad, Telangana, India
| | - Aprotim Mazumder
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serilingampally Manda 500046l, Hyderabad, Telangana, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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29
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Sosa Ponce ML, Moradi-Fard S, Zaremberg V, Cobb JA. SUNny Ways: The Role of the SUN-Domain Protein Mps3 Bridging Yeast Nuclear Organization and Lipid Homeostasis. Front Genet 2020; 11:136. [PMID: 32184804 PMCID: PMC7058695 DOI: 10.3389/fgene.2020.00136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Mps3 is a SUN (Sad1-UNC-84) domain-containing protein that is located in the inner nuclear membrane (INM). Genetic screens with multiple Mps3 mutants have suggested that distinct regions of Mps3 function in relative isolation and underscore the broad involvement of Mps3 in multiple pathways including mitotic spindle formation, telomere maintenance, and lipid metabolism. These pathways have largely been characterized in isolation, without a holistic consideration for how key regulatory events within one pathway might impinge on other aspects of biology at the nuclear membrane. Mps3 is uniquely positioned to function in these multiple pathways as its N- terminus is in the nucleoplasm, where it is important for telomere anchoring at the nuclear periphery, and its C-terminus is in the lumen, where it has links with lipid metabolic processes. Emerging work suggests that the role of Mps3 in nuclear organization and lipid homeostasis are not independent, but more connected. For example, a failure in regulating Mps3 levels through the cell cycle leads to nuclear morphological abnormalities and loss of viability, suggesting a link between the N-terminal domain of Mps3 and nuclear envelope homeostasis. We will highlight work suggesting that Mps3 is pivotal factor in communicating events between the nucleus and the lipid bilayer.
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Affiliation(s)
- Maria Laura Sosa Ponce
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, Calgary, AB, Canada.,Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Sarah Moradi-Fard
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, Calgary, AB, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jennifer A Cobb
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, Calgary, AB, Canada
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30
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King GA, Ünal E. The dynamic nuclear periphery as a facilitator of gamete health and rejuvenation. Curr Genet 2020; 66:487-493. [PMID: 31915924 DOI: 10.1007/s00294-019-01050-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 12/26/2022]
Abstract
The nuclear periphery is a hotspot for the accumulation of age-induced damage in eukaryotic cells. The types of damage that occur at the periphery and their phenotypic consequences have begun to be characterized; however, the mechanisms by which cells repair or eliminate nuclear damage remain poorly understood. Using budding yeast meiosis as a natural system to study cellular rejuvenation, we recently discovered a novel nuclear quality control event, in which age-induced damage is sequestered away from dividing chromosomes to a discarded nuclear compartment that we term the GUNC (for "Gametogenesis Uninherited Nuclear Compartment"). Interestingly, extensive nuclear remodeling occurs even in young cells, including a surprising modularity of the nuclear pore complex, suggesting a general contribution to gamete fitness. In this review, we discuss these findings in the context of recent evidence that the nuclear periphery is a highly dynamic region critical for cellular health.
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Affiliation(s)
- Grant A King
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, 94720, USA.
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31
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Hayashi S, Mori S, Suzuki T, Suzuki T, Yoshihisa T. Impact of intron removal from tRNA genes on Saccharomyces cerevisiae. Nucleic Acids Res 2019; 47:5936-5949. [PMID: 30997502 PMCID: PMC6582322 DOI: 10.1093/nar/gkz270] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/28/2019] [Accepted: 04/04/2019] [Indexed: 12/31/2022] Open
Abstract
In eukaryotes and archaea, tRNA genes frequently contain introns, which are removed during maturation. However, biological roles of tRNA introns remain elusive. Here, we constructed a complete set of Saccharomyces cerevisiae strains in which the introns were removed from all the synonymous genes encoding 10 different tRNA species. All the intronless strains were viable, but the tRNAPheGAA and tRNATyrGUA intronless strains displayed slow growth, cold sensitivity and defective growth under respiratory conditions, indicating physiological importance of certain tRNA introns. Northern analyses revealed that removal of the introns from genes encoding three tRNAs reduced the amounts of the corresponding mature tRNAs, while it did not affect aminoacylation. Unexpectedly, the tRNALeuCAA intronless strain showed reduced 5.8S rRNA levels and abnormal nucleolar morphology. Because pseudouridine (Ψ) occurs at position 34 of the tRNAIleUAU anticodon in an intron-dependent manner, tRNAIleUAU in the intronless strain lost Ψ34. However, in a portion of tRNAIleUAU population, position 34 was converted into 5-carbamoylmethyluridine (ncm5U), which could reduce decoding fidelity. In summary, our results demonstrate that, while introns are dispensable for cell viability, some introns have diverse roles, such as ensuring proper growth under various conditions and controlling the appropriate anticodon modifications for accurate pairing with the codon.
