1
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Marquardt L, Taylor M, Kramer F, Schmitt K, Braus GH, Valerius O, Thumm M. Vacuole fragmentation depends on a novel Atg18-containing retromer-complex. Autophagy 2023; 19:278-295. [PMID: 35574911 PMCID: PMC9809942 DOI: 10.1080/15548627.2022.2072656] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The yeast PROPPIN Atg18 folds as a β-propeller with two binding sites for phosphatidylinositol-3-phosphate (PtdIns3P) and PtdIns(3,5)P2 at its circumference. Membrane insertion of an amphipathic loop of Atg18 leads to membrane tubulation and fission. Atg18 has known functions at the PAS during macroautophagy, but the functional relevance of its endosomal and vacuolar pool is not well understood. Here we show in a proximity-dependent labeling approach and by co-immunoprecipitations that Atg18 interacts with Vps35, a central component of the retromer complex. The binding of Atg18 to Vps35 is competitive with the sorting nexin dimer Vps5 and Vps17. This suggests that Atg18 within the retromer can substitute for both the phosphoinositide binding and the membrane bending capabilities of these sorting nexins. Indeed, we found that Atg18-retromer is required for PtdIns(3,5)P2-dependent vacuolar fragmentation during hyperosmotic stress. The Atg18-retromer is further involved in the normal sorting of the integral membrane protein Atg9. However, PtdIns3P-dependent macroautophagy and the selective cytoplasm-to-vacuole targeting (Cvt) pathway are only partially affected by the Atg18-retromer. We expect that this is due to the plasticity of the different sorting pathways within the endovacuolar system.Abbreviations: BAR: bin/amphiphysin/Rvs; FOA: 5-fluoroorotic acid; PAS: phagophore assembly site; PROPPIN: beta-propeller that binds phosphoinositides; PtdIns3P: phosphatidylinositol-3-phosphate; PX: phox homology.
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Affiliation(s)
- Lisa Marquardt
- Institute of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Matthew Taylor
- Institute of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Florian Kramer
- Institute of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University, Goettingen, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University, Goettingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University, Goettingen, Germany
| | - Michael Thumm
- Institute of Cellular Biochemistry, University Medicine, Goettingen, Germany,CONTACT Michael Thumm ; Institute of Cellular Biochemistry, University Medicine, Humboldtallee 23, D-37073Goettingen, Germany
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2
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Liu S, Jiang L, Miao H, Lv Y, Zhang Q, Ma M, Duan W, Huang Y, Wei X. Autophagy regulation of ATG13 and ATG27 on biofilm formation and antifungal resistance in Candida albicans. BIOFOULING 2022; 38:926-939. [PMID: 36476055 DOI: 10.1080/08927014.2022.2153332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 10/20/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Autophagy is a highly conserved catabolic pathway that is vital for cells; however, the effects of autophagy on the biofilm formation and antifungal resistance of Candida albicans are still unknown. In this study, the potential molecular mechanisms of autophagy in biofilm formation and antifungal resistance were investigated. It was found that 3536 genes were differentially expressed between biofilm and planktonic C. albicans. ATG gene expression and autophagy activity were higher in biofilm than in planktonic C. albicans. Autophagic activities were higher in matured biofilms than that in pre-matured biofilms. Autophagy was involved in C. albicans biofilm formation and its activity increased during biofilm maturation. Further, ALP activity, AO staining cells, and autophagosomes inside cells were obviously reduced in biofilms of atg13Δ/Δ and atg27Δ/Δ strains; moreover, biofilm formation and antifungal resistance were also significantly decreased. Lastly, autophagy regulates biofilm formation and drug resistance of C. albicans and could be served as a new molecular target to the C. albicans biofilm infections.
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Affiliation(s)
- Siqi Liu
- Department of Operative Dentistry and Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Liuliu Jiang
- Department of Operative Dentistry and Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Haochen Miao
- Department of Operative Dentistry and Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Ying Lv
- Department of Operative Dentistry and Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Qinqin Zhang
- Department of Operative Dentistry and Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Ming Ma
- Department of Operative Dentistry and Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Wei Duan
- Department of Operative Dentistry and Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yun Huang
- Department of Operative Dentistry and Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Xin Wei
- Department of Operative Dentistry and Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
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3
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Shortill SP, Frier MS, Wongsangaroonsri P, Davey M, Conibear E. The VINE complex is an endosomal VPS9-domain GEF and SNX-BAR coat. eLife 2022; 11:77035. [PMID: 35938928 PMCID: PMC9507130 DOI: 10.7554/elife.77035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/05/2022] [Indexed: 11/18/2022] Open
Abstract
Membrane trafficking pathways perform important roles in establishing and maintaining the endosomal network. Retrograde protein sorting from the endosome is promoted by conserved SNX-BAR-containing coat complexes including retromer which enrich cargo at tubular microdomains and generate transport carriers. In metazoans, retromer cooperates with VARP, a conserved VPS9-domain GEF, to direct an endosomal recycling pathway. The function of the yeast VARP homolog Vrl1 has been overlooked due to an inactivating mutation found in commonly studied strains. Here, we demonstrate that Vrl1 has features of a SNX-BAR coat protein and forms an obligate complex with Vin1, the paralog of the retromer SNX-BAR protein Vps5. Unique features in the Vin1 N-terminus allow Vrl1 to distinguish it from Vps5, thereby forming a complex that we have named VINE. The VINE complex occupies endosomal tubules and redistributes a conserved mannose 6-phosphate receptor-like protein from endosomes. We also find that membrane recruitment by Vin1 is essential for Vrl1 GEF activity, suggesting that VINE