1
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Sakai Y, Oku M. ATG and ESCRT control multiple modes of microautophagy. FEBS Lett 2024; 598:48-58. [PMID: 37857501 DOI: 10.1002/1873-3468.14760] [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: 07/20/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 10/21/2023]
Abstract
The discovery of microautophagy, the direct engulfment of cytoplasmic material by the lysosome, dates back to 1966 in a morphological study of mammalian cells by Christian de Duve. Since then, studies on microautophagy have shifted toward the elucidation of the physiological significance of the process. However, in contrast to macroautophagy, studies on the molecular mechanisms of microautophagy have been limited. Only recent studies revealed that ATG proteins involved in macroautophagy are also operative in several types of microautophagy and that ESCRT proteins, responsible for the multivesicular body pathway, play a central role in most microautophagy processes. In this review, we summarize our current knowledge on the function of ATG and ESCRT proteins in microautophagy.
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Affiliation(s)
- Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Japan
| | - Masahide Oku
- Department of Bioscience and Biotechnology, Faculty of Bioenvironmental Sciences, Kyoto University of Advanced Science, Kameoka, Japan
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2
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Santana-Sosa S, Matos-Perdomo E, Ayra-Plasencia J, Machín F. A Yeast Mitotic Tale for the Nucleus and the Vacuoles to Embrace. Int J Mol Sci 2023; 24:9829. [PMID: 37372977 DOI: 10.3390/ijms24129829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The morphology of the nucleus is roughly spherical in most eukaryotic cells. However, this organelle shape needs to change as the cell travels through narrow intercellular spaces during cell migration and during cell division in organisms that undergo closed mitosis, i.e., without dismantling the nuclear envelope, such as yeast. In addition, the nuclear morphology is often modified under stress and in pathological conditions, being a hallmark of cancer and senescent cells. Thus, understanding nuclear morphological dynamics is of uttermost importance, as pathways and proteins involved in nuclear shaping can be targeted in anticancer, antiaging, and antifungal therapies. Here, we review how and why the nuclear shape changes during mitotic blocks in yeast, introducing novel data that associate these changes with both the nucleolus and the vacuole. Altogether, these findings suggest a close relationship between the nucleolar domain of the nucleus and the autophagic organelle, which we also discuss here. Encouragingly, recent evidence in tumor cell lines has linked aberrant nuclear morphology to defects in lysosomal function.
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Affiliation(s)
- Silvia Santana-Sosa
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Emiliano Matos-Perdomo
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Jessel Ayra-Plasencia
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Félix Machín
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
- Faculty of Health Sciences, Fernando Pessoa Canarias University, 35450 Santa María de Guía, Spain
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3
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Kümmel D, Herrmann E, Langemeyer L, Ungermann C. Molecular insights into endolysosomal microcompartment formation and maintenance. Biol Chem 2022; 404:441-454. [PMID: 36503831 DOI: 10.1515/hsz-2022-0294] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022]
Abstract
Abstract
The endolysosomal system of eukaryotic cells has a key role in the homeostasis of the plasma membrane, in signaling and nutrient uptake, and is abused by viruses and pathogens for entry. Endocytosis of plasma membrane proteins results in vesicles, which fuse with the early endosome. If destined for lysosomal degradation, these proteins are packaged into intraluminal vesicles, converting an early endosome to a late endosome, which finally fuses with the lysosome. Each of these organelles has a unique membrane surface composition, which can form segmented membrane microcompartments by membrane contact sites or fission proteins. Furthermore, these organelles are in continuous exchange due to fission and fusion events. The underlying machinery, which maintains organelle identity along the pathway, is regulated by signaling processes. Here, we will focus on the Rab5 and Rab7 GTPases of early and late endosomes. As molecular switches, Rabs depend on activating guanine nucleotide exchange factors (GEFs). Over the last years, we characterized the Rab7 GEF, the Mon1-Ccz1 (MC1) complex, and key Rab7 effectors, the HOPS complex and retromer. Structural and functional analyses of these complexes lead to a molecular understanding of their function in the context of organelle biogenesis.
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Affiliation(s)
- Daniel Kümmel
- Institute of Biochemistry, University of Münster , Corrensstraße 36 , D-48149 Münster , Germany
| | - Eric Herrmann
- Institute of Biochemistry, University of Münster , Corrensstraße 36 , D-48149 Münster , Germany
| | - Lars Langemeyer
- Department of Biology/Chemistry, Biochemistry section , Osnabrück University , Barbarastraße 13 , D-49076 Osnabrück , Germany
- Center of Cellular Nanoanalytics (CellNanOs) , Osnabrück University , Barbarastraße 11 , D-49076 Osnabrück , Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry section , Osnabrück University , Barbarastraße 13 , D-49076 Osnabrück , Germany
- Center of Cellular Nanoanalytics (CellNanOs) , Osnabrück University , Barbarastraße 11 , D-49076 Osnabrück , Germany
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4
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Matos-Perdomo E, Santana-Sosa S, Ayra-Plasencia J, Medina-Suárez S, Machín F. The vacuole shapes the nucleus and the ribosomal DNA loop during mitotic delays. Life Sci Alliance 2022; 5:5/10/e202101161. [PMID: 35961781 PMCID: PMC9375157 DOI: 10.26508/lsa.202101161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022] Open
Abstract
Chromosome structuring and condensation is one of the main features of mitosis. Here, Matos-Perdomo et al show how the nuclear envelope reshapes around the vacuole to give rise to the outstanding ribosomal DNA loop in budding yeast. The ribosomal DNA (rDNA) array of Saccharomyces cerevisiae has served as a model to address chromosome organization. In cells arrested before anaphase (mid-M), the rDNA acquires a highly structured chromosomal organization referred to as the rDNA loop, whose length can double the cell diameter. Previous works established that complexes such as condensin and cohesin are essential to attain this structure. Here, we report that the rDNA loop adopts distinct presentations that arise as spatial adaptations to changes in the nuclear morphology triggered during mid-M arrests. Interestingly, the formation of the rDNA loop results in the appearance of a space under the loop (SUL) which is devoid of nuclear components yet colocalizes with the vacuole. We show that the rDNA-associated nuclear envelope (NE) often reshapes into a ladle to accommodate the vacuole in the SUL, with the nucleus becoming bilobed and doughnut-shaped. Finally, we demonstrate that the formation of the rDNA loop and the SUL require TORC1, membrane synthesis and functional vacuoles, yet is independent of nucleus–vacuole junctions and rDNA-NE tethering.
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Affiliation(s)
- Emiliano Matos-Perdomo
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Silvia Santana-Sosa
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jessel Ayra-Plasencia
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Sara Medina-Suárez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain .,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Santa María de Guía, Spain
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5
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Duarte PV, Hardenberg R, Mari M, Walter S, Reggiori F, Fröhlich F, Montoro AG, Ungermann C. The yeast LYST homolog Bph1 is a Rab5 effector and prevents Atg8 lipidation at endosomes. J Cell Sci 2022; 135:274866. [PMID: 35343566 DOI: 10.1242/jcs.259421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/18/2022] [Indexed: 01/18/2023] Open
Abstract
Lysosomes mediate degradation of macromolecules to their precursors for their cellular recycling. Additionally, lysosome-related organelles mediate cell type-specific functions. The Chédiak-Higashi syndrome is an autosomal, recessive disease, in which loss of the protein LYST causes defects in lysosomes and lysosome-related organelles. The molecular function of LYST, however, is largely unknown. Here, we dissected the function of the yeast LYST homolog, Bph1. We show that Bph1 is an endosomal protein, and an effector of the minor Rab5 isoform Ypt52. Strikingly, the bph1▵ mutant has lipidated Atg8 on their endosomes, which is sorted via late endosomes into the vacuole lumen under non-autophagy inducing conditions. In agreement, proteomics of bph1▵ vacuoles reveal an accumulation of Atg8, reduced flux via selective autophagy, and defective endocytosis. Additionally, bph1▵ cells have reduced autophagic flux under starvation conditions. Our observations suggest that Bph1 is a novel Rab5 effector that maintains endosomal functioning. When lost, Atg8 is lipidated at endosomes even during normal growth and ends up in the vacuole lumen. Thus, our results contribute to the understanding of the role of LYST-related proteins and associated diseases.
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Affiliation(s)
- Prado Vargas Duarte
- Osnabrück University, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Ralph Hardenberg
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stefan Walter
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Florian Fröhlich
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany.,Osnabrück University, Department of Biology/Chemistry, Molecular Membrane Biology section, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Ayelén González Montoro
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany.,Osnabrück University, Department of Biology/Chemistry, Cellular Communication Laboratory, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Christian Ungermann
- Osnabrück University, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076 Osnabrück, Germany.,Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
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6
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Konstantinidis G, Tavernarakis N. Autophagy of the Nucleus in Health and Disease. Front Cell Dev Biol 2022; 9:814955. [PMID: 35047516 PMCID: PMC8762222 DOI: 10.3389/fcell.2021.814955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/06/2021] [Indexed: 12/27/2022] Open
Abstract
Nucleophagy is an organelle-selective subtype of autophagy that targets nuclear material for degradation. The macroautophagic delivery of micronuclei to the vacuole, together with the nucleus-vacuole junction-dependent microautophagic degradation of nuclear material, were first observed in yeast. Nuclear pore complexes and ribosomal DNA are typically excluded during conventional macronucleophagy and micronucleophagy, indicating that degradation of nuclear cargo is tightly regulated. In mammals, similarly to other autophagy subtypes, nucleophagy is crucial for cellular differentiation and development, in addition to enabling cells to respond to various nuclear insults and cell cycle perturbations. A common denominator of all nucleophagic processes characterized in diverse organisms is the dependence on the core autophagic machinery. Here, we survey recent studies investigating the autophagic processing of nuclear components. We discuss nucleophagic events in the context of pathology, such as neurodegeneration, cancer, DNA damage, and ageing.