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Affiliation(s)
- Sachiko Hayashi
- Graduate School of Life Science, University of Hyogo, Ako-gun 678-1297, Japan
| | - Shunsuke Mori
- Graduate School of Materials Science, Nagoya University, Nagoya 464-8602, Japan
| | - Takeo Suzuki
- Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Tohru Yoshihisa
- Graduate School of Life Science, University of Hyogo, Ako-gun 678-1297, Japan
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32
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Crane MM, Russell AE, Schafer BJ, Blue BW, Whalen R, Almazan J, Hong MG, Nguyen B, Goings JE, Chen KL, Kelly R, Kaeberlein M. DNA damage checkpoint activation impairs chromatin homeostasis and promotes mitotic catastrophe during aging. eLife 2019; 8:e50778. [PMID: 31714209 PMCID: PMC6850777 DOI: 10.7554/elife.50778] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/30/2019] [Indexed: 02/01/2023] Open
Abstract
Genome instability is a hallmark of aging and contributes to age-related disorders such as cancer and Alzheimer's disease. The accumulation of DNA damage during aging has been linked to altered cell cycle dynamics and the failure of cell cycle checkpoints. Here, we use single cell imaging to study the consequences of increased genomic instability during aging in budding yeast and identify striking age-associated genome missegregation events. This breakdown in mitotic fidelity results from the age-related activation of the DNA damage checkpoint and the resulting degradation of histone proteins. Disrupting the ability of cells to degrade histones in response to DNA damage increases replicative lifespan and reduces genomic missegregations. We present several lines of evidence supporting a model of antagonistic pleiotropy in the DNA damage response where histone degradation, and limited histone transcription are beneficial to respond rapidly to damage but reduce lifespan and genomic stability in the long term.
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Affiliation(s)
- Matthew M Crane
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Adam E Russell
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Brent J Schafer
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Ben W Blue
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Riley Whalen
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Jared Almazan
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Mung Gi Hong
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Bao Nguyen
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Joslyn E Goings
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Kenneth L Chen
- Department of PathologyUniversity of WashingtonSeattleUnited States
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
- Medical Scientist Training ProgramUniversity of WashingtonSeattleUnited States
| | - Ryan Kelly
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Matt Kaeberlein
- Department of PathologyUniversity of WashingtonSeattleUnited States
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33
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Sleiman S, Dragon F. Recent Advances on the Structure and Function of RNA Acetyltransferase Kre33/NAT10. Cells 2019; 8:cells8091035. [PMID: 31491951 PMCID: PMC6770127 DOI: 10.3390/cells8091035] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/23/2019] [Accepted: 08/25/2019] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis is one of the most energy demanding processes in the cell. In eukaryotes, the main steps of this process occur in the nucleolus and include pre-ribosomal RNA (pre-rRNA) processing, post-transcriptional modifications, and assembly of many non-ribosomal factors and ribosomal proteins in order to form mature and functional ribosomes. In yeast and humans, the nucleolar RNA acetyltransferase Kre33/NAT10 participates in different maturation events, such as acetylation and processing of 18S rRNA, and assembly of the 40S ribosomal subunit. Here, we review the structural and functional features of Kre33/NAT10 RNA acetyltransferase, and we underscore the importance of this enzyme in ribosome biogenesis, as well as in acetylation of non-ribosomal targets. We also report on the role of human NAT10 in Hutchinson-Gilford progeria syndrome.
