1
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Ma M, Ganapathi M, Zheng Y, Tan KL, Kanca O, Bove KE, Quintanilla N, Sag SO, Temel SG, LeDuc CA, McPartland AJ, Pereira EM, Shen Y, Hagen J, Thomas CP, Nguyen Galván NT, Pan X, Lu S, Rosenfeld JA, Calame DG, Wangler MF, Lupski JR, Pehlivan D, Hertel PM, Chung WK, Bellen HJ. Homozygous missense variants in YKT6 result in loss of function and are associated with developmental delay, with or without severe infantile liver disease and risk for hepatocellular carcinoma. Genet Med 2024; 26:101125. [PMID: 38522068 DOI: 10.1016/j.gim.2024.101125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
PURPOSE YKT6 plays important roles in multiple intracellular vesicle trafficking events but has not been associated with Mendelian diseases. METHODS We report 3 unrelated individuals with rare homozygous missense variants in YKT6 who exhibited neurological disease with or without a progressive infantile liver disease. We modeled the variants in Drosophila. We generated wild-type and variant genomic rescue constructs of the fly ortholog dYkt6 and compared their ability in rescuing the loss-of-function phenotypes in mutant flies. We also generated a dYkt6KozakGAL4 allele to assess the expression pattern of dYkt6. RESULTS Two individuals are homozygous for YKT6 [NM_006555.3:c.554A>G p.(Tyr185Cys)] and exhibited normal prenatal course followed by failure to thrive, developmental delay, and progressive liver disease. Haplotype analysis identified a shared homozygous region flanking the variant, suggesting a common ancestry. The third individual is homozygous for YKT6 [NM_006555.3:c.191A>G p.(Tyr64Cys)] and exhibited neurodevelopmental disorders and optic atrophy. Fly dYkt6 is essential and is expressed in the fat body (analogous to liver) and central nervous system. Wild-type genomic rescue constructs can rescue the lethality and autophagic flux defects, whereas the variants are less efficient in rescuing the phenotypes. CONCLUSION The YKT6 variants are partial loss-of-function alleles, and the p.(Tyr185Cys) is more severe than p.(Tyr64Cys).
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Affiliation(s)
- Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Yiming Zheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Kai-Li Tan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Kevin E Bove
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Norma Quintanilla
- Department of Pathology and Immunology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Sebnem O Sag
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Sehime G Temel
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
| | | | | | | | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY
| | - Jacob Hagen
- Department of Systems Biology, Columbia University Medical Center, New York, NY
| | - Christie P Thomas
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
| | | | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Baylor Genetics Laboratories, Houston, TX
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Paula M Hertel
- Texas Children's Hospital, Houston, TX; Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX.
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2
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Watanabe H, Urano S, Kikuchi N, Kubo Y, Kikuchi A, Gomi K, Shintani T. Ykt6 functionally overlaps with vacuolar and exocytic R-SNAREs in the yeast Saccharomyces cerevisiae. J Biol Chem 2024; 300:107274. [PMID: 38588809 PMCID: PMC11091695 DOI: 10.1016/j.jbc.2024.107274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 03/17/2024] [Accepted: 03/31/2024] [Indexed: 04/10/2024] Open
Abstract
The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex forms a 4-helix coiled-coil bundle consisting of 16 layers of interacting side chains upon membrane fusion. The central layer (layer 0) is highly conserved and comprises three glutamines (Q) and one arginine (R), and thus SNAREs are classified into Qa-, Qb-, Qc-, and R-SNAREs. Homotypic vacuolar fusion in Saccharomyces cerevisiae requires the SNAREs Vam3 (Qa), Vti1 (Qb), Vam7 (Qc), and Nyv1 (R). However, the yeast strain lacking NYV1 (nyv1Δ) shows no vacuole fragmentation, whereas the vam3Δ and vam7Δ strains display fragmented vacuoles. Here, we provide genetic evidence that the R-SNAREs Ykt6 and Nyv1 are functionally redundant in vacuole homotypic fusion in vivo using a newly isolated ykt6 mutant. We observed the ykt6-104 mutant showed no defect in vacuole morphology, but the ykt6-104 nyv1Δ double mutant had highly fragmented vacuoles. Furthermore, we show the defect in homotypic vacuole fusion caused by the vam7-Q284R mutation was compensated by the nyv1-R192Q or ykt6-R165Q mutations, which maintained the 3Q:1R ratio in the layer 0 of the SNARE complex, indicating that Nyv1 is exchangeable with Ykt6 in the vacuole SNARE complex. Unexpectedly, we found Ykt6 assembled with exocytic Q-SNAREs when the intrinsic exocytic R-SNAREs Snc1 and its paralog Snc2 lose their ability to assemble into the exocytic SNARE complex. These results suggest that Ykt6 may serve as a backup when other R-SNAREs become dysfunctional and that this flexible assembly of SNARE complexes may help cells maintain the robustness of the vesicular transport network.
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Affiliation(s)
- Hayate Watanabe
- Department of Agricultural Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shingo Urano
- Department of Agricultural Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Nozomi Kikuchi
- Department of Agricultural Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Yurika Kubo
- Department of Agricultural Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Ayumi Kikuchi
- Department of Agricultural Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Katsuya Gomi
- Department of Agricultural Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Takahiro Shintani
- Department of Agricultural Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.
