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Yamasaki A, Watanabe Y, Adachi W, Suzuki K, Matoba K, Kirisako H, Kumeta H, Nakatogawa H, Ohsumi Y, Inagaki F, Noda NN. Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates. Cell Rep 2016; 16:19-27. [PMID: 27320913 DOI: 10.1016/j.celrep.2016.05.066] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/29/2016] [Accepted: 05/16/2016] [Indexed: 12/15/2022] Open
Abstract
Selective autophagy mediates the degradation of various cargoes, including protein aggregates and organelles, thereby contributing to cellular homeostasis. Cargo receptors ensure selectivity by tethering specific cargo to lipidated Atg8 at the isolation membrane. However, little is known about the structural requirements underlying receptor-mediated cargo recognition. Here, we report structural, biochemical, and cell biological analysis of the major selective cargo protein in budding yeast, aminopeptidase I (Ape1), and its complex with the receptor Atg19. The Ape1 propeptide has a trimeric coiled-coil structure, which tethers dodecameric Ape1 bodies together to form large aggregates. Atg19 disassembles the propeptide trimer and forms a 2:1 heterotrimer, which not only blankets the Ape1 aggregates but also regulates their size. These receptor activities may promote elongation of the isolation membrane along the aggregate surface, enabling sequestration of the cargo with high specificity.
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Affiliation(s)
- Akinori Yamasaki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | | | - Wakana Adachi
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Kuninori Suzuki
- Bioimaging Center, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Kazuaki Matoba
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Hiromi Kirisako
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Hiroyuki Kumeta
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yoshinori Ohsumi
- Unit for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Fuyuhiko Inagaki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan; Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan.
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Morales Quinones M, Winston JT, Stromhaug PE. Propeptide of aminopeptidase 1 protein mediates aggregation and vesicle formation in cytoplasm-to-vacuole targeting pathway. J Biol Chem 2011; 287:10121-10133. [PMID: 22123825 DOI: 10.1074/jbc.m111.311696] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Misfolded protein aggregation causes disease and aging; autophagy counteracts this by eliminating damaged components, enabling cells to survive starvation. The cytoplasm-to-vacuole targeting pathway in yeast encompasses the aggregation of the premature form of aminopeptidase 1 (prApe1) in cytosol and its sequestration by autophagic proteins into a vesicle for vacuolar transport. We show that the propeptide of Ape1 is important for aggregation and vesicle formation and that it is sufficient for binding to prApe1 and Atg19. Defective aggregation disrupts vacuolar transport, suggesting that aggregate shape is important in vesicle formation, whereas Atg19 binding is not sufficient for vacuolar transport. Aggregation involves hydrophobicity, whereas Atg19 binding requires additional electrostatic interactions. Ape1 dodecamerization may cluster propeptides into trimeric structures, with sufficient affinity to form propeptide hexamers by binding to other dodecamers, causing aggregation. We show that Ape1 aggregates bind Atg19 and Atg8 in vitro; this could be used as a scaffold for an in vitro assay of autophagosome formation to elucidate the mechanisms of autophagy.
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Affiliation(s)
| | - Jared T Winston
- Department of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Per E Stromhaug
- Department of Biological Sciences, University of Missouri, Columbia, Missouri 65211.
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3
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Haldar S, Chattopadhyay K. Effects of arginine and other solution additives on the self-association of different surfactants: an investigation at single-molecule resolution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:5842-5849. [PMID: 21488688 DOI: 10.1021/la200580z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Fluorescence correlation spectroscopy is used to monitor the self-association of SDS and DTAB monomers at single-molecule resolution. Tetramethylrhodamine-5-maleimide (TMR) has been chosen as a probe because rhodamine dyes have been shown to bind surfactant micelles. Correlation functions obtained by FCS experiments have been fit using conventional discrete diffusional component analysis as well as the more recent maximum entropy method (MEM). Hydrodynamic radii calculated from the diffusion time values increase with surfactant concentration as the monomers self-associate. Effects of several solution additives on the self-association property of the surfactants have been studied. Urea and glycerol inhibit self-association, and arginine shows a dual nature. With SDS, arginine favors self-association, and with DTAB, it inhibits micelle formation. We propose surfactant self-association to be a "supersimplified" model of protein aggregation.
