1
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Duan M, Plemel RL, Takenaka T, Lin A, Delgado BM, Nattermann U, Nickerson DP, Mima J, Miller EA, Merz AJ. SNARE chaperone Sly1 directly mediates close-range vesicle tethering. J Cell Biol 2024; 223:e202001032. [PMID: 38478018 PMCID: PMC10943277 DOI: 10.1083/jcb.202001032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024] Open
Abstract
The essential Golgi protein Sly1 is a member of the Sec1/mammalian Unc-18 (SM) family of SNARE chaperones. Sly1 was originally identified through remarkable gain-of-function alleles that bypass requirements for diverse vesicle tethering factors. Employing genetic analyses and chemically defined reconstitutions of ER-Golgi fusion, we discovered that a loop conserved among Sly1 family members is not only autoinhibitory but also acts as a positive effector. An amphipathic lipid packing sensor (ALPS)-like helix within the loop directly binds high-curvature membranes. Membrane binding is required for relief of Sly1 autoinhibition and also allows Sly1 to directly tether incoming vesicles to the Qa-SNARE on the target organelle. The SLY1-20 mutation bypasses requirements for diverse tethering factors but loses this ability if the tethering activity is impaired. We propose that long-range tethers, including Golgins and multisubunit tethering complexes, hand off vesicles to Sly1, which then tethers at close range to initiate trans-SNARE complex assembly and fusion in the early secretory pathway.
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Affiliation(s)
- Mengtong Duan
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rachael L. Plemel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Ariel Lin
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Biology, California State University, San Bernardino, CA, USA
| | | | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Biophysics, Structure, and Design Graduate Program, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Joji Mima
- Institute for Protein Research, Osaka University, Osaka, Japan
| | | | - Alexey J. Merz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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2
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Cauchi RJ. SCFD1 in amyotrophic lateral sclerosis: reconciling a genetic association with in vivo functional analysis. Neural Regen Res 2024; 19:1201-1202. [PMID: 37905864 DOI: 10.4103/1673-5374.386411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/05/2023] [Indexed: 11/02/2023] Open
Affiliation(s)
- Ruben J Cauchi
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building; Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
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3
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D'Souza Z, Pokrovskaya I, Lupashin VV. Syntaxin-5's flexibility in SNARE pairing supports Golgi functions. Traffic 2023; 24:355-379. [PMID: 37340984 PMCID: PMC10330844 DOI: 10.1111/tra.12903] [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: 03/07/2023] [Revised: 05/23/2023] [Accepted: 06/02/2023] [Indexed: 06/22/2023]
Abstract
Deficiency in the conserved oligomeric Golgi (COG) complex that orchestrates SNARE-mediated tethering/fusion of vesicles that recycle the Golgi's glycosylation machinery results in severe glycosylation defects. Although two major Golgi v-SNAREs, GS28/GOSR1, and GS15/BET1L, are depleted in COG-deficient cells, the complete knockout of GS28 and GS15 only modestly affects Golgi glycosylation, indicating the existence of an adaptation mechanism in Golgi SNARE. Indeed, quantitative mass-spectrometry analysis of STX5-interacting proteins revealed two novel Golgi SNARE complexes-STX5/SNAP29/VAMP7 and STX5/VTI1B/STX8/YKT6. These complexes are present in wild-type cells, but their usage is significantly increased in both GS28- and COG-deficient cells. Upon GS28 deletion, SNAP29 increased its Golgi residency in a STX5-dependent manner. While STX5 depletion and Retro2-induced diversion from the Golgi severely affect protein glycosylation, GS28/SNAP29 and GS28/VTI1B double knockouts alter glycosylation similarly to GS28 KO, indicating that a single STX5-based SNARE complex is sufficient to support Golgi glycosylation. Importantly, co-depletion of three Golgi SNARE complexes in GS28/SNAP29/VTI1B TKO cells resulted in severe glycosylation defects and a reduced capacity for glycosylation enzyme retention at the Golgi. This study demonstrates the remarkable plasticity in SXT5-mediated membrane trafficking, uncovering a novel adaptive response to the failure of canonical intra-Golgi vesicle tethering/fusion machinery.
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Affiliation(s)
- Zinia D'Souza
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Irina Pokrovskaya
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Vladimir V Lupashin
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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4
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Borg R, Purkiss A, Cacciottolo R, Herrera P, Cauchi RJ. Loss of amyotrophic lateral sclerosis risk factor SCFD1 causes motor dysfunction in Drosophila. Neurobiol Aging 2023; 126:67-76. [PMID: 36944290 DOI: 10.1016/j.neurobiolaging.2023.02.005] [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: 09/21/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neuromuscular disease mostly resulting from a complex interplay between genetic, environmental and lifestyle factors. Common genetic variants in the Sec1 Family Domain Containing 1 (SCFD1) gene have been associated with increased ALS risk in the most extensive genome-wide association study (GWAS). SCFD1 was also identified as a top-most significant expression Quantitative Trait Locus (eQTL) for ALS. Whether loss of SCFD1 function directly contributes to motor system dysfunction remains unresolved. Here we show that moderate gene silencing of Slh, the Drosophila orthologue of SCFD1, is sufficient to cause climbing and flight defects in adult flies. A more severe knockdown induced a significant reduction in larval mobility and profound neuromuscular junction (NMJ) deficits prior to death before metamorphosis. RNA-seq revealed downregulation of genes encoding chaperones that mediate protein folding downstream of Slh ablation. Our findings support the notion that loss of SCFD1 function is a meaningful contributor to ALS and disease predisposition may result from erosion of the mechanisms protecting against misfolding and protein aggregation.
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Affiliation(s)
- Rebecca Borg
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta; Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Angie Purkiss
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta; Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Rebecca Cacciottolo
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta; Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Paul Herrera
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta; Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Ruben J Cauchi
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta; Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta.
