1
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Prokisch S, Büttner S. Partitioning into ER membrane microdomains impacts autophagic protein turnover during cellular aging. Sci Rep 2024; 14:13653. [PMID: 38871812 DOI: 10.1038/s41598-024-64493-8] [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: 09/29/2023] [Accepted: 06/09/2024] [Indexed: 06/15/2024] Open
Abstract
Eukaryotic membranes are compartmentalized into distinct micro- and nanodomains that rearrange dynamically in response to external and internal cues. This lateral heterogeneity of the lipid bilayer and associated clustering of distinct membrane proteins contribute to the spatial organization of numerous cellular processes. Here, we show that membrane microdomains within the endoplasmic reticulum (ER) of yeast cells are reorganized during metabolic reprogramming and aging. Using biosensors with varying transmembrane domain length to map lipid bilayer thickness, we demonstrate that in young cells, microdomains of increased thickness mainly exist within the nuclear ER, while progressing cellular age drives the formation of numerous microdomains specifically in the cortical ER. Partitioning of biosensors with long transmembrane domains into these microdomains increased protein stability and prevented autophagic removal. In contrast, reporters with short transmembrane domains progressively accumulated at the membrane contact site between the nuclear ER and the vacuole, the so-called nucleus-vacuole junction (NVJ), and were subjected to turnover via selective microautophagy occurring specifically at these sites. Reporters with long transmembrane domains were excluded from the NVJ. Our data reveal age-dependent rearrangement of the lateral organization of the ER and establish transmembrane domain length as a determinant of membrane contact site localization and autophagic degradation.
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Affiliation(s)
- Simon Prokisch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
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2
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Magliozzi JO, Rands TJ, Shrestha S, Simke WC, Hase NE, Juanes MA, Kelley JB, Goode BL. The roles of yeast formins and their regulators Bud6 and Bil2 in the pheromone response. Mol Biol Cell 2024; 35:ar85. [PMID: 38656798 PMCID: PMC11238086 DOI: 10.1091/mbc.e23-11-0459] [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: 11/30/2023] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
In response to pheromone Saccharomyces cerevisiae extend a mating projection. This process depends on the formation of polarized actin cables which direct secretion to the mating tip and translocate the nucleus for karyogamy. Here, we demonstrate that proper mating projection formation requires the formin Bni1, as well as the actin nucleation promoting activities of Bud6, but not the formin Bnr1. Further, Bni1 is required for pheromone gradient tracking. Our work also reveals unexpected new functions for Bil2 in the pheromone response. Previously we identified Bil2 as a direct inhibitor of Bnr1 during vegetative cell growth. Here, we show that Bil2 has Bnr1-independent functions in spatially focusing Bni1-GFP at mating projection tips, and in vitro Bil2 and its binding partner Bud6 organize Bni1 into clusters that nucleate actin assembly. bil2∆ cells also display entangled Bni1-generated actin cable arrays and defects in secretory vesicle transport and nuclear positioning. At low pheromone concentrations, bil2∆ cells are delayed in establishing a polarity axis, and at high concentrations they prematurely form a second and a third mating projection. Together, these results suggest that Bil2 promotes the proper formation and timing of mating projections by organizing Bni1 and maintaining a persistent axis of polarized growth.
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Affiliation(s)
| | - Thomas J. Rands
- Department of Biology, Brandeis University, Waltham, MA 02454
| | - Sudati Shrestha
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469
| | - William C Simke
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469
| | - Niklas E. Hase
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469
| | - M. Angeles Juanes
- Department of Biology, Brandeis University, Waltham, MA 02454
- Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
| | - Joshua B. Kelley
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469
| | - Bruce L. Goode
- Department of Biology, Brandeis University, Waltham, MA 02454
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3
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Reinhard J, Starke L, Klose C, Haberkant P, Hammarén H, Stein F, Klein O, Berhorst C, Stumpf H, Sáenz JP, Hub J, Schuldiner M, Ernst R. MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress. EMBO J 2024; 43:1653-1685. [PMID: 38491296 PMCID: PMC11021466 DOI: 10.1038/s44318-024-00063-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
Biological membranes have a stunning ability to adapt their composition in response to physiological stress and metabolic challenges. Little is known how such perturbations affect individual organelles in eukaryotic cells. Pioneering work has provided insights into the subcellular distribution of lipids in the yeast Saccharomyces cerevisiae, but the composition of the endoplasmic reticulum (ER) membrane, which also crucially regulates lipid metabolism and the unfolded protein response, remains insufficiently characterized. Here, we describe a method for purifying organelle membranes from yeast, MemPrep. We demonstrate the purity of our ER membrane preparations by proteomics, and document the general utility of MemPrep by isolating vacuolar membranes. Quantitative lipidomics establishes the lipid composition of the ER and the vacuolar membrane. Our findings provide a baseline for studying membrane protein biogenesis and have important implications for understanding the role of lipids in regulating the unfolded protein response (UPR). The combined preparative and analytical MemPrep approach uncovers dynamic remodeling of ER membranes in stressed cells and establishes distinct molecular fingerprints of lipid bilayer stress.
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Affiliation(s)
- John Reinhard
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Leonhard Starke
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | | | - Per Haberkant
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | | | - Frank Stein
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | - Ofir Klein
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Charlotte Berhorst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Heike Stumpf
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - James P Sáenz
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | - Jochen Hub
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | - Maya Schuldiner
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Robert Ernst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany.
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany.
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4
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Yoshii SR, Barral Y. Fission-independent compartmentalization of mitochondria during budding yeast cell division. J Cell Biol 2024; 223:e202211048. [PMID: 38180475 PMCID: PMC10783438 DOI: 10.1083/jcb.202211048] [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: 11/13/2022] [Revised: 07/14/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
Lateral diffusion barriers compartmentalize membranes to generate polarity or asymmetrically partition membrane-associated macromolecules. Budding yeasts assemble such barriers in the endoplasmic reticulum (ER) and the outer nuclear envelope at the bud neck to retain aging factors in the mother cell and generate naïve and rejuvenated daughter cells. However, little is known about whether other organelles are similarly compartmentalized. Here, we show that the membranes of mitochondria are laterally compartmentalized at the bud neck and near the cell poles. The barriers in the inner mitochondrial membrane are constitutive, whereas those in the outer membrane form in response to stresses. The strength of mitochondrial diffusion barriers is regulated positively by spatial cues from the septin axis and negatively by retrograde (RTG) signaling. These data indicate that mitochondria are compartmentalized in a fission-independent manner. We propose that these diffusion barriers promote mitochondrial polarity and contribute to mitochondrial quality control.
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Affiliation(s)
- Saori R. Yoshii
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yves Barral
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
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5
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Kaminskiy Y, Ganeeva I, Chasov V, Kudriaeva A, Bulatov E. Asymmetric T-cell division: insights from cutting-edge experimental techniques and implications for immunotherapy. Front Immunol 2024; 15:1301378. [PMID: 38495874 PMCID: PMC10940324 DOI: 10.3389/fimmu.2024.1301378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/02/2024] [Indexed: 03/19/2024] Open
Abstract
Asymmetric cell division is a fundamental process conserved throughout evolution, employed by both prokaryotic and eukaryotic organisms. Its significance lies in its ability to govern cell fate and facilitate the generation of diverse cell types. Therefore, attaining a detailed mechanistic understanding of asymmetric cell division becomes essential for unraveling the complexities of cell fate determination in both healthy and pathological conditions. However, the role of asymmetric division in T-cell biology has only recently been unveiled. Here, we provide an overview of the T-cell asymmetric division field with the particular emphasis on experimental methods and models with the aim to guide the researchers in the selection of appropriate in vitro/in vivo models to study asymmetric division in T cells. We present a comprehensive investigation into the mechanisms governing the asymmetric division in various T-cell subsets underscoring the importance of the asymmetry in fate-determining factor segregation and transcriptional and epigenetic regulation. Furthermore, the intricate interplay of T-cell receptor signaling and the asymmetric division geometry are explored, shedding light on the spatial organization and the impact on cellular fate.
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Affiliation(s)
- Yaroslav Kaminskiy
- Department of Oncology and Pathology, Karolinska Institutet, SciLifeLab, Solna, Sweden
| | - Irina Ganeeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Vitaly Chasov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Anna Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Emil Bulatov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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6
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Piña F, Yan B, Hu J, Niwa M. Reticulons bind sphingolipids to activate the endoplasmic reticulum cell cycle checkpoint, the ER surveillance pathway. Cell Rep 2023; 42:113403. [PMID: 37979174 DOI: 10.1016/j.celrep.2023.113403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/09/2022] [Accepted: 10/23/2023] [Indexed: 11/20/2023] Open
Abstract
The inheritance of a functional endoplasmic reticulum (ER) is ensured by the ER stress surveillance (ERSU) pathway. Here, we made the unexpected discovery that reticulon 1 (Rtn1) and Yop1, well-known ER-curvature-generating proteins, each possess two sphingolipid-binding motifs within their transmembrane domains and that these motifs recognize the ER-stress-induced sphingolipid phytosphingosine (PHS), resulting in an ER inheritance block. Upon binding PHS, Rtn1/Yop1 accumulate on the ER tubule, poised to enter the emerging daughter cell, and cause its misdirection to the bud scars (i.e., previous cell division sites). Amino acid changes in the conserved PHS-binding motifs preclude Rtn1 or Yop1 from binding PHS and diminish their enrichment on the tubular ER, ultimately preventing the ER-stress-induced inheritance block. Conservation of these sphingolipid-binding motifs in human reticulons suggests that sphingolipid binding to Rtn1 and Yop1 represents an evolutionarily conserved mechanism that enables cells to respond to ER stress.
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Affiliation(s)
- Francisco Piña
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, NSB#1, Rm. 5328, 9500 Gilman Drive, San Diego, CA 92093-0377, USA
| | - Bing Yan
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Rm. 6210, Chaoyang District, Beijing 100101, China
| | - Junjie Hu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Rm. 6210, Chaoyang District, Beijing 100101, China
| | - Maho Niwa
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, NSB#1, Rm. 5328, 9500 Gilman Drive, San Diego, CA 92093-0377, USA.