is a multifunctional coat complex that regulates trafficking and signaling events at the endosome. All healthy cells have a highly organized interior: different compartments with specialized roles are in different places, and in order to do their jobs properly, proteins need to be in the right place. Endosomes are membrane-bound compartments that act as transport hubs where proteins are sorted into small vesicles and delivered to other parts of the cell. Two groups of proteins regulate this transport: the first group, known as VPS9 GEFs, switches on the enzymes that recruit the second group of proteins, called the sorting nexins. This second group is responsible for forming the transport vesicles via which proteins are distributed all over the cell. Defects in protein sorting can lead to various diseases, including neurodegenerative conditions such as Parkinson’s disease and juvenile amyotrophic lateral sclerosis. Scientists often use budding yeast cells to study protein sorting, because these cells are similar to human cells, but easier to grow in large numbers and examine in the laboratory. Previous work showed that a yeast protein called Vrl1 is equivalent to a VPS9 GEF from humans called VARP. However, Vrl1 only exists in wild forms of budding yeast, and not in laboratory strains of the organism. Therefore, researchers had not studied Vrl1 in detail, and its roles remained unclear. To learn more about Vrl1, Shortill et al. started by re-introducing the protein into laboratory strains of budding yeast and observing what happened to protein sorting in these cells. Like VARP, Vrl1 was found in the endosomes of budding yeast. However, biochemical experiments revealed that, while human VARP binds to a protein called retromer, Vrl1 does not bind to the equivalent protein in yeast. Instead, Vrl1 itself has features of both the VPS9 GEFs and the sorting nexins. Shortill et al. also found that Vrl1 interacted with a different protein in the sorting nexin family called Vin1. In the absence of Vrl1, Vin1 was found floating around the cell, but once Vrl1 was re-introduced into the budding yeast, Vin1 relocated to the endosomes. Vrl1 uses its VPS9 GEF part to move itself to the endosome membrane, and Vin1 controls this movement, highlighting the interdependence between the two proteins. Once they are at the endosome together, Vrl1 and Vin1 help redistribute proteins to other parts of the cell. This study suggests that, like VARP, Vrl1 cooperates with sorting nexins to transport proteins. Since many previous experiments about protein sorting were carried out in yeast cells lacking Vrl1, it is possible that this process was overlooked despite its potential importance. These new findings could also help other researchers investigating how endosomes and protein sorting work, or do not work, in the context of neurodegenerative diseases.
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Affiliation(s)
- Shawn P Shortill
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Mia S Frier
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | | | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
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4
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Yeast cell death pathway requiring AP-3 vesicle trafficking leads to vacuole/lysosome membrane permeabilization. Cell Rep 2022; 39:110647. [PMID: 35417721 PMCID: PMC9074372 DOI: 10.1016/j.celrep.2022.110647] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/17/2022] [Accepted: 03/16/2022] [Indexed: 12/24/2022] Open
Abstract
Unicellular eukaryotes have been suggested as undergoing self-inflicted destruction. However, molecular details are sparse compared with the mechanisms of programmed/regulated cell death known for human cells and animal models. Here, we report a molecular cell death pathway in Saccharomyces cerevisiae leading to vacuole/lysosome membrane permeabilization. Following a transient cell death stimulus, yeast cells die slowly over several hours, consistent with an ongoing molecular dying process. A genome-wide screen for death-promoting factors identified all subunits of the AP-3 complex, a vesicle trafficking adapter known to transport and install newly synthesized proteins on the vacuole/lysosome membrane. To promote cell death, AP-3 requires its Arf1-GTPase-dependent vesicle trafficking function and the kinase Yck3, which is selectively transported to the vacuole membrane by AP-3. Video microscopy revealed a sequence of events where vacuole permeability precedes the loss of plasma membrane integrity. AP-3-dependent death appears to be conserved in the human pathogenic yeast Cryptococcus neoformans. Details about how mammalian cells die have yielded effective cancer therapies. Similarly, details about fungal cell death may explain failed responses to anti-fungal agents and inform next-generation anti-fungal strategies. Stolp et al. describe a potential mechanism of yeast cell death subversion, by inhibiting AP-3 vesicle trafficking to block vacuole/lysosome permeability.
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5
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Eising S, Esch B, Wälte M, Vargas Duarte P, Walter S, Ungermann C, Bohnert M, Fröhlich F. A lysosomal biogenesis map reveals the cargo spectrum of yeast vacuolar protein targeting pathways. J Cell Biol 2022; 221:213011. [PMID: 35175277 PMCID: PMC8859911 DOI: 10.1083/jcb.202107148] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/20/2021] [Accepted: 01/18/2022] [Indexed: 12/15/2022] Open
Abstract
The lysosome is the major catabolic organelle in the cell that has been established as a key metabolic signaling center. Mutations in many lysosomal proteins have catastrophic effects and cause neurodegeneration, cancer, and age-related diseases. The vacuole is the lysosomal analog of Saccharomyces cerevisiae that harbors many evolutionary conserved proteins. Proteins reach vacuoles via the Vps10-dependent endosomal vacuolar protein sorting pathway, via the alkaline phosphatase (ALP or AP-3) pathway, and via the cytosol-to-vacuole transport (CVT) pathway. A systematic understanding of the cargo spectrum of each pathway is completely lacking. Here, we use quantitative proteomics of purified vacuoles to generate the yeast lysosomal biogenesis map. This dataset harbors information on the cargo-receptor relationship of almost all vacuolar proteins. We map binding motifs of Vps10 and the AP-3 complex and identify a novel cargo of the CVT pathway under nutrient-rich conditions. Our data show how organelle purification and quantitative proteomics can uncover fundamental insights into organelle biogenesis.