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Affiliation(s)
- Shubhasis Haldar
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4 Raja S. C. Mullick Road, Kolkata 700032, India
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Lynch-Day MA, Klionsky DJ. The Cvt pathway as a model for selective autophagy. FEBS Lett 2010; 584:1359-66. [PMID: 20146925 DOI: 10.1016/j.febslet.2010.02.013] [Citation(s) in RCA: 236] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 02/02/2010] [Accepted: 02/04/2010] [Indexed: 01/29/2023]
Abstract
Autophagy is a highly conserved, ubiquitous process that is responsible for the degradation of cytosolic components in response to starvation. Autophagy is generally considered to be non-selective; however, there are selective types of autophagy that use receptor and adaptor proteins to specifically isolate a cargo. One type of selective autophagy in yeast is the cytoplasm to vacuole targeting (Cvt) pathway. The Cvt pathway is responsible for the delivery of the hydrolase aminopeptidase I to the vacuole; as such, it is the only known biosynthetic pathway that utilizes the core machinery of autophagy. Nonetheless, it serves as a model for the study of selective autophagy in other organisms.
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Affiliation(s)
- Melinda A Lynch-Day
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
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5
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Abstract
Autophagy is a highly conserved cellular degradation process in which portions of cytosol and organelles are sequestered into a double-membrane vesicle, an autophagosome, and delivered into a degradative organelle, the vacuole/lysosome, for breakdown and eventual recycling of the resulting macromolecules. This process relieves the cell from various stress conditions. Autophagy plays a critical role during cellular development and differentiation, functions in tumor suppression, and may be linked to life span extension. Autophagy also has diverse roles in innate and adaptive immunity, such as resistance to pathogen invasion. Substantial progress has been made in the identification of many autophagy-related (ATG) genes that are essential to drive this cellular process, including both selective and nonselective types of autophagy. Identification of the ATG genes in yeast, and the finding of orthologs in other organisms, reveals the conservation of the autophagic machinery in all eukaryotes. Here, we summarize our current knowledge about the machinery and molecular mechanism of autophagy.
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Affiliation(s)
- Zhifen Yang
- Life Sciences Institute and Departments of Molecular, Cellular and Developmental Biology and Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-2216, USA
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6
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Yang Z, Klionsky DJ. An overview of the molecular mechanism of autophagy. Curr Top Microbiol Immunol 2009. [PMID: 19802558 DOI: 10.1007/978-3-642-00302-8-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Autophagy is a highly conserved cellular degradation process in which portions of cytosol and organelles are sequestered into a double-membrane vesicle, an autophagosome, and delivered into a degradative organelle, the vacuole/lysosome, for breakdown and eventual recycling of the resulting macromolecules. This process relieves the cell from various stress conditions. Autophagy plays a critical role during cellular development and differentiation, functions in tumor suppression, and may be linked to life span extension. Autophagy also has diverse roles in innate and adaptive immunity, such as resistance to pathogen invasion. Substantial progress has been made in the identification of many autophagy-related (ATG) genes that are essential to drive this cellular process, including both selective and nonselective types of autophagy. Identification of the ATG genes in yeast, and the finding of orthologs in other organisms, reveals the conservation of the autophagic machinery in all eukaryotes. Here, we summarize our current knowledge about the machinery and molecular mechanism of autophagy.
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Affiliation(s)
- Zhifen Yang
- Life Sciences Institute and Departments of Molecular, Cellular and Developmental Biology and Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-2216, USA
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7
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Abstract
Aminopeptidase I is the cargo protein of the cytoplasm-to-vacuole targeting (Cvt), autophagy-like protein-targeting pathway of the yeast Saccharomyces cerevisiae, the nonclassical vacuolar biosynthetic transport route. The second enzyme following this route to the vacuole, alpha-mannosidase, is also transported by direct binding to the Atg19 receptor and to aminopeptidase I. Aminopeptidase I forms a homododecameric complex, which is synthesized and assembled in the cytoplasm, packed in double-membrane vesicles, and transported to the vacuole. Only the homododecameric complex of aminopeptidase I has exopeptidase activity directed against amino-terminal leucine residues. Enzymatic activity can be determined spectrofluorometrically in homogenates and semi-quantitatively after nondenaturing gel electrophoresis and by yeast colony-overlay assay. This chapter describes the methods to determine aminopeptidase I enzymatic activity used to follow complex assembly and vacuolar transport.