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7
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Gräbnitz F, Oxenius A. CD8 T-cell diversification: Asymmetric cell division and its functional implications. Eur J Immunol 2023; 53:e2250225. [PMID: 36788705 DOI: 10.1002/eji.202250225] [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: 11/11/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Establishment of cellular diversity is a basic requirement for the development of multicellular organisms. Cellular diversification can be induced by asymmetric cell division (ACD), during which the emerging two daughter cells unequally inherit lineage specific cargo (including transcription factors, receptors for specific signaling inputs, metabolic platforms, and possibly different epigenetic landscapes), resulting in two daughter cells endowed with different fates. While ACD is strongly involved in lineage choices in mammalian stem cells, its role in fate diversification in lineage committed cell subsets that still exhibit plastic potential, such as T-cells, is currently investigated. In this review, we focus predominantly on the role of ACD in fate diversification of CD8 T-cells. Further, we discuss the impact of differential T-cell receptor stimulation strengths and differentiation history on ACD-mediated fate diversification and highlight a particular importance of ACD in the development of memory CD8 T-cells upon high-affinity stimulation conditions.
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Affiliation(s)
- Fabienne Gräbnitz
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, Zurich, 8093, Switzerland
| | - Annette Oxenius
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, Zurich, 8093, Switzerland
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8
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Yamashita YM. Asymmetric Stem Cell Division and Germline Immortality. Annu Rev Genet 2023; 57:181-199. [PMID: 37552892 DOI: 10.1146/annurev-genet-022123-040039] [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: 08/10/2023]
Abstract
Germ cells are the only cell type that is capable of transmitting genetic information to the next generation, which has enabled the continuation of multicellular life for the last 1.5 billion years. Surprisingly little is known about the mechanisms supporting the germline's remarkable ability to continue in this eternal cycle, termed germline immortality. Even unicellular organisms age at a cellular level, demonstrating that cellular aging is inevitable. Extensive studies in yeast have established the framework of how asymmetric cell division and gametogenesis may contribute to the resetting of cellular age. This review examines the mechanisms of germline immortality-how germline cells reset the aging of cells-drawing a parallel between yeast and multicellular organisms.
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Affiliation(s)
- Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
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9
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Kang L, Ikeda SI, Yang Y, Jeong H, Chen J, Zhang Y, Negishi K, Tsubota K, Kurihara T. Establishment of a novel ER-stress induced myopia model in mice. EYE AND VISION (LONDON, ENGLAND) 2023; 10:44. [PMID: 37907982 PMCID: PMC10619234 DOI: 10.1186/s40662-023-00361-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/08/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND Recent studies have indicated a strong correlation between endoplasmic reticulum (ER) stress and myopia and that eyedrops containing the ER stress inducer tunicamycin (Tm) can induce myopic changes in C57BL/6 J mice. Therefore, this study aimed to create a new myopia model using Tm eyedrops and to explore the mechanism of ER stress-mediated myopia development. METHODS Three-week-old C57BL/6 J mice were treated with different concentrations (0, 25, 50, and 100 μg/mL) and/or number of applications (zero, one, three, and seven) of Tm eyedrops. Refraction and axial length (AL) were measured before and one week after Tm treatment. Scleral collagen alterations were evaluated under polarised light after picrosirius red staining. ER stress-related indicators, such as the expression of collagen I and cleaved collagen were detected using Western blotting. RESULTS Compared with the control group, mice administered eyedrops with 50 μg/mL Tm only once showed the greatest myopic shifts in refraction and AL elongation and reduced scleral expression of collagen I. Picrosirius red staining showed a lower percentage of bundled collagen in the Tm group. Expression of ER-stress indicators increased in the Tm groups. Furthermore, optimised administration of Tm induced matrix metalloproteinase-2 (MMP2) expression in the sclera, which plays a major role in collagen degradation. CONCLUSIONS We have demonstrated that ER stress in the sclera is involved in myopia progression. Tm eyedrops induced myopic changes, loosening of the scleral collagen and decreased expression of collagen I. This process may be associated with ER stress in the sclera, which upregulates the expression of MMP2 leading to collagen degradation.
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Affiliation(s)
- Longdan Kang
- Laboratory of Photobiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
- Department of Ophthalmology, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Shin-Ichi Ikeda
- Laboratory of Photobiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Yajing Yang
- Laboratory of Photobiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Heonuk Jeong
- Laboratory of Photobiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Junhan Chen
- Laboratory of Photobiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Yan Zhang
- Laboratory of Photobiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Kazuno Negishi
- Department of Ophthalmology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Kazuo Tsubota
- Department of Ophthalmology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan.
- Tsubota Laboratory, Inc., 34 Shinanomachi, Shinjuku-Ku, Tokyo, 160-0016, Japan.
| | - Toshihide Kurihara
- Laboratory of Photobiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan.
- Department of Ophthalmology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan.
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10
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Cano-Domínguez N, Callejas-Negrete OA, Pérez-Mozqueda LL, Martínez-Andrade JM, Delgado-Álvarez DL, Castro-Longoria E. The small Ras-like GTPase BUD-1 modulates conidial germination and hyphal growth guidance in the filamentous fungus Neurospora crassa. Fungal Genet Biol 2023; 168:103824. [PMID: 37454888 DOI: 10.1016/j.fgb.2023.103824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/04/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
In filamentous fungi, the hypha orientation is essential for polarized growth and morphogenesis. The ability to re-orient tip growth in response to environmental cues is critical for the colony survival. Therefore, hyphal tip orientation and tip extension are distinct mechanisms that operate in parallel during filamentous growth. In yeast, the axial growth orientation requires a pathway regulated by Rsr1p/Bud1p, a Ras-like GTPase protein, which determines the axial budding pattern. However, in filamentous fungi the function of the Rsr1/Bud1p gene (krev-1 homolog) has not been completely characterized. In this work, we characterized the phenotype of a homokaryon mutant Bud1p orthologous in Neurospora crassa (△bud-1) and tagged BUD-1 with the green fluorescent protein (GFP) to determine its localization and cell dynamics under confocal microscopy. During spore germination BUD-1 was localized at specific points along the plasma membrane and during germ tube emergence it was located at the tip of the germ tubes. In mature hyphae BUD-1 continued to be located at the cell tip and was also present at sites of branch emergence and at the time of septum formation. The △bud-1 mutant showed a delayed germination, and the orientation of hyphae was somewhat disrupted. Also, the hypha diameter was reduced approximately 37 % with respect to the wild type. The lack of BUD-1 affected the Spitzenkörper (Spk) formation, trajectory, the localization of polarisome components BNI-1 and SPA-2, and the actin cytoskeleton polarization. The results presented here suggest that BUD-1 participates in the establishment of a new polarity axis. It may also mediate the delivery of secretory vesicles for the efficient construction of new plasma membrane and cell wall.
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Affiliation(s)
- Nallely Cano-Domínguez
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California, Mexico; Department of Cell Biology and Development, Institute of Cellular Physiology (IFC), National Autonomous University of Mexico (UNAM), Mexico City 04510, Mexico
| | - Olga A Callejas-Negrete
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California, Mexico
| | - Luis L Pérez-Mozqueda
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California, Mexico; Center for Wine and Vine Studies (CEVIT), Technical and Higher Education Center (CETYS), Ensenada, Baja California, Mexico
| | - Juan M Martínez-Andrade
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California, Mexico
| | - Diego L Delgado-Álvarez
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California, Mexico
| | - Ernestina Castro-Longoria
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California, Mexico.
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11
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Schenkel L, Wang X, Le N, Burger M, Kroschewski R. A dedicated cytoplasmic container collects extrachromosomal DNA away from the mammalian nucleus. Mol Biol Cell 2023; 34:ar105. [PMID: 37556227 PMCID: PMC10559310 DOI: 10.1091/mbc.e23-04-0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
Expression from transfected plasmid DNA is generally transient, but it is unclear what process terminates it. We show that DNA entering mammalian cells is rapidly surrounded by a double membrane in the cytoplasm, in some cases after leaving the nucleus. This cytoplasmic container, termed exclusome, frequently also contains extrachromosomal telomeric DNA, and is maintained by the cell over several division cycles. The exclusome envelope contains endoplasmic reticulum proteins and the inner-nuclear membrane proteins Lap2β and Emerin, but differs from the nuclear envelope by its fenestrations and the absence of the Lamin B Receptor and nuclear pore complexes. Reduction of exclusome frequency upon overexpressing Emerin's LEM-domain suggests a role for Emerin in plasmid DNA compartmentalization. Thus, cells distinguish extrachromosomal DNA and chromosomes and wrap them into similar yet distinct envelopes keeping the former in the exclusome but the latter in the nucleus, where transcription occurs.
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Affiliation(s)
- Laura Schenkel
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
- Molecular Life Science PhD Program, Life Science Zurich Graduate School, 8057 Zurich, Switzerland
| | - Xuan Wang
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
- Molecular Life Science PhD Program, Life Science Zurich Graduate School, 8057 Zurich, Switzerland
| | - Nhung Le
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
- Molecular Life Science PhD Program, Life Science Zurich Graduate School, 8057 Zurich, Switzerland
| | - Michael Burger
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Ruth Kroschewski
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
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12
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Paukštytė J, López Cabezas RM, Feng Y, Tong K, Schnyder D, Elomaa E, Gregorova P, Doudin M, Särkkä M, Sarameri J, Lippi A, Vihinen H, Juutila J, Nieminen A, Törönen P, Holm L, Jokitalo E, Krisko A, Huiskonen J, Sarin LP, Hietakangas V, Picotti P, Barral Y, Saarikangas J. Global analysis of aging-related protein structural changes uncovers enzyme-polymerization-based control of longevity. Mol Cell 2023; 83:3360-3376.e11. [PMID: 37699397 DOI: 10.1016/j.molcel.2023.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/18/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023]
Abstract
Aging is associated with progressive phenotypic changes. Virtually all cellular phenotypes are produced by proteins, and their structural alterations can lead to age-related diseases. However, we still lack comprehensive knowledge of proteins undergoing structural-functional changes during cellular aging and their contributions to age-related phenotypes. Here, we conducted proteome-wide analysis of early age-related protein structural changes in budding yeast using limited proteolysis-mass spectrometry (LiP-MS). The results, compiled in online ProtAge catalog, unraveled age-related functional changes in regulators of translation, protein folding, and amino acid metabolism. Mechanistically, we found that folded glutamate synthase Glt1 polymerizes into supramolecular self-assemblies during aging, causing breakdown of cellular amino acid homeostasis. Inhibiting Glt1 polymerization by mutating the polymerization interface restored amino acid levels in aged cells, attenuated mitochondrial dysfunction, and led to lifespan extension. Altogether, this comprehensive map of protein structural changes enables identifying mechanisms of age-related phenotypes and offers opportunities for their reversal.