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Affiliation(s)
- Georgios Konstantinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece.,Department of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece
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7
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Hollenstein DM, Licheva M, Konradi N, Schweida D, Mancilla H, Mari M, Reggiori F, Kraft C. Spatial control of avidity regulates initiation and progression of selective autophagy. Nat Commun 2021; 12:7194. [PMID: 34893607 PMCID: PMC8664900 DOI: 10.1038/s41467-021-27420-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/17/2021] [Indexed: 11/11/2022] Open
Abstract
Autophagosomes form at the endoplasmic reticulum in mammals, and between the vacuole and the endoplasmic reticulum in yeast. However, the roles of these sites and the mechanisms regulating autophagosome formation are incompletely understood. Vac8 is required for autophagy and recruits the Atg1 kinase complex to the vacuole. Here we show that Vac8 acts as a central hub to nucleate the phagophore assembly site at the vacuolar membrane during selective autophagy. Vac8 directly recruits the cargo complex via the Atg11 scaffold. In addition, Vac8 recruits the phosphatidylinositol 3-kinase complex independently of autophagy. Cargo-dependent clustering and Vac8-dependent sequestering of these early autophagy factors, along with local Atg1 activation, promote phagophore assembly site assembly at the vacuole. Importantly, ectopic Vac8 redirects autophagosome formation to the nuclear membrane, indicating that the vacuolar membrane is not specifically required. We propose that multiple avidity-driven interactions drive the initiation and progression of selective autophagy.
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Affiliation(s)
- David M Hollenstein
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Nicole Konradi
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - David Schweida
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Hector Mancilla
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Muriel Mari
- Department of Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
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8
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Liao PC, Garcia EJ, Tan G, Tsang CA, Pon LA. Roles for L o microdomains and ESCRT in ER stress-induced lipid droplet microautophagy in budding yeast. Mol Biol Cell 2021; 32:br12. [PMID: 34668753 PMCID: PMC8694086 DOI: 10.1091/mbc.e21-04-0179] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Microlipophagy (µLP), degradation of lipid droplets (LDs) by microautophagy, occurs by autophagosome-independent direct uptake of LDs at lysosomes/vacuoles in response to nutrient limitations and ER stressors in Saccharomyces cerevisiae. In nutrient-limited yeast, liquid-ordered (Lo) microdomains, sterol-rich raftlike regions in vacuolar membranes, are sites of membrane invagination during LD uptake. The endosome sorting complex required for transport (ESCRT) is required for sterol transport during Lo formation under these conditions. However, ESCRT has been implicated in mediating membrane invagination during µLP induced by ER stressors or the diauxic shift from glycolysis- to respiration-driven growth. Here we report that ER stress induced by lipid imbalance and other stressors induces Lo microdomain formation. This process is ESCRT independent and dependent on Niemann-Pick type C sterol transfer proteins. Inhibition of ESCRT or Lo microdomain formation partially inhibits lipid imbalance-induced µLP, while inhibition of both blocks this µLP. Finally, although the ER stressors dithiothreitol or tunicamycin induce Lo microdomains, µLP in response to these stressors is ESCRT dependent and Lo microdomain independent. Our findings reveal that Lo microdomain formation is a yeast stress response, and stress-induced Lo microdomain formation occurs by stressor-specific mechanisms. Moreover, ESCRT and Lo microdomains play functionally distinct roles in LD uptake during stress-induced µLP.
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Affiliation(s)
- Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Gary Tan
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Catherine A Tsang
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
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9
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Mijaljica D, Klionsky DJ. The necessity of nucleophagic modality. Autophagy 2021; 18:443-448. [PMID: 34643473 DOI: 10.1080/15548627.2021.1971380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Nucleophagy, the selective subtype of autophagy that predominantly targets only a selected and (nonessential) portion of the nucleus, and rarely the nucleus in its entirety, for degradation, reinforces the paradigm that nucleophagy recycling is a meticulous and highly delicate process guarded by fail-safe mechanisms. Our goal in this commentary is to encourage autophagy researchers and other scientists to explore nucleophagy blind spots and gain advanced insights into the diverse roles of this process and its selective modality as they pertain to intranuclear quality control and cellular homeostasis. Identifying and deciphering nucleophagic signaling, regulation, molecular mechanism(s) and its mediators, cargo composition and nuclear membrane dynamics under numerous physiological and/or pathological settings will provide important advances in our understanding of this critical type of organelle-selective autophagy.Abbreviations: INM, inner nuclear membrane; LN, late nucleophagy; mRNA, messenger RNA; NE, nuclear envelope; NL, nuclear lamina; NPC(s), nuclear pore complex(es); NVJ(s), nucleus-vacuole junction(s); ONM, outer nuclear membrane; PMN, piecemeal microautophagy of the nucleus; PND, programmed nuclear death; PNuD, programmed nuclear destruction; rDNA/rRNA, ribosomal DNA/RNA.
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Affiliation(s)
| | - Daniel J Klionsky
- Department of Molecular, Cellular, and Developmental Biology, and the Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
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10
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Mioka T, Guo T, Wang S, Tsuji T, Kishimoto T, Fujimoto T, Tanaka K. Characterization of micron-scale protein-depleted plasma membrane domains in phosphatidylserine-deficient yeast cells. J Cell Sci 2021; 135:261783. [PMID: 34000034 DOI: 10.1242/jcs.256529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
Membrane phase separation to form micron-scale domains of lipids and proteins occurs in artificial membranes; however, a similar large-scale phase separation has not been reported in the plasma membrane of the living cells. We show here that a stable micron-scale protein-depleted region is generated in the plasma membrane of yeast mutants lacking phosphatidylserine at high temperatures. We named this region the 'void zone'. Transmembrane proteins and certain peripheral membrane proteins and phospholipids are excluded from the void zone. The void zone is rich in ergosterol, and requires ergosterol and sphingolipids for its formation. Such properties are also found in the cholesterol-enriched domains of phase-separated artificial membranes, but the void zone is a novel membrane domain that requires energy and various cellular functions for its formation. The formation of the void zone indicates that the plasma membrane in living cells has the potential to undergo phase separation with certain lipid compositions. We also found that void zones were frequently in contact with vacuoles, in which a membrane domain was also formed at the contact site.
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Affiliation(s)
- Tetsuo Mioka
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido 060-0815, Japan
| | - Tian Guo
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido 060-0815, Japan
| | - Shiyao Wang
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido 060-0815, Japan
| | - Takuma Tsuji
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Takuma Kishimoto
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido 060-0815, Japan
| | - Toyoshi Fujimoto
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kazuma Tanaka
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido 060-0815, Japan
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11
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Zhang Z, Cottignie I, Van Zeebroeck G, Thevelein JM. Nutrient transceptors physically interact with the yeast S6/protein kinase B homolog, Sch9, a TOR kinase target. Biochem J 2021; 478:357-375. [PMID: 33394033 PMCID: PMC7850899 DOI: 10.1042/bcj20200722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 12/18/2022]
Abstract
Multiple starvation-induced, high-affinity nutrient transporters in yeast function as receptors for activation of the protein kinase A (PKA) pathway upon re-addition of their substrate. We now show that these transceptors may play more extended roles in nutrient regulation. The Gap1 amino acid, Mep2 ammonium, Pho84 phosphate and Sul1 sulfate transceptors physically interact in vitro and in vivo with the PKA-related Sch9 protein kinase, the yeast homolog of mammalian S6 protein kinase and protein kinase B. Sch9 is a phosphorylation target of TOR and well known to affect nutrient-controlled cellular processes, such as growth rate. Mapping with peptide microarrays suggests specific interaction domains in Gap1 for Sch9 binding. Mutagenesis of the major domain affects the upstart of growth upon the addition of L-citrulline to nitrogen-starved cells to different extents but apparently does not affect in vitro binding. It also does not correlate with the drop in L-citrulline uptake capacity or transceptor activation of the PKA target trehalase by the Gap1 mutant forms. Our results reveal a nutrient transceptor-Sch9-TOR axis in which Sch9 accessibility for phosphorylation by TOR may be affected by nutrient transceptor-Sch9 interaction under conditions of nutrient starvation or other environmental challenges.
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Affiliation(s)
- Zhiqiang Zhang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Ines Cottignie
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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12
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Tosal-Castano S, Peselj C, Kohler V, Habernig L, Berglund LL, Ebrahimi M, Vögtle FN, Höög J, Andréasson C, Büttner S. Snd3 controls nucleus-vacuole junctions in response to glucose signaling. Cell Rep 2021; 34:108637. [PMID: 33472077 DOI: 10.1016/j.celrep.2020.108637] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 12/08/2020] [Accepted: 12/21/2020] [Indexed: 12/29/2022] Open
Abstract
Membrane contact sites facilitate the exchange of metabolites between organelles to support interorganellar communication. The nucleus-vacuole junctions (NVJs) establish physical contact between the perinuclear endoplasmic reticulum (ER) and the vacuole. Although the NVJ tethers are known, how NVJ abundance and composition are controlled in response to metabolic cues remains elusive. Here, we identify the ER protein Snd3 as central factor for NVJ formation. Snd3 interacts with NVJ tethers, supports their targeting to the contacts, and is essential for NVJ formation. Upon glucose exhaustion, Snd3 relocalizes from the ER to NVJs and promotes contact expansion regulated by central glucose signaling pathways. Glucose replenishment induces the rapid dissociation of Snd3 from the NVJs, preceding the slow disassembly of the junctions. In sum, this study identifies a key factor required for formation and regulation of NVJs and provides a paradigm for metabolic control of membrane contact sites.
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Affiliation(s)
- Sergi Tosal-Castano
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Carlotta Peselj
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Lukas Habernig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Lisa Larsson Berglund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Sweden
| | - Mahsa Ebrahimi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Stefan-Meier-Straße 17, 79104 Freiburg, Germany; Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Johanna Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, 8010 Graz, Austria.
