1
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Ji J, Yu Y, Wu S, Wang D, Weng J, Wang W. Different conformational dynamics of SNARE protein Ykt6 among yeast and mammals. J Biol Chem 2023; 299:104968. [PMID: 37380075 PMCID: PMC10388204 DOI: 10.1016/j.jbc.2023.104968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/29/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
Ykt6 is one of the most conserved SNARE (N-ethylmaleimide-sensitive factor attachment protein receptor) proteins involved in multiple intracellular membrane trafficking processes. The membrane-anchoring function of Ykt6 has been elucidated to result from its conformational transition from a closed state to an open state. Two ways of regulating the conformational transition were proposed: the C-terminal lipidation and the phosphorylation at the SNARE core. Despite many aspects of common properties, Ykt6 displays differential cellular localizations and functional behaviors in different species, such as yeast, mammals, and worms. The structure-function relationship underlying these differences remains elusive. Here, we combined biochemical characterization, single-molecule FRET measurement, and molecular dynamics simulation to compare the conformational dynamics of yeast and rat Ykt6. Compared to rat Ykt6 (rYkt6), yeast Ykt6 (yYkt6) has more open conformations and could not bind dodecylphosphocholine that inhibits rYkt6 in the closed state. A point mutation T46L/Q57A was shown to be able to convert yYkt6 to a more closed and dodecylphosphocholine-bound state, where Leu46 contributes key hydrophobic interactions for the closed state. We also demonstrated that the phospho-mutation S174D could shift the conformation of rYkt6 to a more open state, but the corresponding mutation S176D in yYkt6 leads to a slightly more closed conformation. These observations shed light on the regulatory mechanism underlying the variations of Ykt6 functions across species.
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Affiliation(s)
- Jie Ji
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China
| | - Yiping Yu
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China
| | - Shaowen Wu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | | | - Jingwei Weng
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China.
| | - Wenning Wang
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China.
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2
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Rikitake Y. Regulation of the SNARE Protein Ykt6 Function by Diprenylation and Phosphorylation. J Biochem 2022; 172:337-340. [PMID: 36166826 DOI: 10.1093/jb/mvac076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
For proper intracellular vesicle transport, it is essential for transport vesicle membranes to fuse with the appropriate target membranes. Ykt6 is a SNARE protein with functions in diverse vesicle transport pathways, including secretory, endocytotic, and autophagic pathways. To exert these functions, the association of Ykt6 with vesicle membranes and the change of its conformation from closed to open play key roles. Recent studies have revealed regulatory mechanisms involved in Ykt6 membrane association and conformation change. When in the cytosol, the vicinal cysteine residues within the C-terminal CCAIM sequence of Ykt6 undergo diprenylation (farnesylation of the distal cysteine residues by farnesyltransferase; this is followed by geranylgeranylation of the proximal cysteine residue by geranylgeranyltransferase-III). Phosphorylation of a serine residue within the SNARE domain triggers the conversion of the Ykt6 conformation from closed to open, allowing Ykt6 membrane association. In this commentary, I briefly summarize and discuss the recently revealed regulatory mechanisms of Ykt6 function by diprenylation and phosphorylation.