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Affiliation(s)
- Jurgita Paukštytė
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Rosa María López Cabezas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Yuehan Feng
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Kai Tong
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Ellinoora Elomaa
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Pavlina Gregorova
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Matteo Doudin
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Meeri Särkkä
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Jesse Sarameri
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Alice Lippi
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helena Vihinen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Juhana Juutila
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Anni Nieminen
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Petri Törönen
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Liisa Holm
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Anita Krisko
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Juha Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - L Peter Sarin
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Ville Hietakangas
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Paola Picotti
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Juha Saarikangas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland.
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13
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Kalli S, Vallieres C, Violet J, Sanders JW, Chapman J, Vincken JP, Avery SV, Araya-Cloutier C. Cellular Responses and Targets in Food Spoilage Yeasts Exposed to Antifungal Prenylated Isoflavonoids. Microbiol Spectr 2023; 11:e0132723. [PMID: 37428107 PMCID: PMC10433819 DOI: 10.1128/spectrum.01327-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/17/2023] [Indexed: 07/11/2023] Open
Abstract
Prenylated isoflavonoids are phytochemicals with promising antifungal properties. Recently, it was shown that glabridin and wighteone disrupted the plasma membrane (PM) of the food spoilage yeast Zygosaccharomyces parabailii in distinct ways, which led us to investigate further their modes of action (MoA). Transcriptomic profiling with Z. parabailii showed that genes encoding transmembrane ATPase transporters, including Yor1, and genes homologous to the pleiotropic drug resistance (PDR) subfamily in Saccharomyces cerevisiae were upregulated in response to both compounds. Gene functions involved in fatty acid and lipid metabolism, proteostasis, and DNA replication processes were overrepresented among genes upregulated by glabridin and/or wighteone. Chemogenomic analysis using the genome-wide deletant collection for S. cerevisiae further suggested an important role for PM lipids and PM proteins. Deletants of gene functions involved in biosynthesis of very-long-chain fatty acids (constituents of PM sphingolipids) and ergosterol were hypersensitive to both compounds. Using lipid biosynthesis inhibitors, we corroborated roles for sphingolipids and ergosterol in prenylated isoflavonoid action. The PM ABC transporter Yor1 and Lem3-dependent flippases conferred sensitivity and resistance, respectively, to the compounds, suggesting an important role for PM phospholipid asymmetry in their MoAs. Impaired tryptophan availability, likely linked to perturbation of the PM tryptophan permease Tat2, was evident in response to glabridin. Finally, substantial evidence highlighted a role of the endoplasmic reticulum (ER) in cellular responses to wighteone, including gene functions associated with ER membrane stress or with phospholipid biosynthesis, the primary lipid of the ER membrane. IMPORTANCE Preservatives, such as sorbic acid and benzoic acid, inhibit the growth of undesirable yeast and molds in foods. Unfortunately, preservative tolerance and resistance in food spoilage yeast, such as Zygosaccharomyces parabailii, is a growing challenge in the food industry, which can compromise food safety and increase food waste. Prenylated isoflavonoids are the main defense phytochemicals in the Fabaceae family. Glabridin and wighteone belong to this group of compounds and have shown potent antifungal activity against food spoilage yeasts. The present study demonstrated the mode of action of these compounds against food spoilage yeasts by using advanced molecular tools. Overall, the cellular actions of these two prenylated isoflavonoids share similarities (at the level of the plasma membrane) but also differences. Tryptophan import was specifically affected by glabridin, whereas endoplasmic reticulum membrane stress was specifically induced by wighteone. Understanding the mode of action of these novel antifungal agents is essential for their application in food preservation.
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Affiliation(s)
- Sylvia Kalli
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Cindy Vallieres
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Joseph Violet
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - John Chapman
- Unilever Foods Innovation Centre, Wageningen, the Netherlands
| | - Jean-Paul Vincken
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Simon V. Avery
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Carla Araya-Cloutier
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
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14
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Béziat C, Jaillais Y. Should I stay or should I go: the functional importance and regulation of lipid diffusion in biological membranes. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2479-2488. [PMID: 36738265 DOI: 10.1093/jxb/erad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 01/23/2023] [Indexed: 06/06/2023]
Abstract
Biological membranes are highly dynamic, in particular due to the constant exchange of vesicles between the different compartments of the cell. In addition, the dynamic nature of membranes is also caused by their inherently fluid properties, with the diffusion of both proteins and lipids within their leaflets. Lipid diffusion is particularly difficult to study in vivo but recent advances in optical microscopy and lipid visualization now enable the characterization of lipid lateral motion, and here we review these methods in plants. We then discuss the parameters that affect lipid diffusion in membranes and explore their consequences on the formation of membrane domains at different scales. Finally, we consider how controlled lipid diffusion affects membrane functions during cell signaling, development, and environmental interactions.
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Affiliation(s)
- Chloé Béziat
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
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15
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Howell-Bray T, Byrne L. The effect of prions on cellular metabolism: The metabolic impact of the [RNQ +] prion and potential role of native Rnq1p. RESEARCH SQUARE 2023:rs.3.rs-2511186. [PMID: 36909567 PMCID: PMC10002837 DOI: 10.21203/rs.3.rs-2511186/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Within the field of amyloid and prion disease there is a need for a more comprehensive understanding of the fundamentals of disease biology. In order to facilitate the progression treatment and underpin comprehension of toxicity, fundamental understanding of the disruption to normal cellular biochemistry and trafficking is needed. Here, by removing the complex biochemistry of the brain, we have utilised known prion forming strains of Saccharomyces cerevisiae carrying different conformational variants of the Rnq1p to obtain Liquid Chromatography-Mass Spectrometry (LC-MS) metabolic profiles and identify key perturbations of prion presence. These studies reveal that prion containing [RNQ+] cells display a significant reduction in amino acid biosynthesis and distinct perturbations in sphingolipid metabolism, with significant downregulation in metabolites within these pathways. Moreover, that native Rnq1p appears to downregulate ubiquinone biosynthesis pathways within cells, suggesting that Rnq1p may play a lipid/mevalonate-based cytoprotective role as a regulator of ubiquinone production. These findings contribute to the understanding of how prion proteins interact in vivo in both their prion and non-prion confirmations and indicate potential targets for the mitigation of these effects. We demonstrate specific sphingolipid centred metabolic disruptions due to prion presence and give insight into a potential cytoprotective role of the native Rnq1 protein. This provides evidence of metabolic similarities between yeast and mammalian cells as a consequence of prion presence and establishes the application of metabolomics as a tool to investigate prion/amyloid-based phenomena.
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16
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Septin Defects Favour Symmetric Inheritance of the Budding Yeast Deceptive Courtship Memory. Int J Mol Sci 2023; 24:ijms24033003. [PMID: 36769325 PMCID: PMC9917509 DOI: 10.3390/ijms24033003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Mnemons are prion-like elements that encode cellular memories of past cellular adaptations and do not spread to progenies during cell divisions. During the deceptive courtship in budding yeast, the Whi3 mnemon (Whi3mnem) condenses into a super-assembly to encode a mating pheromone refractory state established in the mother cell. Whi3mnem is confined to the mother cell such that their daughter cells have the ability to respond to the mating pheromone. Confinement of Whi3mnem involves its association with the endoplasmic reticulum membranes and the compartmentalization of these membranes by the lateral membrane diffusion barrier at the bud neck, the limit between the mother cell and the bud. However, during the first cell division after the establishment of the pheromone refractory state, this adaptation is more likely to be inherited by the daughter cell than in subsequent cell divisions. Here, we show that the first cell division is associated with larger daughter cells and cytokinesis defects, traits that are not observed in subsequent cell divisions. The cytoskeletal septin protein shows aberrant localisation in these divisions and the septin-dependent endoplasmic reticulum membrane diffusion barrier is weakened. Overall, these data suggest that cytokinesis defects associated with prolonged cell division can alter the confinement and inheritance pattern of a cellular memory.
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17
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Chen P, Levy DL. Regulation of organelle size and organization during development. Semin Cell Dev Biol 2023; 133:53-64. [PMID: 35148938 PMCID: PMC9357868 DOI: 10.1016/j.semcdb.2022.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 12/11/2022]
Abstract
During early embryogenesis, as cells divide in the developing embryo, the size of intracellular organelles generally decreases to scale with the decrease in overall cell size. Organelle size scaling is thought to be important to establish and maintain proper cellular function, and defective scaling may lead to impaired development and disease. However, how the cell regulates organelle size and organization are largely unanswered questions. In this review, we summarize the process of size scaling at both the cell and organelle levels and discuss recently discovered mechanisms that regulate this process during early embryogenesis. In addition, we describe how some recently developed techniques and Xenopus as an animal model can be used to investigate the underlying mechanisms of size regulation and to uncover the significance of proper organelle size scaling and organization.
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Affiliation(s)
- Pan Chen
- Institute of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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18
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Benoit B, Poüs C, Baillet A. Septins as membrane influencers: direct play or in association with other cytoskeleton partners. Front Cell Dev Biol 2023; 11:1112319. [PMID: 36875762 PMCID: PMC9982393 DOI: 10.3389/fcell.2023.1112319] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/23/2023] [Indexed: 02/19/2023] Open
Abstract
The cytoskeleton comprises three polymerizing structures that have been studied for a long time, actin microfilaments, microtubules and intermediate filaments, plus more recently investigated dynamic assemblies like septins or the endocytic-sorting complex required for transport (ESCRT) complex. These filament-forming proteins control several cell functions through crosstalks with each other and with membranes. In this review, we report recent works that address how septins bind to membranes, and influence their shaping, organization, properties and functions, either by binding to them directly or indirectly through other cytoskeleton elements.