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5
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Gu XJ, Su WM, Dou M, Jiang Z, Duan QQ, Wang H, Ren YL, Cao B, Wang Y, Chen YP. Identifying novel genes for amyotrophic lateral sclerosis by integrating human brain proteomes with genome-wide association data. J Neurol 2023:10.1007/s00415-023-11757-4. [PMID: 37148340 DOI: 10.1007/s00415-023-11757-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND Genome-Wide Association Studies (GWAS) have identified numerous risk genes for Amyotrophic Lateral Sclerosis (ALS); however, the mechanisms by which these loci confer ALS risk are uncertain. This study aims to identify novel causal proteins in the brains of patients with ALS using an integrative analytical pipeline. METHODS Using the datasets of Protein Quantitative Trait Loci (pQTL) (NpQTL1 = 376, NpQTL2 = 152), expression QTL (eQTL) (N = 452), and the largest ALS GWAS (NALS=27,205, NControls = 110,881), we performed a systematic analytical pipeline including Proteome-Wide Association Study (PWAS), Mendelian Randomization (MR), Bayesian colocalization, and Transcriptome-Wide Association Study (TWAS) to identify novel causal proteins for ALS in the brain. RESULTS Using PWAS, we found that the altered protein abundance of 12 genes in the brain was associated with ALS. Three genes (SCFD1, SARM1 and CAMLG) were identified as lead causal genes for ALS with solid evidence (False discovery rate < 0.05, in MR analysis; PPH4 > 80% for Bayesian colocalization). Specifically, an increased abundance of SCFD1 and CAMLG led to an increased risk of ALS, whereas a higher abundance of SARM1 led to a decreased risk of developing ALS. TWAS showed that SCFD1 and CAMLG were related to ALS at the transcriptional level. CONCLUSIONS SCFD1, CAMLG, and SARM1 exhibited robust associations and causality with ALS. The study findings provide novel clues for identifying potential therapeutic targets in ALS. Further studies are required to explore the mechanisms underlying the identified genes.
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Affiliation(s)
- Xiao-Jing Gu
- Mental Health Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Wei-Ming Su
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Institute of Brain Science and Brain-Inspired Technology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Centre for Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Meng Dou
- Chengdu Institute of Computer Application, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Zheng Jiang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Institute of Brain Science and Brain-Inspired Technology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Centre for Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Qing-Qing Duan
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Institute of Brain Science and Brain-Inspired Technology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Centre for Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Han Wang
- Department of Pathophysiology, West China College of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yan-Ling Ren
- Department of Pathophysiology, West China College of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Bei Cao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Institute of Brain Science and Brain-Inspired Technology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Centre for Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yi Wang
- Department of Pathophysiology, West China College of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yong-Ping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- Institute of Brain Science and Brain-Inspired Technology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- Centre for Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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6
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Khakurel A, Lupashin VV. Role of GARP Vesicle Tethering Complex in Golgi Physiology. Int J Mol Sci 2023; 24:6069. [PMID: 37047041 PMCID: PMC10094427 DOI: 10.3390/ijms24076069] [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: 02/22/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 04/14/2023] Open
Abstract
The Golgi associated retrograde protein complex (GARP) is an evolutionarily conserved component of Golgi membrane trafficking machinery that belongs to the Complexes Associated with Tethering Containing Helical Rods (CATCHR) family. Like other multisubunit tethering complexes such as COG, Dsl1, and Exocyst, the GARP is believed to function by tethering and promoting fusion of the endosome-derived small trafficking intermediate. However, even twenty years after its discovery, the exact structure and the functions of GARP are still an enigma. Recent studies revealed novel roles for GARP in Golgi physiology and identified human patients with mutations in GARP subunits. In this review, we summarized our knowledge of the structure of the GARP complex, its protein partners, GARP functions related to Golgi physiology, as well as cellular defects associated with the dysfunction of GARP subunits.
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Affiliation(s)
| | - Vladimir V. Lupashin
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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7
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Abstract
Cargo delivery from one compartment to the next relies on the fusion of vesicles with different cellular organelles in a process that requires the concerted action of tethering factors. Although all tethers act to bridge vesicle membranes to mediate fusion, they form very diverse groups as they differ in composition, and in their overall architecture and size, as well as their protein interactome. However, their conserved function relies on a common design. Recent data on class C Vps complexes indicates that tethers play a significant role in membrane fusion beyond vesicle capturing. Furthermore, these studies provide additional mechanistic insights into membrane fusion events and reveal that tethers should be considered as key players of the fusion machinery. Moreover, the discovery of the novel tether FERARI complex has changed our understanding of cargo transport in the endosomal system as it has been shown to mediate 'kiss-and-run' vesicle-target membrane interactions. In this Cell Science at a Glance and the accompanying poster, we compare the structure of the coiled-coil and the multisubunit CATCHR and class C Vps tether families on the basis of their functional analogy. We discuss the mechanism of membrane fusion, and summarize how tethers capture vesicles, mediate membrane fusion at different cellular compartments and regulate cargo traffic.
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Affiliation(s)
| | - Anne Spang
- Biozentrum, University of Basel, 4056 Basel, Switzerland
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8
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Sumya FT, Pokrovskaya ID, D'Souza Z, Lupashin VV. Acute COG complex inactivation unveiled its immediate impact on Golgi and illuminated the nature of intra-Golgi recycling vesicles. Traffic 2023; 24:52-75. [PMID: 36468177 PMCID: PMC9969905 DOI: 10.1111/tra.12876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/12/2022] [Accepted: 11/29/2022] [Indexed: 12/07/2022]
Abstract
Conserved Oligomeric Golgi (COG) complex controls Golgi trafficking and glycosylation, but the precise COG mechanism is unknown. The auxin-inducible acute degradation system was employed to investigate initial defects resulting from COG dysfunction. We found that acute COG inactivation caused a massive accumulation of COG-dependent (CCD) vesicles that carry the bulk of Golgi enzymes and resident proteins. v-SNAREs (GS15, GS28) and v-tethers (giantin, golgin84, and TMF1) were relocalized into CCD vesicles, while t-SNAREs (STX5, YKT6), t-tethers (GM130, p115), and most of Rab proteins remained Golgi-associated. Airyscan microscopy and velocity gradient analysis revealed that different Golgi residents are segregated into different populations of CCD vesicles. Acute COG depletion significantly affected three Golgi-based vesicular coats-COPI, AP1, and GGA, suggesting that COG uniquely orchestrates tethering of multiple types of intra-Golgi CCD vesicles produced by different coat machineries. This study provided the first detailed view of primary cellular defects associated with COG dysfunction in human cells.