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3
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Ma T, Tan JR, Lu JY, Li S, Zhang Y. S-acylation of YKT61 modulates its unconventional participation in the formation of SNARE complexes in Arabidopsis. J Genet Genomics 2024:S1673-8527(24)00077-8. [PMID: 38642801 DOI: 10.1016/j.jgg.2024.04.007] [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: 02/02/2024] [Revised: 04/11/2024] [Accepted: 04/13/2024] [Indexed: 04/22/2024]
Abstract
Hetero-tetrameric soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) complexes are critical for vesicle-target membrane fusion within the endomembrane system of eukaryotic cells. SNARE assembly involves four different SNARE motifs, Qa, Qb, Qc, and R, provided by three or four SNARE proteins. YKT6 is an atypical R-SNARE that lacks a transmembrane domain and is involved in multiple vesicle-target membrane fusions. Although YKT6 is evolutionarily conserved and essential, its function and regulation in different phyla seem distinct. Arabidopsis YKT61, the yeast and metazoan YKT6 homologue, is essential for gametophytic development, plays a critical role in sporophytic cells, and mediates multiple vesicle-target membrane fusion. However, its molecular regulation is unclear. We report here that YKT61 is S-acylated. Abolishing its S-acylation by a C195S mutation dissociates YKT61 from endomembrane structures and causes its functional loss. Although interacting with various SNARE proteins, YKT61 functions not as a canonical R-SNARE but coordinates with other R-SNAREs to participate in the formation of SNARE complexes. Phylum-specific molecular regulation of YKT6 may be evolved to allow more efficient SNARE assembly in different eukaryotic cells.
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Affiliation(s)
- Ting Ma
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Jun-Ru Tan
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jin-Yu Lu
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Sha Li
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Yan Zhang
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China.
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4
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Sakamaki JI, Mizushima N. Cell biology of protein-lipid conjugation. Cell Struct Funct 2023; 48:99-112. [PMID: 37019684 PMCID: PMC10721952 DOI: 10.1247/csf.23016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
Protein-lipid conjugation is a widespread modification involved in many biological processes. Various lipids, including fatty acids, isoprenoids, sterols, glycosylphosphatidylinositol, sphingolipids, and phospholipids, are covalently linked with proteins. These modifications direct proteins to intracellular membranes through the hydrophobic nature of lipids. Some of these membrane-binding processes are reversible through delipidation or by reducing the affinity to membranes. Many signaling molecules undergo lipid modification, and their membrane binding is important for proper signal transduction. The conjugation of proteins to lipids also influences the dynamics and function of organellar membranes. Dysregulation of lipidation has been associated with diseases such as neurodegenerative diseases. In this review, we first provide an overview of diverse forms of protein-lipid conjugation and then summarize the catalytic mechanisms, regulation, and roles of these modifications.Key words: lipid, lipidation, membrane, organelle, protein modification.
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Affiliation(s)
- Jun-ichi Sakamaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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5
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Zhang X, G. Dapar ML, Zhang X, Chen Y. A pan-cancer analysis of the oncogenic role of YKT6 in human tumors. Medicine (Baltimore) 2023; 102:e33546. [PMID: 37058019 PMCID: PMC10101269 DOI: 10.1097/md.0000000000033546] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/27/2023] [Indexed: 04/15/2023] Open
Abstract
YKT6, as a Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein with vesicle trafficking, plays an essential role in the development and progression of tumor. However, the gene of YKT6 has not been fully assessed in pan-cancer studies. We aim to investigate the gene of YKT6 across 33 different types of tumor by using the Cancer Genome Atlas, Gene Expression Omnibus database, and other several kinds of bioinformatic tools. YKT6 is significantly up-regulated in most tumors, and we found that overexpression of YKT6 is positively associated with poor prognosis of overall survival and poor disease-free survival prognosis in several tumors, such as Adrenocortical carcinoma, Bladder Urothelial Carcinoma, Head and Neck squamous cell carcinoma. We also detected distinct associations exist between YKT6 and tumor mutational burden or microsatellite instability with tumors. YKT6 expression was positively related to cancer-associated fibroblasts for TCGA tumors of colon adenocarcinoma and LGG. Furthermore, we discovered a significantly positively correlation between YKT6 expression and endothelial cell in tumors of colon adenocarcinoma, HNSC-HPV+, OV, READ and THCA. While a negative relationship was obtained between YKT6 expression and endothelial cell in KIRC. Moreover, "Syntaxin binding," "SNARE complex," "vesicle fusion" and "DNA replication" are involved in the influence of YKT6 on tumor pathogenesis. Our pan-cancer analysis offers a deep comprehending the gene of YKT6 in tumoeigenesis from viewpoint of clinical tumor samples.
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Affiliation(s)
- Xuezhong Zhang
- Department of Biology, College of Arts and Sciences, Central Mindanao University, Musuan, Philippines
- Department of Laboratory Medicine, Zibo Central Hospital, Zibo, China
| | - Mark Lloyd G. Dapar
- Department of Biology, College of Arts and Sciences, Central Mindanao University, Musuan, Philippines
- Center for Biodiversity Research and Extension in Mindanao, Central Mindanao University, Musuan, Philippines
- Microtechnique and Systematics Laboratory, Natural Science Research Center, Musuan, Philippines
| | - Xin Zhang
- Department of Laboratory Medicine, Zibo Central Hospital, Zibo, China
| | - Yingjun Chen
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, China
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6
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Sánchez-Martín P, Kriegenburg F, Alves L, Adam J, Elsaesser J, Babic R, Mancilla H, Licheva M, Tascher G, Münch C, Eimer S, Kraft C. ULK1-mediated phosphorylation regulates the conserved role of YKT6 in autophagy. J Cell Sci 2023; 136:jcs260546. [PMID: 36644903 PMCID: PMC10022743 DOI: 10.1242/jcs.260546] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/06/2023] [Indexed: 01/17/2023] Open
Abstract
Autophagy is a catabolic process during which cytosolic material is enwrapped in a newly formed double-membrane structure called the autophagosome, and subsequently targeted for degradation in the lytic compartment of the cell. The fusion of autophagosomes with the lytic compartment is a tightly regulated step and involves membrane-bound SNARE proteins. These play a crucial role as they promote lipid mixing and fusion of the opposing membranes. Among the SNARE proteins implicated in autophagy, the essential SNARE protein YKT6 is the only SNARE protein that is evolutionarily conserved from yeast to humans. Here, we show that alterations in YKT6 function, in both mammalian cells and nematodes, produce early and late autophagy defects that result in reduced survival. Moreover, mammalian autophagosomal YKT6 is phospho-regulated by the ULK1 kinase, preventing premature bundling with the lysosomal SNARE proteins and thereby inhibiting autophagosome-lysosome fusion. Together, our findings reveal that timely regulation of the YKT6 phosphorylation status is crucial throughout autophagy progression and cell survival.