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13
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Plasma Membrane Protein Nce102 Modulates Morphology and Function of the Yeast Vacuole. Biomolecules 2020; 10:biom10111476. [PMID: 33114062 PMCID: PMC7690685 DOI: 10.3390/biom10111476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 01/02/2023] Open
Abstract
Membrane proteins are targeted not only to specific membranes in the cell architecture, but also to distinct lateral microdomains within individual membranes to properly execute their biological functions. Yeast tetraspan protein Nce102 has been shown to migrate between such microdomains within the plasma membrane in response to an acute drop in sphingolipid levels. Combining microscopy and biochemistry methods, we show that upon gradual ageing of a yeast culture, when sphingolipid demand increases, Nce102 migrates from the plasma membrane to the vacuole. Instead of being targeted for degradation it localizes to V-ATPase-poor, i.e., ergosterol-enriched, domains of the vacuolar membrane, analogous to its plasma membrane localization. We discovered that, together with its homologue Fhn1, Nce102 modulates vacuolar morphology, dynamics, and physiology. Specifically, the fusing of vacuoles, accompanying a switch of fermenting yeast culture to respiration, is retarded in the strain missing both proteins. Furthermore, the absence of either causes an enlargement of ergosterol-rich vacuolar membrane domains, while the vacuoles themselves become smaller. Our results clearly show decreased stability of the V-ATPase in the absence of either Nce102 or Fhn1, a possible result of the disruption of normal microdomain morphology of the vacuolar membrane. Therefore, the functionality of the vacuole as a whole might be compromised in these cells.
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14
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Schuck S. Microautophagy - distinct molecular mechanisms handle cargoes of many sizes. J Cell Sci 2020; 133:133/17/jcs246322. [PMID: 32907930 DOI: 10.1242/jcs.246322] [Citation(s) in RCA: 220] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Autophagy is fundamental for cell and organismal health. Two types of autophagy are conserved in eukaryotes: macroautophagy and microautophagy. During macroautophagy, autophagosomes deliver cytoplasmic constituents to endosomes or lysosomes, whereas during microautophagy lytic organelles take up cytoplasm directly. While macroautophagy has been investigated extensively, microautophagy has received much less attention. Nonetheless, it has become clear that microautophagy has a broad range of functions in biosynthetic transport, metabolic adaptation, organelle remodeling and quality control. This Review discusses the selective and non-selective microautophagic processes known in yeast, plants and animals. Based on the molecular mechanisms for the uptake of microautophagic cargo into lytic organelles, I propose to distinguish between fission-type microautophagy, which depends on ESCRT proteins, and fusion-type microautophagy, which requires the core autophagy machinery and SNARE proteins. Many questions remain to be explored, but the functional versatility and mechanistic diversity of microautophagy are beginning to emerge.
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Affiliation(s)
- Sebastian Schuck
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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15
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Bo Otto F, Thumm M. Nucleophagy-Implications for Microautophagy and Health. Int J Mol Sci 2020; 21:ijms21124506. [PMID: 32599961 PMCID: PMC7352367 DOI: 10.3390/ijms21124506] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Nucleophagy, the selective subtype of autophagy that targets nuclear material for autophagic degradation, was not only shown to be a model system for the study of selective macroautophagy, but also for elucidating the role of the core autophagic machinery within microautophagy. Nucleophagy also emerged as a system associated with a variety of disease conditions including cancer, neurodegeneration and ageing. Nucleophagic processes are part of natural cell development, but also act as a response to various stress conditions. Upon releasing small portions of nuclear material, micronuclei, the autophagic machinery transfers these micronuclei to the vacuole for subsequent degradation. Despite sharing many cargos and requiring the core autophagic machinery, recent investigations revealed the aspects that set macro- and micronucleophagy apart. Central to the discrepancies found between macro- and micronucleophagy is the nucleus vacuole junction, a large membrane contact site formed between nucleus and vacuole. Exclusion of nuclear pore complexes from the junction and its exclusive degradation by micronucleophagy reveal compositional differences in cargo. Regarding their shared reliance on the core autophagic machinery, micronucleophagy does not involve normal autophagosome biogenesis observed for macronucleophagy, but instead maintains a unique role in overall microautophagy, with the autophagic machinery accumulating at the neck of budding vesicles.
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16
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Munzel L, Neumann P, Otto FB, Krick R, Metje-Sprink J, Kroppen B, Karedla N, Enderlein J, Meinecke M, Ficner R, Thumm M. Atg21 organizes Atg8 lipidation at the contact of the vacuole with the phagophore. Autophagy 2020; 17:1458-1478. [PMID: 32515645 DOI: 10.1080/15548627.2020.1766332] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Coupling of Atg8 to phosphatidylethanolamine is crucial for the expansion of the crescent-shaped phagophore during cargo engulfment. Atg21, a PtdIns3P-binding beta-propeller protein, scaffolds Atg8 and its E3-like complex Atg12-Atg5-Atg16 during lipidation. The crystal structure of Atg21, in complex with the Atg16 coiled-coil domain, showed its binding at the bottom side of the Atg21 beta-propeller. Our structure allowed detailed analyses of the complex formation of Atg21 with Atg16 and uncovered the orientation of the Atg16 coiled-coil domain with respect to the membrane. We further found that Atg21 was restricted to the phagophore edge, near the vacuole, known as the vacuole isolation membrane contact site (VICS). We identified a specialized vacuolar subdomain at the VICS, typical of organellar contact sites, where the membrane protein Vph1 was excluded, while Vac8 was concentrated. Furthermore, Vac8 was required for VICS formation. Our results support a specialized organellar contact involved in controlling phagophore elongation. Abbreviations: FCCS: fluorescence cross correlation spectroscopy; NVJ: nucleus-vacuole junction; PAS: phagophore assembly site; PE: phosphatidylethanolamine; PROPPIN: beta-propeller that binds phosphoinositides; PtdIns3P: phosphatidylinositol- 3-phosphate; VICS: vacuole isolation membrane contact site.
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Affiliation(s)
- Lena Munzel
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Florian B Otto
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Roswitha Krick
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Janina Metje-Sprink
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Benjamin Kroppen
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Narain Karedla
- Physics Department III, University of Goettingen, Goettingen, Germany
| | - Jörg Enderlein
- Physics Department III, University of Goettingen, Goettingen, Germany
| | - Michael Meinecke
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Michael Thumm
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
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17
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Kohler V, Aufschnaiter A, Büttner S. Closing the Gap: Membrane Contact Sites in the Regulation of Autophagy. Cells 2020; 9:E1184. [PMID: 32397538 PMCID: PMC7290522 DOI: 10.3390/cells9051184] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
In all eukaryotic cells, intracellular organization and spatial separation of incompatible biochemical processes is established by individual cellular subcompartments in form of membrane-bound organelles. Virtually all of these organelles are physically connected via membrane contact sites (MCS), allowing interorganellar communication and a functional integration of cellular processes. These MCS coordinate the exchange of diverse metabolites and serve as hubs for lipid synthesis and trafficking. While this of course indirectly impacts on a plethora of biological functions, including autophagy, accumulating evidence shows that MCS can also directly regulate autophagic processes. Here, we focus on the nexus between interorganellar contacts and autophagy in yeast and mammalian cells, highlighting similarities and differences. We discuss MCS connecting the ER to mitochondria or the plasma membrane, crucial for early steps of both selective and non-selective autophagy, the yeast-specific nuclear-vacuolar tethering system and its role in microautophagy, the emerging function of distinct autophagy-related proteins in organellar tethering as well as novel MCS transiently emanating from the growing phagophore and mature autophagosome.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden;
| | - Andreas Aufschnaiter
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden;
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden;
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
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18
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Abstract
Nucleophagy, the mechanism for autophagic degradation of nuclear material, occurs in both a macro- and micronucleophagic manner. Upon nitrogen deprivation, we observed, in an in-depth fluorescence microscopy study, the formation of micronuclei: small parts of superfluous nuclear components surrounded by perinuclear ER. We identified two types of micronuclei associated with a corresponding autophagic mode. Our results showed that macronucleophagy degraded these smaller micronuclei. Engulfed in Atg8-positive phagophores and containing cargo receptor Atg39, macronucleophagic structures revealed finger-like extensions when observed in 3-dimensional reconstitutions of fluorescence microscopy images, suggesting directional growth. Interestingly, in the late stages of phagophore elongation, the adjacent vacuolar membrane showed a reduction of integral membrane protein Pho8. This change in membrane composition could indicate the formation of a specialized vacuolar domain, required for autophagosomal fusion. Significantly larger micronuclei formed at nucleus vacuole junctions and were identified as a substrate of piecemeal microautophagy of the nucleus (PMN), by the presence of the integral membrane protein Nvj1. Micronuclei sequestered by vacuolar invaginations also contained Atg39. A detailed investigation revealed that both Atg39 and Atg8 accumulated between the vacuolar tips. These findings suggest a role for Atg39 in micronucleophagy. Indeed, following the degradation of Nvj1, an exclusive substrate of PMN, in immunoblots, we could confirm the essential role of Atg39 for PMN. Our study thus details the involvement of Atg8 in both macronucleophagy and PMN and identifies Atg39 as the general cargo receptor for nucleophagic processes.Abbreviations: DIC: Differential interference contrast, FWHM: Full width at half maximum, IQR: Interquartile range, MIPA: Micropexophagy-specific membrane apparatus, NLS: Nuclear localization signal, NVJ: Nucleus vacuole junction, PMN: Piecemeal microautophagy of the nucleus, pnER: Perinuclear ER.
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Affiliation(s)
- Florian B Otto
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Michael Thumm
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
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19
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Abstract
Autophagy is a major intracellular degradation system that derives its degradative abilities from the lysosome. The most well-studied form of autophagy is macroautophagy, which delivers cytoplasmic material to lysosomes via the double-membraned autophagosome. Other forms of autophagy, namely chaperone-mediated autophagy and microautophagy, occur directly on the lysosome. Besides providing the means for degradation, lysosomes are also involved in autophagy regulation and can become substrates of autophagy when damaged. During autophagy, they exhibit notable changes, including increased acidification, enhanced enzymatic activity, and perinuclear localization. Despite their importance to autophagy, details on autophagy-specific regulation of lysosomes remain relatively scarce. This review aims to provide a summary of current understanding on the behaviour of lysosomes during autophagy and outline unexplored areas of autophagy-specific lysosome research.