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Affiliation(s)
- Béatrice Benoit
- INSERM UMR-S 1193, UFR de Pharmacie, University Paris-Saclay, Orsay, France
| | - Christian Poüs
- INSERM UMR-S 1193, UFR de Pharmacie, University Paris-Saclay, Orsay, France.,Laboratoire de Biochimie-Hormonologie, Hôpital Antoine Béclère, AP-HP, Hôpitaux Universitaires Paris-Saclay, Clamart, France
| | - Anita Baillet
- INSERM UMR-S 1193, UFR de Pharmacie, University Paris-Saclay, Orsay, France
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19
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Gupta V, Mahata T, Roy R, Gharai PK, Jana A, Garg S, Ghosh S. Discovery of imidazole-based GSK-3 β inhibitors for transdifferentiation of human mesenchymal stem cells to neurons: A potential single-molecule neurotherapeutic foresight. Front Mol Neurosci 2022; 15:1002419. [PMID: 36590911 PMCID: PMC9797524 DOI: 10.3389/fnmol.2022.1002419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/11/2022] [Indexed: 12/16/2022] Open
Abstract
The transdifferentiation of human mesenchymal stem cells (hMSC) to functional neurons is crucial for the development of future neuro-regenerative therapeutics. Currently, transdifferentiation of hMSCs to neurons requires a "chemical cocktail" along with neural growth factors. The role of the individual molecules present in a "chemical cocktail" is poorly understood and may cause unwanted toxicity or adverse effects. Toward, this goal, we have showcased the discovery of an imidazole-based "single-molecule" transdifferentiation initiator SG-145C. This discovery was achieved via screening of a small molecule library through extensive in silico studies to shortlist the best-fitting molecules. This discovery evolved through a careful selection to target Glycogen synthase kinase-3β (GSK-3β), which is one of the important proteins responsible for neurogenesis. Rigorous computational experiments, as well as extensive biological assays, confirmed that SG-145C has significant potential to transdifferentiate hMSCs to neurons. Interestingly, our results suggest that SG-145C can inhibit the proteasomal degradation of phosphorylated β-catenin, in turn promoting transdifferentiation of hMSCs into neurons via the Wnt pathway.
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Affiliation(s)
- Varsha Gupta
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Tanushree Mahata
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Rajsekhar Roy
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Karwar, Rajasthan, India
| | - Prabir Kumar Gharai
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Aniket Jana
- Smart Healthcare, Interdisciplinary Research Platform, Indian Institute of Technology Jodhpur, Karwar, Rajasthan, India
| | - Shubham Garg
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Karwar, Rajasthan, India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India,Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Karwar, Rajasthan, India,Smart Healthcare, Interdisciplinary Research Platform, Indian Institute of Technology Jodhpur, Karwar, Rajasthan, India,*Correspondence: Surajit Ghosh,
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20
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Sing TL, Brar GA, Ünal E. Gametogenesis: Exploring an Endogenous Rejuvenation Program to Understand Cellular Aging and Quality Control. Annu Rev Genet 2022; 56:89-112. [PMID: 35878627 PMCID: PMC9712276 DOI: 10.1146/annurev-genet-080320-025104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gametogenesis is a conserved developmental program whereby a diploid progenitor cell differentiates into haploid gametes, the precursors for sexually reproducing organisms. In addition to ploidy reduction and extensive organelle remodeling, gametogenesis naturally rejuvenates the ensuing gametes, leading to resetting of life span. Excitingly, ectopic expression of the gametogenesis-specific transcription factor Ndt80 is sufficient to extend life span in mitotically dividing budding yeast, suggesting that meiotic rejuvenation pathways can be repurposed outside of their natural context. In this review, we highlight recent studies of gametogenesis that provide emerging insight into natural quality control, organelle remodeling, and rejuvenation strategies that exist within a cell. These include selective inheritance, programmed degradation, and de novo synthesis, all of which are governed by the meiotic gene expression program entailing many forms of noncanonical gene regulation. Finally, we highlight critical questions that remain in the field and provide perspective on the implications of gametogenesis research on human health span.
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Affiliation(s)
- Tina L Sing
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
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21
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bin Imtiaz MK, Royall LN, Gonzalez-Bohorquez D, Jessberger S. Human neural progenitors establish a diffusion barrier in the endoplasmic reticulum membrane during cell division. Development 2022; 149:275957. [PMID: 35815653 PMCID: PMC9440750 DOI: 10.1242/dev.200613] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/20/2022] [Indexed: 11/20/2022]
Abstract
Asymmetric segregation of cellular components regulates the fate and behavior of somatic stem cells. Similar to dividing budding yeast and precursor cells in Caenorhabditis elegans, it has been shown that mouse neural progenitors establish a diffusion barrier in the membrane of the endoplasmic reticulum (ER), which has been associated with asymmetric partitioning of damaged proteins and cellular age. However, the existence of an ER diffusion barrier in human cells remains unknown. Here, we used fluorescence loss in photobleaching (FLIP) imaging to show that human embryonic stem cell (hESC)- and induced pluripotent stem cell (iPSC)-derived neural progenitor cells establish an ER diffusion barrier during cell division. The human ER diffusion barrier is regulated via lamin-dependent mechanisms and is associated with asymmetric segregation of mono- and polyubiquitylated damaged proteins. Further, forebrain regionalized organoids derived from hESCs were used to show the establishment of an ER membrane diffusion barrier in more naturalistic tissues, mimicking early steps of human brain development. Thus, the data provided here show that human neural progenitors establish a diffusion barrier during cell division in the membrane of the ER, which may allow for asymmetric segregation of cellular components, contributing to the fate and behavior of human neural progenitor cells. Summary: Asymmetric segregation of cellular components, which may contribute to the fate and behavior of human neural progenitors, is allowed by a diffusion barrier in the endoplasmic reticulum membrane during cell division.
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Affiliation(s)
- Muhammad Khadeesh bin Imtiaz
- Laboratory of Neural Plasticity , Faculties of Medicine and Science , , 8057 Zurich , Switzerland
- Brain Research Institute, University of Zurich , Faculties of Medicine and Science , , 8057 Zurich , Switzerland
| | - Lars N. Royall
- Laboratory of Neural Plasticity , Faculties of Medicine and Science , , 8057 Zurich , Switzerland
- Brain Research Institute, University of Zurich , Faculties of Medicine and Science , , 8057 Zurich , Switzerland
| | - Daniel Gonzalez-Bohorquez
- Laboratory of Neural Plasticity , Faculties of Medicine and Science , , 8057 Zurich , Switzerland
- Brain Research Institute, University of Zurich , Faculties of Medicine and Science , , 8057 Zurich , Switzerland
| | - Sebastian Jessberger
- Laboratory of Neural Plasticity , Faculties of Medicine and Science , , 8057 Zurich , Switzerland
- Brain Research Institute, University of Zurich , Faculties of Medicine and Science , , 8057 Zurich , Switzerland
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22
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Koga A, Takayama C, Ishibashi Y, Kono Y, Matsuzaki M, Tani M. Loss of tolerance to multiple environmental stresses due to limitation of structural diversity of complex sphingolipids. Mol Biol Cell 2022; 33:ar105. [PMID: 35895092 DOI: 10.1091/mbc.e22-04-0117] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Structural diversity of complex sphingolipids is important for maintenance of various cellular functions; however, the overall picture of the significance of this structural diversity remains largely unknown. To investigate the physiological importance of the structural diversity of complex sphingolipids, we here constructed a complex sphingolipid structural diversity disruption library in budding yeast, which comprises 11 mutants including with combinations of deletions of sphingolipid-metabolizing enzyme genes. The sensitivity of the mutants to various environmental stresses revealed that the more the structural variation of complex sphingolipids is limited, the more stress sensitivity tends to increase. Moreover, it was found that in mutant cells with only one subtype of complex sphingolipid, Slt2 MAP kinase and Msn2/4 transcriptional factors are essential for maintenance of a normal growth and compensation for reduced tolerance of multiple stresses caused by loss of complex sphingolipid diversity. Slt2 and Msn2/4 are involved in compensation for impaired integrity of cell walls and plasma membranes caused by loss of complex sphingolipid diversity, respectively. From these findings, it was suggested that loss of structural diversity of complex sphingolipids affects the environment of the cell surface, including both plasma membranes and cell walls, which could cause multiple environmental stress hypersensitivity.
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Affiliation(s)
- Ayano Koga
- Department of Chemistry, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Chihiro Takayama
- Department of Chemistry, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yohei Ishibashi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yushi Kono
- Department of Chemistry, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Momoko Matsuzaki
- Department of Chemistry, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Motohiro Tani
- Department of Chemistry, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
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23
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A Nuclear Belt Fastens on Neural Cell Fate. Cells 2022; 11:cells11111761. [PMID: 35681456 PMCID: PMC9179901 DOI: 10.3390/cells11111761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/22/2022] Open
Abstract
Successful embryonic and adult neurogenesis require proliferating neural stem and progenitor cells that are intrinsically and extrinsically guided into a neuronal fate. In turn, migration of new-born neurons underlies the complex cytoarchitecture of the brain. Proliferation and migration are therefore essential for brain development, homeostasis and function in adulthood. Among several tightly regulated processes involved in brain formation and function, recent evidence points to the nuclear envelope (NE) and NE-associated components as critical new contributors. Classically, the NE was thought to merely represent a barrier mediating selective exchange between the cytoplasm and nucleoplasm. However, research over the past two decades has highlighted more sophisticated and diverse roles for NE components in progenitor fate choice and migration of their progeny by tuning gene expression via interactions with chromatin, transcription factors and epigenetic factors. Defects in NE components lead to neurodevelopmental impairments, whereas age-related changes in NE components are proposed to influence neurodegenerative diseases. Thus, understanding the roles of NE components in brain development, maintenance and aging is likely to reveal new pathophysiological mechanisms for intervention. Here, we review recent findings for the previously underrepresented contribution of the NE in neuronal commitment and migration, and envision future avenues for investigation.
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24
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Meinema AC, Marzelliusardottir A, Mirkovic M, Aspert T, Lee SS, Charvin G, Barral Y. DNA circles promote yeast ageing in part through stimulating the reorganization of nuclear pore complexes. eLife 2022; 11:71196. [PMID: 35373738 PMCID: PMC9020822 DOI: 10.7554/elife.71196] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 04/03/2022] [Indexed: 11/13/2022] Open
Abstract
The nuclear pore complex (NPC) mediates nearly all exchanges between nucleus and cytoplasm, and in many species it changes composition as the organism ages. However, how these changes arise and whether they contribute themselves to ageing is poorly understood. We show that SAGA-dependent attachment of DNA circles to NPCs in replicatively ageing yeast cells causes NPCs to lose their nuclear basket and cytoplasmic complexes. These NPCs were not recognized as defective by the NPC quality control machinery (SINC) and not targeted by ESCRTs. They interacted normally or more effectively with protein import and export factors but specifically lost mRNA export factors. Acetylation of Nup60 drove the displacement of basket and cytoplasmic complexes from circle-bound NPCs. Mutations preventing this remodeling extended the replicative lifespan of the cells. Thus, our data suggest that the anchorage of accumulating circles locks NPCs in a specialized state and that this process is intrinsically linked to the mechanisms by which ERCs promote ageing.