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Affiliation(s)
- Pablo Sánchez-Martín
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Franziska Kriegenburg
- 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
| | - Ludovico Alves
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Julius Adam
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Jana Elsaesser
- 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
| | - Riccardo Babic
- 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
| | - Hector Mancilla
- 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
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Stefan Eimer
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - 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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7
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Karuna M P, Witte L, Linnemannstoens K, Choezom D, Danieli-Mackay A, Honemann-Capito M, Gross JC. Phosphorylation of Ykt6 SNARE Domain Regulates Its Membrane Recruitment and Activity. Biomolecules 2020; 10:biom10111560. [PMID: 33207719 PMCID: PMC7696345 DOI: 10.3390/biom10111560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/17/2022] Open
Abstract
Sensitive factor attachment protein receptors (SNARE) proteins are important mediators of protein trafficking that regulate the membrane fusion of specific vesicle populations and their target organelles. The SNARE protein Ykt6 lacks a transmembrane domain and attaches to different organelle membranes. Mechanistically, Ykt6 activity is thought to be regulated by a conformational change from a closed cytosolic form to an open membrane-bound form, yet the mechanism that regulates this transition is unknown. We identified phosphorylation sites in the SNARE domain of Ykt6 that mediate Ykt6 membrane recruitment and are essential for cellular growth. Using proximity-dependent labeling and membrane fractionation, we found that phosphorylation regulates Ykt6 conversion from a closed to an open conformation. This conformational switch recruits Ykt6 to several organelle membranes, where it functionally regulates the trafficking of Wnt proteins and extracellular vesicle secretion in a concentration-dependent manner. We propose that phosphorylation of its SNARE domain leads to a conformational switch from a cytosolic, auto-inhibited Ykt6 to an active SNARE at different membranes.
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Affiliation(s)
- Pradhipa Karuna M
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Leonie Witte
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Karen Linnemannstoens
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Dolma Choezom
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Adi Danieli-Mackay
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Mona Honemann-Capito
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Julia Christina Gross
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
- HMU Health and Medical University Potsdam, 14471 Potsdam, Germany
- Correspondence:
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8
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Gao J, Kurre R, Rose J, Walter S, Fröhlich F, Piehler J, Reggiori F, Ungermann C. Function of the SNARE Ykt6 on autophagosomes requires the Dsl1 complex and the Atg1 kinase complex. EMBO Rep 2020; 21:e50733. [PMID: 33025734 PMCID: PMC7726795 DOI: 10.15252/embr.202050733] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/04/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022] Open
Abstract
The mechanism and regulation of fusion between autophagosomes and lysosomes/vacuoles are still only partially understood in both yeast and mammals. In yeast, this fusion step requires SNARE proteins, the homotypic vacuole fusion and protein sorting (HOPS) tethering complex, the RAB7 GTPase Ypt7, and its guanine nucleotide exchange factor (GEF) Mon1‐Ccz1. We and others recently identified Ykt6 as the autophagosomal SNARE protein. However, it has not been resolved when and how lipid‐anchored Ykt6 is recruited onto autophagosomes. Here, we show that Ykt6 is recruited at an early stage of the formation of these carriers through a mechanism that depends on endoplasmic reticulum (ER)‐resident Dsl1 complex and COPII‐coated vesicles. Importantly, Ykt6 activity on autophagosomes is regulated by the Atg1 kinase complex, which inhibits Ykt6 through direct phosphorylation. Thus, our findings indicate that the Ykt6 pool on autophagosomal membranes is kept inactive by Atg1 phosphorylation, and once an autophagosome is ready to fuse with vacuole, Ykt6 dephosphorylation allows its engagement in the fusion event.
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Affiliation(s)
- Jieqiong Gao
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany
| | - Rainer Kurre
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics, Integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
| | - Jaqueline Rose
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany
| | - Stefan Walter
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Florian Fröhlich
- Department of Biology/Chemistry, Molecular Membrane Biology Group, University of Osnabrück, Osnabrück, Germany
| | - Jacob Piehler
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics, Integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany.,Department of Biology/Chemistry, Biophysics Section, University of Osnabrück, Osnabrück, Germany
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany
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9
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Kriegenburg F, Bas L, Gao J, Ungermann C, Kraft C. The multi-functional SNARE protein Ykt6 in autophagosomal fusion processes. Cell Cycle 2019; 18:639-651. [PMID: 30836834 PMCID: PMC6464585 DOI: 10.1080/15384101.2019.1580488] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/06/2019] [Accepted: 01/29/2019] [Indexed: 01/01/2023] Open
Abstract
Autophagy is a degradative pathway in which cytosolic material is enwrapped within double membrane vesicles, so-called autophagosomes, and delivered to lytic organelles. SNARE (Soluble N-ethylmaleimide sensitive factor attachment protein receptor) proteins are key to drive membrane fusion of the autophagosome and the lytic organelles, called lysosomes in higher eukaryotes or vacuoles in plants and yeast. Therefore, the identification of functional SNARE complexes is central for understanding fusion processes and their regulation. The SNARE proteins Syntaxin 17, SNAP29 and Vamp7/VAMP8 are responsible for the fusion of autophagosomes with lysosomes in higher eukaryotes. Recent studies reported that the R-SNARE Ykt6 is an additional SNARE protein involved in autophagosome-lytic organelle fusion in yeast, Drosophila, and mammals. These current findings point to an evolutionarily conserved role of Ykt6 in autophagosome-related fusion events. Here, we briefly summarize the principal mechanisms of autophagosome-lytic organelle fusion, with a special focus on Ykt6 to highlight some intrinsic features of this unusual SNARE protein.