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Affiliation(s)
- Sophie Sleiman
- Département des Sciences Biologiques and Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada.
| | - Francois Dragon
- Département des Sciences Biologiques and Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada.
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34
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Barbosa AD, Lim K, Mari M, Edgar JR, Gal L, Sterk P, Jenkins BJ, Koulman A, Savage DB, Schuldiner M, Reggiori F, Wigge PA, Siniossoglou S. Compartmentalized Synthesis of Triacylglycerol at the Inner Nuclear Membrane Regulates Nuclear Organization. Dev Cell 2019; 50:755-766.e6. [PMID: 31422915 PMCID: PMC6859503 DOI: 10.1016/j.devcel.2019.07.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 04/22/2019] [Accepted: 07/03/2019] [Indexed: 01/08/2023]
Abstract
Cells dynamically adjust organelle organization in response to growth and environmental cues. This requires regulation of synthesis of phospholipids, the building blocks of organelle membranes, or remodeling of their fatty-acyl (FA) composition. FAs are also the main components of triacyglycerols (TGs), which enable energy storage in lipid droplets. How cells coordinate FA metabolism with organelle biogenesis during cell growth remains unclear. Here, we show that Lro1, an acyltransferase that generates TGs from phospholipid-derived FAs in yeast, relocates from the endoplasmic reticulum to a subdomain of the inner nuclear membrane. Lro1 nuclear targeting is regulated by cell cycle and nutrient starvation signals and is inhibited when the nucleus expands. Lro1 is active at this nuclear subdomain, and its compartmentalization is critical for nuclear integrity. These data suggest that Lro1 nuclear targeting provides a site of TG synthesis, which is coupled with nuclear membrane remodeling. Nutrients regulate the phospholipid:diacylglycerol acyltransferase Lro1 Lro1 targets the INM subdomain bordering the nucleolus Lro1 is active at the INM and can sustain cell survival during starvation Compartmentalized synthesis of nuclear TG is important for nuclear envelope integrity
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Affiliation(s)
- Antonio D Barbosa
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Koini Lim
- Metabolic Research Laboratories, Wellcome Trust-Medical Research, Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Muriel Mari
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, 9713AV Groningen, Netherlands
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Lihi Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Peter Sterk
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Benjamin J Jenkins
- NIHR BRC Core Metabolomics and Lipidomics Laboratory and University of Cambridge Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Albert Koulman
- NIHR BRC Core Metabolomics and Lipidomics Laboratory and University of Cambridge Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - David B Savage
- Metabolic Research Laboratories, Wellcome Trust-Medical Research, Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, 9713AV Groningen, Netherlands
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Symeon Siniossoglou
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
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35
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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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36
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Walters AD, Amoateng K, Wang R, Chen JH, McDermott G, Larabell CA, Gadal O, Cohen-Fix O. Nuclear envelope expansion in budding yeast is independent of cell growth and does not determine nuclear volume. Mol Biol Cell 2018; 30:131-145. [PMID: 30379612 PMCID: PMC6337908 DOI: 10.1091/mbc.e18-04-0204] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Most cells exhibit a constant ratio between nuclear and cell volume. The mechanism dictating this constant ratio and the nuclear component(s) that scale with cell size are not known. To address this, we examined the consequences to the size and shape of the budding yeast nucleus when cell expansion is inhibited by down-regulating components of the secretory pathway. We find that under conditions where cell size increase is restrained, the nucleus becomes bilobed, with the bulk of the DNA in one lobe and the nucleolus in the other. The formation of bilobed nuclei is dependent on fatty acid and phospholipid synthesis, suggesting that it is associated with nuclear membrane expansion. Bilobed nuclei appeared predominantly after spindle pole body separation, suggesting that nuclear envelope expansion follows cell-cycle cues rather than cell size. Importantly, cells with bilobed nuclei had the same nuclear:cell volume ratio as cells with round nuclei. Therefore, the bilobed nucleus could be a consequence of continued NE expansion as cells traverse the cell cycle without an accompanying increase in nuclear volume due to the inhibition of cell growth. Our data suggest that nuclear volume is not determined by nuclear envelope availability but by one or more nucleoplasmic factors.