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Affiliation(s)
- Willa Wen-You Yim
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
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20
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Abdrakhmanov A, Gogvadze V, Zhivotovsky B. To Eat or to Die: Deciphering Selective Forms of Autophagy. Trends Biochem Sci 2020; 45:347-364. [PMID: 32044127 DOI: 10.1016/j.tibs.2019.11.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/09/2019] [Accepted: 11/18/2019] [Indexed: 12/23/2022]
Abstract
Autophagy is an evolutionarily conserved process whereby damaged and redundant components of the cell are degraded in structures called autophagolysosomes. Currently, three main types of autophagy are recognized: macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA). However, we still know little about some specific types of autophagy that are linked to various intracellular compartments and their roles in the physiology of the whole organism and connections to various diseases. Here, we aim to shed light on the latest insights on and mechanisms of several selective forms of autophagy.
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Affiliation(s)
- Alibek Abdrakhmanov
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir Gogvadze
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden
| | - Boris Zhivotovsky
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden.
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21
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Prinz WA, Toulmay A, Balla T. The functional universe of membrane contact sites. Nat Rev Mol Cell Biol 2020; 21:7-24. [PMID: 31732717 PMCID: PMC10619483 DOI: 10.1038/s41580-019-0180-9] [Citation(s) in RCA: 425] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 12/13/2022]
Abstract
Organelles compartmentalize eukaryotic cells, enhancing their ability to respond to environmental and developmental changes. One way in which organelles communicate and integrate their activities is by forming close contacts, often called 'membrane contact sites' (MCSs). Interest in MCSs has grown dramatically in the past decade as it is has become clear that they are ubiquitous and have a much broader range of critical roles in cells than was initially thought. Indeed, functions for MCSs in intracellular signalling (particularly calcium signalling, reactive oxygen species signalling and lipid signalling), autophagy, lipid metabolism, membrane dynamics, cellular stress responses and organelle trafficking and biogenesis have now been reported.
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Affiliation(s)
- William A Prinz
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Alexandre Toulmay
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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22
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Park J, Kim HI, Jeong H, Lee M, Jang SH, Yoon SY, Kim H, Park ZY, Jun Y, Lee C. Quaternary structures of Vac8 differentially regulate the Cvt and PMN pathways. Autophagy 2019; 16:991-1006. [PMID: 31512555 PMCID: PMC7469494 DOI: 10.1080/15548627.2019.1659615] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Armadillo (ARM) repeat proteins constitute a large protein family with diverse and fundamental functions in all organisms, and armadillo repeat domains share high structural similarity. However, exactly how these structurally similar proteins can mediate diverse functions remains a long-standing question. Vac8 (vacuole related 8) is a multifunctional protein that plays pivotal roles in various autophagic pathways, including piecemeal microautophagy of the nucleus (PMN) and cytoplasm-to-vacuole targeting (Cvt) pathways in the budding yeast Saccharomyces cerevisiae. Vac8 comprises an H1 helix at the N terminus, followed by 12 armadillo repeats. Herein, we report the crystal structure of Vac8 bound to Atg13, a key component of autophagic machinery. The 70-Å extended loop of Atg13 binds to the ARM domain of Vac8 in an antiparallel manner. Structural, biochemical, and in vivo experiments demonstrated that the H1 helix of Vac8 intramolecularly associates with the first ARM and regulates its self-association, which is crucial for Cvt and PMN pathways. The structure of H1 helix-deleted Vac8 complexed with Atg13 reveals that Vac8[Δ19–33]-Atg13 forms a heterotetramer and adopts an extended superhelical structure exclusively employed in the Cvt pathway. Most importantly, comparison of Vac8-Nvj1 and Vac8-Atg13 provides a molecular understanding of how a single ARM domain protein adopts different quaternary structures depending on its associated proteins to differentially regulate 2 closely related but distinct cellular pathways. Abbreviations Ape1: aminopeptidase I; ARM: armadillo repeat; Atg: autophagy-related; AUC: analytical ultracentrifugation; Cvt: cytoplasm-to-vacuole targeting; DIC: differential interference contrast; GFP: green fluorescent protein; GST: glutathione-S-transferase; ITC: isothermal titration calorimetry; NVJ: nucleus-vacuole junction; PDB: protein data bank; PMN: piecemeal microautophagy of the nucleus; prApe1: precursor Ape1; RMSD: root-mean-square deviation; SAXS: small-angle X-ray scattering; SD-N: nitrogen starvation medium; SEC: size-exclusion chromatography; tAtg13: Atg13 construct comprising residues 567–695; tNvj1: Nvj1 construct comprising residues 229–321; tVac8: Vac8 construct comprising residues 10–515; Vac8: vacuole related 8
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Affiliation(s)
- Jumi Park
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology , Ulsan, Republic of Korea.,Cell Logistics Research Center, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea
| | - Hye-In Kim
- Cell Logistics Research Center, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea.,School of Life Sciences, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea
| | - Hanbin Jeong
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology , Ulsan, Republic of Korea.,Cell Logistics Research Center, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea
| | - Miriam Lee
- Cell Logistics Research Center, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea.,School of Life Sciences, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea
| | - Se Hwan Jang
- School of Life Sciences, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea
| | - So Young Yoon
- Cell Logistics Research Center, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea.,School of Life Sciences, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea
| | - Hyejin Kim
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology , Ulsan, Republic of Korea.,Cell Logistics Research Center, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea
| | - Zee-Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea
| | - Youngsoo Jun
- Cell Logistics Research Center, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea.,School of Life Sciences, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea
| | - Changwook Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology , Ulsan, Republic of Korea.,Cell Logistics Research Center, Gwangju Institute of Science and Technology , Gwangju, Republic of Korea
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23
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Def1 mediates the degradation of excess nucleolar protein Nop1 in budding yeast. Biochem Biophys Res Commun 2019; 519:302-308. [PMID: 31506176 DOI: 10.1016/j.bbrc.2019.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/01/2019] [Indexed: 01/22/2023]
Abstract
Nucleolar proteins such as Nop1/fibrillarin are degraded by nucleophagy in nutrient-starved conditions. However, whether and how excess nucleolar proteins are removed in normal conditions is unknown. Here we show that overexpressed nucleolar protein Nop1 is toxic and degraded in nutrient-rich conditions in budding yeast. The degradation was dependent on proteasomes. The CUE domain-containing protein Def1 mediated the degradation via the CUE domain and alleviated toxicity of Nop1 overexpression. Def1 was recruited to overexpressed Nop1 in the nucleolus. Ubiquitin mutants compromised this recruitment. This study revealed that Def1 is a novel factor for ubiquitin-dependent degradation of excess nucleolar proteins.
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24
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Ganesan S, Sosa Ponce ML, Tavassoli M, Shabits BN, Mahadeo M, Prenner EJ, Terebiznik MR, Zaremberg V. Metabolic control of cytosolic-facing pools of diacylglycerol in budding yeast. Traffic 2019; 20:226-245. [PMID: 30569465 DOI: 10.1111/tra.12632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022]
Abstract
Diacylglycerol (DAG) is a key signaling lipid and intermediate in lipid metabolism. Our knowledge of DAG distribution and dynamics in cell membranes is limited. Using live-cell fluorescence microscopy we investigated the localization of yeast cytosolic-facing pools of DAG in response to conditions where lipid homeostasis and DAG levels were known to be altered. Two main pools were monitored over time using DAG sensors. One pool was associated with vacuolar membranes and the other localized to sites of polarized growth. Dynamic changes in DAG distribution were observed during resumption of growth from stationary phase, when DAG is used to support phospholipid synthesis for membrane proliferation. Vacuolar membranes experienced constant morphological changes displaying DAG enriched microdomains coexisting with liquid-disordered areas demarcated by Vph1. Formation of these domains was dependent on triacylglycerol (TAG) lipolysis. DAG domains and puncta were closely connected to lipid droplets. Lack of conversion of DAG to phosphatidate in growth conditions dependent on TAG mobilization, led to the accumulation of DAG in a vacuolar-associated compartment, impacting the polarized distribution of DAG at budding sites. DAG polarization was also regulated by phosphatidylserine synthesis/traffic and sphingolipid synthesis in the Golgi.
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Affiliation(s)
| | - Maria L Sosa Ponce
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Marjan Tavassoli
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Brittney N Shabits
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Mark Mahadeo
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Elmar J Prenner
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Mauricio R Terebiznik
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.,Department of Cell and System Biology, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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25
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Starr ML, Fratti RA. The Participation of Regulatory Lipids in Vacuole Homotypic Fusion. Trends Biochem Sci 2018; 44:546-554. [PMID: 30587414 DOI: 10.1016/j.tibs.2018.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/27/2018] [Accepted: 12/03/2018] [Indexed: 12/28/2022]
Abstract
In eukaryotes, organelles and vesicles modulate their contents and identities through highly regulated membrane fusion events. Membrane trafficking and fusion are carried out through a series of stages that lead to the formation of SNARE complexes between cellular compartment membranes to trigger fusion. Although the protein catalysts of membrane fusion are well characterized, their response to their surrounding microenvironment, provided by the lipid composition of the membrane, remains to be fully understood. Membranes are composed of bulk lipids (e.g., phosphatidylcholine), as well as regulatory lipids that undergo constant modifications by kinases, phosphatases, and lipases. These lipids include phosphoinositides, diacylglycerol, phosphatidic acid, and cholesterol/ergosterol. Here we describe the roles of these lipids throughout the stages of yeast vacuole homotypic fusion.
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Affiliation(s)
- Matthew L Starr
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rutilio A Fratti
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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26
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Verlhac P, Reggiori F. Sorting the trash: Micronucleophagy gets selective. J Cell Biol 2018; 217:2605-2607. [PMID: 30006460 PMCID: PMC6080933 DOI: 10.1083/jcb.201806127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
During micronucleophagy, the nucleolus is targeted by autophagic degradation, but although nucleolar proteins are recycled, ribosomal DNA is spared. Mostofa et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201706164) reveal that the separation of these two nucleolar components is mediated by the CLIP and cohibin complexes and is vital for cell survival during starvation.