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Affiliation(s)
| | | | | | - Théo Aspert
- Department of Developmental Biology and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| | - Sung Sik Lee
- Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Gilles Charvin
- Department of Developmental Biology and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| | - Yves Barral
- Department of Biology, ETH Zürich, Zürich, Switzerland
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25
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A role for cell polarity in lifespan and mitochondrial quality control in the budding yeast Saccharomyces cerevisiae. iScience 2022; 25:103957. [PMID: 35281729 PMCID: PMC8914336 DOI: 10.1016/j.isci.2022.103957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/15/2021] [Accepted: 02/17/2022] [Indexed: 01/03/2023] Open
Abstract
Babies are born young, largely independent of the age of their mothers. Mother-daughter age asymmetry in yeast is achieved, in part, by inheritance of higher-functioning mitochondria by buds and retention of some high-functioning mitochondria in mother cells. The mitochondrial F box protein, Mfb1p, tethers mitochondria at both poles in a cell cycle-regulated manner: it localizes to and anchors mitochondria at the mother cell tip throughout the cell cycle and at the bud tip before cytokinesis. Here, we report that cell polarity and polarized localization of Mfb1p decline with age in Saccharomyces cerevisiae. Moreover, deletion of genes (BUD1, BUD2, and BUD5) that mediate symmetry breaking during establishment of cell polarity and asymmetric yeast cell division cause depolarized Mfb1p localization and defects in mitochondrial distribution and quality control. Our results support a role for the polarity machinery in lifespan through modulating Mfb1 function in asymmetric inheritance of mitochondria during yeast cell division. Budding polarity declines with age Polarization of a mitochondrial tether, Mfb1p, within mother cells declines with age Defects in budding polarity disrupt Mfb1p polarization and mitochondrial distribution Polarity defects affect Mfb1p-mediated mitochondrial quality and lifespan control
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26
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Lau Y, Oamen HP, Grogg M, Parfenova I, Saarikangas J, Hannay R, Nichols RA, Hilvert D, Barral Y, Caudron F. Whi3 mnemon association with endoplasmic reticulum membranes confines the memory of deceptive courtship to the yeast mother cell. Curr Biol 2022; 32:963-974.e7. [PMID: 35085498 PMCID: PMC8938615 DOI: 10.1016/j.cub.2022.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 12/17/2022]
Abstract
Prion-like proteins are involved in many aspects of cellular physiology, including cellular memory. In response to deceptive courtship, budding yeast escapes pheromone-induced cell-cycle arrest through the coalescence of the G1/S inhibitor Whi3 into a dominant, inactive super-assembly. Whi3 is a mnemon (Whi3mnem), a protein that conformational change maintains as a trait in the mother cell but is not inherited by the daughter cells. How the maintenance and asymmetric inheritance of Whi3mnem are achieved is unknown. Here, we report that Whi3mnem is closely associated with endoplasmic reticulum (ER) membranes and is retained in the mother cell by the lateral diffusion barriers present at the bud neck. Strikingly, barrier defects made Whi3mnem propagate in a mitotically stable, prion-like manner. The amyloid-forming glutamine-rich domain of Whi3 was required for both mnemon and prion-like behaviors. Thus, we propose that Whi3mnem is in a self-templating state, lending temporal maintenance of memory, whereas its association with the compartmentalized membranes of the ER prevents infectious propagation to the daughter cells. These results suggest that confined self-templating super-assembly is a powerful mechanism for the long-term encoding of information in a spatially defined manner. Yeast courtship may provide insights on how individual synapses become potentiated in neuronal memory.
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Affiliation(s)
- Yasmin Lau
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Henry Patrick Oamen
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Marcel Grogg
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg, 8093 Zürich, Switzerland
| | - Iuliia Parfenova
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg, 8093 Zürich, Switzerland
| | - Juha Saarikangas
- Helsinki Institute of Life Science HiLIFE, Viikinkaari 5, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, Viikinkaari 5, 00790 Helsinki, Finland; Neuroscience Center, University of Helsinki, Viikinkaari 5, 00790 Helsinki, Finland
| | - Robin Hannay
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Richard Alan Nichols
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg, 8093 Zürich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg, 8093 Zürich, Switzerland
| | - Fabrice Caudron
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; IGMM, Univ Montpellier, CNRS, Route de Mende, 34293 Montpellier, France.
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27
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Abstract
Membrane lateral heterogeneity, historically referred to as the lipid raft hypothesis, has been extensively investigated through physiochemical experiments on model membranes. Currently, the basic principles are well understood; however, the physiological relevance of these structures in living organisms is still not clear. Thus, studying membrane organization in vivo is extremely important and elucidates the role of such structures in various membrane-associated processes. This is particularly true when a whole single-celled organism can be studied rather than an isolated cell. The ordered and disordered membrane phases are characterized by the degree of acyl chain packing in the lipid bilayer. Polar water molecules can penetrate into the low-density lipid packing of the disordered phase, but are more excluded from the tightly packed ordered phase. Here, polarity-sensitive probes, embedded in the lipid bilayer, are used to report on membrane organization and to quantitate this parameter via 2-channel fluorescence microscopy. Coupling genetic approaches, which are easily accessible in yeast model organisms, with the imaging approach described here provides a great opportunity to investigate how membrane heterogeneity impacts physiology.
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Affiliation(s)
- Maria Makarova
- School of Biosciences, University of Birmingham, Birmingham, UK.
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
- School of Mathematics, University of Birmingham, Birmingham, UK
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28
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Schuster T, Geiger H. Septins in Stem Cells. Front Cell Dev Biol 2021; 9:801507. [PMID: 34957123 PMCID: PMC8695968 DOI: 10.3389/fcell.2021.801507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/24/2021] [Indexed: 12/01/2022] Open
Abstract
Septins were first described in yeast. Due to extensive research in non-yeast cells, Septins are now recognized across all species as important players in the regulation of the cytoskeleton, in the establishment of polarity, for migration, vesicular trafficking and scaffolding. Stem cells are primarily quiescent cells, and this actively maintained quiescent state is critical for proper stem cell function. Equally important though, stem cells undergo symmetric or asymmetric division, which is likely linked to the level of symmetry found in the mother stem cell. Due to the ability to organize barriers and be able to break symmetry in cells, Septins are thought to have a significant impact on organizing quiescence as well as the mode (symmetric vs asymmetric) of stem cell division to affect self-renewal versus differentiation. Mechanisms of regulating mammalian quiescence and symmetry breaking by Septins are though still somewhat elusive. Within this overview article, we summarize current knowledge on the role of Septins in stem cells ranging from yeast to mice especially with respect to quiescence and asymmetric division, with a special focus on hematopoietic stem cells.
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Affiliation(s)
| | - Hartmut Geiger
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
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29
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Schlarmann P, Ikeda A, Funato K. Membrane Contact Sites in Yeast: Control Hubs of Sphingolipid Homeostasis. MEMBRANES 2021; 11:971. [PMID: 34940472 PMCID: PMC8707754 DOI: 10.3390/membranes11120971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 01/02/2023]
Abstract
Sphingolipids are the most diverse class of membrane lipids, in terms of their structure and function. Structurally simple sphingolipid precursors, such as ceramides, act as intracellular signaling molecules in various processes, including apoptosis, whereas mature and complex forms of sphingolipids are important structural components of the plasma membrane. Supplying complex sphingolipids to the plasma membrane, according to need, while keeping pro-apoptotic ceramides in check is an intricate task for the cell and requires mechanisms that tightly control sphingolipid synthesis, breakdown, and storage. As each of these processes takes place in different organelles, recent studies, using the budding yeast Saccharomyces cerevisiae, have investigated the role of membrane contact sites as hubs that integrate inter-organellar sphingolipid transport and regulation. In this review, we provide a detailed overview of the findings of these studies and put them into the context of established regulatory mechanisms of sphingolipid homeostasis. We have focused on the role of membrane contact sites in sphingolipid metabolism and ceramide transport, as well as the mechanisms that prevent toxic ceramide accumulation.
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Affiliation(s)
| | | | - Kouichi Funato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan; (P.S.); (A.I.)
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30
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Otto GM, Cheunkarndee T, Leslie JM, Brar GA. Programmed cortical ER collapse drives selective ER degradation and inheritance in yeast meiosis. J Cell Biol 2021; 220:212710. [PMID: 34661602 PMCID: PMC8562846 DOI: 10.1083/jcb.202108105] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022] Open
Abstract
The endoplasmic reticulum (ER) carries out essential and conserved cellular functions, which depend on the maintenance of its structure and subcellular distribution. Here, we report developmentally regulated changes in ER morphology and composition during budding yeast meiosis, a conserved differentiation program that gives rise to gametes. A subset of the cortical ER collapses away from the plasma membrane at anaphase II, thus separating into a spatially distinct compartment. This programmed collapse depends on the transcription factor Ndt80, conserved ER membrane structuring proteins Lnp1 and reticulons, and the actin cytoskeleton. A subset of ER is retained at the mother cell plasma membrane and excluded from gamete cells via the action of ER-plasma membrane tethering proteins. ER remodeling is coupled to ER degradation by selective autophagy, which relies on ER collapse and is regulated by timed expression of the autophagy receptor Atg40. Thus, developmentally programmed changes in ER morphology determine the selective degradation or inheritance of ER subdomains by gametes.