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Affiliation(s)
- Farhana Taher Sumya
- Department of Physiology and Cell Biology University of Arkansas for Medical Sciences Little Rock Arkansas USA
| | - Irina D. Pokrovskaya
- Department of Physiology and Cell Biology University of Arkansas for Medical Sciences Little Rock Arkansas USA
| | - Zinia D'Souza
- Department of Physiology and Cell Biology University of Arkansas for Medical Sciences Little Rock Arkansas USA
| | - Vladimir V. Lupashin
- Department of Physiology and Cell Biology University of Arkansas for Medical Sciences Little Rock Arkansas USA
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9
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Kubitz L, Bitsch S, Zhao X, Schmitt K, Deweid L, Roehrig A, Barazzone EC, Valerius O, Kolmar H, Béthune J. Engineering of ultraID, a compact and hyperactive enzyme for proximity-dependent biotinylation in living cells. Commun Biol 2022; 5:657. [PMID: 35788163 PMCID: PMC9253107 DOI: 10.1038/s42003-022-03604-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/20/2022] [Indexed: 12/11/2022] Open
Abstract
Proximity-dependent biotinylation (PDB) combined with mass spectrometry analysis has established itself as a key technology to study protein-protein interactions in living cells. A widespread approach, BioID, uses an abortive variant of the E. coli BirA biotin protein ligase, a quite bulky enzyme with slow labeling kinetics. To improve PDB versatility and speed, various enzymes have been developed by different approaches. Here we present a small-size engineered enzyme: ultraID. We show its practical use to probe the interactome of Argonaute-2 after a 10 min labeling pulse and expression at physiological levels. Moreover, using ultraID, we provide a membrane-associated interactome of coatomer, the coat protein complex of COPI vesicles. To date, ultraID is the smallest and most efficient biotin ligase available for PDB and offers the possibility of investigating interactomes at a high temporal resolution. A small-size engineered enzyme, ultraID, is presented for proximity-dependent biotinylation, that shows efficient labeling in mammalian cell culture, E. coli and S. cerevisiae.
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Affiliation(s)
- Lea Kubitz
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Sebastian Bitsch
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Xiyan Zhao
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Kerstin Schmitt
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Georg-August-University Göttingen, Göttingen, Germany
| | - Lukas Deweid
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.,Ferring Pharmaceuticals, Copenhagen, Denmark
| | - Amélie Roehrig
- Heidelberg University Biochemistry Center, Heidelberg, Germany.,Inserm UMRS1138 - FunGeST team, Paris, France
| | - Elisa Cappio Barazzone
- Heidelberg University Biochemistry Center, Heidelberg, Germany.,Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Oliver Valerius
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Georg-August-University Göttingen, Göttingen, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Julien Béthune
- Department of Biotechnology, Hamburg University of Applied Sciences, Hamburg, Germany.
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10
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Galesloot TE, Grotenhuis AJ, Kolev D, Aben KK, Bryan RT, Catto JWF, Cheng KK, Conroy S, Dyrskjøt L, Fleshner NE, James ND, Lamy P, Lindskrog SV, Malats N, Mengual L, Verhaegh G, Zeegers MP, Kiemeney LALM, Vermeulen SH. Genome-wide Meta-analysis Identifies Novel Genes Associated with Recurrence and Progression in Non-muscle-invasive Bladder Cancer. Eur Urol Oncol 2021; 5:70-83. [PMID: 34353775 DOI: 10.1016/j.euo.2021.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/15/2021] [Accepted: 07/01/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Non-muscle-invasive bladder cancer (NMIBC) is characterized by frequent recurrences and a risk of progression in stage and grade. Increased knowledge of underlying biological mechanisms is needed. OBJECTIVE To identify single nucleotide polymorphisms (SNPs) associated with recurrence-free (RFS) and progression-free (PFS) survival in NMIBC. DESIGN, SETTING, AND PARTICIPANTS We analyzed outcome data from 3400 newly diagnosed NMIBC patients from the Netherlands, the UK, Canada, and Spain. We generated genome-wide germline SNP data using Illumina OmniExpress and Infinium Global Screening Array in combination with genotype imputation. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Cohort-specific genome-wide association studies (GWASs) for RFS and PFS were performed using a Cox proportional hazard model. Results were combined in a fixed-effect inverse-variance weighted meta-analysis. Candidate genes for the identified SNP associations were prioritized using functional annotation, gene-based analysis, expression quantitative trait locus analysis, and transcription factor binding site databases. Tumor expression levels of prioritized genes were tested for association with RFS and PFS in an independent NMIBC cohort. RESULTS AND LIMITATIONS This meta-analysis revealed a genome-wide significant locus for RFS on chromosome 14 (lead SNP rs12885353, hazard ratio [HR] C vs T allele 1.55, 95% confidence interval [CI] 1.33-1.82, p = 4.0 × 10-8), containing genes G2E3 and SCFD1. Higher expression of SCFD1 was associated with increased RFS (HR 0.70, 95% CI 0.59-0.84, pFDR = 0.003). Twelve other loci were suggestively associated with RFS (p < 10-5), pointing toward 18 additional candidate genes. For PFS, ten loci showed suggestive evidence of association, indicating 36 candidate genes. Expression levels of ten of these genes were statistically significantly associated with PFS, of which four (IFT140, UBE2I, FAHD1, and NME3) showed directional consistency with our meta-analysis results and published literature. CONCLUSIONS In this first prognostic GWAS in NMIBC, we identified several novel candidate loci and five genes that showed convincing associations with recurrence or progression. PATIENT SUMMARY In this study, we searched for inherited DNA changes that affect the outcome of non-muscle-invasive bladder cancer (NMIBC). We identified several genes that are associated with disease recurrence and progression. The roles and mechanisms of these genes in NMIBC prognosis should be investigated in future studies.
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Affiliation(s)
- Tessel E Galesloot
- Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands.