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Affiliation(s)
- Alison D Walters
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Kwabena Amoateng
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Renjie Wang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Jian-Hua Chen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Gerry McDermott
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Carolyn A Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Orna Cohen-Fix
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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37
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Deregulation of the G1/S-phase transition is the proximal cause of mortality in old yeast mother cells. Genes Dev 2018; 32:1075-1084. [PMID: 30042134 PMCID: PMC6075151 DOI: 10.1101/gad.312140.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/14/2018] [Indexed: 01/02/2023]
Abstract
In this study, Neurohr et al. investigated why old yeast cells stop dividing and die. They show that age-induced accumulation of the G1/S-phase inhibitor Whi5 and defects in G1/S cyclin transcription cause cell cycle delays and genomic instability that result in cell death, thus identifying deregulation of the G1/S-phase transition as the proximal cause of age-induced proliferation decline and cell death in budding yeast. Budding yeast cells produce a finite number of daughter cells before they die. Why old yeast cells stop dividing and die is unclear. We found that age-induced accumulation of the G1/S-phase inhibitor Whi5 and defects in G1/S cyclin transcription cause cell cycle delays and genomic instability that result in cell death. We further identified extrachromosomal rDNA (ribosomal DNA) circles (ERCs) to cause the G1/S cyclin expression defect in old cells. Spontaneous segregation of Whi5 and ERCs into daughter cells rejuvenates old mothers, but daughters that inherit these aging factors die rapidly. Our results identify deregulation of the G1/S-phase transition as the proximal cause of age-induced proliferation decline and cell death in budding yeast.
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38
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Sing TL, Hung MP, Ohnuki S, Suzuki G, San Luis BJ, McClain M, Unruh JR, Yu Z, Ou J, Marshall-Sheppard J, Huh WK, Costanzo M, Boone C, Ohya Y, Jaspersen SL, Brown GW. The budding yeast RSC complex maintains ploidy by promoting spindle pole body insertion. J Cell Biol 2018; 217:2445-2462. [PMID: 29875260 PMCID: PMC6028538 DOI: 10.1083/jcb.201709009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 02/13/2018] [Accepted: 05/09/2018] [Indexed: 01/31/2023] Open
Abstract
Sing et al. characterize an unanticipated role for the Saccharomyces cerevisiae RSC complex in ploidy maintenance. They show that RSC promotes the distribution of Nbp1 and Ndc1 to the spindle pole body (SPB) to facilitate SPB maturation and accurate chromosome segregation. Ploidy is tightly regulated in eukaryotic cells and is critical for cell function and survival. Cells coordinate multiple pathways to ensure replicated DNA is segregated accurately to prevent abnormal changes in chromosome number. In this study, we characterize an unanticipated role for the Saccharomyces cerevisiae “remodels the structure of chromatin” (RSC) complex in ploidy maintenance. We show that deletion of any of six nonessential RSC genes causes a rapid transition from haploid to diploid DNA content because of nondisjunction events. Diploidization is accompanied by diagnostic changes in cell morphology and is stably maintained without further ploidy increases. We find that RSC promotes chromosome segregation by facilitating spindle pole body (SPB) duplication. More specifically, RSC plays a role in distributing two SPB insertion factors, Nbp1 and Ndc1, to the new SPB. Thus, we provide insight into a role for a SWI/SNF family complex in SPB duplication and ploidy maintenance.