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Affiliation(s)
- George Maxwell Otto
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Tia Cheunkarndee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Jessica Mae Leslie
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA.,Center for Computational Biology, University of California, Berkeley, Berkeley, CA
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31
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Bhattacharya M, Chatterjee S, Sharma AR, Agoramoorthy G, Chakraborty C. D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Appl Microbiol Biotechnol 2021; 105:9035-9045. [PMID: 34755213 PMCID: PMC8578012 DOI: 10.1007/s00253-021-11676-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022]
Abstract
The progression of the COVID-19 pandemic has generated numerous emerging variants of SARS-CoV-2 on a global scale. These variants have gained evolutionary advantages, comprising high virulence and serious infectivity due to multiple spike glycoprotein mutations. As a reason, variants are demonstrating significant abilities to escape the immune responses of the host. The D614G mutation in the S-glycoprotein of SARS-CoV-2 variants has shown the most efficient interaction with the ACE2 receptor of the cells. This explicit mutation at amino acid position 614 (aspartic acid-to-glycine substitution) is the prime cause of infection and re-infection. It changes the conformation of RBD and cleavage patterns S-glycoprotein with higher stability, replication fitness, and fusion efficiencies. Therefore, this review aims to provide several crucial pieces of information associated with the D614 mutational occurrence of SARS-CoV-2 variants and their infectivity patterns. This review will also effectively emphasize the mechanism of action of D614G mutant variants, immune escape, and partial vaccine escape of this virus. Furthermore, the viral characteristic changes leading to the current global pandemic condition have been highlighted. Here, we have tried to illustrate a novel direction for future researchers to develop effective therapeutic approaches and counterweight strategies to minimize the spread of COVID-19.Key points• D614G mutation arises within the S-glycoprotein of significant SARS-CoV-2 variants.• The D614G mutation affects infection, re-infection, cleavage patterns of S-glycoprotein, and replication fitness of SARS-CoV-2 variants.• The D614G mutation influences the immunity and partial vaccine escape.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756020, Odisha, India
| | - Srijan Chatterjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Kolkata, West Bengal, 700126, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | | | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Kolkata, West Bengal, 700126, India.
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32
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Lenoir G, D'Ambrosio JM, Dieudonné T, Čopič A. Transport Pathways That Contribute to the Cellular Distribution of Phosphatidylserine. Front Cell Dev Biol 2021; 9:737907. [PMID: 34540851 PMCID: PMC8440936 DOI: 10.3389/fcell.2021.737907] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/10/2021] [Indexed: 12/05/2022] Open
Abstract
Phosphatidylserine (PS) is a negatively charged phospholipid that displays a highly uneven distribution within cellular membranes, essential for establishment of cell polarity and other processes. In this review, we discuss how combined action of PS biosynthesis enzymes in the endoplasmic reticulum (ER), lipid transfer proteins (LTPs) acting within membrane contact sites (MCS) between the ER and other compartments, and lipid flippases and scramblases that mediate PS flip-flop between membrane leaflets controls the cellular distribution of PS. Enrichment of PS in specific compartments, in particular in the cytosolic leaflet of the plasma membrane (PM), requires input of energy, which can be supplied in the form of ATP or by phosphoinositides. Conversely, coupling between PS synthesis or degradation, PS flip-flop and PS transfer may enable PS transfer by passive flow. Such scenario is best documented by recent work on the formation of autophagosomes. The existence of lateral PS nanodomains, which is well-documented in the case of the PM and postulated for other compartments, can change the steepness or direction of PS gradients between compartments. Improvements in cellular imaging of lipids and membranes, lipidomic analysis of complex cellular samples, reconstitution of cellular lipid transport reactions and high-resolution structural data have greatly increased our understanding of cellular PS homeostasis. Our review also highlights how budding yeast has been instrumental for our understanding of the organization and transport of PS in cells.
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Affiliation(s)
- Guillaume Lenoir
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Juan Martín D'Ambrosio
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Thibaud Dieudonné
- Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alenka Čopič
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
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33
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Woods BL, Cannon KS, Vogt EJD, Crutchley JM, Gladfelter AS. Interplay of septin amphipathic helices in sensing membrane-curvature and filament bundling. Mol Biol Cell 2021; 32:br5. [PMID: 34319771 PMCID: PMC8684760 DOI: 10.1091/mbc.e20-05-0303] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The curvature of the membrane defines cell shape. Septins are GTP-binding proteins that assemble into heteromeric complexes and polymerize into filaments at areas of micron-scale membrane curvature. An amphipathic helix (AH) domain within the septin complex is necessary and sufficient for septins to preferentially assemble onto micron-scale curvature. Here we report that the nonessential fungal septin, Shs1, also has an AH domain capable of recognizing membrane curvature. In a septin mutant strain lacking a fully functional Cdc12 AH domain (cdc12-6), the C-terminal extension of Shs1, containing an AH domain, becomes essential. Additionally, we find that the Cdc12 AH domain is important for regulating septin filament bundling, suggesting septin AH domains have multiple, distinct functions and that bundling and membrane binding may be coordinately controlled.
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Affiliation(s)
- Benjamin L Woods
- Biology Department, University of North Carolina, Chapel Hill, NC 27599
| | - Kevin S Cannon
- Biology Department, University of North Carolina, Chapel Hill, NC 27599
| | - Ellysa J D Vogt
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - John M Crutchley
- Biology Department, University of North Carolina, Chapel Hill, NC 27599
| | - Amy S Gladfelter
- Biology Department, University of North Carolina, Chapel Hill, NC 27599.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599.,Marine Biological Laboratory, Woods Hole, MA 02543
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34
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Bin Imtiaz MK, Jessberger S. Isolation of adult mouse hippocampal neural stem cells for fluorescence loss in photobleaching assays. STAR Protoc 2021; 2:100695. [PMID: 34382020 PMCID: PMC8339235 DOI: 10.1016/j.xpro.2021.100695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
This protocol describes the isolation and culturing of primary neural stem cells (NSCs) from the adult mouse hippocampus, followed by the experimental approach for fluorescence loss in photobleaching assays, previously used to characterize the presence of an endoplasmic reticulum (ER) membrane diffusion barrier. The assay described here can be used to study live asymmetry in the ER membrane or other organelles that is established in dividing NSCs. For complete details on the use and execution of this protocol, please refer to Clay et al. (2014); bin Imtiaz et al. (2021); Lee et al. (2016); Luedeke et al. (2005); Moore et al. (2015); Shcheprova et al. (2008). Protocol describes the isolation of hippocampal neural stem cells (NSCs) Approach to culture NSCs for fluorescence loss in photobleaching (FLIP) assays FLIP assays of NSCs explained step by step
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Affiliation(s)
- Muhammad Khadeesh Bin Imtiaz
- Brain Research Institute, University of Zurich, Zurich 8057, Switzerland.,Department of Genetics and Development, Columbia University Medical Center, New York, NY 10033, USA
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35
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Spiliotis ET, McMurray MA. Masters of asymmetry - lessons and perspectives from 50 years of septins. Mol Biol Cell 2021; 31:2289-2297. [PMID: 32991244 PMCID: PMC7851956 DOI: 10.1091/mbc.e19-11-0648] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Septins are a unique family of GTPases, which were discovered 50 years ago as essential genes for the asymmetric cell shape and division of budding yeast. Septins assemble into filamentous nonpolar polymers, which associate with distinct membrane macrodomains and subpopulations of actin filaments and microtubules. While structurally a cytoskeleton-like element, septins function predominantly as spatial regulators of protein localization and interactions. Septin scaffolds and barriers have provided a long-standing paradigm for the generation and maintenance of asymmetry in cell membranes. Septins also promote asymmetry by regulating the spatial organization of the actin and microtubule cytoskeleton, and biasing the directionality of membrane traffic. In this 50th anniversary perspective, we highlight how septins have conserved and adapted their roles as effectors of membrane and cytoplasmic asymmetry across fungi and animals. We conclude by outlining principles of septin function as a module of symmetry breaking, which alongside the monomeric small GTPases provides a core mechanism for the biogenesis of molecular asymmetry and cell polarity.
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Affiliation(s)
| | - Michael A McMurray
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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36
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Mela A, Momany M. Septins coordinate cell wall integrity and lipid metabolism in a sphingolipid-dependent process. J Cell Sci 2021; 135:256543. [PMID: 33912961 DOI: 10.1242/jcs.258336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/31/2020] [Indexed: 01/09/2023] Open
Abstract
Septins colocalize with membrane sterol-rich regions and facilitate recruitment of cell wall synthases during wall remodeling. We show that null mutants missing an Aspergillus nidulans core septin present in hexamers and octamers (ΔaspAcdc11, ΔaspBcdc3 or ΔaspCcdc12) are sensitive to multiple cell wall-disturbing agents that activate the cell wall integrity MAPK pathway. The null mutant missing the octamer-exclusive core septin (ΔaspDcdc10) showed similar sensitivity, but only to a single cell wall-disturbing agent and the null mutant missing the noncore septin (ΔaspE) showed only very mild sensitivity to a different single agent. Core septin mutants showed changes in wall polysaccharide composition and chitin synthase localization. Mutants missing any of the five septins resisted ergosterol-disrupting agents. Hexamer mutants showed increased sensitivity to sphingolipid-disrupting agents. Core septins mislocalized after treatment with sphingolipid-disrupting agents, but not after ergosterol-disrupting agents. Our data suggest that the core septins are involved in cell wall integrity signaling, that all five septins are involved in monitoring ergosterol metabolism, that the hexamer septins are required for sphingolipid metabolism and that septins require sphingolipids to coordinate the cell wall integrity response.
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Affiliation(s)
- Alexander Mela
- Fungal Biology Group and Plant Biology Department, University of Georgia, 2502 Miller Plant Science Building, Athens, GA 30602, USA
| | - Michelle Momany
- Fungal Biology Group and Plant Biology Department, University of Georgia, 2502 Miller Plant Science Building, Athens, GA 30602, USA
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37
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Dawes IW, Perrone GG. Stress and ageing in yeast. FEMS Yeast Res 2021; 20:5670642. [PMID: 31816015 DOI: 10.1093/femsyr/foz085] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023] Open
Abstract
There has long been speculation about the role of various stresses in ageing. Some stresses have beneficial effects on ageing-dependent on duration and severity of the stress, others have negative effects and the question arises whether these negative effects are causative of ageing or the result of the ageing process. Cellular responses to many stresses are highly coordinated in a concerted way and hence there is a great deal of cross-talk between different stresses. Here the relevant aspects of the coordination of stress responses and the roles of different stresses on yeast cell ageing are discussed, together with the various functions that are involved. The cellular processes that are involved in alleviating the effects of stress on ageing are considered, together with the possible role of early stress events on subsequent ageing of cells.