| | - Anne J Grotenhuis
- Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands
| | - Dimitar Kolev
- Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands
| | - Katja K Aben
- Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands; Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - Richard T Bryan
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK; Bladder Cancer Research Centre, University of Birmingham, Birmingham, UK
| | - James W F Catto
- Academic Urology Unit, University of Sheffield, Sheffield, UK
| | - Kar K Cheng
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Samantha Conroy
- Academic Urology Unit, University of Sheffield, Sheffield, UK
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Neil E Fleshner
- Department of Urology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Nicholas D James
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Sia Viborg Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain; CIBERONC, Madrid, Spain
| | - Lourdes Mengual
- Department and Laboratory of Urology, Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Gerald Verhaegh
- Department of Urology, Radboud university medical center, Nijmegen, The Netherlands
| | - Maurice P Zeegers
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK; Department of Complex Genetics and Epidemiology, School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands; CAPHRI School for Public Health and Primary Care, University of Maastricht, Maastricht, The Netherlands
| | - Lambertus A L M Kiemeney
- Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands; Department of Urology, Radboud university medical center, Nijmegen, The Netherlands
| | - Sita H Vermeulen
- Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands
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11
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Pérez-Rodriguez S, Wulff T, Voldborg BG, Altamirano C, Trujillo-Roldán MA, Valdez-Cruz NA. Compartmentalized Proteomic Profiling Outlines the Crucial Role of the Classical Secretory Pathway during Recombinant Protein Production in Chinese Hamster Ovary Cells. ACS OMEGA 2021; 6:12439-12458. [PMID: 34056395 PMCID: PMC8154153 DOI: 10.1021/acsomega.0c06030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 05/11/2023]
Abstract
Different cellular processes that contribute to protein production in Chinese hamster ovary (CHO) cells have been previously investigated by proteomics. However, although the classical secretory pathway (CSP) has been well documented as a bottleneck during recombinant protein (RP) production, it has not been well represented in previous proteomic studies. Hence, the significance of this pathway for production of RP was assessed by identifying its own proteins that were associated to changes in RP production, through subcellular fractionation coupled to shot-gun proteomics. Two CHO cell lines producing a monoclonal antibody with different specific productivities were used as cellular models, from which 4952 protein groups were identified, which represent a coverage of 59% of the Chinese hamster proteome. Data are available via ProteomeXchange with identifier PXD021014. By using SAM and ROTS algorithms, 493 proteins were classified as differentially expressed, of which about 80% was proposed as novel targets and one-third were assigned to the CSP. Endoplasmic reticulum (ER) stress, unfolded protein response, calcium homeostasis, vesicle traffic, glycosylation, autophagy, proteasomal activity, protein synthesis and translocation into ER lumen, and secretion of extracellular matrix components were some of the affected processes that occurred in the secretory pathway. Processes from other cellular compartments, such as DNA replication, transcription, cytoskeleton organization, signaling, and metabolism, were also modified. This study gives new insights into the molecular traits of higher producer cells and provides novel targets for development of new sub-lines with improved phenotypes for RP production.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Tune Wulff
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Bjørn G. Voldborg
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Claudia Altamirano
- Laboratorio
de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085 Valparaíso, Chile
| | - Mauricio A. Trujillo-Roldán
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Norma A. Valdez-Cruz
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
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12
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Abstract
SNARE proteins and Sec1/Munc18 (SM) proteins constitute the core molecular engine that drives nearly all intracellular membrane fusion and exocytosis. While SNAREs are known to couple their folding and assembly to membrane fusion, the physiological pathways of SNARE assembly and the mechanistic roles of SM proteins have long been enigmatic. Here, we review recent advances in understanding the SNARE-SM fusion machinery with an emphasis on biochemical and biophysical studies of proteins that mediate synaptic vesicle fusion. We begin by discussing the energetics, pathways, and kinetics of SNARE folding and assembly in vitro. Then, we describe diverse interactions between SM and SNARE proteins and their potential impact on SNARE assembly in vivo. Recent work provides strong support for the idea that SM proteins function as chaperones, their essential role being to enable fast, accurate SNARE assembly. Finally, we review the evidence that SM proteins collaborate with other SNARE chaperones, especially Munc13-1, and briefly discuss some roles of SNARE and SM protein deficiencies in human disease.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA;
| | - Frederick M Hughson
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA;
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13
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Rich KA, Roggenbuck J, Kolb SJ. Searching Far and Genome-Wide: The Relevance of Association Studies in Amyotrophic Lateral Sclerosis. Front Neurosci 2021; 14:603023. [PMID: 33584177 PMCID: PMC7873947 DOI: 10.3389/fnins.2020.603023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/03/2020] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies (GWAS) and rare variant association studies (RVAS) are applied across many areas of complex disease to analyze variation in whole genomes of thousands of unrelated patients. These approaches are able to identify variants and/or biological pathways which are associated with disease status and, in contrast to traditional linkage studies or candidate gene approaches, do so without requiring multigenerational affected families, prior hypotheses, or known genes of interest. However, the novel associations identified by these methods typically have lower effect sizes than those found in classical family studies. In the motor neuron disease amyotrophic lateral sclerosis (ALS), GWAS, and RVAS have been used to identify multiple disease-associated genes but have not yet resulted in novel therapeutic interventions. There is significant urgency within the ALS community to identify additional genetic markers of disease to uncover novel biological mechanisms, stratify genetic subgroups of disease, and drive drug development. Given the widespread and increasing application of genetic association studies of complex disease, it is important to recognize the strengths and limitations of these approaches. Here, we review ALS gene discovery via GWAS and RVAS.
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Affiliation(s)
- Kelly A Rich
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Jennifer Roggenbuck
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Stephen J Kolb
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, United States.,Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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14
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van Berkel AA, Santos TC, Shaweis H, van Weering JRT, Toonen RF, Verhage M. Loss of MUNC18-1 leads to retrograde transport defects in neurons. J Neurochem 2020; 157:450-466. [PMID: 33259669 PMCID: PMC8247427 DOI: 10.1111/jnc.15256] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022]
Abstract
Loss of the exocytic Sec1/MUNC18 protein MUNC18-1 or its target-SNARE partners SNAP25 and syntaxin-1 results in rapid, cell-autonomous and unexplained neurodegeneration, which is independent of their known role in synaptic vesicle exocytosis. cis-Golgi abnormalities are the earliest cellular phenotypes before degeneration occurs. Here, we investigated whether loss of MUNC18-1 causes defects in intracellular membrane transport pathways in primary murine neurons that may explain neurodegeneration. Electron, confocal and super resolution microscopy confirmed that loss of MUNC18-1 expression results in a smaller cis-Golgi. In addition, we now show that medial-Golgi and the trans-Golgi Network are also affected. However, stacking and cisternae ultrastructure of the Golgi were normal. Overall, ultrastructure of null mutant neurons was remarkably normal just hours before cell death occurred. By synchronizing protein trafficking by conditional cargo retention in the endoplasmic reticulum using selective hooks (RUSH) and immunocytochemistry, we show that anterograde Endoplasmic Reticulum-to-Golgi and Golgi exit of endogenous and exogenous proteins were normal. In contrast, loss of MUNC18-1 caused reduced retrograde Cholera Toxin B-subunit transport from the plasma membrane to the Golgi. In addition, MUNC18-1-deficiency resulted in abnormalities in retrograde TrkB trafficking in an antibody uptake assay. We conclude that MUNC18-1 deficient neurons have normal anterograde but reduced retrograde transport to the Golgi. The impairments in retrograde pathways suggest a role of MUNC18-1 in endosomal SNARE-dependent fusion and provide a plausible explanation for the observed Golgi abnormalities and cell death in MUNC18-1 deficient neurons.