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Affiliation(s)
- Sebastian Eising
- Molecular Membrane Biology Group, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Bianca Esch
- Molecular Membrane Biology Group, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Mike Wälte
- Institute of Cell Dynamics and Imaging, University of Münster, Münster, Germany
| | - Prado Vargas Duarte
- Biochemistry Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Stefan Walter
- Center of Cellular Nanoanalytics Osnabrück, Osnabrück University, Osnabrück, Germany
| | - Christian Ungermann
- Biochemistry Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany.,Center of Cellular Nanoanalytics Osnabrück, Osnabrück University, Osnabrück, Germany
| | - Maria Bohnert
- Institute of Cell Dynamics and Imaging, University of Münster, Münster, Germany.,Cells in Motion Interfaculty Centre, University of Münster, Münster, Germany
| | - Florian Fröhlich
- Molecular Membrane Biology Group, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany.,Biochemistry Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
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6
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Goyal S, Segarra VA, N, Stecher AM, Truman AW, Reitzel AM, Chi RJ. Vps501, a novel vacuolar SNX-BAR protein cooperates with the SEA complex to regulate TORC1 signaling. Traffic 2022; 23. [PMID: 35098628 PMCID: PMC9305297 DOI: 10.1111/tra.12833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 12/01/2022]
Abstract
The sorting nexins (SNX), constitute a diverse family of molecules that play varied roles in membrane trafficking, cell signaling, membrane remodeling, organelle motility and autophagy. In particular, the SNX-BAR proteins, a SNX subfamily characterized by a C-terminal dimeric Bin/Amphiphysin/Rvs (BAR) lipid curvature domain and a conserved Phox-homology domain, are of great interest. In budding yeast, many SNX-BARs proteins have well-characterized endo-vacuolar trafficking roles. Phylogenetic analyses allowed us to identify an additional SNX-BAR protein, Vps501, with a novel endo-vacuolar role. We report that Vps501 uniquely localizes to the vacuolar membrane and has physical and genetic interactions with the SEA complex to regulate TORC1 inactivation. We found cells displayed a severe deficiency in starvation-induced/nonselective autophagy only when SEA complex subunits are ablated in combination with Vps501, indicating a cooperative role with the SEA complex during TORC1 signaling during autophagy induction. Additionally, we found the SEACIT complex becomes destabilized in vps501Δsea1Δ cells, which resulted in aberrant endosomal TORC1 activity and subsequent Atg13 hyperphosphorylation. We have also discovered that the vacuolar localization of Vps501 is dependent upon a direct interaction with Sea1 and a unique lipid binding specificity that is also required for its function. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shreya Goyal
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | | | - Nitika
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Aaron M. Stecher
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Andrew W. Truman
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Adam M. Reitzel
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Richard J. Chi
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
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7
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Sturgeon CM, Zanghi N, Smith HM, Davis EK, Robinson MR, Cabrera E, Holbrook MC, Segarra VA. YML018C protein localizes to the vacuolar membrane independently of Atg27p. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000391. [PMID: 33997660 PMCID: PMC8116935 DOI: 10.17912/micropub.biology.000391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The function of the budding yeast YML018C protein remains to be determined. High-throughput studies have reported that the YML018C protein localizes to the vacuolar membrane and physically interacts with the autophagy-related protein Atg27p. While this evidence suggests a potential role for this uncharacterized protein in the process of autophagy, the function of this putative interaction remains uncharacterized. In this micropublication, we report our finding that the localization of the YML018C protein to the vacuolar membrane does not require Atg27p.
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Affiliation(s)
| | - Nicholas Zanghi
- Department of Biology, High Point University, High Point, NC, USA 27268
| | - Hannah M. Smith
- Department of Biology, High Point University, High Point, NC, USA 27268
| | - Emily K. Davis
- Department of Biology, High Point University, High Point, NC, USA 27268
| | | | - Elizabeth Cabrera
- Department of Biology, High Point University, High Point, NC, USA 27268
| | - Molly C. Holbrook
- Department of Biology, High Point University, High Point, NC, USA 27268,
Department of Biological Sciences, University of North Carolina, Charlotte, USA 28223
| | - Verónica A. Segarra
- Department of Biology, High Point University, High Point, NC, USA 27268,
Correspondence to: Verónica A. Segarra ()
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8
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Segarra VA, Sharma A, Lemmon SK. Atg27p localization is clathrin- and Ent3p/5p-dependent. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 33817565 PMCID: PMC8008256 DOI: 10.17912/micropub.biology.000381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The autophagy-related protein Atg27p has been previously shown to localize to the autophagy-specific pre-autophagosomal structure (PAS) as well as to several organelles, including the late Golgi, the vacuolar membrane, and the endosome. Given that Atg27p localization to the vacuolar membrane in particular has been shown to be dependent on both its C-terminal tyrosine sorting motif and the AP-3 adaptor, and that Atg27p can be found in clathrin-coated vesicles, we set out to determine whether Atg27p localization inside cells is dependent on clathrin or on any of its cargo adaptors. We report that Atg27p localization is clathrin- and Ent3p/5p-dependent.