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Affiliation(s)
- Pauline Verlhac
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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27
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Mostofa MG, Rahman MA, Koike N, Yeasmin AM, Islam N, Waliullah TM, Hosoyamada S, Shimobayashi M, Kobayashi T, Hall MN, Ushimaru T. CLIP and cohibin separate rDNA from nucleolar proteins destined for degradation by nucleophagy. J Cell Biol 2018; 217:2675-2690. [PMID: 29959231 PMCID: PMC6080932 DOI: 10.1083/jcb.201706164] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 02/15/2018] [Accepted: 05/02/2018] [Indexed: 12/16/2022] Open
Abstract
Nutrient starvation or inactivation of TORC1 induces separation of rDNA and nucleolar proteins in yeast. Mostofa et al. report that the rDNA tethering CLIP–cohibin system repositions nucleolar proteins to sites proximal to the nuclear–vacuolar junction (NVJ), where micronucleophagy occurs, whereas rDNA moves to regions distal to the NVJ. Nutrient starvation or inactivation of target of rapamycin complex 1 (TORC1) in budding yeast induces nucleophagy, a selective autophagy process that preferentially degrades nucleolar components. DNA, including ribosomal DNA (rDNA), is not degraded by nucleophagy, even though rDNA is embedded in the nucleolus. Here, we show that TORC1 inactivation promotes relocalization of nucleolar proteins and rDNA to different sites. Nucleolar proteins move to sites proximal to the nuclear–vacuolar junction (NVJ), where micronucleophagy (or piecemeal microautophagy of the nucleus) occurs, whereas rDNA dissociates from nucleolar proteins and moves to sites distal to NVJs. CLIP and cohibin, which tether rDNA to the inner nuclear membrane, were required for repositioning of nucleolar proteins and rDNA, as well as effective nucleophagic degradation of the nucleolar proteins. Furthermore, micronucleophagy itself was necessary for the repositioning of rDNA and nucleolar proteins. However, rDNA escaped from nucleophagic degradation in CLIP- or cohibin-deficient cells. This study reveals that rDNA–nucleolar protein separation is important for the nucleophagic degradation of nucleolar proteins.
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Affiliation(s)
- Md Golam Mostofa
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | | | - Naoki Koike
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Akter Mst Yeasmin
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Nafisa Islam
- Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | | | - Shun Hosoyamada
- Laboratory of Genome Regeneration, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
| | | | - Takehiko Kobayashi
- Laboratory of Genome Regeneration, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
| | | | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan .,Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
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28
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Bingol B. Autophagy and lysosomal pathways in nervous system disorders. Mol Cell Neurosci 2018; 91:167-208. [PMID: 29729319 DOI: 10.1016/j.mcn.2018.04.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 04/26/2018] [Accepted: 04/28/2018] [Indexed: 12/12/2022] Open
Abstract
Autophagy is an evolutionarily conserved pathway for delivering cytoplasmic cargo to lysosomes for degradation. In its classically studied form, autophagy is a stress response induced by starvation to recycle building blocks for essential cellular processes. In addition, autophagy maintains basal cellular homeostasis by degrading endogenous substrates such as cytoplasmic proteins, protein aggregates, damaged organelles, as well as exogenous substrates such as bacteria and viruses. Given their important role in homeostasis, autophagy and lysosomal machinery are genetically linked to multiple human disorders such as chronic inflammatory diseases, cardiomyopathies, cancer, and neurodegenerative diseases. Multiple targets within the autophagy and lysosomal pathways offer therapeutic opportunities to benefit patients with these disorders. Here, I will summarize the mechanisms of autophagy pathways, the evidence supporting a pathogenic role for disturbed autophagy and lysosomal degradation in nervous system disorders, and the therapeutic potential of autophagy modulators in the clinic.
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Affiliation(s)
- Baris Bingol
- Genentech, Inc., Department of Neuroscience, 1 DNA Way, South San Francisco 94080, United States.
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29
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Oku M, Sakai Y. Three Distinct Types of Microautophagy Based on Membrane Dynamics and Molecular Machineries. Bioessays 2018; 40:e1800008. [PMID: 29708272 DOI: 10.1002/bies.201800008] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/02/2018] [Indexed: 01/13/2023]
Abstract
Microautophagy is originally defined as lysosomal (vacuolar) membrane dynamics to directly enwrap and transport cytosolic components into the lumen of the lytic organelle. Molecular details of microautophagy had remained unknown until genetic studies in yeast identified a set of proteins required for the process. Subsequent studies with other experimental model organisms resulted in a series of discoveries that accompanied an expansion of the definition of microautophagy to also encompass endosomal membrane dynamics. These findings, however, still impose puzzling, non-integrated images as to the molecular mechanism of microautophagy. By reviewing recent studies on microautophagy in various experimental systems, we propose the classification of microautophagy into three types, as the basis for developing a comprehensive view of the process.
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Affiliation(s)
- Masahide Oku
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.,Research Unit for Physiological Chemistry, The Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, 606-8502, Japan
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30
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Kakimoto Y, Tashiro S, Kojima R, Morozumi Y, Endo T, Tamura Y. Visualizing multiple inter-organelle contact sites using the organelle-targeted split-GFP system. Sci Rep 2018; 8:6175. [PMID: 29670150 PMCID: PMC5906596 DOI: 10.1038/s41598-018-24466-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/04/2018] [Indexed: 12/18/2022] Open
Abstract
Functional integrity of eukaryotic organelles relies on direct physical contacts between distinct organelles. However, the entity of organelle-tethering factors is not well understood due to lack of means to analyze inter-organelle interactions in living cells. Here we evaluate the split-GFP system for visualizing organelle contact sites in vivo and show its advantages and disadvantages. We observed punctate GFP signals from the split-GFP fragments targeted to any pairs of organelles among the ER, mitochondria, peroxisomes, vacuole and lipid droplets in yeast cells, which suggests that these organelles form contact sites with multiple organelles simultaneously although it is difficult to rule out the possibilities that these organelle contacts sites are artificially formed by the irreversible associations of the split-GFP probes. Importantly, split-GFP signals in the overlapped regions of the ER and mitochondria were mainly co-localized with ERMES, an authentic ER-mitochondria tethering structure, suggesting that split-GFP assembly depends on the preexisting inter-organelle contact sites. We also confirmed that the split-GFP system can be applied to detection of the ER-mitochondria contact sites in HeLa cells. We thus propose that the split-GFP system is a potential tool to observe and analyze inter-organelle contact sites in living yeast and mammalian cells.
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Affiliation(s)
- Yuriko Kakimoto
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan
| | - Shinya Tashiro
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan
| | - Rieko Kojima
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan
| | - Yuki Morozumi
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Yasushi Tamura
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan.
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31
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Demine S, Tejerina S, Bihin B, Thiry M, Reddy N, Renard P, Raes M, Jadot M, Arnould T. Mild mitochondrial uncoupling induces HSL/ATGL-independent lipolysis relying on a form of autophagy in 3T3-L1 adipocytes. J Cell Physiol 2017; 233:1247-1265. [PMID: 28488768 DOI: 10.1002/jcp.25994] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 05/08/2017] [Indexed: 12/15/2022]
Abstract
Obesity is characterized by an excessive triacylglycerol accumulation in white adipocytes. Various mechanisms allowing the tight regulation of triacylglycerol storage and mobilization by lipid droplet-associated proteins as well as lipolytic enzymes have been identified. Increasing energy expenditure by inducing a mild uncoupling of mitochondria in adipocytes might represent a putative interesting anti-obesity strategy as it reduces the adipose tissue triacylglycerol content (limiting alterations caused by cell hypertrophy) by stimulating lipolysis through yet unknown mechanisms, limiting the adverse effects of adipocyte hypertrophy. Herein, the molecular mechanisms involved in lipolysis induced by a mild uncoupling of mitochondria in white 3T3-L1 adipocytes were characterized. Mitochondrial uncoupling-induced lipolysis was found to be independent from canonical pathways that involve lipolytic enzymes such as HSL and ATGL. Finally, enhanced lipolysis in response to mitochondrial uncoupling relies on a form of autophagy as lipid droplets are captured by endolysosomal vesicles. This new mechanism of triacylglycerol breakdown in adipocytes exposed to mild uncoupling provides new insights on the biology of adipocytes dealing with mitochondria forced to dissipate energy.
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Affiliation(s)
- Stéphane Demine
- Laboratory of Biochemistry and Cell Biology (URBC), NARILIS (Namur Research Institute for Life Sciences), University of Namur (UNamur), Namur, Belgium
| | - Silvia Tejerina
- Laboratory of Biochemistry and Cell Biology (URBC), NARILIS (Namur Research Institute for Life Sciences), University of Namur (UNamur), Namur, Belgium
| | - Benoît Bihin
- Laboratory of Biochemistry and Cell Biology (URBC), NARILIS (Namur Research Institute for Life Sciences), University of Namur (UNamur), Namur, Belgium
| | - Marc Thiry
- Laboratory of Cell Biology, GIGA-R, University of Liège, Liège, Belgium
| | - Nagabushana Reddy
- Laboratory of Biochemistry and Cell Biology (URBC), NARILIS (Namur Research Institute for Life Sciences), University of Namur (UNamur), Namur, Belgium
| | - Patricia Renard
- Laboratory of Biochemistry and Cell Biology (URBC), NARILIS (Namur Research Institute for Life Sciences), University of Namur (UNamur), Namur, Belgium
| | - Martine Raes
- Laboratory of Biochemistry and Cell Biology (URBC), NARILIS (Namur Research Institute for Life Sciences), University of Namur (UNamur), Namur, Belgium
| | - Michel Jadot
- Laboratory of Molecular Physiology (URPhyM), NARILIS (Namur Research Institute for Life Sciences), University of Namur (UNamur), Namur, Belgium
| | - Thierry Arnould
- Laboratory of Biochemistry and Cell Biology (URBC), NARILIS (Namur Research Institute for Life Sciences), University of Namur (UNamur), Namur, Belgium
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32
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Mechanistic insight into the nucleus-vacuole junction based on the Vac8p-Nvj1p crystal structure. Proc Natl Acad Sci U S A 2017; 114:E4539-E4548. [PMID: 28533415 DOI: 10.1073/pnas.1701030114] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Formation of the nucleus-vacuole junction (NVJ) is mediated by direct interaction between the vacuolar protein Vac8p and the outer nuclear endoplasmic reticulum membrane protein Nvj1p. Herein we report the crystal structure of Vac8p bound to Nvj1p at 2.4-Å resolution. Vac8p comprises a flexibly connected N-terminal H1 helix followed by 12 armadillo repeats (ARMs) that form a right-handed superhelical structure. The extended 80-Å-long loop of Nvj1p specifically binds the highly conserved inner groove formed from ARM1-12 of Vac8p. Disruption of the Nvj1p-Vac8p interaction results in the loss of tight NVJs, which impairs piecemeal microautophagy of the nucleus in Saccharomyces cerevisiae Vac8p cationic triad (Arg276, Arg317, and Arg359) motifs interacting with Nvj1p are also critical to the recognition of Atg13p, a key component of the cytoplasm-to-vacuole targeting (CVT) pathway, indicating competitive binding to Vac8p. Indeed, mutation of the cationic triad abolishes CVT of Ape1p in vivo. Combined with biochemical data, the crystal structure reveals a Vac8p homodimer formed from ARM1, and this self-association, likely regulated by the flexible H1 helix and the C terminus of Nvj1p, is critical for Vac8p cellular functions.