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Affiliation(s)
- Tina L Sing
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Minnie P Hung
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Godai Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Bryan-Joseph San Luis
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO
| | - Jiongwen Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jesse Marshall-Sheppard
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Won-Ki Huh
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO.,Department of Molecular and Integrative Physiology, University of Kansas Medical Centre, Kansas City, KS
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
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39
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Matos-Perdomo E, Machín F. The ribosomal DNA metaphase loop of Saccharomyces cerevisiae gets condensed upon heat stress in a Cdc14-independent TORC1-dependent manner. Cell Cycle 2018; 17:200-215. [PMID: 29166821 PMCID: PMC5884360 DOI: 10.1080/15384101.2017.1407890] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Chromosome morphology in Saccharomyces cerevisiae is only visible at the microscopic level in the ribosomal DNA array (rDNA). The rDNA has been thus used as a model to characterize condensation and segregation of sister chromatids in mitosis. It has been established that the metaphase structure ("loop") depends, among others, on the condensin complex; whereas its segregation also depends on that complex, the Polo-like kinase Cdc5 and the cell cycle master phosphatase Cdc14. In addition, Cdc14 also drives rDNA hypercondensation in telophase. Remarkably, since all these components are essential for cell survival, their role on rDNA condensation and segregation was established by temperature-sensitive (ts) alleles. Here, we show that the heat stress (HS) used to inactivate ts alleles (25 ºC to 37 ºC shift) causes rDNA loop condensation in metaphase-arrested wild type cells, a result that can also be mimicked by other stresses that inhibit the TORC1 pathway. Because this condensation might challenge previous findings with ts alleles, we have repeated classical experiments of rDNA condensation and segregation, yet using instead auxin-driven degradation alleles (aid alleles). We have undertaken the protein degradation at lower temperatures (25 ºC) and concluded that the classical roles for condensin, Cdc5, Cdc14 and Cdc15 still prevailed. Thus, condensin degradation disrupts rDNA higher organization, Cdc14 and Cdc5 degradation precludes rDNA segregation and Cdc15 degradation still allows rDNA hypercompaction in telophase. Finally, we provide direct genetic evidence that this HS-mediated rDNA condensation is dependent on TORC1 but, unlike the one observed in anaphase, is independent of Cdc14.
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Affiliation(s)
- Emiliano Matos-Perdomo
- a Unidad de Investigación , Hospital Universitario Ntra Sra de Candelaria , Ctra del Rosario 145, 38010 , Santa Cruz de Tenerife , Spain.,b Universidad de La Laguna , Tenerife , Spain
| | - Félix Machín
- a Unidad de Investigación , Hospital Universitario Ntra Sra de Candelaria , Ctra del Rosario 145, 38010 , Santa Cruz de Tenerife , Spain
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40
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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: 148] [Impact Index Per Article: 21.1] [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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41
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Blank HM, Perez R, He C, Maitra N, Metz R, Hill J, Lin Y, Johnson CD, Bankaitis VA, Kennedy BK, Aramayo R, Polymenis M. Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. EMBO J 2017; 36:487-502. [PMID: 28057705 PMCID: PMC5694946 DOI: 10.15252/embj.201695050] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 11/09/2016] [Accepted: 11/18/2016] [Indexed: 02/04/2023] Open
Abstract
Translational control during cell division determines when cells start a new cell cycle, how fast they complete it, the number of successive divisions, and how cells coordinate proliferation with available nutrients. The translational efficiencies of mRNAs in cells progressing synchronously through the mitotic cell cycle, while preserving the coupling of cell division with cell growth, remain uninvestigated. We now report comprehensive ribosome profiling of a yeast cell size series from the time of cell birth, to identify mRNAs under periodic translational control. The data reveal coordinate translational activation of mRNAs encoding lipogenic enzymes late in the cell cycle including Acc1p, the rate-limiting enzyme acetyl-CoA carboxylase. An upstream open reading frame (uORF) confers the translational control of ACC1 and adjusts Acc1p protein levels in different nutrients. The ACC1 uORF is relevant for cell division because its ablation delays cell cycle progression, reduces cell size, and suppresses the replicative longevity of cells lacking the Sch9p protein kinase regulator of ribosome biogenesis. These findings establish an unexpected relationship between lipogenesis and protein synthesis in mitotic cell divisions.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Ricardo Perez