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Affiliation(s)
| | - Anupam Sharma
- Department of Microbiology, University of Georgia, Athens, GA, USA 30602
| | - Sandra K Lemmon
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA 33101
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9
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Segarra VA, Sharma A, Lemmon SK. Atg27p co-fractionates with clathrin-coated vesicles in budding yeast. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 33817564 PMCID: PMC8008255 DOI: 10.17912/micropub.biology.000380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Atg27p, a single-pass transmembrane protein that functions in autophagy, localizes to a variety of cellular compartments including the pre-autophagosomal structure, late Golgi, vacuolar membrane, as well as early and late endosomes. Its cytoplasmic C-terminus contains a tyrosine sorting motif that allows for its transport to the vacuolar membrane and an additional sequence that allows for its retrieval from the vacuolar membrane to the endosome. Since clathrin is well known to mediate vesicular transport in the endomembrane system, the trafficking of Atg27p and its tyrosine sorting motif suggested that it might be trafficked inside clathrin-coated vesicles (CCVs). In our previous studies, Atg27p was identified by mass spectrometry as a potential component in CCVs, as it was present in CCVs isolated from both WT and auxilin-depleted cells. We now confirm that Atg27p is a component of CCVs using immunoblotting and additional mass spectrometry data.
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Affiliation(s)
| | - Anupam Sharma
- Department of Microbiology, University of Georgia, Athens, GA, USA 30602
| | - Sandra K Lemmon
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA 33101
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10
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Tremblay O, Thow Z, Merrill AR. Several New Putative Bacterial ADP-Ribosyltransferase Toxins Are Revealed from In Silico Data Mining, Including the Novel Toxin Vorin, Encoded by the Fire Blight Pathogen Erwinia amylovora. Toxins (Basel) 2020; 12:E792. [PMID: 33322547 PMCID: PMC7764402 DOI: 10.3390/toxins12120792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/28/2020] [Accepted: 12/10/2020] [Indexed: 12/31/2022] Open
Abstract
Mono-ADP-ribosyltransferase (mART) toxins are secreted by several pathogenic bacteria that disrupt vital host cell processes in deadly diseases like cholera and whooping cough. In the last two decades, the discovery of mART toxins has helped uncover the mechanisms of disease employed by pathogens impacting agriculture, aquaculture, and human health. Due to the current abundance of mARTs in bacterial genomes, and an unprecedented availability of genomic sequence data, mART toxins are amenable to discovery using an in silico strategy involving a series of sequence pattern filters and structural predictions. In this work, a bioinformatics approach was used to discover six bacterial mART sequences, one of which was a functional mART toxin encoded by the plant pathogen, Erwinia amylovora, called Vorin. Using a yeast growth-deficiency assay, we show that wild-type Vorin inhibited yeast cell growth, while catalytic variants reversed the growth-defective phenotype. Quantitative mass spectrometry analysis revealed that Vorin may cause eukaryotic host cell death by suppressing the initiation of autophagic processes. The genomic neighbourhood of Vorin indicated that it is a Type-VI-secreted effector, and co-expression experiments showed that Vorin is neutralized by binding of a cognate immunity protein, VorinI. We demonstrate that Vorin may also act as an antibacterial effector, since bacterial expression of Vorin was not achieved in the absence of VorinI. Vorin is the newest member of the mART family; further characterization of the Vorin/VorinI complex may help refine inhibitor design for mART toxins from other deadly pathogens.
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Affiliation(s)
| | | | - A. Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (O.T.); (Z.T.)
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11
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Steinfeld N, Lahiri V, Morrison A, Metur SP, Klionsky DJ, Weisman LS. Elevating PI3P drives select downstream membrane trafficking pathways. Mol Biol Cell 2020; 32:143-156. [PMID: 33237833 PMCID: PMC8120694 DOI: 10.1091/mbc.e20-03-0191] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Phosphoinositide signaling lipids are essential for several cellular processes. The requirement for a phosphoinositide is conventionally studied by depleting the corresponding lipid kinase. However, there are very few reports on the impact of elevating phosphoinositides. That phosphoinositides are dynamically elevated in response to stimuli suggests that, in addition to being required, phosphoinositides drive downstream pathways. To test this hypothesis, we elevated the levels of phosphatidylinositol-3-phosphate (PI3P) by generating hyperactive alleles of the yeast phosphatidylinositol 3-kinase, Vps34. We find that hyperactive Vps34 drives certain pathways, including phosphatidylinositol-3,5-bisphosphate synthesis and retrograde transport from the vacuole. This demonstrates that PI3P is rate limiting in some pathways. Interestingly, hyperactive Vps34 does not affect endosomal sorting complexes required for transport (ESCRT) function. Thus, elevating PI3P does not always increase the rate of PI3P-dependent pathways. Elevating PI3P can also delay a pathway. Elevating PI3P slowed late steps in autophagy, in part by delaying the disassembly of autophagy proteins from mature autophagosomes as well as delaying fusion of autophagosomes with the vacuole. This latter defect is likely due to a more general defect in vacuole fusion, as assessed by changes in vacuole morphology. These studies suggest that stimulus-induced elevation of phosphoinositides provides a way for these stimuli to selectively regulate downstream processes.