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Affiliation(s)
- Yoshiyuki Rikitake
- Laboratory of Medical Pharmaceutics, Kobe Pharmaceutical University, 4-19-1, Motoyamakitamachi, Higashinada-ku, Kobe 658-8558, Japan
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3
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Li H, Li X, Xu Z, Lu J, Cao C, You W, Yu Z, Shen H, Chen G. Unbalanced Regulation of Sec22b and Ykt6 Blocks Autophagosome Axonal Retrograde Flux in Neuronal Ischemia-Reperfusion Injury. J Neurosci 2022; 42:5641-5654. [PMID: 35654605 PMCID: PMC9295843 DOI: 10.1523/jneurosci.2030-21.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
Cerebral ischemia-reperfusion (I/R) injury in ischemic penumbra is accountable for poor outcome of ischemic stroke patients receiving recanalization therapy. Compelling evidence previously demonstrated a dual role of autophagy in stroke. This study aimed to understand the traits of autophagy in the ischemic penumbra and the potential mechanism that switches the dual role of autophagy. We found that autophagy induction by rapamycin and lithium carbonate performed before ischemia reduced neurologic deficits and infarction, while autophagy induction after reperfusion had the opposite effect in the male murine middle cerebral artery occlusion/reperfusion (MCAO/R) model, both of which were eliminated in mice lacking autophagy (Atg7flox/flox; Nestin-Cre). Autophagic flux determination showed that reperfusion led to a blockage of axonal autophagosome retrograde transport in neurons, which then led to autophagic flux damage. Then, we found that I/R induced changes in the protein levels of Sec22b and Ykt6 in neurons, two autophagosome transport-related factors, in which Sec22b significantly increased and Ykt6 significantly decreased. In the absence of exogenous autophagy induction, Sec22b knock-down and Ykt6 overexpression significantly alleviated autophagic flux damage, infarction, and neurologic deficits in neurons or murine exposed to cerebral I/R in an autophagy-dependent manner. Furthermore, Sec22b knock-down and Ykt6 overexpression switched the outcome of rapamycin posttreatment from deterioration to neuroprotection. Thus, Sec22b and Ykt6 play key roles in neuronal autophagic flux, and modest regulation of Sec22b and Ykt6 may help to reverse the failure of targeting autophagy induction to improve the prognosis of ischemic stroke.SIGNIFICANCE STATEMENT The highly polarized architecture of neurons with neurites presents challenges for material transport, such as autophagosomes, which form at the neurite tip and need to be transported to the cell soma for degradation. Here, we demonstrate that Sec22b and Ykt6 act as autophagosome porters and play an important role in maintaining the integrity of neuronal autophagic flux. Ischemia-reperfusion (I/R)-induced excess Sec22b and loss of Ykt6 in neurons lead to axonal autophagosome retrograde trafficking failure, autophagic flux damage, and finally neuronal injury. Facilitated axonal autophagosome retrograde transport by Sec22b knock-down and Ykt6 overexpression may reduce I/R-induced neuron injury and extend the therapeutic window of pharmacological autophagy induction for neuroprotection.
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Affiliation(s)
- Haiying Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province 215006, China
| | - Xiang Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province 215006, China
| | - Zhongmou Xu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province 215006, China
| | - Jinxin Lu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province 215006, China
| | - Chang Cao
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province 215006, China
| | - Wanchun You
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province 215006, China
| | - Zhengquan Yu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province 215006, China
| | - Haitao Shen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province 215006, China
| | - Gang Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province 215006, China
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4
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Pokrywka NJ, Bush S, Nick SE. The R-SNARE Ykt6 is required for multiple events during oogenesis in Drosophila. Cells Dev 2021; 169:203759. [PMID: 34856414 DOI: 10.1016/j.cdev.2021.203759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/31/2021] [Accepted: 11/21/2021] [Indexed: 11/30/2022]
Abstract
Ykt6 has emerged as a key protein involved in a wide array of trafficking events, and has also been implicated in a number of human pathologies, including the progression of several cancers. It is a complex protein that simultaneously exhibits a high degree of structural and functional homology, and yet adopts differing roles in different cellular contexts. Because Ykt6 has been implicated in a variety of vesicle fusion events, we characterized the role of Ykt6 in oogenesis by observing the phenotype of Ykt6 germline clones. Immunofluorescence was used to visualize the expression of membrane proteins, organelles, and vesicular trafficking markers in mutant egg chambers. We find that Ykt6 germline clones have morphological and actin defects affecting both the nurse cells and oocyte, consistent with a role in regulating membrane growth during mid-oogenesis. Additionally, these egg chambers exhibit defects in bicoid and oskar RNA localization, and in the trafficking of Gurken during mid-to-late oogenesis. Finally, we show that Ykt6 mutations result in defects in late endosomal pathways, including endo- and exocytosis. These findings suggest a role for Ykt6 in endosome maturation and in the movement of membranes to and from the cell surface.