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Affiliation(s)
- Franziska Kriegenburg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Levent Bas
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Jieqiong Gao
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Christian Ungermann
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg
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10
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Khurana GK, Vishwakarma P, Puri N, Lynn AM. Phylogenetic Analysis of the vesicular fusion SNARE machinery revealing its functional divergence across Eukaryotes. Bioinformation 2018; 14:361-368. [PMID: 30262973 PMCID: PMC6143360 DOI: 10.6026/97320630014361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 07/12/2018] [Accepted: 07/30/2018] [Indexed: 12/23/2022] Open
Abstract
Proteins of the SNARE (Soluble N-ethylmaleimide-sensitive factor attachment protein receptors) family play a significant role in all
vesicular fusion events involved in endocytic and exocytic pathways. These proteins act as molecular machines that assemble into tight
four-helix bundle complex, bridging the opposing membranes into close proximity forming membrane fusion. Almost all SNARE
proteins share a 53 amino acid coiled-coil domain, which is mostly linked to the transmembrane domain at the C-terminal end. Despite
significant variations between SNARE sequences across species, the SNARE mediated membrane fusion is evolutionary conserved in
all eukaryotes. It is of interest to compare the functional divergence of SNARE proteins across various eukaryotic groups during
evolution. Here, we report an exhaustive phylogeny of the SNARE proteins retrieved from SNARE database including plants, animals,
fungi and protists. The Initial phylogeny segregated SNARE protein sequences into five well-supported clades Qa, Qb, Qc, Qbc and R
reflective of their positions in the four-helix SNARE complex. Further to improve resolution the Qa, Qb, Qc and R family specific trees
were reconstructed, each of these were further segregated into organelle specific clades at first and later diverged into lineage specific
subgroups. This revealed that most of the SNARE orthologs are conserved at subcellular locations or at trafficking pathways across
various species during eukaryotic evolution. The paralogous expansion in SNARE repertoire was observed at metazoans (animals) and
plants independently during eukaryotic evolution. However, results also show that the multi-cellular and saprophytic fungi have
limited SNAREs.
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Affiliation(s)
- Gagandeep K Khurana
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India- 110067
| | - Poonam Vishwakarma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India-110067
| | - Niti Puri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India- 110067
| | - Andrew Michael Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India-110067
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11
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Takáts S, Glatz G, Szenci G, Boda A, Horváth GV, Hegedűs K, Kovács AL, Juhász G. Non-canonical role of the SNARE protein Ykt6 in autophagosome-lysosome fusion. PLoS Genet 2018; 14:e1007359. [PMID: 29694367 PMCID: PMC5937789 DOI: 10.1371/journal.pgen.1007359] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 05/07/2018] [Accepted: 04/11/2018] [Indexed: 11/25/2022] Open
Abstract
The autophagosomal SNARE Syntaxin17 (Syx17) forms a complex with Snap29 and Vamp7/8 to promote autophagosome-lysosome fusion via multiple interactions with the tethering complex HOPS. Here we demonstrate that, unexpectedly, one more SNARE (Ykt6) is also required for autophagosome clearance in Drosophila. We find that loss of Ykt6 leads to large-scale accumulation of autophagosomes that are unable to fuse with lysosomes to form autolysosomes. Of note, loss of Syx5, the partner of Ykt6 in ER-Golgi trafficking does not prevent autolysosome formation, pointing to a more direct role of Ykt6 in fusion. Indeed, Ykt6 localizes to lysosomes and autolysosomes, and forms a SNARE complex with Syx17 and Snap29. Interestingly, Ykt6 can be outcompeted from this SNARE complex by Vamp7, and we demonstrate that overexpression of Vamp7 rescues the fusion defect of ykt6 loss of function cells. Finally, a point mutant form with an RQ amino acid change in the zero ionic layer of Ykt6 protein that is thought to be important for fusion-competent SNARE complex assembly retains normal autophagic activity and restores full viability in mutant animals, unlike palmitoylation or farnesylation site mutant Ykt6 forms. As Ykt6 and Vamp7 are both required for autophagosome-lysosome fusion and are mutually exclusive subunits in a Syx17-Snap29 complex, these data suggest that Vamp7 is directly involved in membrane fusion and Ykt6 acts as a non-conventional, regulatory SNARE in this process. SNARE proteins are critical executors of most vesicle fusion events in eukaryotic cells. 4 SNARE domains assemble into a bundle to promote fusion. We have previously shown that Syntaxin 17, Snap29 (contributing 2 SNARE domains) and Vamp7 form the SNARE complex executing autophagosome-lysosome fusion in Drosophila. Surprisingly, one more SNARE protein (Ykt6) is also required in vivo for autophagosome-lysosome fusion. We find that Ykt6 can form a less stable complex with Syntaxin 17 and Snap29 than Vamp7, because Vamp7 outcompetes Ykt6. Ykt6, Vamp7 and Syntaxin 17 all bind to the tethering complex HOPS to promote vesicle fusion. Ykt6 likely plays a non-canonical role in autophagosome-lysosome fusion, because its mutant form (which is thought to be unable to assemble into a fusion-competent SNARE complex) still rescues the fusion defect of ykt6 mutant cells, and it restores viability in mutant animals.