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33
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Seo AY, Lau PW, Feliciano D, Sengupta P, Gros MAL, Cinquin B, Larabell CA, Lippincott-Schwartz J. AMPK and vacuole-associated Atg14p orchestrate μ-lipophagy for energy production and long-term survival under glucose starvation. eLife 2017; 6. [PMID: 28394250 PMCID: PMC5407857 DOI: 10.7554/elife.21690] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/09/2017] [Indexed: 12/22/2022] Open
Abstract
Dietary restriction increases the longevity of many organisms, but the cell signaling and organellar mechanisms underlying this capability are unclear. We demonstrate that to permit long-term survival in response to sudden glucose depletion, yeast cells activate lipid-droplet (LD) consumption through micro-lipophagy (µ-lipophagy), in which fat is metabolized as an alternative energy source. AMP-activated protein kinase (AMPK) activation triggered this pathway, which required Atg14p. More gradual glucose starvation, amino acid deprivation or rapamycin did not trigger µ-lipophagy and failed to provide the needed substitute energy source for long-term survival. During acute glucose restriction, activated AMPK was stabilized from degradation and interacted with Atg14p. This prompted Atg14p redistribution from ER exit sites onto liquid-ordered vacuole membrane domains, initiating µ-lipophagy. Our findings that activated AMPK and Atg14p are required to orchestrate µ-lipophagy for energy production in starved cells is relevant for studies on aging and evolutionary survival strategies of different organisms. DOI:http://dx.doi.org/10.7554/eLife.21690.001
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Affiliation(s)
- Arnold Y Seo
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Cell Biology and Metabolism Program, National Institutes of Health, Bethesda, United States
| | - Pick-Wei Lau
- Cell Biology and Metabolism Program, National Institutes of Health, Bethesda, United States
| | - Daniel Feliciano
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Cell Biology and Metabolism Program, National Institutes of Health, Bethesda, United States
| | - Prabuddha Sengupta
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Cell Biology and Metabolism Program, National Institutes of Health, Bethesda, United States
| | - Mark A Le Gros
- Department of Anatomy, University of California, San Francisco, San Francisco, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Bertrand Cinquin
- Department of Anatomy, University of California, San Francisco, San Francisco, United States
| | - Carolyn A Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Jennifer Lippincott-Schwartz
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Cell Biology and Metabolism Program, National Institutes of Health, Bethesda, United States
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34
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Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Mol Cell 2017; 65:761-774.e5. [PMID: 28132844 DOI: 10.1016/j.molcel.2016.12.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 11/21/2016] [Accepted: 12/22/2016] [Indexed: 12/15/2022]
Abstract
We have developed a general progressive procedure, Active Interaction Mapping, to guide assembly of the hierarchy of functions encoding any biological system. Using this process, we assemble an ontology of functions comprising autophagy, a central recycling process implicated in numerous diseases. A first-generation model, built from existing gene networks in Saccharomyces, captures most known autophagy components in broad relation to vesicle transport, cell cycle, and stress response. Systematic analysis identifies synthetic-lethal interactions as most informative for further experiments; consequently, we saturate the model with 156,364 such measurements across autophagy-activating conditions. These targeted interactions provide more information about autophagy than all previous datasets, producing a second-generation ontology of 220 functions. Approximately half are previously unknown; we confirm roles for Gyp1 at the phagophore-assembly site, Atg24 in cargo engulfment, Atg26 in cytoplasm-to-vacuole targeting, and Ssd1, Did4, and others in selective and non-selective autophagy. The procedure and autophagy hierarchy are at http://atgo.ucsd.edu/.
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35
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Luo M, Zhao X, Song Y, Cheng H, Zhou R. Nuclear autophagy: An evolutionarily conserved mechanism of nuclear degradation in the cytoplasm. Autophagy 2016; 12:1973-1983. [PMID: 27541589 DOI: 10.1080/15548627.2016.1217381] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Macroautophagy/autophagy is a catabolic process that is essential for cellular homeostasis. Studies on autophagic degradation of cytoplasmic components have generated interest in nuclear autophagy. Although its mechanisms and roles have remained elusive, tremendous progress has been made toward understanding nuclear autophagy. Nuclear autophagy is evolutionarily conserved in eukaryotes that may target various nuclear components through a series of processes, including nuclear sensing, nuclear export, autophagic substrate encapsulation and autophagic degradation in the cytoplasm. However, the molecular processes and regulatory mechanisms involved in nuclear autophagy remain largely unknown. Numerous studies have highlighted the importance of nuclear autophagy in physiological and pathological processes such as cancer. This review focuses on current advances in nuclear autophagy and provides a summary of its research history and landmark discoveries to offer new perspectives.
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Affiliation(s)
- Majing Luo
- a Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences , Wuhan University , Wuhan , China
| | - Xueya Zhao
- a Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences , Wuhan University , Wuhan , China
| | - Ying Song
- a Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences , Wuhan University , Wuhan , China
| | - Hanhua Cheng
- a Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences , Wuhan University , Wuhan , China
| | - Rongjia Zhou
- a Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences , Wuhan University , Wuhan , China
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36
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Meseroll RA, Cohen-Fix O. The Malleable Nature of the Budding Yeast Nuclear Envelope: Flares, Fusion, and Fenestrations. J Cell Physiol 2016; 231:2353-60. [PMID: 26909870 DOI: 10.1002/jcp.25355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 02/19/2016] [Indexed: 11/10/2022]
Abstract
In eukaryotes, the nuclear envelope (NE) physically separates nuclear components and activities from rest of the cell. The NE also provides rigidity to the nucleus and contributes to chromosome organization. At the same time, the NE is highly dynamic; it must change shape and rearrange its components during development and throughout the cell cycle, and its morphology can be altered in response to mutation and disease. Here we focus on the NE of budding yeast, Saccharomyces cerevisiae, which has several unique features: it remains intact throughout the cell cycle, expands symmetrically during interphase, elongates during mitosis and, expands asymmetrically during mitotic delay. Moreover, its NE is safely breached during mating and when large structures, such as nuclear pore complexes and the spindle pole body, are embedded into its double membrane. The budding yeast NE lacks lamins and yet the nucleus is capable of maintaining a spherical shape throughout interphase. Despite these eccentricities, studies of the budding yeast NE have uncovered interesting, and likely conserved, processes that contribute to NE dynamics. In particular, we discuss the processes that drive and enable NE expansion and the dramatic changes in the NE that lead to extensions and fenestrations. J. Cell. Physiol. 231: 2353-2360, 2016. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Rebecca A Meseroll
- The Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Orna Cohen-Fix
- The Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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37
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New Insight Into the Roles of Membrane Microdomains in Physiological Activities of Fungal Cells. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:119-80. [PMID: 27241220 DOI: 10.1016/bs.ircmb.2016.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The organization of biological membranes into structurally and functionally distinct lateral microdomains is generally accepted. From bacteria to mammals, laterally compartmentalized membranes seem to be a vital attribute of life. The crucial fraction of our current knowledge about the membrane microdomains has been gained from studies on fungi. In this review we summarize the evidence of the microdomain organization of membranes from fungal cells, with accent on their enormous diversity in composition, temporal dynamics, modes of formation, and recognized engagement in the cell physiology. A special emphasis is laid on the fact that in addition to their other biological functions, membrane microdomains also mediate the communication among different membranes within a eukaryotic cell and coordinate their functions. Involvement of fungal membrane microdomains in stress sensing, regulation of lipid homeostasis, and cell differentiation is discussed more in detail.
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38
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Barbosa AD, Sembongi H, Su WM, Abreu S, Reggiori F, Carman GM, Siniossoglou S. Lipid partitioning at the nuclear envelope controls membrane biogenesis. Mol Biol Cell 2015; 26:3641-57. [PMID: 26269581 PMCID: PMC4603934 DOI: 10.1091/mbc.e15-03-0173] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/22/2015] [Accepted: 08/06/2015] [Indexed: 12/11/2022] Open
Abstract
Partitioning of lipid precursors between membranes and storage is crucial for cell growth, and its disruption underlies pathologies such as cancer, obesity, and type 2 diabetes. However, the mechanisms and signals that regulate this process are largely unknown. In yeast, lipid precursors are mainly used for phospholipid synthesis in nutrient-rich conditions in order to sustain rapid proliferation but are redirected to triacylglycerol (TAG) stored in lipid droplets during starvation. Here we investigate how cells reprogram lipid metabolism in the endoplasmic reticulum. We show that the conserved phosphatidate (PA) phosphatase Pah1, which generates diacylglycerol from PA, targets a nuclear membrane subdomain that is in contact with growing lipid droplets and mediates TAG synthesis. We find that cytosol acidification activates the master regulator of Pah1, the Nem1-Spo7 complex, thus linking Pah1 activity to cellular metabolic status. In the absence of TAG storage capacity, Pah1 still binds the nuclear membrane, but lipid precursors are redirected toward phospholipids, resulting in nuclear deformation and a proliferation of endoplasmic reticulum membrane. We propose that, in response to growth signals, activation of Pah1 at the nuclear envelope acts as a switch to control the balance between membrane biogenesis and lipid storage.