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Affiliation(s)
- Noah Steinfeld
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Vikramjit Lahiri
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Anna Morrison
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Shree Padma Metur
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Lois S Weisman
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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12
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Garr C, Sturgeon CM, Franks N, Segarra VA. Autophagy as an on-ramp to scientific discovery. Autophagy 2020; 17:837-839. [PMID: 32543335 DOI: 10.1080/15548627.2020.1769972] [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: 10/24/2022] Open
Abstract
The common view of art and science as polar opposites along the educational spectrum can sometimes mask the degree to which they inform one another. In fact, art can also serve as a way to foster interest in querying the natural world, ultimately allowing us to recruit highly creative individuals to join the scientific community. We have experienced firsthand how cellular processes, such as autophagy, which are not usually highlighted or described in detail in foundational cell biology textbooks, have served as an on-ramp for artists at the undergraduate and high school levels in the context of scientific research and science outreach, respectively. We discuss our experiences in this article and highlight the ways in which art's many dimensions are well-suited, not only for forging connections between scientists and their communities but also for encouraging creativity in the way scientists engage with visually and conceptually complex phenomena, such as autophagy.Abbreviations: AP-3: adaptor protein complex 3; Atg27: autophagy related protein 27; STEAM: science, technology, engineering, arts, and mathematics; STEM: science, technology, engineering and math.
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Affiliation(s)
- Casey Garr
- Department of Biology, High Point University, High Point, NC, USA 27268.,Garr Biomedical Visuals, Chapel Hill, NC, USA 27514
| | | | - Noah Franks
- Penn Griffin School for the Arts, High Point, NC, USA 27260
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13
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Nakatogawa H. Mechanisms governing autophagosome biogenesis. Nat Rev Mol Cell Biol 2020; 21:439-458. [PMID: 32372019 DOI: 10.1038/s41580-020-0241-0] [Citation(s) in RCA: 449] [Impact Index Per Article: 112.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
Abstract
Autophagosomes are double-membrane vesicles newly formed during autophagy to engulf a wide range of intracellular material and transport this autophagic cargo to lysosomes (or vacuoles in yeasts and plants) for subsequent degradation. Autophagosome biogenesis responds to a plethora of signals and involves unique and dynamic membrane processes. Autophagy is an important cellular mechanism allowing the cell to meet various demands, and its disruption compromises homeostasis and leads to various diseases, including metabolic disorders, neurodegeneration and cancer. Thus, not surprisingly, the elucidation of the molecular mechanisms governing autophagosome biogenesis has attracted considerable interest. Key molecules and organelles involved in autophagosome biogenesis, including autophagy-related (ATG) proteins and the endoplasmic reticulum, have been discovered, and their roles and relationships have been investigated intensely. However, several fundamental questions, such as what supplies membranes/lipids to build the autophagosome and how the membrane nucleates, expands, bends into a spherical shape and finally closes, have proven difficult to address. Nonetheless, owing to recent studies with new approaches and technologies, we have begun to unveil the mechanisms underlying these processes on a molecular level. We now know that autophagosome biogenesis is a highly complex process, in which multiple proteins and lipids from various membrane sources, supported by the formation of membrane contact sites, cooperate with biophysical phenomena, including membrane shaping and liquid-liquid phase separation, to ensure seamless segregation of the autophagic cargo. Together, these studies pave the way to obtaining a holistic view of autophagosome biogenesis.
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Affiliation(s)
- Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
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14
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Ma M, Burd CG. Retrograde trafficking and plasma membrane recycling pathways of the budding yeast Saccharomyces cerevisiae. Traffic 2019; 21:45-59. [PMID: 31471931 DOI: 10.1111/tra.12693] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
The endosomal system functions as a network of protein and lipid sorting stations that receives molecules from endocytic and secretory pathways and directs them to the lysosome for degradation, or exports them from the endosome via retrograde trafficking or plasma membrane recycling pathways. Retrograde trafficking pathways describe endosome-to-Golgi transport while plasma membrane recycling pathways describe trafficking routes that return endocytosed molecules to the plasma membrane. These pathways are crucial for lysosome biogenesis, nutrient acquisition and homeostasis and for the physiological functions of many types of specialized cells. Retrograde and recycling sorting machineries of eukaryotic cells were identified chiefly through genetic screens using the budding yeast Saccharomyces cerevisiae system and discovered to be highly conserved in structures and functions. In this review, we discuss advances regarding retrograde trafficking and recycling pathways, including new discoveries that challenge existing ideas about the organization of the endosomal system, as well as how these pathways intersect with cellular homeostasis pathways.
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Affiliation(s)
- Mengxiao Ma
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
| | - Christopher G Burd
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
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15
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Sturgeon CM, Robinson MR, Penton MC, Clemmer DC, Trujillo MA, Khawaja AU, Segarra VA. Kinetic assay of starvation sensitivity in yeast autophagy mutants allows for the identification of intermediary phenotypes. BMC Res Notes 2019; 12:505. [PMID: 31412956 PMCID: PMC6694668 DOI: 10.1186/s13104-019-4545-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVE A classical method to quantitatively determine the starvation sensitivity phenotype of autophagy mutant budding yeast strains is to starve them for a period of time and then to assess the proportion of cells that retain the ability to form colonies when the availability of nutrients is restored. The readout of this colony-formation assay is generally evaluated after a fixed period of time following the restoration of nutrients, so that it can be considered an endpoint assay. One drawback we have identified is the inability to characterize subtle intermediary phenotypes that are detectable at the molecular level but fail to reach statistical significance in the colony formation experiment. We set out to determine whether a more dynamic measurement of growth during recovery after starvation would increase the sensitivity with which we are able to detect partial loss-of-function phenotypes. RESULTS We describe a 96-well plate-based assay to kinetically assess starvation sensitivity in budding yeast that allows for the quantitative detection of very modest starvation sensitivity phenotypes with statistical significance in autophagy mutant yeast strains lacking the ATG27 gene.