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Chong He
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Richard Metz
- Genomics and Bioinformatics Services, Texas A&M Agrilife Research, College Station, TX, USA
| | - Joshua Hill
- Genomics and Bioinformatics Services, Texas A&M Agrilife Research, College Station, TX, USA
| | - Yuhong Lin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Charles D Johnson
- Genomics and Bioinformatics Services, Texas A&M Agrilife Research, College Station, TX, USA
| | - Vytas A Bankaitis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Department of Molecular & Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, USA
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | | | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
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42
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Smoyer CJ, Katta SS, Gardner JM, Stoltz L, McCroskey S, Bradford WD, McClain M, Smith SE, Slaughter BD, Unruh JR, Jaspersen SL. Analysis of membrane proteins localizing to the inner nuclear envelope in living cells. J Cell Biol 2016; 215:575-590. [PMID: 27831485 PMCID: PMC5119940 DOI: 10.1083/jcb.201607043] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/03/2016] [Accepted: 10/18/2016] [Indexed: 12/31/2022] Open
Abstract
Understanding the protein composition of the inner nuclear membrane (INM) is fundamental to elucidating its role in normal nuclear function and in disease; however, few tools exist to examine the INM in living cells, and the INM-specific proteome remains poorly characterized. Here, we adapted split green fluorescent protein (split-GFP) to systematically localize known and predicted integral membrane proteins in Saccharomyces cerevisiae to the INM as opposed to the outer nuclear membrane. Our data suggest that components of the endoplasmic reticulum (ER) as well as other organelles are able to access the INM, particularly if they contain a small extraluminal domain. By pairing split-GFP with fluorescence correlation spectroscopy, we compared the composition of complexes at the INM and ER, finding that at least one is unique: Sbh2, but not Sbh1, has access to the INM. Collectively, our work provides a comprehensive analysis of transmembrane protein localization to the INM and paves the way for further research into INM composition and function.
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Affiliation(s)
| | | | | | - Lynn Stoltz
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Scott McCroskey
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | | | - Sarah E Smith
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO 64110 .,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160
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43
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Wang R, Kamgoue A, Normand C, Léger-Silvestre I, Mangeat T, Gadal O. High resolution microscopy reveals the nuclear shape of budding yeast during cell cycle and in various biological states. J Cell Sci 2016; 129:4480-4495. [PMID: 27831493 PMCID: PMC5201014 DOI: 10.1242/jcs.188250] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 11/01/2016] [Indexed: 01/10/2023] Open
Abstract
How spatial organization of the genome depends on nuclear shape is unknown, mostly because accurate nuclear size and shape measurement is technically challenging. In large cell populations of the yeast Saccharomyces cerevisiae, we assessed the geometry (size and shape) of nuclei in three dimensions with a resolution of 30 nm. We improved an automated fluorescence localization method by implementing a post-acquisition correction of the spherical microscopic aberration along the z-axis, to detect the three dimensional (3D) positions of nuclear pore complexes (NPCs) in the nuclear envelope. Here, we used a method called NucQuant to accurately estimate the geometry of nuclei in 3D throughout the cell cycle. To increase the robustness of the statistics, we aggregated thousands of detected NPCs from a cell population in a single representation using the nucleolus or the spindle pole body (SPB) as references to align nuclei along the same axis. We could detect asymmetric changes of the nucleus associated with modification of nucleolar size. Stereotypical modification of the nucleus toward the nucleolus further confirmed the asymmetric properties of the nuclear envelope. Summary: This novel method to explore 3D geometry of the nuclear envelope with enhanced resolution and post-acquisition correction of z-axis aberration revealed increased NPC density near the SPB and the nucleolus.