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Affiliation(s)
- Nancy Jo Pokrywka
- Department of Biology, Vassar College, Poughkeepsie, NY 12604, United States of America.
| | - Setse Bush
- Department of Biology, Vassar College, Poughkeepsie, NY 12604, United States of America
| | - Sophie E Nick
- Department of Biology, Vassar College, Poughkeepsie, NY 12604, United States of America
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5
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McGrath K, Agarwal S, Tonelli M, Dergai M, Gaeta AL, Shum AK, Lacoste J, Zhang Y, Wen W, Chung D, Wiersum G, Shevade A, Zaichick S, van Rossum DB, Shuvalova L, Savas JN, Kuchin S, Taipale M, Caldwell KA, Caldwell GA, Fasshauer D, Caraveo G. A conformational switch driven by phosphorylation regulates the activity of the evolutionarily conserved SNARE Ykt6. Proc Natl Acad Sci U S A 2021; 118:e2016730118. [PMID: 33723042 DOI: 10.1073/pnas.2016730118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ykt6 is a conserved SNARE that plays critical roles along multiple vesicular pathways. To achieve its function, Ykt6 cycles between the cytosol and membrane-bound compartments through reversible lipidation. The mechanism that regulates these transitions is unknown. Ykt6 function is disrupted by α-synuclein, a protein critically implicated in synucleinopathies such as Parkinson’s Disease. Through a multidisciplinary approach, we report that phosphorylation regulated by Ca2+ signaling drives a conformational change that allows Ykt6 to switch from a closed cytosolic to an open membrane-bound form. Phosphorylation is also a critical determinant for Ykt6 protein interactions with functional consequences in the secretory and autophagy pathways under normal and α-synuclein conditions. This work provides a mechanistic insight into Ykt6 regulation with therapeutic implications for synucleinopathies. Ykt6 is a soluble N-ethylmaleimide sensitive factor activating protein receptor (SNARE) critically involved in diverse vesicular fusion pathways. While most SNAREs rely on transmembrane domains for their activity, Ykt6 dynamically cycles between the cytosol and membrane-bound compartments where it is active. The mechanism that regulates these transitions and allows Ykt6 to achieve specificity toward vesicular pathways is unknown. Using a Parkinson’s disease (PD) model, we found that Ykt6 is phosphorylated at an evolutionarily conserved site which is regulated by Ca2+ signaling. Through a multidisciplinary approach, we show that phosphorylation triggers a conformational change that allows Ykt6 to switch from a closed cytosolic to an open membrane-bound form. In the phosphorylated open form, the spectrum of protein interactions changes, leading to defects in both the secretory and autophagy pathways, enhancing toxicity in PD models. Our studies reveal a mechanism by which Ykt6 conformation and activity are regulated with potential implications for PD.
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6
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Sakata N, Shirakawa R, Goto K, Trinh DA, Horiuchi H. Double prenylation of SNARE protein Ykt6 is required for lysosomal hydrolase trafficking. J Biochem 2021; 169:363-370. [PMID: 33035318 DOI: 10.1093/jb/mvaa111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/18/2020] [Indexed: 11/14/2022] Open
Abstract
Ykt6 is an evolutionarily conserved SNARE protein regulating Golgi membrane fusion and other diverse membrane trafficking pathways. Unlike most SNARE proteins, Ykt6 lacks a transmembrane domain but instead has a tandem cysteine motif at the C-terminus. Recently, we have demonstrated that Ykt6 undergoes double prenylation at the C-terminal two cysteines first by farnesyltransferase and then by a newly identified protein prenyltransferase named geranylgeranyltransferase type-III (GGTase-III). GGTase-III consists of a novel α subunit prenyltransferase alpha subunit repeat containing 1 (PTAR1) and the β subunit of Rab geranylgeranyltransferase. PTAR1 knockout (KO) cells, where Ykt6 is singly prenylated with a farnesyl moiety, exhibit structural and functional abnormalities in the Golgi apparatus with delayed intra-Golgi trafficking and impaired protein glycosylation. It remains unclear whether the second prenylation of Ykt6 is required for proper trafficking of lysosomal hydrolases from Golgi to lysosomes. Here, we show that lysosomal hydrolases, cathepsin D and β-hexosaminidase, were missorted at the trans-Golgi network and secreted into the extracellular space in PTAR1 KO cells. Moreover, maturation of these hydrolases was disturbed. LC3B, an autophagy marker, was accumulated in PTAR1 KO cells, suggesting defects in cellular degradation pathways. Thus, doubly prenylated Ykt6, but not singly prenylated Ykt6, is critical for the efficient sorting and trafficking of acid hydrolases to lysosomes.