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Affiliation(s)
- Szabolcs Takáts
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
- Hungarian Academy of Sciences, Premium Postdoctoral Research Program, Budapest, Hungary
- * E-mail: (ST); (GJ)
| | - Gábor Glatz
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Győző Szenci
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Attila Boda
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Gábor V. Horváth
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Krisztina Hegedűs
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Attila L. Kovács
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Gábor Juhász
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail: (ST); (GJ)
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12
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Karim MA, Samyn DR, Mattie S, Brett CL. Distinct features of multivesicular body-lysosome fusion revealed by a new cell-free content-mixing assay. Traffic 2017; 19:138-149. [DOI: 10.1111/tra.12543] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 11/07/2017] [Accepted: 11/09/2017] [Indexed: 01/18/2023]
Affiliation(s)
| | | | - Sevan Mattie
- Department of Biology; Concordia University; Montreal Canada
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13
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D'Agostino M, Risselada HJ, Mayer A. Steric hindrance of SNARE transmembrane domain organization impairs the hemifusion-to-fusion transition. EMBO Rep 2016; 17:1590-1608. [PMID: 27644261 DOI: 10.15252/embr.201642209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/12/2016] [Indexed: 11/09/2022] Open
Abstract
SNAREs fuse membranes in several steps. Trans-SNARE complexes juxtapose membranes, induce hemifused stalk structures, and open the fusion pore. A recent penetration model of fusion proposed that SNAREs force the hydrophilic C-termini of their transmembrane domains through the hydrophobic core of the membrane(s). In contrast, the indentation model suggests that the C-termini open the pore by locally compressing and deforming the stalk. Here we test these models in the context of yeast vacuole fusion. Addition of small hydrophilic tags renders bilayer penetration by the C-termini energetically unlikely. It preserves fusion activity, however, arguing against the penetration model. Addition of large protein tags to the C-termini permits SNARE activation, trans-SNARE pairing, and hemifusion but abolishes pore opening. Fusion proceeds if the tags are detached from the membrane by a hydrophilic spacer or if only one side of the trans-SNARE complex carries a protein tag. Thus, both sides of a trans-SNARE complex can drive pore opening. Our results are consistent with an indentation model in which multiple SNARE C-termini cooperate in opening the fusion pore by locally deforming the inner leaflets.
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Affiliation(s)
- Massimo D'Agostino
- Département de Biochimie, Université de Lausanne, Epalinges, Switzerland
| | - Herre Jelger Risselada
- Department of Theoretical Physics, Georg-August University, Goettingen, Germany.,Leibniz-Institut für Oberflächenmodifizierung, Leipzig, Germany
| | - Andreas Mayer
- Département de Biochimie, Université de Lausanne, Epalinges, Switzerland
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14
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Manandhar SP, Calle EN, Gharakhanian E. Distinct palmitoylation events at the amino-terminal conserved cysteines of Env7 direct its stability, localization, and vacuolar fusion regulation in S. cerevisiae. J Biol Chem 2014; 289:11431-11442. [PMID: 24610781 DOI: 10.1074/jbc.m113.524082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Palmitoylation at cysteine residues is the only known reversible form of lipidation and has been implicated in protein membrane association as well as function. Many palmitoylated proteins have regulatory roles in dynamic cellular processes, including membrane fusion. Recently, we identified Env7 as a conserved and palmitoylated protein kinase involved in negative regulation of membrane fusion at the lysosomal vacuole. Env7 contains a palmitoylation consensus sequence, and substitution of its three consecutive cysteines (Cys(13)-Cys(15)) results in a non-palmitoylated and cytoplasmic Env7. In this study, we further dissect and define the role(s) of individual cysteines of the consensus sequence in various properties of Env7 in vivo. Our results indicate that more than one of the cysteines serve as palmitoylation substrates, and any pairwise combination is essential and sufficient for near wild type levels of Env7 palmitoylation, membrane localization, and phosphorylation. Furthermore, individually, each cysteine can serve as a minimum requirement for distinct aspects of Env7 behavior and function in cells. Cys(13) is sufficient for membrane association, Cys(15) is essential for the fusion regulatory function of membrane-bound Env7, and Cys(14) and Cys(15) are redundantly essential for protection of membrane-bound Env7 from proteasomal degradation. A role for Cys(14) and Cys(15) in correct sorting at the membrane is also discussed. Thus, palmitoylation at the N-terminal cysteines of Env7 directs not only its membrane association but also its stability, phosphorylation, and cellular function.
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Affiliation(s)
- Surya P Manandhar
- Department of Biological Sciences, California State University, Long Beach, California 90840
| | - Erika N Calle
- Department of Biological Sciences, California State University, Long Beach, California 90840
| | - Editte Gharakhanian
- Department of Biological Sciences, California State University, Long Beach, California 90840.
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15
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Saccharomyces cerevisiae Env7 is a novel serine/threonine kinase 16-related protein kinase and negatively regulates organelle fusion at the lysosomal vacuole. Mol Cell Biol 2012; 33:526-42. [PMID: 23166297 DOI: 10.1128/mcb.01303-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Membrane fusion depends on conserved components and is responsible for organelle biogenesis and vesicular trafficking. Yeast vacuoles are dynamic structures analogous to mammalian lysosomes. We report here that yeast Env7 is a novel palmitoylated protein kinase ortholog that negatively regulates vacuolar membrane fusion. Microscopic and biochemical studies confirmed the localization of tagged Env7 at the vacuolar membrane and implicated membrane association via the palmitoylation of its N-terminal Cys13 to -15. In vitro kinase assays established Env7 as a protein kinase. Site-directed mutagenesis of the Env7 alanine-proline-glutamic acid (APE) motif Glu269 to alanine results in an unstable kinase-dead allele that is stabilized and redistributed to the detergent-resistant fraction by interruption of the proteasome system in vivo. Palmitoylation-deficient Env7C13-15S is also kinase dead and mislocalizes to the cytoplasm. Microscopy studies established that env7Δ is defective in maintaining fragmented vacuoles during hyperosmotic response and in buds. ENV7 function is not redundant with a similar role of vacuolar membrane kinase Yck3, as the two do not share a substrate, and ENV7 is not a suppressor of yck3Δ. Bayesian phylogenetic analyses strongly support ENV7 as an ortholog of the gene encoding human STK16, a Golgi apparatus protein kinase with undefined function. We propose that Env7 function in fusion/fission dynamics may be conserved within the endomembrane system.