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Affiliation(s)
- Annemiek A van Berkel
- Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), University Medical Center Amsterdam, Amsterdam, The Netherlands.,Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands
| | - Tatiana C Santos
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands
| | - Hesho Shaweis
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands
| | - Jan R T van Weering
- Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), University Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Ruud F Toonen
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands
| | - Matthijs Verhage
- Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), University Medical Center Amsterdam, Amsterdam, The Netherlands.,Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, Amsterdam, The Netherlands
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15
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The Close Relationship between the Golgi Trafficking Machinery and Protein Glycosylation. Cells 2020; 9:cells9122652. [PMID: 33321764 PMCID: PMC7764369 DOI: 10.3390/cells9122652] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022] Open
Abstract
Glycosylation is the most common post-translational modification of proteins; it mediates their correct folding and stability, as well as their transport through the secretory transport. Changes in N- and O-linked glycans have been associated with multiple pathological conditions including congenital disorders of glycosylation, inflammatory diseases and cancer. Glycoprotein glycosylation at the Golgi involves the coordinated action of hundreds of glycosyltransferases and glycosidases, which are maintained at the correct location through retrograde vesicle trafficking between Golgi cisternae. In this review, we describe the molecular machinery involved in vesicle trafficking and tethering at the Golgi apparatus and the effects of mutations in the context of glycan biosynthesis and human diseases.
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16
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D'Souza Z, Taher FS, Lupashin VV. Golgi inCOGnito: From vesicle tethering to human disease. Biochim Biophys Acta Gen Subj 2020; 1864:129694. [PMID: 32730773 PMCID: PMC7384418 DOI: 10.1016/j.bbagen.2020.129694] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022]
Abstract
The Conserved Oligomeric Golgi (COG) complex, a multi-subunit vesicle tethering complex of the CATCHR (Complexes Associated with Tethering Containing Helical Rods) family, controls several aspects of cellular homeostasis by orchestrating retrograde vesicle traffic within the Golgi. The COG complex interacts with all key players regulating intra-Golgi trafficking, namely SNAREs, SNARE-interacting proteins, Rabs, coiled-coil tethers, and vesicular coats. In cells, COG deficiencies result in the accumulation of non-tethered COG-complex dependent (CCD) vesicles, dramatic morphological and functional abnormalities of the Golgi and endosomes, severe defects in N- and O- glycosylation, Golgi retrograde trafficking, sorting and protein secretion. In humans, COG mutations lead to severe multi-systemic diseases known as COG-Congenital Disorders of Glycosylation (COG-CDG). In this report, we review the current knowledge of the COG complex and analyze COG-related trafficking and glycosylation defects in COG-CDG patients.
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Affiliation(s)
- Zinia D'Souza
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Farhana S Taher
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Vladimir V Lupashin
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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17
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Wang X, Gong J, Zhu L, Wang S, Yang X, Xu Y, Yang X, Ma C. Munc13 activates the Munc18-1/syntaxin-1 complex and enables Munc18-1 to prime SNARE assembly. EMBO J 2020; 39:e103631. [PMID: 32643828 PMCID: PMC7429736 DOI: 10.15252/embj.2019103631] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/20/2020] [Accepted: 06/02/2020] [Indexed: 11/09/2022] Open
Abstract
Priming of synaptic vesicles involves Munc13-catalyzed transition of the Munc18-1/syntaxin-1 complex to the SNARE complex in the presence of SNAP-25 and synaptobrevin-2; Munc13 drives opening of syntaxin-1 via the MUN domain while Munc18-1 primes SNARE assembly via domain 3a. However, the underlying mechanism remains unclear. In this study, we have identified a number of residues in domain 3a of Munc18-1 that are crucial for Munc13 and Munc18-1 actions in SNARE complex assembly and synaptic vesicle priming. Our results showed that two residues (Q301/K308) at the side of domain 3a mediate the interaction between the Munc18-1/syntaxin-1 complex and the MUN domain. This interaction enables the MUN domain to drive the opening of syntaxin-1 linker region, thereby leading to the extension of domain 3a and promoting synaptobrevin-2 binding. In addition, we identified two residues (K332/K333) at the bottom of domain 3a that mediate the interaction between Munc18-1 and the SNARE motif of syntaxin-1. This interaction ensures Munc18-1 to persistently associate with syntaxin-1 during the conformational change of syntaxin-1 from closed to open, which reinforces the role of Munc18-1 in templating SNARE assembly. Taken together, our data suggest a mechanism by which Munc13 activates the Munc18-1/syntaxin-1 complex and enables Munc18-1 to prime SNARE assembly.
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Affiliation(s)
- Xianping Wang
- Key Laboratory of Molecular Biophysics of the Ministry of EducationCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Jihong Gong
- Key Laboratory of Molecular Biophysics of the Ministry of EducationCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Le Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of EducationCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Shen Wang
- Key Laboratory of Molecular Biophysics of the Ministry of EducationCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Xiaoyu Yang
- Key Laboratory of Molecular Biophysics of the Ministry of EducationCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Yuanyuan Xu
- Key Laboratory of Molecular Biophysics of the Ministry of EducationCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Xiaofei Yang
- Key Laboratory of Cognitive ScienceHubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & TreatmentLaboratory of Membrane Ion Channels and MedicineCollege of Biomedical EngineeringSouth‐Central University for NationalitiesWuhanChina
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of the Ministry of EducationCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Brain ResearchHuazhong University of Science and TechnologyWuhanChina
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18
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Gao G, Banfield DK. Multiple features within the syntaxin Sed5p mediate its Golgi localization. Traffic 2020; 21:274-296. [DOI: 10.1111/tra.12720] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Guanbin Gao
- The Division of Life ScienceThe Hong Kong University of Science and Technology Hong Kong
| | - David K. Banfield
- The Division of Life ScienceThe Hong Kong University of Science and Technology Hong Kong
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19
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Blackburn JB, D'Souza Z, Lupashin VV. Maintaining order: COG complex controls Golgi trafficking, processing, and sorting. FEBS Lett 2019; 593:2466-2487. [PMID: 31381138 PMCID: PMC6771879 DOI: 10.1002/1873-3468.13570] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
Abstract
The conserved oligomeric Golgi (COG) complex, a multisubunit tethering complex of the CATCHR (complexes associated with tethering containing helical rods) family, controls membrane trafficking and ensures Golgi homeostasis by orchestrating retrograde vesicle targeting within the Golgi. In humans, COG defects lead to severe multisystemic diseases known as COG-congenital disorders of glycosylation (COG-CDG). The COG complex both physically and functionally interacts with all classes of molecules maintaining intra-Golgi trafficking, namely SNAREs, SNARE-interacting proteins, Rabs, coiled-coil tethers, and vesicular coats. Here, we review our current knowledge of COG-related trafficking and glycosylation defects in humans and model organisms, and analyze possible scenarios for the molecular mechanism of the COG orchestrated vesicle targeting.