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González-Díaz H, González-Díaz Y, Santana L, Ubeira FM, Uriarte E. Proteomics, networks and connectivity indices. Proteomics 2008; 8:750-78. [DOI: 10.1002/pmic.200700638] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Andrei-Selmer C, Knuppel A, Satyanarayana C, Heese C, Schu PV. A new class of mutants deficient in dodecamerization of aminopeptidase 1 and vacuolar transport. J Biol Chem 2001; 276:11606-14. [PMID: 11152450 DOI: 10.1074/jbc.m003846200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vacuolar aminopeptidase 1 is transported to the vacuole by cytoplasmic double-membrane vesicles, the nonclassic Cvt pathway. The cytosolic protein dodecamerizes and is enclosed in a double-membrane vesicle, which is transported to and fuses with the vacuole releasing a single-membrane autophagic body into the vacuolar lumen. This is degraded and the precursor sequence of aminopeptidase 1 is removed. This pathway resembles autophagy, and most proteins identified to function in the Cvt pathway are also required for autophagy and vice versa. The cytosolic precursor protein and the matured vacuolar protein form a homododecameric complex, and only this complex has enzymatic activity. We developed a new genetic screen to isolate mutants in the biogenesis of vacuolar aminopeptidase 1 based on its enzymatic activity. The sensitivity of this assay made it possible for us to search for mutants under conditions where autophagy is down-regulated, and we describe two new mutants defective in the biogenesis pathway of vacuolar aminopeptidase 1. Mutants are defective in dodecamerization of pApe1p and in Cvt vesicle formation. Complex assembly and transport vesicle formation appear to be linked processes. This mechanism can control the potentially harmful cytoplasmic proteolytic activity and could be the driving force for this nonclassic mechanism of vacuolar enzyme transport.
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Affiliation(s)
- C Andrei-Selmer
- Zentrum für Biochemie und Molekulare Zellbiologie, Department Biochemie II, Universität Göttingen, Heinrich-Düker-Weg 12, Göttingen D-37073, Germany
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Kim J, Klionsky DJ. Autophagy, cytoplasm-to-vacuole targeting pathway, and pexophagy in yeast and mammalian cells. Annu Rev Biochem 2001; 69:303-42. [PMID: 10966461 DOI: 10.1146/annurev.biochem.69.1.303] [Citation(s) in RCA: 281] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The sequestration and delivery of cytoplasmic material to the yeast vacuole and mammalian lysosome require the dynamic mobilization of cellular membranes and specialized protein machinery. Under nutrient deprivation conditions, double-membrane vesicles form around bulk cytoplasmic cargo destined for degradation and recycling in the vacuole/lysosome. A similar process functions to remove excess organelles under vegetative conditions in which they are no longer needed. Biochemical, morphological, and molecular genetic studies in yeasts and mammalian cells have begun to elucidate the molecular details of this autophagy process. In addition, the overlap of macroautophagy with the process of pexophagy and with the biosynthetic cytoplasm-to-vacuole targeting pathway, which delivers the resident vacuolar hydrolase aminopeptidase I, indicates that these three pathways are related mechanistically. Identification and characterization of the autophagic/cytoplasm-to-vacuole protein-targeting components have revealed the essential roles for various functional classes of proteins, including a novel protein conjugation system and the machinery for vesicle formation and fusion.
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Affiliation(s)
- J Kim
- Section of Microbiology, University of California, Davis, California 95616, USA.
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11
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Silles E, Mazón MJ, Gevaert K, Goethals M, Vandekerckhove J, Leber R, Sandoval IV. Targeting of aminopeptidase I to the yeast vacuole is mediated by Ssa1p, a cytosolic member of the 70-kDa stress protein family. J Biol Chem 2000; 275:34054-9. [PMID: 10903313 DOI: 10.1074/jbc.m003514200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The two cytosolic members of the highly conserved 70-kDa stress protein family, Ssa1p and Ssa2p, were specifically retained by the prepro-NH(2) extension of the vacuolar aminopeptidase I precursor (pAPI) conjugated to agarose (Sulfolink). A temperature-sensitive mutant strain a1(ts)a234 (ssa1(ts) ssa2 ssa3 ssa4), when incubated at the restrictive temperature, was able to assemble the API precursor into dodecamers, but failed to pack pAPI into vesicles and to convert it into mature API (mAPI), a process that occurs in the vacuole. Altogether these results indicate that Ssa1p mediates the targeting of pAPI to the vacuole.
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Affiliation(s)
- E Silles
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior Investigaciones Cientificas-Universidad Autónoma de Madrid, 28029 Madrid, Spain.
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12
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Satyanarayana C, Schröder-Köhne S, Craig EA, Schu PV, Horst M. Cytosolic Hsp70s are involved in the transport of aminopeptidase 1 from the cytoplasm into the vacuole. FEBS Lett 2000; 470:232-8. [PMID: 10745074 DOI: 10.1016/s0014-5793(00)01324-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Eukaryotic 70 kDa heat shock proteins (Hsp70s) are localized in various cellular compartments and exhibit functions such as protein translocation across membranes, protein folding and assembly. Here we demonstrate that the constitutively expressed members of the yeast cytoplasmic Ssa subfamily, Ssa1/2p, are involved in the transport of the vacuolar hydrolase aminopeptidase 1 from the cytoplasm into the vacuole. The Ssap family members displayed overlapping functions in the transport of aminopeptidase 1. In SSAI and SSAII deletion mutants the precursor of aminopeptidase 1 accumulated in a dodecameric complex that is packaged in prevacuolar transport vesicles. Ssa1/2p was prominently localized to the vacuolar membrane, consistent with the role we propose for Ssa proteins in the fusion of transport vesicles with the vacuolar membrane.