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Affiliation(s)
- Antonio Daniel Barbosa
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Hiroshi Sembongi
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Wen-Min Su
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ 08901
| | - Susana Abreu
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 A Groningen, Netherlands
| | - Fulvio Reggiori
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 A Groningen, Netherlands
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ 08901
| | - Symeon Siniossoglou
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
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39
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Hernández A, Serrano-Bueno G, Perez-Castiñeira JR, Serrano A. 8-Dehydrosterols induce membrane traffic and autophagy defects through V-ATPase dysfunction in Saccharomyces cerevisae. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2945-56. [PMID: 26344037 DOI: 10.1016/j.bbamcr.2015.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/01/2015] [Indexed: 12/11/2022]
Abstract
8-Dehydrosterols are present in a wide range of biologically relevant situations, from human rare diseases to amine fungicide-treated fungi and crops. However, the molecular bases of their toxicity are still obscure. We show here that 8-dehydrosterols, but not other sterols, affect yeast vacuole acidification through V-ATPases. Moreover, erg2Δ cells display reductions in proton pumping rates consistent with ion-transport uncoupling in vitro. Concomitantly, subunit Vph1p shows conformational changes in the presence of 8-dehydrosterols. Expression of a plant vacuolar H(+)-pumping pyrophosphatase as an alternative H(+)-pump relieves Vma(-)-like phenotypes in erg2Δ-derived mutant cells. As a consequence of these acidification defects, endo- and exo-cytic traffic deficiencies that can be alleviated with a H(+)-pumping pyrophosphatase are also observed. Despite their effect on membrane traffic, 8-dehydrosterols do not induce endoplasmic reticulum stress or assembly defects on the V-ATPase. Autophagy is a V-ATPase dependent process and erg2Δ mutants accumulate autophagic bodies under nitrogen starvation similar to Vma(-) mutants. In contrast to classical Atg(-) mutants, this defect is not accompanied by impairment of traffic through the CVT pathway, processing of Pho8Δ60p, GFP-Atg8p localisation or difficulties to survive under nitrogen starvation conditions, but it is concomitant to reduced vacuolar protease activity. All in all, erg2Δ cells are autophagy mutants albeit some of their phenotypic features differ from classical Atg(-) defective cells. These results may pave the way to understand the aetiology of sterol-related diseases, the cytotoxic effect of amine fungicides, and may explain the tolerance to these compounds observed in plants.
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Affiliation(s)
- Agustín Hernández
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Avda Américo Vespucio 48, 41092 Sevilla, Spain.
| | - Gloria Serrano-Bueno
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Avda Américo Vespucio 48, 41092 Sevilla, Spain
| | - José Román Perez-Castiñeira
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Avda Américo Vespucio 48, 41092 Sevilla, Spain
| | - Aurelio Serrano
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Avda Américo Vespucio 48, 41092 Sevilla, Spain.
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40
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Raiborg C, Wenzel EM, Stenmark H. ER-endosome contact sites: molecular compositions and functions. EMBO J 2015; 34:1848-58. [PMID: 26041457 DOI: 10.15252/embj.201591481] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/31/2015] [Indexed: 01/05/2023] Open
Abstract
Recent studies have revealed the existence of numerous contact sites between the endoplasmic reticulum (ER) and endosomes in mammalian cells. Such contacts increase during endosome maturation and play key roles in cholesterol transfer, endosome positioning, receptor dephosphorylation, and endosome fission. At least 7 distinct contact sites between the ER and endosomes have been identified to date, which have diverse molecular compositions. Common to these contact sites is that they impose a close apposition between the ER and endosome membranes, which excludes membrane fusion while allowing the flow of molecular signals between the two membranes, in the form of enzymatic modifications, or ion, lipid, or protein transfer. Thus, ER-endosome contact sites ensure coordination of molecular activities between the two compartments while keeping their general compositions intact. Here, we review the molecular architectures and cellular functions of known ER-endosome contact sites and discuss their implications for human health.
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Affiliation(s)
- Camilla Raiborg
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway Department of Molecular Cell Biology, Institute for Cancer Research Oslo University Hospital, Oslo, Norway
| | - Eva M Wenzel
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway Department of Molecular Cell Biology, Institute for Cancer Research Oslo University Hospital, Oslo, Norway
| | - Harald Stenmark
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway Department of Molecular Cell Biology, Institute for Cancer Research Oslo University Hospital, Oslo, Norway Centre of Molecular Inflammation Research, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
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41
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Okamoto K. Organellophagy: eliminating cellular building blocks via selective autophagy. ACTA ACUST UNITED AC 2014; 205:435-45. [PMID: 24862571 PMCID: PMC4033777 DOI: 10.1083/jcb.201402054] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Maintenance of organellar quality and quantity is critical for cellular homeostasis and adaptation to variable environments. Emerging evidence demonstrates that this kind of control is achieved by selective elimination of organelles via autophagy, termed organellophagy. Organellophagy consists of three key steps: induction, cargo tagging, and sequestration, which involve signaling pathways, organellar landmark molecules, and core autophagy-related proteins, respectively. In addition, posttranslational modifications such as phosphorylation and ubiquitination play important roles in recruiting and tailoring the autophagy machinery to each organelle. The basic principles underlying organellophagy are conserved from yeast to mammals, highlighting its biological relevance in eukaryotic cells.
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Affiliation(s)
- Koji Okamoto
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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42
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Hönscher C, Ungermann C. A close-up view of membrane contact sites between the endoplasmic reticulum and the endolysosomal system: from yeast to man. Crit Rev Biochem Mol Biol 2014; 49:262-8. [PMID: 24382115 DOI: 10.3109/10409238.2013.875512] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Maintenance of organelle identity is crucial for the functionality of eukaryotic cells. Hence, transfer reactions between different compartments must be highly efficient and tightly regulated at the same time. Membrane contact sites (MCSs) represent an important route for inter-organelle transport and communication independent of vesicular trafficking. Due to extensive research, the mechanistic understanding of these sites increases constantly. However, how the formation and the versatile functions of MCSs are regulated is mainly unclear. Within this review, we focus on one well-known MCS, the nucleus-vacuole junction in yeast and discuss its analogy to endoplasmic reticulum-late endosome contacts in metazoan. Formation of the junction in yeast requires Vac8, a protein that is involved in various cellular processes at the yeast vacuole and a target of multiple posttranslational modifications. We discuss the possibility that dual functionality of proteins involved in contact formation is a common principle to coordinate inter-organelle transfer with organellar biogenesis.
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Affiliation(s)
- Carina Hönscher
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück , Osnabrück , Germany
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43
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Montefusco DJ, Matmati N, Hannun YA. The yeast sphingolipid signaling landscape. Chem Phys Lipids 2014; 177:26-40. [PMID: 24220500 PMCID: PMC4211598 DOI: 10.1016/j.chemphyslip.2013.10.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/18/2013] [Accepted: 10/19/2013] [Indexed: 12/13/2022]
Abstract
Sphingolipids are recognized as signaling mediators in a growing number of pathways, and represent potential targets to address many diseases. The study of sphingolipid signaling in yeast has created a number of breakthroughs in the field, and has the potential to lead future advances. The aim of this article is to provide an inclusive view of two major frontiers in yeast sphingolipid signaling. In the first section, several key studies in the field of sphingolipidomics are consolidated to create a yeast sphingolipidome that ranks nearly all known sphingolipid species by their level in a resting yeast cell. The second section presents an overview of most known phenotypes identified for sphingolipid gene mutants, presented with the intention of illuminating not yet discovered connections outside and inside of the field.
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Affiliation(s)
- David J Montefusco
- Dept. Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States.
| | - Nabil Matmati
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, United States
| | - Yusuf A Hannun
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, United States.
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44
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Abstract
Autophagy refers to a group of processes that involve degradation of cytoplasmic components including cytosol, macromolecular complexes, and organelles, within the vacuole or the lysosome of higher eukaryotes. The various types of autophagy have attracted increasing attention for at least two reasons. First, autophagy provides a compelling example of dynamic rearrangements of subcellular membranes involving issues of protein trafficking and organelle identity, and thus it is fascinating for researchers interested in questions pertinent to basic cell biology. Second, autophagy plays a central role in normal development and cell homeostasis, and, as a result, autophagic dysfunctions are associated with a range of illnesses including cancer, diabetes, myopathies, some types of neurodegeneration, and liver and heart diseases. That said, this review focuses on autophagy in yeast. Many aspects of autophagy are conserved from yeast to human; in particular, this applies to the gene products mediating these pathways as well as some of the signaling cascades regulating it, so that the information we relate is relevant to higher eukaryotes. Indeed, as with many cellular pathways, the initial molecular insights were made possible due to genetic studies in Saccharomyces cerevisiae and other fungi.