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Affiliation(s)
- Jessica B. Blackburn
- Department of Physiology and BiophysicsUniversity of Arkansas for Medical SciencesLittle RockARUSA
- Present address:
Division of Allergy, Pulmonary and Critical Care MedicineDepartment of MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Zinia D'Souza
- Department of Physiology and BiophysicsUniversity of Arkansas for Medical SciencesLittle RockARUSA
| | - Vladimir V. Lupashin
- Department of Physiology and BiophysicsUniversity of Arkansas for Medical SciencesLittle RockARUSA
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20
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Linders PT, Horst CVD, Beest MT, van den Bogaart G. Stx5-Mediated ER-Golgi Transport in Mammals and Yeast. Cells 2019; 8:cells8080780. [PMID: 31357511 PMCID: PMC6721632 DOI: 10.3390/cells8080780] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 01/12/2023] Open
Abstract
The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) syntaxin 5 (Stx5) in mammals and its ortholog Sed5p in Saccharomyces cerevisiae mediate anterograde and retrograde endoplasmic reticulum (ER)-Golgi trafficking. Stx5 and Sed5p are structurally highly conserved and are both regulated by interactions with other ER-Golgi SNARE proteins, the Sec1/Munc18-like protein Scfd1/Sly1p and the membrane tethering complexes COG, p115, and GM130. Despite these similarities, yeast Sed5p and mammalian Stx5 are differently recruited to COPII-coated vesicles, and Stx5 interacts with the microtubular cytoskeleton, whereas Sed5p does not. In this review, we argue that these different Stx5 interactions contribute to structural differences in ER-Golgi transport between mammalian and yeast cells. Insight into the function of Stx5 is important given its essential role in the secretory pathway of eukaryotic cells and its involvement in infections and neurodegenerative diseases.
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Affiliation(s)
- Peter Ta Linders
- Tumor Immunology Lab, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Chiel van der Horst
- Tumor Immunology Lab, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Martin Ter Beest
- Tumor Immunology Lab, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Geert van den Bogaart
- Tumor Immunology Lab, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands.
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
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21
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Ungermann C, Kümmel D. Structure of membrane tethers and their role in fusion. Traffic 2019; 20:479-490. [DOI: 10.1111/tra.12655] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Christian Ungermann
- Biochemistry Section, Department of Biology/ChemistryUniversity of Osnabrück Osnabrück Germany
- Center for Cellular Nanoanalytics (CellNanOs)University of Osnabrück Osnabrück Germany
| | - Daniel Kümmel
- Biochemistry & Structural Biology Section, Institute of BiochemistryUniversity of Münster Münster Germany
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22
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Dingjan I, Linders PTA, Verboogen DRJ, Revelo NH, Ter Beest M, van den Bogaart G. Endosomal and Phagosomal SNAREs. Physiol Rev 2018; 98:1465-1492. [PMID: 29790818 DOI: 10.1152/physrev.00037.2017] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein family is of vital importance for organelle communication. The complexing of cognate SNARE members present in both the donor and target organellar membranes drives the membrane fusion required for intracellular transport. In the endocytic route, SNARE proteins mediate trafficking between endosomes and phagosomes with other endosomes, lysosomes, the Golgi apparatus, the plasma membrane, and the endoplasmic reticulum. The goal of this review is to provide an overview of the SNAREs involved in endosomal and phagosomal trafficking. Of the 38 SNAREs present in humans, 30 have been identified at endosomes and/or phagosomes. Many of these SNAREs are targeted by viruses and intracellular pathogens, which thereby reroute intracellular transport for gaining access to nutrients, preventing their degradation, and avoiding their detection by the immune system. A fascinating picture is emerging of a complex transport network with multiple SNAREs being involved in consecutive trafficking routes.
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Affiliation(s)
- Ilse Dingjan
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Peter T A Linders
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Danielle R J Verboogen
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Natalia H Revelo
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Martin Ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
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23
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Li M, Du W, Zhou M, Zheng L, Song E, Hou J. Proteomic analysis of insulin secretory granules in INS-1 cells by protein correlation profiling. BIOPHYSICS REPORTS 2018; 4:329-338. [PMID: 30596141 PMCID: PMC6276070 DOI: 10.1007/s41048-018-0061-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/08/2018] [Indexed: 11/30/2022] Open
Abstract
Abstract Insulin secretory granules (ISGs), a group of distinguishing organelles in pancreatic β cells, are responsible for the storage and secretion of insulin to maintain blood glucose homeostasis. The molecular mechanisms of ISG biogenesis, maturation, transportation, and exocytosis are still largely unknown because the proteins involved in these distinct steps have not been fully identified. Subcellular fractionation by density gradient centrifugation has been successfully employed to analyze the proteomes of numerous organelles. However, use of this method to elucidate the ISG proteome is limited by co-fractionated contaminants because ISGs are very dynamic and have abundant exchanges or contacts with other organelles, such as the Golgi apparatus, lysosomes, and endosomes. In this study, we developed a new strategy for identifying ISG proteins by protein correlation profiling (PCP)-based proteomics, which included ISG purification by OptiPrep density gradient centrifugation, label-free quantitative proteome, and identification of ISG proteins by correlating fractionation profiles between candidates and known ISG markers. Using this approach, we were able to identify 81 ISG proteins. Among them, TM9SF3, a nine-transmembrane protein, was considered a high confidence ISG candidate protein highlighted in the PCP network. Further biochemical and immunofluorescence assays indicated that TM9SF3 localized in ISGs, suggesting that it is a potential new ISG marker. Graphical abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s41048-018-0061-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Li
- 1National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China.,2College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wen Du
- 1National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Maoge Zhou
- 1National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Li Zheng
- 1National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Eli Song
- 1National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Junjie Hou
- 1National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
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24
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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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25
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Anderson NS, Mukherjee I, Bentivoglio CM, Barlowe C. The Golgin protein Coy1 functions in intra-Golgi retrograde transport and interacts with the COG complex and Golgi SNAREs. Mol Biol Cell 2017; 28:mbc.E17-03-0137. [PMID: 28794270 PMCID: PMC5620376 DOI: 10.1091/mbc.e17-03-0137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 07/12/2017] [Accepted: 07/31/2017] [Indexed: 01/09/2023] Open
Abstract
Extended coiled-coil proteins of the Golgin family play prominent roles in maintaining the structure and function of the Golgi complex. Here we further investigate the Golgin protein Coy1 and document its function in retrograde transport between early Golgi compartments. Cells that lack Coy1 displayed a reduced half-life of the Och1 mannosyltransferase, an established cargo of intra-Golgi retrograde transport. Combining the coy1Δ mutation with deletions in other putative retrograde Golgins (sgm1Δ and rud3Δ) caused strong glycosylation and growth defects and reduced membrane association of the Conserved Oligomeric Golgi complex. In contrast, overexpression of COY1 inhibited the growth of mutant strains deficient in fusion activity at the Golgi (sed5-1 and sly1-ts). To map Coy1 protein interactions, co-immunoprecipitation experiments revealed an association with the Conserved Oliogmeric Golgi (COG) complex and with intra-Golgi SNARE proteins. These physical interactions are direct, as Coy1 was efficiently captured in vitro by Lobe A of the COG complex and the purified SNARE proteins Gos1, Sed5 and Sft1. Thus, our genetic, in vivo, and biochemical data indicate a role for Coy1 in regulating COG complex-dependent fusion of retrograde-directed COPI vesicles.