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Affiliation(s)
- Renjie Wang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
| | - Alain Kamgoue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
| | - Christophe Normand
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
| | - Isabelle Léger-Silvestre
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
| | - Thomas Mangeat
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
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44
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Joshi AS, Huang X, Choudhary V, Levine TP, Hu J, Prinz WA. A family of membrane-shaping proteins at ER subdomains regulates pre-peroxisomal vesicle biogenesis. J Cell Biol 2016; 215:515-529. [PMID: 27872254 PMCID: PMC5119935 DOI: 10.1083/jcb.201602064] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 07/29/2016] [Accepted: 10/21/2016] [Indexed: 11/22/2022] Open
Abstract
Saccharomyces cerevisiae contains three conserved reticulon and reticulon-like proteins that help maintain ER structure by stabilizing high membrane curvature in ER tubules and the edges of ER sheets. A mutant lacking all three proteins has dramatically altered ER morphology. We found that ER shape is restored in this mutant when Pex30p or its homologue Pex31p is overexpressed. Pex30p can tubulate membranes both in cells and when reconstituted into proteoliposomes, indicating that Pex30p is a novel ER-shaping protein. In contrast to the reticulons, Pex30p is low abundance, and we found that it localizes to subdomains in the ER. We show that these ER subdomains are the sites where most preperoxisomal vesicles (PPVs) are generated. In addition, overproduction or deletion of Pex30p or Pex31p alters the size, shape, and number of PPVs. Our findings suggest that Pex30p and Pex31p help shape and generate regions of the ER where PPV biogenesis occurs.
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Affiliation(s)
- Amit S Joshi
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Xiaofang Huang
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.,Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China
| | - Vineet Choudhary
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Tim P Levine
- University College London Institute of Ophthalmology, London EC1V 9EL, England, UK
| | - Junjie Hu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.,Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - William A Prinz
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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45
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Převorovský M, Oravcová M, Zach R, Jordáková A, Bähler J, Půta F, Folk P. CSL protein regulates transcription of genes required to prevent catastrophic mitosis in fission yeast. Cell Cycle 2016; 15:3082-3093. [PMID: 27687771 DOI: 10.1080/15384101.2016.1235100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
For every eukaryotic cell to grow and divide, intricately coordinated action of numerous proteins is required to ensure proper cell-cycle progression. The fission yeast Schizosaccharomyces pombe has been instrumental in elucidating the fundamental principles of cell-cycle control. Mutations in S. pombe 'cut' (cell untimely torn) genes cause failed coordination between cell and nuclear division, resulting in catastrophic mitosis. Deletion of cbf11, a fission yeast CSL transcription factor gene, triggers a 'cut' phenotype, but the precise role of Cbf11 in promoting mitotic fidelity is not known. We report that Cbf11 directly activates the transcription of the acetyl-coenzyme A carboxylase gene cut6, and the biotin uptake/biosynthesis genes vht1 and bio2, with the former 2 implicated in mitotic fidelity. Cbf11 binds to a canonical, metazoan-like CSL response element (GTGGGAA) in the cut6 promoter. Expression of Cbf11 target genes shows apparent oscillations during the cell cycle using temperature-sensitive cdc25-22 and cdc10-M17 block-release experiments, but not with other synchronization methods. The penetrance of catastrophic mitosis in cbf11 and cut6 mutants is nutrient-dependent. We also show that drastic decrease in biotin availability arrests cell proliferation but does not cause mitotic defects. Taken together, our results raise the possibility that CSL proteins play conserved roles in regulating cell-cycle progression, and they could guide experiments into mitotic CSL functions in mammals.
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Affiliation(s)
- Martin Převorovský
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
| | - Martina Oravcová
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
| | - Róbert Zach
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
| | - Anna Jordáková
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
| | - Jürg Bähler
- b Research Department of Genetics , Evolution & Environment and UCL Cancer Institute, University College London , Gower Street, London , UK
| | - František Půta
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
| | - Petr Folk
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
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46
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Chemudupati M, Osmani AH, Osmani SA. A mitotic nuclear envelope tether for Gle1 also impacts nuclear and nucleolar architecture. Mol Biol Cell 2016; 27:mbc.E16-07-0544. [PMID: 27630260 PMCID: PMC5170558 DOI: 10.1091/mbc.e16-07-0544] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/06/2016] [Accepted: 09/08/2016] [Indexed: 01/16/2023] Open
Abstract
During Aspergillus nidulans mitosis peripheral nuclear pore complex (NPC) proteins (Nups) disperse from the core NPC structure. Unexpectedly, one predicted peripheral Nup, Gle1, remains at the mitotic NE via an unknown mechanism. Gle1 affinity purification identified MtgA ( M: itotic T: ether for G: le1), which tethers Gle1 to the NE during mitosis, but not during interphase when Gle1 is at NPCs. MtgA is the ortholog of the Schizosaccharomyces pombe telomere-anchoring inner nuclear membrane protein Bqt4. Like Bqt4, MtgA has meiotic roles but is functionally distinct from Bqt4 as MtgA is not required for tethering telomeres to the NE. Domain analyses revealed MtgA targeting to the NE requires its C-terminal transmembrane domain and a nuclear localization signal. Importantly, MtgA functions beyond Gle1 mitotic targeting and meiosis and impacts nuclear and nucleolar architecture when deleted or overexpressed. Deletion of MtgA generates small, round nuclei whereas overexpressing MtgA generates larger nuclei with altered nuclear compartmentalization resulting from NE expansion around the nucleolus. The accumulation of MtgA around the nucleolus promotes a similar accumulation of the endoplasmic reticulum (ER) protein Erg24 lowering its levels in the ER. This study extends the functions of Bqt4-like proteins to include mitotic Gle1 targeting and modulation of nuclear and nucleolar architecture.