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16
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Abstract
Intracellular membrane fusion requires R-SNAREs and Q-SNAREs to assemble into a four-helical parallel coiled-coil, with their hydrophobic anchors spanning the two apposed membranes. Based on the fusion properties of chemically defined SNARE- proteoliposomes, it has been proposed that the assembly of this helical bundle transduces force through the entire bilayer via the transmembrane SNARE anchor domains to drive fusion. However, an R-SNARE, Nyv1p, with a genetically engineered lipid anchor that spans half of the bilayer suffices for the fusion of isolated vacuoles, although this organelle has other R-SNAREs. To demonstrate unequivocally the fusion activity of lipid-anchored Nyv1p, we reconstituted proteoliposomes with purified lipid-anchored Nyv1p as the only protein. When these proteoliposomes were incubated with those bearing cognate Q-SNAREs, there was trans-SNARE complex assembly but, in accord with prior studies of the neuronal SNAREs, little lipid mixing. However, the addition of physiological fusion accessory proteins (HOPS, Sec17p, and Sec18p) allows lipid-anchored Nyv1p to support fusion, suggesting that trans-SNARE complex function is not limited to force transduction across the bilayers through the transmembrane domains.
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17
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Epp N, Rethmeier R, Krämer L, Ungermann C. Membrane dynamics and fusion at late endosomes and vacuoles – Rab regulation, multisubunit tethering complexes and SNAREs. Eur J Cell Biol 2011; 90:779-85. [DOI: 10.1016/j.ejcb.2011.04.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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18
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Ayong L, DaSilva T, Mauser J, Allen CM, Chakrabarti D. Evidence for prenylation-dependent targeting of a Ykt6 SNARE in Plasmodium falciparum. Mol Biochem Parasitol 2011; 175:162-8. [DOI: 10.1016/j.molbiopara.2010.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 11/01/2010] [Accepted: 11/05/2010] [Indexed: 10/18/2022]
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19
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Zabrocki P, Bastiaens I, Delay C, Bammens T, Ghillebert R, Pellens K, De Virgilio C, Van Leuven F, Winderickx J. Phosphorylation, lipid raft interaction and traffic of alpha-synuclein in a yeast model for Parkinson. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1783:1767-80. [PMID: 18634833 DOI: 10.1016/j.bbamcr.2008.06.010] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2007] [Revised: 05/08/2008] [Accepted: 06/02/2008] [Indexed: 01/04/2023]
Abstract
Parkinson's disease is a neurodegenerative disorder characterized by the formation of Lewy bodies containing aggregated alpha-synuclein. We used a yeast model to screen for deletion mutants with mislocalization and enhanced inclusion formation of alpha-synuclein. Many of the mutants were affected in functions related to vesicular traffic but especially mutants in endocytosis and vacuolar degradation combined inclusion formation with enhanced alpha-synuclein-mediated toxicity. The screening also allowed for identification of casein kinases responsible for alpha-synuclein phosphorylation at the plasma membrane as well as transacetylases that modulate the alpha-synuclein membrane interaction. In addition, alpha-synuclein was found to associate with lipid rafts, a phenomenon dependent on the ergosterol content. Together, our data suggest that toxicity of alpha-synuclein in yeast is at least in part associated with endocytosis of the protein, vesicular recycling back to the plasma membrane and vacuolar fusion defects, each contributing to the obstruction of different vesicular trafficking routes.
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Affiliation(s)
- Piotr Zabrocki
- Laboratory of Functional Biology, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
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20
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Meiringer CTA, Auffarth K, Hou H, Ungermann C. Depalmitoylation of Ykt6 prevents its entry into the multivesicular body pathway. Traffic 2008; 9:1510-21. [PMID: 18541004 DOI: 10.1111/j.1600-0854.2008.00778.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The dually lipidated SNARE Ykt6 is found on intracellular membranes and in the cytosol. In this study, we show that Ykt6 localizes to the Golgi as well as endosomal and vacuolar membranes in vivo. The ability of Ykt6 to cycle between the cytosol and the membranes depends on the intramolecular interaction of the N-terminal longin and C-terminal SNARE domains and not on either domain alone. A mutant deficient in this interaction accumulates on membranes and--in contrast to the wild-type protein--does not get released from vacuoles. Our data also indicate that Ykt6 is a substrate of the DHHC (Asp-His-His-Cys) acyltransferase network. Overexpression of the vacuolar acyltransferase Pfa3 drives the F42S mutant not only to the vacuole but also into the vacuolar lumen. Thus, depalmitoylation and release of Ykt6 are needed for its recycling and to circumvent its entry into the endosomal multivesicular body pathway.