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45
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Tsai IT, Lin JL, Chiang YH, Chuang YC, Liang SS, Chuang CN, Huang TN, Wang TF. Interorganelle interactions and inheritance patterns of nuclei and vacuoles in budding yeast meiosis. Autophagy 2013; 10:285-95. [PMID: 24345927 PMCID: PMC5396080 DOI: 10.4161/auto.27192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Many of the mechanisms by which organelles are inherited by spores during meiosis are not well understood. Dramatic chromosome motion and bouquet formation are evolutionarily conserved characteristics of meiotic chromosomes. The budding yeast bouquet genes (NDJ1, MPS3, CSM4) mediate these movements via telomere attachment to the nuclear envelope (NE). Here, we report that during meiosis the NE is in direct contact with vacuoles via nucleus-vacuole junctions (NVJs). We show that in meiosis NVJs are assembled through the interaction of the outer NE-protein Nvj1 and the vacuolar membrane protein Vac8. Notably, NVJs function as diffusion barriers that exclude the nuclear pore complexes, the bouquet protein Mps3 and NE-tethered telomeres from the outer nuclear membrane and nuclear ER, resulting in distorted NEs during early meiosis. An increase in NVJ area resulting from Nvj1-GFP overexpression produced a moderate bouquet mutant-like phenotype in wild-type cells. NVJs, as the vacuolar contact sites of the nucleus, were found to undergo scission alongside the NE during meiotic nuclear division. The zygotic NE and NVJs were partly segregated into 4 spores. Lastly, new NVJs were also revealed to be synthesized de novo to rejoin the zygotic NE with the newly synthesized vacuoles in the mature spores. In conclusion, our results revealed that budding yeast nuclei and vacuoles exhibit dynamic interorganelle interactions and different inheritance patterns in meiosis, and also suggested that nvj1Δ mutant cells may be useful to resolve the technical challenges pertaining to the isolation of intact nuclei for the biochemical study of meiotic nuclear proteins.
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Affiliation(s)
- I-Ting Tsai
- Department of Life Sciences and Institute of Genome Sciences; National Yang-Ming University; Taipei, Taiwan; Institute of Molecular Biology; Academia Sinica; Taipei, Taiwan
| | - Jyun-Liang Lin
- Institute of Molecular Biology; Academia Sinica; Taipei, Taiwan
| | - Yi-Hsuan Chiang
- Department of Life Sciences and Institute of Genome Sciences; National Yang-Ming University; Taipei, Taiwan; Institute of Molecular Biology; Academia Sinica; Taipei, Taiwan
| | - Yu-Chien Chuang
- Institute of Molecular Biology; Academia Sinica; Taipei, Taiwan; Taiwan International Graduate Program in Molecular and Cellular Biology; Academia Sinica; Taipei, Taiwan
| | - Shu-Shan Liang
- Institute of Molecular Biology; Academia Sinica; Taipei, Taiwan; Institute of Biochemical Sciences; National Taiwan University; Taipei, Taiwan
| | - Chi-Ning Chuang
- Institute of Molecular Biology; Academia Sinica; Taipei, Taiwan
| | - Tzyy-Nan Huang
- Institute of Molecular Biology; Academia Sinica; Taipei, Taiwan
| | - Ting-Fang Wang
- Department of Life Sciences and Institute of Genome Sciences; National Yang-Ming University; Taipei, Taiwan; Institute of Molecular Biology; Academia Sinica; Taipei, Taiwan; Taiwan International Graduate Program in Molecular and Cellular Biology; Academia Sinica; Taipei, Taiwan; Institute of Biochemical Sciences; National Taiwan University; Taipei, Taiwan
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46
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Cervantes S, Bunnik EM, Saraf A, Conner CM, Escalante A, Sardiu ME, Ponts N, Prudhomme J, Florens L, Le Roch KG. The multifunctional autophagy pathway in the human malaria parasite, Plasmodium falciparum. Autophagy 2013; 10:80-92. [PMID: 24275162 PMCID: PMC4028325 DOI: 10.4161/auto.26743] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Autophagy is a catabolic pathway typically induced by nutrient starvation to recycle amino acids, but can also function in removing damaged organelles. In addition, this pathway plays a key role in eukaryotic development. To date, not much is known about the role of autophagy in apicomplexan parasites and more specifically in the human malaria parasite Plasmodium falciparum. Comparative genomic analysis has uncovered some, but not all, orthologs of autophagy-related (ATG) genes in the malaria parasite genome. Here, using a genome-wide in silico analysis, we confirmed that ATG genes whose products are required for vesicle expansion and completion are present, while genes involved in induction of autophagy and cargo packaging are mostly absent. We subsequently focused on the molecular and cellular function of P. falciparum ATG8 (PfATG8), an autophagosome membrane marker and key component of the autophagy pathway, throughout the parasite asexual and sexual erythrocytic stages. In this context, we showed that PfATG8 has a distinct and atypical role in parasite development. PfATG8 localized in the apicoplast and in vesicles throughout the cytosol during parasite development. Immunofluorescence assays of PfATG8 in apicoplast-minus parasites suggest that PfATG8 is involved in apicoplast biogenesis. Furthermore, treatment of parasite cultures with bafilomycin A 1 and chloroquine, both lysosomotropic agents that inhibit autophagosome and lysosome fusion, resulted in dramatic morphological changes of the apicoplast, and parasite death. Furthermore, deep proteomic analysis of components associated with PfATG8 indicated that it may possibly be involved in ribophagy and piecemeal microautophagy of the nucleus. Collectively, our data revealed the importance and specificity of the autophagy pathway in the malaria parasite and offer potential novel therapeutic strategies.
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Affiliation(s)
- Serena Cervantes
- Graduate Program in Cell, Molecular, and Developmental Biology; University of California, Riverside; Riverside, CA USA; Department of Cell Biology and Neuroscience; University of California, Riverside; Riverside, CA USA
| | - Evelien M Bunnik
- Department of Cell Biology and Neuroscience; University of California, Riverside; Riverside, CA USA
| | - Anita Saraf
- Stowers Institute for Medical Research; Kansas City, MO USA
| | - Christopher M Conner
- Department of Cell Biology and Neuroscience; University of California, Riverside; Riverside, CA USA
| | - Aster Escalante
- Department of Cell Biology and Neuroscience; University of California, Riverside; Riverside, CA USA
| | | | - Nadia Ponts
- Department of Cell Biology and Neuroscience; University of California, Riverside; Riverside, CA USA
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience; University of California, Riverside; Riverside, CA USA
| | | | - Karine G Le Roch
- Department of Cell Biology and Neuroscience; University of California, Riverside; Riverside, CA USA
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47
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Helle SC, Kanfer G, Kolar K, Lang A, Michel AH, Kornmann B. Organization and function of membrane contact sites. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - MOLECULAR CELL RESEARCH 2013. [DOI: 10.1016.j.bbamcr.2013.01.02810.1016/j.bbamcr.2013.01.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Toulmay A, Prinz WA. Direct imaging reveals stable, micrometer-scale lipid domains that segregate proteins in live cells. ACTA ACUST UNITED AC 2013; 202:35-44. [PMID: 23836928 PMCID: PMC3704982 DOI: 10.1083/jcb.201301039] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Stable raftlike lipid domains form and segregate membrane proteins in the yeast vacuole in response to various stresses. It has been proposed that membrane rafts, which are sterol- and sphingolipid-enriched liquid-ordered (Lo) domains, segregate proteins in membranes and play critical roles in numerous processes in cells. However, rafts remain controversial because they are difficult to observe in cells without invasive methods and seem to be very small (nanoscale) and short lived, leading many to question whether they exist or are physiologically relevant. In this paper, we show that micrometer-scale, stable lipid domains formed in the yeast vacuole membrane in response to nutrient deprivation, changes in the pH of the growth medium, and other stresses. All vacuolar membrane proteins tested segregated to one of two domains. These domains formed quasi-symmetrical patterns strikingly similar to those found in liposomes containing coexisting Lo and liquid-disordered regions. Indeed, we found that one of these domains is probably sterol enriched and Lo. Domain formation was shown to be regulated by the pH-responsive Rim101 signaling pathway and may also require vesicular trafficking to vacuoles.
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Affiliation(s)
- Alexandre Toulmay
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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49
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Abstract
Under certain circumstances, the removal of damaged or non-essential parts of the nucleus, or even an entire nucleus, is crucial in order to promote cell longevity and enable proper function. A selective form of autophagy, known as nucleophagy, can be used to accomplish the degradation of nucleus-derived material. In this Cell Science at a Glance article and the accompanying poster, we summarize the similarities and differences between the divergent modes of nucleophagy that have been described to date, emphasizing, where possible, the molecular mechanism, the membrane interactions and rearrangements, and the nature of the nucleus-derived material that is degraded. In turn, we will consider nucleophagy processes in the lower eukaryotes, the budding yeast Saccharomyces cerevisiae, filamentous fungi Aspergillus and Magnaporthe oryzae and the ciliated protozoan Tetrahymena thermophila, and finally in mammalian cells. We will also briefly discuss the emerging links between nucleophagy and human disease.
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Affiliation(s)
- Dalibor Mijaljica
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton campus, VIC 3800, Australia
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50
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Helle SCJ, Kanfer G, Kolar K, Lang A, Michel AH, Kornmann B. Organization and function of membrane contact sites. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2526-41. [PMID: 23380708 DOI: 10.1016/j.bbamcr.2013.01.028] [Citation(s) in RCA: 349] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/18/2013] [Accepted: 01/21/2013] [Indexed: 11/16/2022]
Abstract
Membrane-bound organelles are a wonderful evolutionary acquisition of the eukaryotic cell, allowing the segregation of sometimes incompatible biochemical reactions into specific compartments with tailored microenvironments. On the flip side, these isolating membranes that crowd the interior of the cell, constitute a hindrance to the diffusion of metabolites and information to all corners of the cell. To ensure coordination of cellular activities, cells use a network of contact sites between the membranes of different organelles. These membrane contact sites (MCSs) are domains where two membranes come to close proximity, typically less than 30nm. Such contacts create microdomains that favor exchange between two organelles. MCSs are established and maintained in durable or transient states by tethering structures, which keep the two membranes in proximity, but fusion between the membranes does not take place. Since the endoplasmic reticulum (ER) is the most extensive cellular membrane network, it is thus not surprising to find the ER involved in most MCSs within the cell. The ER contacts diverse compartments such as mitochondria, lysosomes, lipid droplets, the Golgi apparatus, endosomes and the plasma membrane. In this review, we will focus on the common organizing principles underlying the many MCSs found between the ER and virtually all compartments of the cell, and on how the ER establishes a network of MCSs for the trafficking of vital metabolites and information. This article is part of a Special Issue entitled: Functional and structural diversity of endoplasmic reticulum.
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Affiliation(s)
- Sebastian C J Helle
- Institute of Biochemistry, ETH Zürich, HPM G16 Schafmattstrasse, Zürich, Switzerland
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