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Affiliation(s)
- Candyce M Sturgeon
- Department of Biology, High Point University, One University Parkway, High Point, NC, 27268, USA
| | - Meaghan R Robinson
- Department of Biology, High Point University, One University Parkway, High Point, NC, 27268, USA
| | - Molly C Penton
- Department of Biology, High Point University, One University Parkway, High Point, NC, 27268, USA.,Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223-0001, USA
| | - Deanna C Clemmer
- Department of Biology, High Point University, One University Parkway, High Point, NC, 27268, USA.,Cystic Fibrosis Center/Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7248, USA
| | - Maria A Trujillo
- Department of Biology, High Point University, One University Parkway, High Point, NC, 27268, USA.,Department of Human Genetics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Ambar U Khawaja
- International Baccalaureate Program, High Point Central High School, High Point, NC, 27262, USA.,Campus Y Program (Global Gap Year), University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Verónica A Segarra
- Department of Biology, High Point University, One University Parkway, High Point, NC, 27268, USA.
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16
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Chung T. How phosphoinositides shape autophagy in plant cells. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:146-158. [PMID: 30824047 DOI: 10.1016/j.plantsci.2019.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/10/2019] [Accepted: 01/19/2019] [Indexed: 05/06/2023]
Abstract
Plant cells use autophagy to degrade their own cytoplasm in vacuoles, thereby not only recycling their breakdown products, but also ensuring the homeostasis of essential cytoplasmic constituents and organelles. Plants and other eukaryotes have a conserved set of core Autophagy-related (ATG) genes involved in the biogenesis of the autophagosome, the main autophagic compartment destined for the lytic vacuole. In the past decade, the core ATG genes were isolated from several plant species. The core ATG proteins include the components of the VACUOLAR PROTEIN SORTING 34 (VPS34) complex that is responsible for the local production of phosphatidylinositol 3-phosphate (PI3P) at the site of autophagosome formation. Dissecting the roles of PI3P and its effectors in autophagy is challenging, because of the multi-faceted links between autophagosomal and endosomal systems. This review highlights recent studies on putative plant PI3P effectors involved in autophagosome dynamics. Molecular mechanisms underlying the requirement of PI3P for autophagosome biogenesis and trafficking are also discussed.
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Affiliation(s)
- Taijoon Chung
- Department of Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea.
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17
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Seaman MNJ. Back From the Brink: Retrieval of Membrane Proteins From Terminal Compartments: Unexpected Pathways for Membrane Protein Retrieval From Vacuoles and Endolysosomes. Bioessays 2019; 41:e1800146. [PMID: 30706963 DOI: 10.1002/bies.201800146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/03/2018] [Indexed: 11/12/2022]
Abstract
It has long been believed that membrane proteins present in degradative compartments such as endolysosomes or vacuoles would be destined for destruction. Now however, it appears that mechanisms and machinery exist in simple eukaryotes such as yeast and more complex organisms such as mammals that can rescue potentially "doomed" membrane proteins by retrieving them from these "late" compartments and recycling them back to the Golgi complex. In yeast, a sorting nexin dimer containing Snx4p can recognize and retrieve the Atg27p membrane protein while in mammals, the AP5 complex (with SPG11 and SPG15) directs the recycling of Golgi-localized proteins along with the cation-independent mannose 6-phosphate receptor (CIMPR). Although the respective machinery is different, there is much commonality between yeast and mammals regarding the mechanisms of retrieval and the physiological importance of these late recycling pathways.
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Affiliation(s)
- Matthew N J Seaman
- University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Addenbrookes Hospital, CB2 0XY, UK
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18
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Sardana R, Zhu L, Emr SD. Rsp5 Ubiquitin ligase-mediated quality control system clears membrane proteins mistargeted to the vacuole membrane. J Cell Biol 2018; 218:234-250. [PMID: 30361468 PMCID: PMC6314561 DOI: 10.1083/jcb.201806094] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/06/2018] [Accepted: 10/01/2018] [Indexed: 11/22/2022] Open
Abstract
Sardana et al. show that protein quality control systems on multiple endocytic organelles cooperate to prevent aberrant protein accumulation and maintain proteostasis. By mistargeting PM proteins de novo to the yeast vacuolar membrane, they uncover a “fail-safe” mechanism that ensures degradation of diverse endocytic cargos. Maintenance of organelle identity is profoundly dependent on the coordination between correct targeting of proteins and removal of mistargeted and damaged proteins. This task is mediated by organelle-specific protein quality control (QC) systems. In yeast, the endocytosis and QC of most plasma membrane (PM) proteins requires the Rsp5 ubiquitin ligase and ART adaptor network. We show that intracellular adaptors of Rsp5, Ear1, and Ssh4 mediate recognition and vacuolar degradation of PM proteins that escape or bypass PM QC systems. This second tier of surveillance helps to maintain cell integrity upon heat stress and protects from proteotoxicity. To understand the mechanism of the recognition of aberrant PM cargos by Ssh4–Rsp5, we mistarget multiple PM proteins de novo to the vacuolar membrane. We found that Ssh4–Rsp5 can target and ubiquitinate multiple lysines within a restricted distance from the membrane, providing a fail-safe mechanism for a diverse cargo repertoire. The mistargeting or misfolding of PM proteins likely exposes these lysines or shifts them into the “ubiquitination zone” accessible to the Ssh4–Rsp5 complex.