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Affiliation(s)
- Ian W Dawes
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Gabriel G Perrone
- School of Science and Health, Western Sydney University, Campbelltown, NSW 2560, Australia
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38
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Szuba A, Bano F, Castro-Linares G, Iv F, Mavrakis M, Richter RP, Bertin A, Koenderink GH. Membrane binding controls ordered self-assembly of animal septins. eLife 2021; 10:63349. [PMID: 33847563 PMCID: PMC8099429 DOI: 10.7554/elife.63349] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Septins are conserved cytoskeletal proteins that regulate cell cortex mechanics. The mechanisms of their interactions with the plasma membrane remain poorly understood. Here, we show by cell-free reconstitution that binding to flat lipid membranes requires electrostatic interactions of septins with anionic lipids and promotes the ordered self-assembly of fly septins into filamentous meshworks. Transmission electron microscopy reveals that both fly and mammalian septin hexamers form arrays of single and paired filaments. Atomic force microscopy and quartz crystal microbalance demonstrate that the fly filaments form mechanically rigid, 12- to 18-nm thick, double layers of septins. By contrast, C-terminally truncated septin mutants form 4-nm thin monolayers, indicating that stacking requires the C-terminal coiled coils on DSep2 and Pnut subunits. Our work shows that membrane binding is required for fly septins to form ordered arrays of single and paired filaments and provides new insights into the mechanisms by which septins may regulate cell surface mechanics.
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Affiliation(s)
- Agata Szuba
- AMOLF, Department of Living Matter, Biological Soft Matter group, Amsterdam, Netherlands
| | - Fouzia Bano
- School of Biomedical Sciences, Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, United Kingdom.,Bragg Centre for Materials Research, University of Leeds, Leeds, United Kingdom
| | - Gerard Castro-Linares
- AMOLF, Department of Living Matter, Biological Soft Matter group, Amsterdam, Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Francois Iv
- Institut Fresnel, CNRS, Aix-Marseille Univ, Centrale Marseille, Marseille, France
| | - Manos Mavrakis
- Institut Fresnel, CNRS, Aix-Marseille Univ, Centrale Marseille, Marseille, France
| | - Ralf P Richter
- School of Biomedical Sciences, Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, United Kingdom.,Bragg Centre for Materials Research, University of Leeds, Leeds, United Kingdom
| | - Aurélie Bertin
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Paris, France.,Sorbonne Université, Paris, France
| | - Gijsje H Koenderink
- AMOLF, Department of Living Matter, Biological Soft Matter group, Amsterdam, Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
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39
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Santos FC, Marquês JT, Bento‐Oliveira A, Almeida RF. Sphingolipid‐enriched domains in fungi. FEBS Lett 2020; 594:3698-3718. [DOI: 10.1002/1873-3468.13986] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/21/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Filipa C. Santos
- Centro de Química Estrutural Faculdade de Ciências, Universidade de Lisboa Campo Grande Portugal
| | - Joaquim T. Marquês
- Centro de Química Estrutural Faculdade de Ciências, Universidade de Lisboa Campo Grande Portugal
| | - Andreia Bento‐Oliveira
- Centro de Química Estrutural Faculdade de Ciências, Universidade de Lisboa Campo Grande Portugal
| | - Rodrigo F.M. Almeida
- Centro de Química Estrutural Faculdade de Ciências, Universidade de Lisboa Campo Grande Portugal
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40
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Wang HY, Bharti D, Levental I. Membrane Heterogeneity Beyond the Plasma Membrane. Front Cell Dev Biol 2020; 8:580814. [PMID: 33330457 PMCID: PMC7710808 DOI: 10.3389/fcell.2020.580814] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/02/2020] [Indexed: 01/21/2023] Open
Abstract
The structure and organization of cellular membranes have received intense interest, particularly in investigations of the raft hypothesis. The vast majority of these investigations have focused on the plasma membrane of mammalian cells, yielding significant progress in understanding membrane heterogeneity in terms of lipid composition, molecular structure, dynamic regulation, and functional relevance. In contrast, investigations on lipid organization in other membrane systems have been comparatively scarce, despite the likely relevance of membrane domains in these contexts. In this review, we summarize recent observations on lipid organization in organellar membranes, including endoplasmic reticulum, Golgi, endo-lysosomes, lipid droplets, and secreted membranes like lung surfactant, milk fat globule membranes, and viral membranes. Across these non-plasma membrane systems, it seems that the biophysical principles underlying lipid self-organization contribute to lateral domains.
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Affiliation(s)
- Hong-Yin Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
| | - Deepti Bharti
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
- National Institute of Technology, Rourkela, India
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
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41
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Goodman JS, King GA, Ünal E. Cellular quality control during gametogenesis. Exp Cell Res 2020; 396:112247. [PMID: 32882217 PMCID: PMC7572901 DOI: 10.1016/j.yexcr.2020.112247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/18/2020] [Accepted: 08/23/2020] [Indexed: 12/12/2022]
Abstract
A hallmark of aging is the progressive accumulation of cellular damage. Age-induced damage arises due to a decrease in organelle function along with a decline in protein quality control. Although somatic tissues deteriorate with age, the germline must maintain cellular homeostasis in order to ensure the production of healthy progeny. While germline quality control has been primarily studied in multicellular organisms, recent evidence suggests the existence of gametogenesis-specific quality control mechanisms in unicellular eukaryotes, highlighting the evolutionary conservation of meiotic events beyond chromosome morphogenesis. Notably, budding yeast eliminates age-induced damage during meiotic differentiation, employing novel organelle and protein quality control mechanisms to produce young and healthy gametes. Similarly, organelle and protein quality control is present in metazoan gametogenesis; however, whether and how these mechanisms contribute to cellular rejuvenation requires further investigation. Here, we summarize recent findings that describe organelle and protein quality control in budding yeast gametogenesis, examine similar quality control mechanisms in metazoan development, and identify research directions that will improve our understanding of meiotic cellular rejuvenation.
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Affiliation(s)
- Jay S Goodman
- Department of Molecular and Cell Biology, University of California Berkeley, 94720, USA
| | - Grant A King
- Department of Molecular and Cell Biology, University of California Berkeley, 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California Berkeley, 94720, USA.
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42
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Prasad R, Sliwa-Gonzalez A, Barral Y. Mapping bilayer thickness in the ER membrane. SCIENCE ADVANCES 2020; 6:6/46/eaba5130. [PMID: 33177076 PMCID: PMC7673731 DOI: 10.1126/sciadv.aba5130] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 09/23/2020] [Indexed: 05/20/2023]
Abstract
In the plasma membrane and in synthetic membranes, resident lipids may laterally unmix to form domains of distinct biophysical properties. Whether lipids also drive the lateral organization of intracellular membranes is largely unknown. Here, we describe genetically encoded fluorescent reporters visualizing local variations in bilayer thickness. Using them, we demonstrate that long-chained ceramides promote the formation of discrete domains of increased bilayer thickness in the yeast ER, particularly in the future plane of cleavage and at ER-trans-Golgi contact sites. Thickening of the ER membrane in the cleavage plane contributed to the formation of lateral diffusion barriers, which restricted the passage of short, but not long, protein transmembrane domains between the mother and bud ER compartments. Together, our data establish that the ER membrane is laterally organized and that ceramides drive this process, and provide insights into the physical nature and biophysical mechanisms of the lateral diffusion barriers that compartmentalize the ER.
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Affiliation(s)
- Rupali Prasad
- Institute of Biochemistry, Department of Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Andrzej Sliwa-Gonzalez
- Institute of Biochemistry, Department of Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, Department of Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
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43
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Ardham VR, Zoni V, Adamowicz S, Campomanes P, Vanni S. Accurate Estimation of Membrane Capacitance from Atomistic Molecular Dynamics Simulations of Zwitterionic Lipid Bilayers. J Phys Chem B 2020; 124:8278-8286. [PMID: 32856913 DOI: 10.1021/acs.jpcb.0c03145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Lipid membranes are indispensable to life, and they regulate countless cellular processes. To investigate the properties of membranes under controlled conditions, numerous reconstitution methods have been developed over the last few decades. Several of these methods result in the formation of lipid bilayers containing residual hydrophobic molecules between the two monolayers. These contaminants might alter membrane properties, including bilayer thickness, that is usually inferred from measurements of membrane capacitance assuming a simple slab model. However, recent measurements on solvent-free bilayers raised significant questions on the reliability of this approach. To reconcile the observed discrepancies, we developed a protocol to predict membrane capacitance from the dielectric profile of lipid bilayers computed from molecular dynamics simulations. Our methodology shows excellent agreement against available data on solvent-free noncharged bilayers, and it confirms that the uniform slab model is a reliable approximation from which to infer membrane capacitance. We find that the effective electrical thickness contributing to membrane capacitance is different from the hydrophobic thickness inferred from X-ray scattering form factors. We apply our model to estimate the concentration of residual solvent in reconstituted systems, and we propose that our protocol could be used to infer membrane properties in the presence of hydrophobic solvents.
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Affiliation(s)
- Vikram Reddy Ardham
- Chemin du Musée 10, Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Valeria Zoni
- Chemin du Musée 10, Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Sylvain Adamowicz
- Chemin du Musée 10, Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Pablo Campomanes
- Chemin du Musée 10, Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Stefano Vanni
- Chemin du Musée 10, Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
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44
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Niwa M. A cell cycle checkpoint for the endoplasmic reticulum. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118825. [PMID: 32828757 DOI: 10.1016/j.bbamcr.2020.118825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
The generation of new cells is one of the most fundamental aspects of cell biology. Proper regulation of the cell cycle is critical for human health, as underscored by many diseases associated with errors in cell cycle regulation, including both cancer and hereditary diseases. A large body of work has identified regulatory mechanisms and checkpoints that ensure accurate and timely replication and segregation of chromosomal DNA. However, few studies have evaluated the extent to which similar checkpoints exist for the division of cytoplasmic components, including organelles. Such checkpoint mechanisms might be crucial for compartments that cannot be generated de novo, such as the endoplasmic reticulum (ER). In this review, we highlight recent work in the model organism Saccharomyces cerevisiae that led to the discovery of such a checkpoint that ensures that cells inherit functional ER into the daughter cell.
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Affiliation(s)
- Maho Niwa
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, NSB#1, Rm 5328, 9500 Gilman Drive, La Jolla, CA 92093-0377, United States of America.