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Affiliation(s)
- Mahesh Chemudupati
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Aysha H Osmani
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Stephen A Osmani
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
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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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48
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Yang PL, Hsu TH, Wang CW, Chen RH. Lipid droplets maintain lipid homeostasis during anaphase for efficient cell separation in budding yeast. Mol Biol Cell 2016; 27:2368-80. [PMID: 27307588 PMCID: PMC4966979 DOI: 10.1091/mbc.e16-02-0106] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/08/2016] [Indexed: 11/11/2022] Open
Abstract
The neutral lipids steryl ester and triacylglycerol (TAG) are stored in the membrane-bound organelle lipid droplet (LD) in essentially all eukaryotic cells. It is unclear what physiological conditions require the mobilization or storage of these lipids. Here, we study the budding yeast mutant are1Δ are2Δ dga1Δ lro1Δ, which cannot synthesize the neutral lipids and therefore lacks LDs. This quadruple mutant is delayed at cell separation upon release from mitotic arrest. The cells have abnormal septa, unstable septin assembly during cytokinesis, and prolonged exocytosis at the division site at the end of cytokinesis. Lipidomic analysis shows a marked increase of diacylglycerol (DAG) and phosphatidic acid, the precursors for TAG, in the mutant during mitotic exit. The cytokinesis and separation defects are rescued by adding phospholipid precursors or inhibiting fatty acid synthesis, which both reduce DAG levels. Our results suggest that converting excess lipids to neutral lipids for storage during mitotic exit is important for proper execution of cytokinesis and efficient cell separation.
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Affiliation(s)
- Po-Lin Yang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Tzu-Han Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chao-Wen Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Rey-Huei Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
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49
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Sanchez-Alvarez M, Zhang Q, Finger F, Wakelam MJO, Bakal C. Cell cycle progression is an essential regulatory component of phospholipid metabolism and membrane homeostasis. Open Biol 2016; 5:150093. [PMID: 26333836 PMCID: PMC4593667 DOI: 10.1098/rsob.150093] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We show that phospholipid anabolism does not occur uniformly during the metazoan cell cycle. Transition to S-phase is required for optimal mobilization of lipid precursors, synthesis of specific phospholipid species and endoplasmic reticulum (ER) homeostasis. Average changes observed in whole-cell phospholipid composition, and total ER lipid content, upon stimulation of cell growth can be explained by the cell cycle distribution of the population. TORC1 promotes phospholipid anabolism by slowing S/G2 progression. The cell cycle stage-specific nature of lipid biogenesis is dependent on p53. We propose that coupling lipid metabolism to cell cycle progression is a means by which cells have evolved to coordinate proliferation with cell and organelle growth.
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Affiliation(s)
- Miguel Sanchez-Alvarez
- Division of Cancer Biology, Chester Beatty Laboratories, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Qifeng Zhang
- Lipidomics Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | - Fabian Finger
- Division of Cancer Biology, Chester Beatty Laboratories, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | | | - Chris Bakal
- Division of Cancer Biology, Chester Beatty Laboratories, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
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50
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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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