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Affiliation(s)
- Nadine S Anderson
- Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Indrani Mukherjee
- Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Christine M Bentivoglio
- Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Charles Barlowe
- Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
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26
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Golgi trafficking defects in postnatal microcephaly: The evidence for “Golgipathies”. Prog Neurobiol 2017; 153:46-63. [DOI: 10.1016/j.pneurobio.2017.03.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/22/2017] [Accepted: 03/29/2017] [Indexed: 12/17/2022]
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27
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Climer LK, Hendrix RD, Lupashin VV. Conserved Oligomeric Golgi and Neuronal Vesicular Trafficking. Handb Exp Pharmacol 2017; 245:227-247. [PMID: 29063274 DOI: 10.1007/164_2017_65] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The conserved oligomeric Golgi (COG) complex is an evolutionary conserved multi-subunit vesicle tethering complex essential for the majority of Golgi apparatus functions: protein and lipid glycosylation and protein sorting. COG is present in neuronal cells, but the repertoire of COG function in different Golgi-like compartments is an enigma. Defects in COG subunits cause alteration of Golgi morphology, protein trafficking, and glycosylation resulting in human congenital disorders of glycosylation (CDG) type II. In this review we summarize and critically analyze recent advances in the function of Golgi and Golgi-like compartments in neuronal cells and functions and dysfunctions of the COG complex and its partner proteins.
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Affiliation(s)
- Leslie K Climer
- College of Medicine, Physiology and Biophysics, UAMS, Little Rock, AR, USA
| | - Rachel D Hendrix
- College of Medicine, Neurobiology and Developmental Sciences, UAMS, Little Rock, AR, USA
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28
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Hou N, Yang Y, Scott IC, Lou X. The Sec domain protein Scfd1 facilitates trafficking of ECM components during chondrogenesis. Dev Biol 2016; 421:8-15. [PMID: 27851892 DOI: 10.1016/j.ydbio.2016.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 10/12/2016] [Accepted: 11/13/2016] [Indexed: 01/31/2023]
Abstract
Chondrogenesis in the developing skeleton requires transformation of chondrocytes from a simple mesenchymal condensation to cells with a highly enriched extracellular matrix (ECM). This transition is in part accomplished by alterations in the chondrocyte protein transport machinery to cope with both the increased amount and large size of ECM components. In a zebrafish mutagenesis screen to identify genes essential for cartilage development, we uncovered a mutant that disrupts the gene encoding Sec1 family domain containing 1 (scfd1). Homozygous scfd1 mutant embryos exhibit a profound craniofacial abnormality caused by a failure of chondrogenesis. Loss of scfd1 was found to hinder ER to Golgi transport of ECM proteins and is accompanied with activation of the unfolded protein response in chondrocytes. We further demonstrate a conserved role for Scfd1 in differentiation of mammalian chondrocytes, in which loss of either SCFD1 or STX18, a SLY1 interacting t-SNARE, severely impair transport of type II collagen. These results show that the existence of a specific export pathway, mediated by a complex containing SCFD1 and STX18 that plays an essential role in secretion of large ECM proteins during chondrogenesis.
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Affiliation(s)
- Ningning Hou
- Model Animal Research Center, Nanjing University, China
| | - Yuxi Yang
- Model Animal Research Center, Nanjing University, China
| | - Ian C Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Canada; Department of Molecular Genetics, University of Toronto, Canada
| | - Xin Lou
- Model Animal Research Center, Nanjing University, China.
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29
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Chou HT, Dukovski D, Chambers MG, Reinisch KM, Walz T. CATCHR, HOPS and CORVET tethering complexes share a similar architecture. Nat Struct Mol Biol 2016; 23:761-3. [PMID: 27428774 PMCID: PMC4972687 DOI: 10.1038/nsmb.3264] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/20/2016] [Indexed: 01/09/2023]
Abstract
We show that the Saccharomyces cerevisiae GARP complex and the Cog1-4 subcomplex of the COG complex, both members of the complexes associated with tethering containing helical rods (CATCHR) family of multisubunit tethering complexes, share the same subunit organization. We also show that the HOPS complex, a tethering complex acting in the endolysosomal pathway, shares a similar architecture, suggesting that multisubunit tethering complexes use related structural frameworks.
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Affiliation(s)
- Hui-Ting Chou
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Danijela Dukovski
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Melissa G Chambers
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Karin M Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
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30
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Willett R, Blackburn JB, Climer L, Pokrovskaya I, Kudlyk T, Wang W, Lupashin V. COG lobe B sub-complex engages v-SNARE GS15 and functions via regulated interaction with lobe A sub-complex. Sci Rep 2016; 6:29139. [PMID: 27385402 PMCID: PMC4935880 DOI: 10.1038/srep29139] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/14/2016] [Indexed: 01/03/2023] Open
Abstract
The conserved oligomeric Golgi (COG) complex is a peripheral membrane protein complex which orchestrates tethering of intra-Golgi vesicles. We found that COG1-4 (lobe A) and 5-8 (lobe B) protein assemblies are present as independent sub-complexes on cell membranes. Super-resolution microscopy demonstrates that COG sub-complexes are spatially separated on the Golgi with lobe A preferential localization on Golgi stacks and the presence of lobe B on vesicle-like structures, where it physically interacts with v-SNARE GS15. The localization and specific interaction of the COG sub-complexes with the components of vesicle tethering/fusion machinery suggests their different roles in the vesicle tethering cycle. We propose and test a novel model that employs association/disassociation of COG sub-complexes as a mechanism that directs vesicle tethering at Golgi membranes. We demonstrate that defective COG assembly or restriction of tethering complex disassembly by a covalent COG1-COG8 linkage is inhibitory to COG complex activity, supporting the model.