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21
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Cabrera M, Ungermann C. Chapter Thirteen Purification and In Vitro Analysis of Yeast Vacuoles. Methods Enzymol 2008; 451:177-96. [DOI: 10.1016/s0076-6879(08)03213-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Jun Y, Xu H, Thorngren N, Wickner W. Sec18p and Vam7p remodel trans-SNARE complexes to permit a lipid-anchored R-SNARE to support yeast vacuole fusion. EMBO J 2007; 26:4935-45. [PMID: 18007597 DOI: 10.1038/sj.emboj.7601915] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Accepted: 10/15/2007] [Indexed: 11/09/2022] Open
Abstract
Intracellular membrane fusion requires SNARE proteins in a trans-complex, anchored to apposed membranes. Proteoliposome studies have suggested that SNAREs drive fusion by stressing the lipid bilayer via their transmembrane domains (TMDs), and that SNARE complexes require a TMD in each docked membrane to promote fusion. Yeast vacuole fusion is believed to require three Q-SNAREs from one vacuole and the R-SNARE Nyv1p from its fusion partner. In accord with this model, we find that fusion is abolished when the TMD of Nyv1p is replaced by lipid anchors, even though lipid-anchored Nyv1p assembles into trans-SNARE complexes. However, normal fusion is restored by the addition of both Sec18p and the soluble SNARE Vam7p. In restoring fusion, Sec18p promotes the disassembly of trans-SNARE complexes, and Vam7p enhances their assembly. Thus, either the TMD of this R-SNARE is not essential for fusion, and TMD-mediated membrane stress is not the only mode of trans-SNARE complex action, or these SNAREs have more flexibility than heretofore appreciated to form alternate functional complexes that violate the 3Q:1R rule.
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Affiliation(s)
- Youngsoo Jun
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755-3844, USA
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23
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Meiringer CTA, Ungermann C. Probing protein palmitoylation at the yeast vacuole. Methods 2006; 40:171-6. [PMID: 17012029 DOI: 10.1016/j.ymeth.2006.06.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2006] [Accepted: 06/23/2006] [Indexed: 11/15/2022] Open
Abstract
A protein's function depends on its localization to the right cellular compartment. A number of proteins require lipidation to associate with membranes. Protein palmitoylation is a reversible lipid modification and has been shown to mediate both membrane localization and control protein function. At the yeast vacuole, several palmitoylated proteins have been identified that are required for vacuole biogenesis, including the fusion factor Vac8, the SNARE Ykt6 and the casein kinase Yck3. Moreover, both the DHHC-CRD acyltransferase Pfa3 and Ykt6 are involved in palmitoylation at the vacuole Here, we present and discuss methods to probe for protein palmitoylation at vacuoles.
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24
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Kümmel D, Heinemann U, Veit M. Unique self-palmitoylation activity of the transport protein particle component Bet3: a mechanism required for protein stability. Proc Natl Acad Sci U S A 2006; 103:12701-6. [PMID: 16908848 PMCID: PMC1562543 DOI: 10.1073/pnas.0603513103] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Indexed: 11/18/2022] Open
Abstract
Bet3 is a component of the transport protein particle complex involved in vesicular trafficking to and through the Golgi complex. X-ray structural analysis of human and mouse Bet3 revealed a hydrophobic tunnel inside the protein, which is occupied by a fatty acid linked to cysteine-68. We show here that Bet3 has strong self-palmitoylating activity. Incubation of purified Bet3 with [3H]palmitoyl-CoA (Pal-CoA) leads to a rapid and stoichiometric attachment of fatty acids to cysteine-68. Bet3 has an intrinsic affinity for Pal-CoA, and the palmitoylation reaction occurs at physiological pH values and Pal-CoA concentrations. Moreover, Bet3 is also efficiently palmitoylated at cysteine-68 inside vertebrate cells. Palmitoylation can occur late after Bet3 synthesis, but once the fatty acids are bound they are not removed, not even by disassembly of the Golgi complex. Narrowing the hydrophobic tunnel by exchange of alanine-82 with bulkier amino acids inhibits palmitoylation, both in vitro and inside cells, indicating that the fatty acid must insert into the tunnel for stable attachment. Finally, we show that palmitoylation of Bet3 plays a structural role. CD spectroscopy reveals that chemically deacylated Bet3 has a reduced melting temperature. As a consequence of its structural defect nonacylated Bet3 does not bind to TPC6, a further subunit of the transport protein particle complex, and is degraded inside cells.
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Affiliation(s)
- Daniel Kümmel
- *Max Delbrück Center for Molecular Medicine, Robert-Rössle Strasse 10, 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Free University, Takustrasse 6, 14195 Berlin, Germany; and
| | - Udo Heinemann
- *Max Delbrück Center for Molecular Medicine, Robert-Rössle Strasse 10, 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Free University, Takustrasse 6, 14195 Berlin, Germany; and
| | - Michael Veit
- Department of Immunology and Molecular Biology, Free University, Philippstrasse 13, 10115 Berlin, Germany
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25
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Roth AF, Wan J, Bailey AO, Sun B, Kuchar JA, Green WN, Phinney BS, Yates JR, Davis NG. Global analysis of protein palmitoylation in yeast. Cell 2006; 125:1003-13. [PMID: 16751107 PMCID: PMC2246083 DOI: 10.1016/j.cell.2006.03.042] [Citation(s) in RCA: 428] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2005] [Revised: 02/23/2006] [Accepted: 03/23/2006] [Indexed: 11/20/2022]
Abstract
Protein palmitoylation is a reversible lipid modification that regulates membrane tethering for key proteins in cell signaling, cancer, neuronal transmission, and membrane trafficking. Palmitoylation has proven to be a difficult study: Specifying consensuses for predicting palmitoylation remain unavailable, and first-example palmitoylation enzymes--i.e., protein acyltransferases (PATs)--were identified only recently. Here, we use a new proteomic methodology that purifies and identifies palmitoylated proteins to characterize the palmitoyl proteome of the yeast Saccharomyces cerevisiae. Thirty-five new palmitoyl proteins are identified, including many SNARE proteins and amino acid permeases as well as many other participants in cellular signaling and membrane trafficking. Analysis of mutant yeast strains defective for members of the DHHC protein family, a putative PAT family, allows a matching of substrate palmitoyl proteins to modifying PATs and reveals the DHHC family to be a family of diverse PAT specificities responsible for most of the palmitoylation within the cell.