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Affiliation(s)
- Richa Sardana
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | - Lu Zhu
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | - Scott D Emr
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
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19
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Wei Y, Liu M, Li X, Liu J, Li H. Origin of the Autophagosome Membrane in Mammals. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1012789. [PMID: 30345294 PMCID: PMC6174804 DOI: 10.1155/2018/1012789] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/18/2018] [Accepted: 09/03/2018] [Indexed: 12/20/2022]
Abstract
Autophagy begins with the nucleation of phagophores, which then expand to give rise to the double-membrane autophagosomes. Autophagosomes ultimately fuse with lysosomes, where the cytosolic cargoes are degraded. Accumulation of autophagosomes is a hallmark of autophagy and neurodegenerative disorders including Alzheimer's and Huntington's disease. In recent years, the sources of autophagosome membrane have attracted a great deal of interests, even so, the membrane donors for autophagosomes are still under debate. In this review, we describe the probable sources of autophagosome membrane.
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Affiliation(s)
- Yun Wei
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Meixia Liu
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Xianxiao Li
- Department of Oncology, Air Force General Hospital, Beijing 100142, China
| | - Jiangang Liu
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Hao Li
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
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20
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Suzuki SW, Emr SD. Membrane protein recycling from the vacuole/lysosome membrane. J Cell Biol 2018; 217:1623-1632. [PMID: 29511122 PMCID: PMC5940307 DOI: 10.1083/jcb.201709162] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/24/2018] [Accepted: 02/13/2018] [Indexed: 12/23/2022] Open
Abstract
The lysosome (or vacuole in yeast) is the central organelle responsible for cellular degradation and nutrient storage. Lysosomes receive cargo from the secretory, endocytic, and autophagy pathways. Many of these proteins and lipids are delivered to the lysosome membrane, and some are degraded in the lysosome lumen, whereas others appear to be recycled through unknown pathways. In this study, we identify the transmembrane autophagy protein Atg27 as a physiological cargo recycled from the vacuole. We reveal that Atg27 is delivered to the vacuole membrane and then recycled using a two-step recycling process. First, Atg27 is recycled from the vacuole to the endosome via the Snx4 complex and then from the endosome to the Golgi via the retromer complex. During the process of vacuole-to-endosome retrograde trafficking, Snx4 complexes assemble on the vacuolar surface and recognize specific residues in the cytoplasmic tail of Atg27. This novel pathway maintains the normal composition and function of the vacuole membrane.
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Affiliation(s)
- Sho W Suzuki
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Scott D Emr
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
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21
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Autophagy in the context of the cellular membrane-trafficking system: the enigma of Atg9 vesicles. Biochem Soc Trans 2017; 45:1323-1331. [PMID: 29150528 PMCID: PMC5730941 DOI: 10.1042/bst20170128] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 12/15/2022]
Abstract
Macroautophagy is an intracellular degradation system that involves the de novo formation of membrane structures called autophagosomes, although the detailed process by which membrane lipids are supplied during autophagosome formation is yet to be elucidated. Macroautophagy is thought to be associated with canonical membrane trafficking, but several mechanistic details are still missing. In this review, the current understanding and potential mechanisms by which membrane trafficking participates in macroautophagy are described, with a focus on the enigma of the membrane protein Atg9, for which the proximal mechanisms determining its movement are disputable, despite its key role in autophagosome formation.
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22
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Zou S, Sun D, Liang Y. The Roles of the SNARE Protein Sed5 in Autophagy in Saccharomyces cerevisiae. Mol Cells 2017; 40:643-654. [PMID: 28927260 PMCID: PMC5638772 DOI: 10.14348/molcells.2017.0030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/10/2017] [Accepted: 07/19/2017] [Indexed: 12/15/2022] Open
Abstract
Autophagy is a degradation pathway in eukaryotic cells in which aging proteins and organelles are sequestered into double-membrane vesicles, termed autophagosomes, which fuse with vacuoles to hydrolyze cargo. The key step in autophagy is the formation of autophagosomes, which requires different kinds of vesicles, including COPII vesicles and Atg9-containing vesicles, to transport lipid double-membranes to the phagophore assembly site (PAS). In yeast, the cis-Golgi localized t-SNARE protein Sed5 plays a role in endoplasmic reticulum (ER)-Golgi and intra-Golgi vesicular transport. We report that during autophagy, sed5-1 mutant cells could not properly transport Atg8 to the PAS, resulting in multiple Atg8 dots being dispersed into the cytoplasm. Some dots were trapped in the Golgi apparatus. Sed5 regulates the antero-grade trafficking of Atg9-containing vesicles to the PAS by participating in the localization of Atg23 and Atg27 to the Golgi apparatus. Furthermore, we found that overexpression of SFT1 or SFT2 (suppressor of sed5 ts) rescued the autophagy defects in sed5-1 mutant cells. Our data suggest that Sed5 plays a novel role in autophagy, by regulating the formation of Atg9-containing vesicles in the Golgi apparatus, and the genetic interaction between Sft1/2 and Sed5 is essential for autophagy.