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Affiliation(s)
- C Satyanarayana
- Institut für Molekulare Zellbiologie und Biochemie, Abteilung Biochemie II, Universität Göttingen, Heinrich-Düker Weg 12, D-37073, Göttingen, Germany
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13
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Abstract
Many cellular processes require a balance between protein synthesis and protein degradation. The vacuole/lysosome is the main site of protein and organellar turnover within the cell due to its ability to sequester numerous hydrolases within a membrane-enclosed compartment. Several mechanisms are used to deliver substrates, as well as resident hydrolases, to this organelle. The delivery processes involve dynamic rearrangements of membrane. In addition, continual adjustments are made to respond to changes in environmental conditions. In this review, we focus on recent progress made in analyzing these delivery processes at a molecular level. The identification of protein components involved in the recognition, sequestration, and transport events has begun to provide information about this important area of eukaryotic cell physiology.
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Affiliation(s)
- D J Klionsky
- Section of Microbiology, University of California, Davis 95616, USA.
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14
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Martinez E, Seguí-Real B, Silles E, Mazón MJ, Sandoval IV. The prepropeptide of vacuolar aminopeptidase I is necessary and sufficient to target the fluorescent reporter protein GFP to the vacuole of yeast by the Ccvt pathway. Mol Microbiol 1999; 33:52-62. [PMID: 10411723 DOI: 10.1046/j.1365-2958.1999.01446.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have studied the capacity of the prepro amino extension of vacuolar protease leucine aminopeptidase I (API) to target the fluorescent reporter protein GFP to the vacuole of yeast. The preproGFP chimera constructed by extending the amino end of GFP with the prepro-part of API is rapidly degraded in both wild-type WCG cells and WCG 11/21a cells deficient in the proteasome. In contrast, the chimera expressed in WCG-PP cells deficient in both proteasome activity and vacuolar proteinase A accumulates in the vacuole, where it remains stable. Replacement of Gly by Ile-7, a substitution that prevents folding of the pre-part into an amphipathic helix and inhibits the targeting of the API precursor to the vacuole, inhibits the targeting of preproGFP to the vacuole. The separated pre- and pro-parts of the API precursor do not target GFP to the vacuole. Targeting of preproGFP to the vacuole is independent of its levels of expression, as the fluorescent protein localizes to the vacuole in cells expressing the protein under the control of both the GAL 1/10 or the API promoter. The preproGFP expressed under both promoters is recovered as monomers from cytosolic cell extracts. PreproGFP expressed under the API promoter is packed into cytoplasmic bodies that penetrate into the vacuolar lumen to release the protein. Altogether our results show that the prepro-part of the API precursor is necessary and sufficient to target the green fluorescent reporter protein to the vacuole.
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Affiliation(s)
- E Martinez
- Centro de Biologia Molecular Severo Ochoa, CSIC, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
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De Matteis MA, Morrow JS. The role of ankyrin and spectrin in membrane transport and domain formation. Curr Opin Cell Biol 1998; 10:542-9. [PMID: 9719877 DOI: 10.1016/s0955-0674(98)80071-9] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recent discoveries reveal a Golgi-centric spectrin-ankyrin skeleton required for Golgi integrity and anterograde protein trafficking. Identification of specific functional domains in spectrin that mediate its association with motor proteins and the Golgi complex has allowed novel insights into the structure and function of the secretory pathway, and into how this process is controlled by ADP-ribosylation factor and phosphoinositides. Alternative models of Golgi spectrin function that have been recently proposed are reviewed.
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Affiliation(s)
- M A De Matteis
- Department of Cell Biology and Oncology, Consorzio Mario Negri Sud, Santa Maria Imbaro, Chieti, Italy.
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Abstract
The vacuole/lysosome is a primary catabolic site in the eukaryotic cell. One implication of its cellular role is that delivery systems must exist to target both hydrolytic enzymes and substrates destined for degradation to this organelle. A number of nonclassical vacuolar targeting pathways that deliver degradative substrates and at least one resident enzyme from the cytosol to the vacuole have recently been described. The pathways identified so far include cytoplasm to vacuole targeting, macroautophagy, pexophagy and vacuolar import and degradation. Cytological, genetic and molecular genetic approaches have begun to provide insight into the molecular basis of these processes.
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Affiliation(s)
- S V Scott
- Section of Microbiology, University of California, Davis 95616, USA
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Affiliation(s)
- D J Klionsky
- Section of Microbiology, University of California, Davis, California 95616, USA.
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