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Affiliation(s)
- Amy F. Roth
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Junmei Wan
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Aaron O. Bailey
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Beimeng Sun
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jason A. Kuchar
- Department of Biochemistry, Michigan State University, East Lansing, MI 48824, USA
| | - William N. Green
- Department of Neurobiology, Pharmacology and Physiology, University of Chicago, Chicago, IL 60637, USA
| | - Brett S. Phinney
- Department of Biochemistry, Michigan State University, East Lansing, MI 48824, USA
| | - John R. Yates
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas G. Davis
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- *Contact:
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26
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Stroupe C, Collins KM, Fratti RA, Wickner W. Purification of active HOPS complex reveals its affinities for phosphoinositides and the SNARE Vam7p. EMBO J 2006; 25:1579-89. [PMID: 16601699 PMCID: PMC1440844 DOI: 10.1038/sj.emboj.7601051] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Accepted: 02/27/2006] [Indexed: 12/24/2022] Open
Abstract
Coupling of Rab GTPase activation and SNARE complex assembly during membrane fusion is poorly understood. The homotypic fusion and vacuole protein sorting (HOPS) complex links these two processes: it is an effector for the vacuolar Rab GTPase Ypt7p and is required for vacuolar SNARE complex assembly. We now report that pure, active HOPS complex binds phosphoinositides and the PX domain of the vacuolar SNARE protein Vam7p. These binding interactions support HOPS complex association with the vacuole and explain its enrichment at the same microdomains on docked vacuoles as phosphoinositides, Ypt7p, Vam7p, and the other SNARE proteins. Concentration of the HOPS complex at these microdomains may be a key factor for coupling Rab GTPase activation to SNARE complex assembly.
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Affiliation(s)
| | - Kevin M Collins
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH, USA
| | - Rutilio A Fratti
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH, USA
| | - William Wickner
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH, USA
- Department of Biochemistry, Dartmouth Medical School, 7200 Vail Building, Room 425 Remsen, Hanover, NH 03755-3844, USA. Tel.: +1 603 650 1701; Fax: +1 603 650 1353; E-mail: , URL: http://www.dartmouth.edu/~wickner
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27
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Ungermann C, Langosch D. Functions of SNAREs in intracellular membrane fusion and lipid bilayer mixing. J Cell Sci 2005; 118:3819-28. [PMID: 16129880 DOI: 10.1242/jcs.02561] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Intracellular membrane fusion occurs with exquisite coordination and specificity. Each fusion event requires three basic components: Rab-GTPases organize the fusion site; SNARE proteins act during fusion; and N-ethylmaleimide-sensitive factor (NSF) plus its cofactor alpha-SNAP are required for recycling or activation of the fusion machinery. Whereas Rab-GTPases seem to mediate the initial membrane contact, SNAREs appear to lie at the center of the fusion process. It is known that formation of complexes between SNAREs from apposed membranes is a prerequisite for lipid bilayer mixing; however, the biophysics and many details of SNARE function are still vague. Nevertheless, recent observations are shedding light on the role of SNAREs in membrane fusion. Structural studies are revealing the mechanisms by which SNARES form complexes and interact with other proteins. Furthermore, it is now apparent that the SNARE transmembrane segment not only anchors the protein but engages in SNARE-SNARE interactions and plays an active role in fusion. Recent work indicates that the fusion process itself may comprise two stages and proceed via a hemifusion intermediate.
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Affiliation(s)
- Christian Ungermann
- Biochemie Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
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28
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Current awareness on yeast. Yeast 2005. [DOI: 10.1002/yea.1168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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29
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Munro S. The Golgi apparatus: defining the identity of Golgi membranes. Curr Opin Cell Biol 2005; 17:395-401. [PMID: 15975778 DOI: 10.1016/j.ceb.2005.06.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Accepted: 06/07/2005] [Indexed: 02/01/2023]
Abstract
The Golgi apparatus is a stack of compartments that serves as a central junction for membrane traffic, with carriers moving through the stack as well as arriving from, and departing toward, many other destinations in the cell. This requires that the different compartments in the Golgi recruit from the cytosol a distinct set of proteins to mediate accurate membrane traffic. This recruitment appears to reflect recognition of small GTPases of the Rab and Arf family, or of lipid species such as PtdIns(4)P and diacylglycerol, which provide a unique "identity" for each compartment. Recent work is starting to reveal the mechanisms by which these labile landmarks are generated in a spatially restricted manner on specific parts of the Golgi.
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Affiliation(s)
- Sean Munro
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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30
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Dietrich LEP, LaGrassa TJ, Rohde J, Cristodero M, Meiringer CTA, Ungermann C. ATP-independent control of Vac8 palmitoylation by a SNARE subcomplex on yeast vacuoles. J Biol Chem 2005; 280:15348-55. [PMID: 15701652 DOI: 10.1074/jbc.m410582200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yeast vacuole fusion requires palmitoylated Vac8. We previously showed that Vac8 acylation occurs early in the fusion reaction, is blocked by antibodies against Sec18 (yeast N-ethylmaleimide-sensitive fusion protein (NSF)), and is mediated by the R-SNARE Ykt6. Here we analyzed the regulation of this reaction on purified vacuoles. We show that Vac8 acylation is restricted to a narrow time window, is independent of ATP hydrolysis by Sec18, and is stimulated by the ion chelator EDTA. Analysis of vacuole protein complexes indicated that Ykt6 is part of a complex distinct from the second R-SNARE, Nyv1. We speculate that during vacuole fusion, Nyv1 is the classical R-SNARE, whereas the Ykt6-containing complex has a novel function in Vac8 palmitoylation.
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Affiliation(s)
- Lars E P Dietrich
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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