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Affiliation(s)
- Natsumi Sakata
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Ryutaro Shirakawa
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Kota Goto
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Duc Anh Trinh
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Hisanori Horiuchi
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
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7
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Barz S, Kriegenburg F, Henning A, Bhattacharya A, Mancilla H, Sánchez-Martín P, Kraft C. Atg1 kinase regulates autophagosome-vacuole fusion by controlling SNARE bundling. EMBO Rep 2020; 21:e51869. [PMID: 33274589 PMCID: PMC7726815 DOI: 10.15252/embr.202051869] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/26/2022] Open
Abstract
Autophagy mediates the degradation of cytoplasmic material. Upon autophagy induction, autophagosomes form a sealed membrane around the cargo and fuse with the lytic compartment to release the cargo for degradation. In order to avoid premature fusion of immature autophagosomal membranes with the lytic compartment, this process needs to be tightly regulated. Several factors mediating autophagosome–vacuole fusion have recently been identified. In budding yeast, autophagosome–vacuole fusion requires the R‐SNARE Ykt6 on the autophagosome, together with the three Q‐SNAREs Vam3, Vam7, and Vti1 on the vacuole. However, how these SNAREs are regulated during the fusion process is poorly understood. In this study, we investigate the regulation of Ykt6. We found that Ykt6 is directly phosphorylated by Atg1 kinase, which keeps this SNARE in an inactive state. Ykt6 phosphorylation prevents SNARE bundling by disrupting its interaction with the vacuolar SNAREs Vam3 and Vti1, thereby preventing premature autophagosome–vacuole fusion. These findings shed new light on the regulation of autophagosome–vacuole fusion and reveal a further step in autophagy controlled by the Atg1 kinase.
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Affiliation(s)
- Saskia Barz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Franziska Kriegenburg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anna Henning
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anuradha Bhattacharya
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Hector Mancilla
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Pablo Sánchez-Martín
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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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: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Shirakawa R, Goto-Ito S, Goto K, Wakayama S, Kubo H, Sakata N, Trinh DA, Yamagata A, Sato Y, Masumoto H, Cheng J, Fujimoto T, Fukai S, Horiuchi H. A SNARE geranylgeranyltransferase essential for the organization of the Golgi apparatus. EMBO J 2020; 39:e104120. [PMID: 32128853 DOI: 10.15252/embj.2019104120] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/22/2020] [Accepted: 01/31/2020] [Indexed: 01/08/2023] Open
Abstract
Protein prenylation is essential for many cellular processes including signal transduction, cytoskeletal reorganization, and membrane trafficking. Here, we identify a novel type of protein prenyltransferase, which we named geranylgeranyltransferase type-III (GGTase-III). GGTase-III consists of prenyltransferase alpha subunit repeat containing 1 (PTAR1) and the β subunit of RabGGTase. Using a biotinylated geranylgeranyl analogue, we identified the Golgi SNARE protein Ykt6 as a substrate of GGTase-III. GGTase-III transfers a geranylgeranyl group to mono-farnesylated Ykt6, generating doubly prenylated Ykt6. The crystal structure of GGTase-III in complex with Ykt6 provides structural basis for Ykt6 double prenylation. In GGTase-III-deficient cells, Ykt6 remained in a singly prenylated form, and the Golgi SNARE complex assembly was severely impaired. Consequently, the Golgi apparatus was structurally disorganized, and intra-Golgi protein trafficking was delayed. Our findings reveal a fourth type of protein prenyltransferase that generates geranylgeranyl-farnesyl Ykt6. Double prenylation of Ykt6 is essential for the structural and functional organization of the Golgi apparatus.