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45
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Zaman MF, Nenadic A, Radojičić A, Rosado A, Beh CT. Sticking With It: ER-PM Membrane Contact Sites as a Coordinating Nexus for Regulating Lipids and Proteins at the Cell Cortex. Front Cell Dev Biol 2020; 8:675. [PMID: 32793605 PMCID: PMC7387695 DOI: 10.3389/fcell.2020.00675] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/03/2020] [Indexed: 12/31/2022] Open
Abstract
Membrane contact sites between the cortical endoplasmic reticulum (ER) and the plasma membrane (PM) provide a direct conduit for small molecule transfer and signaling between the two largest membranes of the cell. Contact is established through ER integral membrane proteins that physically tether the two membranes together, though the general mechanism is remarkably non-specific given the diversity of different tethering proteins. Primary tethers including VAMP-associated proteins (VAPs), Anoctamin/TMEM16/Ist2p homologs, and extended synaptotagmins (E-Syts), are largely conserved in most eukaryotes and are both necessary and sufficient for establishing ER-PM association. In addition, other species-specific ER-PM tether proteins impart unique functional attributes to both membranes at the cell cortex. This review distils recent functional and structural findings about conserved and species-specific tethers that form ER-PM contact sites, with an emphasis on their roles in the coordinate regulation of lipid metabolism, cellular structure, and responses to membrane stress.
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Affiliation(s)
- Mohammad F Zaman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Aleksa Nenadic
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Ana Radojičić
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Abel Rosado
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Christopher T Beh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,The Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada
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46
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Abstract
Asymmetric cell division (ACD) is an evolutionarily conserved mechanism used by prokaryotes and eukaryotes alike to control cell fate and generate cell diversity. A detailed mechanistic understanding of ACD is therefore necessary to understand cell fate decisions in health and disease. ACD can be manifested in the biased segregation of macromolecules, the differential partitioning of cell organelles, or differences in sibling cell size or shape. These events are usually preceded by and influenced by symmetry breaking events and cell polarization. In this Review, we focus predominantly on cell intrinsic mechanisms and their contribution to cell polarization, ACD and binary cell fate decisions. We discuss examples of polarized systems and detail how polarization is established and, whenever possible, how it contributes to ACD. Established and emerging model organisms will be considered alike, illuminating both well-documented and underexplored forms of polarization and ACD.
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Affiliation(s)
- Bharath Sunchu
- Department of Biology, University of Washington, Life Science Building, Seattle, WA 98195, USA
| | - Clemens Cabernard
- Department of Biology, University of Washington, Life Science Building, Seattle, WA 98195, USA
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47
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Khmelinskaia A, Marquês JMT, Bastos AEP, Antunes CAC, Bento-Oliveira A, Scolari S, Lobo GMDS, Malhó R, Herrmann A, Marinho HS, de Almeida RFM. Liquid-Ordered Phase Formation by Mammalian and Yeast Sterols: A Common Feature With Organizational Differences. Front Cell Dev Biol 2020; 8:337. [PMID: 32596234 PMCID: PMC7304482 DOI: 10.3389/fcell.2020.00337] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/17/2020] [Indexed: 11/13/2022] Open
Abstract
Here, biophysical properties of membranes enriched in three metabolically related sterols are analyzed both in vitro and in vivo. Unlike cholesterol and ergosterol, the common metabolic precursor zymosterol is unable to induce the formation of a liquid ordered (l o) phase in model lipid membranes and can easily accommodate in a gel phase. As a result, Zym has a marginal ability to modulate the passive membrane permeability of lipid vesicles with different compositions, contrary to cholesterol and ergosterol. Using fluorescence-lifetime imaging microscopy of an aminostyryl dye in living mammalian and yeast cells we established a close parallel between sterol-dependent membrane biophysical properties in vivo and in vitro. This approach unraveled fundamental differences in yeast and mammalian plasma membrane organization. It is often suggested that, in eukaryotes, areas that are sterol-enriched are also rich in sphingolipids, constituting highly ordered membrane regions. Our results support that while cholesterol is able to interact with saturated lipids, ergosterol seems to interact preferentially with monounsaturated phosphatidylcholines. Taken together, we show that different eukaryotic kingdoms developed unique solutions for the formation of a sterol-rich plasma membrane, a common evolutionary trait that accounts for sterol structural diversity.
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Affiliation(s)
- Alena Khmelinskaia
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Joaquim M T Marquês
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - André E P Bastos
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Catarina A C Antunes
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Andreia Bento-Oliveira
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Silvia Scolari
- Department of Biology, Molecular Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gerson M da S Lobo
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Rui Malhó
- Faculdade de Ciências, BioISI, Universidade de Lisboa, Lisbon, Portugal
| | - Andreas Herrmann
- Department of Biology, Molecular Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - H Susana Marinho
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Rodrigo F M de Almeida
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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48
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Bento-Oliveira A, Santos FC, Marquês JT, Paulo PMR, Korte T, Herrmann A, Marinho HS, de Almeida RFM. Yeast Sphingolipid-Enriched Domains and Membrane Compartments in the Absence of Mannosyldiinositolphosphorylceramide. Biomolecules 2020; 10:biom10060871. [PMID: 32517183 PMCID: PMC7356636 DOI: 10.3390/biom10060871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/25/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
The relevance of mannosyldiinositolphosphorylceramide [M(IP)2C] synthesis, the terminal complex sphingolipid class in the yeast Saccharomyces cerevisiae, for the lateral organization of the plasma membrane, and in particular for sphingolipid-enriched gel domains, was investigated by fluorescence spectroscopy and microscopy. We also addressed how changing the complex sphingolipid profile in the plasma membrane could influence the membrane compartments (MC) containing either the arginine/ H+ symporter Can1p (MCC) or the proton ATPase Pma1p (MCP). To achieve these goals, wild-type (wt) and ipt1Δ cells, which are unable to synthesize M(IP)2C accumulating mannosylinositolphosphorylceramide (MIPC), were compared. Living cells, isolated plasma membrane and giant unilamellar vesicles reconstituted from plasma membrane lipids were labelled with various fluorescent membrane probes that report the presence and organization of distinct lipid domains, global order, and dielectric properties. Can1p and Pma1p were tagged with GFP and mRFP, respectively, in both yeast strains, to evaluate their lateral organization using confocal fluorescence intensity and fluorescence lifetime imaging. The results show that IPT1 deletion strongly affects the rigidity of gel domains but not their relative abundance, whereas no significant alterations could be perceived in ergosterol-enriched domains. Moreover, in these cells lacking M(IP)2C, a clear alteration in Pma1p membrane distribution, but no significant changes in Can1p distribution, were observed. Thus, this work reinforces the notion that sphingolipid-enriched domains distinct from ergosterol-enriched regions are present in the S. cerevisiae plasma membrane and suggests that M(IP)2C is important for a proper hydrophobic chain packing of sphingolipids in the gel domains of wt cells. Furthermore, our results strongly support the involvement of sphingolipid domains in the formation and stability of the MCP, possibly being enriched in this compartment.
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Affiliation(s)
- Andreia Bento-Oliveira
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (A.B.-O.); (F.C.S.); (J.T.M.); (H.S.M.)
| | - Filipa C. Santos
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (A.B.-O.); (F.C.S.); (J.T.M.); (H.S.M.)
| | - Joaquim Trigo Marquês
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (A.B.-O.); (F.C.S.); (J.T.M.); (H.S.M.)
| | - Pedro M. R. Paulo
- Centro de Química Estrutural, Instituto Superior Técnico, 1049-001 Lisbon, Portugal;
| | - Thomas Korte
- Department of Biology, Molecular Biophysics, IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (T.K.); (A.H.)
| | - Andreas Herrmann
- Department of Biology, Molecular Biophysics, IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; (T.K.); (A.H.)
| | - H. Susana Marinho
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (A.B.-O.); (F.C.S.); (J.T.M.); (H.S.M.)
| | - Rodrigo F. M. de Almeida
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (A.B.-O.); (F.C.S.); (J.T.M.); (H.S.M.)
- Correspondence: ; Tel.: +351-217-500-925
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49
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Lau Y, Oamen HP, Caudron F. Protein Phase Separation during Stress Adaptation and Cellular Memory. Cells 2020; 9:cells9051302. [PMID: 32456195 PMCID: PMC7291175 DOI: 10.3390/cells9051302] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022] Open
Abstract
Cells need to organise and regulate their biochemical processes both in space and time in order to adapt to their surrounding environment. Spatial organisation of cellular components is facilitated by a complex network of membrane bound organelles. Both the membrane composition and the intra-organellar content of these organelles can be specifically and temporally controlled by imposing gates, much like bouncers controlling entry into night-clubs. In addition, a new level of compartmentalisation has recently emerged as a fundamental principle of cellular organisation, the formation of membrane-less organelles. Many of these structures are dynamic, rapidly condensing or dissolving and are therefore ideally suited to be involved in emergency cellular adaptation to stresses. Remarkably, the same proteins have also the propensity to adopt self-perpetuating assemblies which properties fit the needs to encode cellular memory. Here, we review some of the principles of phase separation and the function of membrane-less organelles focusing particularly on their roles during stress response and cellular memory.
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50
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Manzano-López J, Monje-Casas F. Asymmetric cell division and replicative aging: a new perspective from the spindle poles. Curr Genet 2020; 66:719-727. [PMID: 32266430 DOI: 10.1007/s00294-020-01074-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/26/2020] [Accepted: 03/28/2020] [Indexed: 12/25/2022]
Abstract
Although cell division is usually portrayed as an equitable process by which a progenitor cell originates two identical daughter cells, there are multiple examples of asymmetric divisions that generate two cells that differ in their content, morphology and/or proliferative potential. The capacity of the cells to generate asymmetry during their division is of paramount biological relevance, playing essential roles during embryonic development, cellular regeneration and tissue morphogenesis. Problems with the proper establishment of asymmetry and polarity during cell division can give rise to cancer and neurodevelopmental disorders, as well as to also accelerate cellular aging. Interestingly, the microtubule organizing centers that orchestrate the formation of the mitotic spindle have been described among the cellular structures that can be differentially allocated during asymmetric cell divisions. This mini-review focuses on recent research from our group and others uncovering a role for the non-random distribution of the spindle-associated microtubule organizing centers in the differential distribution of aging factors during asymmetric mitoses and therefore in the maintenance of the replicative lifespan of the cells.
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Affiliation(s)
- Javier Manzano-López
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC) - University of Seville - University Pablo de Olavide, Avda. Américo Vespucio, 24, P.C.T. Cartuja 93, 41092, Sevilla, Spain.
| | - Fernando Monje-Casas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC) - University of Seville - University Pablo de Olavide, Avda. Américo Vespucio, 24, P.C.T. Cartuja 93, 41092, Sevilla, Spain.
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