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Affiliation(s)
- Shenshen Zou
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095,
China
| | - Dan Sun
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095,
China
| | - Yongheng Liang
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095,
China
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23
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Ma M, Burd CG, Chi RJ. Distinct complexes of yeast Snx4 family SNX-BARs mediate retrograde trafficking of Snc1 and Atg27. Traffic 2017; 18:134-144. [PMID: 28026081 DOI: 10.1111/tra.12462] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/06/2016] [Accepted: 12/06/2016] [Indexed: 12/31/2022]
Abstract
The yeast SNX4 sub-family of sorting nexin containing a Bin-Amphiphysin-Rvs domain (SNX-BAR) proteins, Snx4/Atg24, Snx41 and Atg20/Snx42, are required for endocytic recycling and selective autophagy. Here, we show that Snx4 forms 2 functionally distinct heterodimers: Snx4-Atg20 and Snx4-Snx41. Each heterodimer coats an endosome-derived tubule that mediates retrograde sorting of distinct cargo; the v-SNARE, Snc1, is a cargo of the Snx4-Atg20 pathway, and Snx4-Snx41 mediates retrograde sorting of Atg27, an integral membrane protein implicated in selective autophagy. Live cell imaging of individual endosomes shows that Snx4 and the Vps5-Vps17 retromer SNX-BAR heterodimer operate concurrently on a maturing endosome. Consistent with this, the yeast dynamin family protein, Vps1, which was previously shown to promote fission of retromer-coated tubules, promotes fission of Snx4-Atg20 coated tubules. The results indicate that the yeast SNX-BAR proteins coat 3 distinct types of endosome-derived carriers that mediate endosome-to-Golgi retrograde trafficking.
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Affiliation(s)
- Mengxiao Ma
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
| | - Christopher G Burd
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
| | - Richard J Chi
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina
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24
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Bean BDM, Davey M, Conibear E. Cargo selectivity of yeast sorting nexins. Traffic 2017; 18:110-122. [PMID: 27883263 DOI: 10.1111/tra.12459] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/21/2016] [Accepted: 11/21/2016] [Indexed: 01/09/2023]
Abstract
Sorting nexins are PX domain-containing proteins that bind phospholipids and often act in membrane trafficking where they help to select cargo. However, the functions and cargo specificities of many sorting nexins are unknown. Here, a high-throughput imaging screen was used to identify new sorting nexin cargo in the yeast Saccharomyces cerevisiae. Deletions of 9 different sorting nexins were screened for mislocalization of a set of green fluorescent protein (GFP)-tagged membrane proteins found at the plasma membrane, Golgi or endosomes. This identified 27 proteins that require 1 or more sorting nexins for their correct localization, 23 of which represent novel sorting nexin cargo. Nine hits whose sorting was dependent on Snx4, the sorting nexin-containing retromer complex, or both retromer and Snx3, were examined in detail to search for potential sorting motifs. We identified cytosolic domains of Ear1, Ymd8 and Ymr010w that conferred retromer-dependent sorting on a chimeric reporter and identified conserved residues required for this sorting in a functional assay. This work defined a consensus sequence for retromer and Snx3-dependent sorting.
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Affiliation(s)
- Björn D M Bean
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
| | - Michael Davey
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
| | - Elizabeth Conibear
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
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25
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Gómez-Sánchez R, Sánchez-Wandelmer J, Reggiori F. Monitoring the Formation of Autophagosomal Precursor Structures in Yeast Saccharomyces cerevisiae. Methods Enzymol 2017; 588:323-365. [DOI: 10.1016/bs.mie.2016.09.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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26
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The AP-3 adaptor complex mediates sorting of yeast and mammalian PQ-loop-family basic amino acid transporters to the vacuolar/lysosomal membrane. Sci Rep 2015; 5:16665. [PMID: 26577948 PMCID: PMC4649669 DOI: 10.1038/srep16665] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/19/2015] [Indexed: 01/31/2023] Open
Abstract
The limiting membrane of lysosomes in animal cells and that of the vacuole in yeast
include a wide variety of transporters, but little is known about how these proteins
reach their destination membrane. The mammalian PQLC2 protein catalyzes efflux of
basic amino acids from the lysosome, and the similar Ypq1, −2, and
−3 proteins of yeast perform an equivalent function at the vacuole. We
here show that the Ypq proteins are delivered to the vacuolar membrane via the
alkaline phosphatase (ALP) trafficking pathway, which requires the AP-3 adaptor
complex. When traffic via this pathway is deficient, the Ypq proteins pass through
endosomes from where Ypq1 and Ypq2 properly reach the vacuolar membrane whereas Ypq3
is missorted to the vacuolar lumen via the multivesicular body pathway. When
produced in yeast, PQLC2 also reaches the vacuolar membrane via the ALP pathway, but
tends to sort to the vacuolar lumen if AP-3 is defective. Finally, in HeLa cells,
inhibiting the synthesis of an AP-3 subunit also impairs sorting of PQLC2 to
lysosomes. Our results suggest the existence of a conserved AP-3-dependent
trafficking pathway for proper delivery of basic amino acid exporters to the yeast
vacuole and to lysosomes of human cells.
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