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Affiliation(s)
- Ryutaro Shirakawa
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Sakurako Goto-Ito
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan
| | - Kota Goto
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Shonosuke Wakayama
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Haremaru Kubo
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Natsumi Sakata
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Duc Anh Trinh
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Atsushi Yamagata
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan
| | - Yusuke Sato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Masumoto
- Biomedical Research Support Center, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Jinglei Cheng
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toyoshi Fujimoto
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shuya Fukai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan
| | - Hisanori Horiuchi
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
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10
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Abstract
Studying the mechanism of autophagosome-vacuole fusion has proven difficult in live yeast cells. Developing a novel in vitro fusion assay, we identified Ykt6 as the missing R-SNARE (Soluble N-ethylmaleimide sensitive factor attachment protein receptor) in this process and pinpoint the place of action of all four SNAREs involved. Parallel studies have confirmed our findings in other organisms.
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Affiliation(s)
- Levent Bas
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Daniel Papinski
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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11
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Wu S, Wang D, Weng J, Liu J, Wang W. A revisit of the conformational dynamics of SNARE protein r Ykt6. Biochem Biophys Res Commun 2018; 503:2841-2847. [PMID: 30119892 DOI: 10.1016/j.bbrc.2018.08.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins are involved in the fusion of vesicles with their target membranes. R-SNARE protein Ykt6 is one of the most conserved SNARE in eukaryotes. The conformational state of Ykt6 is regulated by the lipidations at its C-terminal motif. Previous studies show that the binding of dodecylphosphocholine (DPC) can stabilize a closed conformation of rat Ykt6 (rYkt6) and mimic the farnesylated rYkt6. Despite this model, the detailed conformational dynamics of Ykt6 is still unclear. Here, we combined smFRET and MD simulation to demonstrate that the un-lipidated rYkt6 adopts five major conformational states. DPC binding shifts the conformational distribution toward the more closed states. At the same time, there remain considerable fractions of open and semi-open conformations in the presence of DPC. These newly revealed dynamic features of rYkt6 are consistent with its unique functional diversity in neuronal cells.
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Affiliation(s)
- Shaowen Wu
- Multiscale Research Institute of Complex Systems, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, PR China
| | - Dongdong Wang
- Multiscale Research Institute of Complex Systems, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, PR China
| | - Jingwei Weng
- Multiscale Research Institute of Complex Systems, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, PR China
| | - Jianwei Liu
- Multiscale Research Institute of Complex Systems, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, PR China.
| | - Wenning Wang
- Multiscale Research Institute of Complex Systems, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, PR China.
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Banerjee H, Rachubinski RA. Involvement of SNARE protein Ykt6 in glycosome biogenesis in Trypanosoma brucei. Mol Biochem Parasitol 2017; 218:28-37. [PMID: 29107734 DOI: 10.1016/j.molbiopara.2017.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 10/02/2017] [Accepted: 10/21/2017] [Indexed: 11/30/2022]
Abstract
The kinetoplastid parasites Trypanosoma and Leishmania are etiologic agents of diseases like African sleeping sickness, Chagas and leishmaniasis that inflict many tropical and subtropical parts of the world. These parasites are distinctive in that they compartmentalize most of the usually cytosolic enzymes of the glycolytic pathway within a peroxisome-like organelle called the glycosome. Functional glycosomes are essential in both the procyclic and bloodstream forms of trypanosomatid parasites, and mislocalization of glycosomal enzymes to the cytosol is fatal for the parasite. The life cycle of these parasites is intimately linked to their efficient protein and vesicular trafficking machinery that helps them in immune evasion, host-pathogen interaction and organelle biogenesis and integrity. Soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) proteins play important roles in vesicular trafficking and mediate a wide range of protein-protein interactions in eukaryotes. We show here that the SNARE protein Ykt6 is necessary for glycosome biogenesis and function in Trypanosoma brucei. RNAi-mediated depletion of Ykt6 in both the procyclic and bloodstream forms of T. brucei leads to mislocalization of glycosomal matrix proteins to the cytosol, pronounced reduction in glycosome number, and cell death. GFP-tagged Ykt6 appears as punctate structures in the T. brucei cell and colocalizes in part to glycosomes. Our results constitute the first demonstration of a role for SNARE proteins in the biogenesis of peroxisomal organelles.
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Affiliation(s)
- Hiren Banerjee
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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