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Affiliation(s)
- Rose Willett
- Department of Physiology and Biophysics, UAMS, Little Rock, AR, USA
| | | | - Leslie Climer
- Department of Physiology and Biophysics, UAMS, Little Rock, AR, USA
| | | | - Tetyana Kudlyk
- Department of Physiology and Biophysics, UAMS, Little Rock, AR, USA
| | - Wei Wang
- Department of Physiology and Biophysics, UAMS, Little Rock, AR, USA
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31
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Abstract
Intracellular membrane fusion is mediated in most cases by membrane-bridging complexes of soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs). However, the assembly of such complexes in vitro is inefficient, and their uncatalysed disassembly is undetectably slow. Here, we focus on the cellular machinery that orchestrates assembly and disassembly of SNARE complexes, thereby regulating processes ranging from vesicle trafficking to organelle fusion to neurotransmitter release. Rapid progress is being made on many fronts, including the development of more realistic cell-free reconstitutions, the application of single-molecule biophysics, and the elucidation of X-ray and high-resolution electron microscopy structures of the SNARE assembly and disassembly machineries 'in action'.
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Affiliation(s)
- Richard W Baker
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.,Present address: Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Frederick M Hughson
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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32
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Vukašinović N, Žárský V. Tethering Complexes in the Arabidopsis Endomembrane System. Front Cell Dev Biol 2016; 4:46. [PMID: 27243010 PMCID: PMC4871884 DOI: 10.3389/fcell.2016.00046] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/02/2016] [Indexed: 12/30/2022] Open
Abstract
Targeting of endomembrane transport containers is of the utmost importance for proper land plant growth and development. Given the immobility of plant cells, localized membrane vesicle secretion and recycling are amongst the main processes guiding proper cell, tissue and whole plant morphogenesis. Cell wall biogenesis and modification are dependent on vectorial membrane traffic, not only during normal development, but also in stress responses and in plant defense against pathogens and/or symbiosis. It is surprising how little we know about these processes in plants, from small GTPase regulation to the tethering complexes that act as their effectors. Tethering factors are single proteins or protein complexes mediating first contact between the target membrane and arriving membrane vesicles. In this review we focus on the tethering complexes of the best-studied plant model—Arabidopsis thaliana. Genome-based predictions indicate the presence of all major tethering complexes in plants that are known from a hypothetical last eukaryotic common ancestor (LECA). The evolutionary multiplication of paralogs of plant tethering complex subunits has produced the massively expanded EXO70 family, indicating a subfunctionalization of the terminal exocytosis machinery in land plants. Interpretation of loss of function (LOF) mutant phenotypes has to consider that related, yet clearly functionally-specific complexes often share some common core subunits. It is therefore impossible to conclude with clarity which version of the complex is responsible for the phenotypic deviations observed. Experimental interest in the analysis of plant tethering complexes is growing and we hope to contribute with this review by attracting even more attention to this fascinating field of plant cell biology.
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Affiliation(s)
- Nemanja Vukašinović
- Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University Prague, Czech Republic
| | - Viktor Žárský
- Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University Prague, Czech Republic
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33
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Dubuke ML, Munson M. The Secret Life of Tethers: The Role of Tethering Factors in SNARE Complex Regulation. Front Cell Dev Biol 2016; 4:42. [PMID: 27243006 PMCID: PMC4860414 DOI: 10.3389/fcell.2016.00042] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/25/2016] [Indexed: 02/03/2023] Open
Abstract
Trafficking in eukaryotic cells is a tightly regulated process to ensure correct cargo delivery to the proper destination organelle or plasma membrane. In this review, we focus on how the vesicle fusion machinery, the SNARE complex, is regulated by the interplay of the multisubunit tethering complexes (MTC) with the SNAREs and Sec1/Munc18 (SM) proteins. Although these factors are used in different stages of membrane trafficking, e.g., Golgi to plasma membrane transport vs. vacuolar fusion, and in a variety of diverse eukaryotic cell types, many commonalities between their functions are being revealed. We explore the various protein-protein interactions and findings from functional reconstitution studies in order to highlight both their common features and the differences in their modes of regulation. These studies serve as a starting point for mechanistic explorations in other systems.
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Affiliation(s)
- Michelle L Dubuke
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, MA USA
| | - Mary Munson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, MA USA
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34
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Fisher P, Ungar D. Bridging the Gap between Glycosylation and Vesicle Traffic. Front Cell Dev Biol 2016; 4:15. [PMID: 27014691 PMCID: PMC4781848 DOI: 10.3389/fcell.2016.00015] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/22/2016] [Indexed: 11/24/2022] Open
Abstract
Glycosylation is recognized as a vitally important posttranslational modification. The structure of glycans that decorate proteins and lipids is largely dictated by biosynthetic reactions occurring in the Golgi apparatus. This biosynthesis relies on the relative distribution of glycosyltransferases and glycosidases, which is maintained by retrograde vesicle traffic between Golgi cisternae. Tethering of vesicles at the Golgi apparatus prior to fusion is regulated by Rab GTPases, coiled-coil tethers termed golgins and the multisubunit tethering complex known as the conserved oligomeric Golgi (COG) complex. In this review we discuss the mechanisms involved in vesicle tethering at the Golgi apparatus and highlight the importance of tethering in the context of glycan biosynthesis and a set of diseases known as congenital disorders of glycosylation.
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Affiliation(s)
- Peter Fisher
- Department of Biology, University of York York, UK
| | - Daniel Ungar
- Department of Biology, University of York York, UK
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35
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Climer LK, Dobretsov M, Lupashin V. Defects in the COG complex and COG-related trafficking regulators affect neuronal Golgi function. Front Neurosci 2015; 9:405. [PMID: 26578865 PMCID: PMC4621299 DOI: 10.3389/fnins.2015.00405] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/12/2015] [Indexed: 12/22/2022] Open
Abstract
The Conserved Oligomeric Golgi (COG) complex is an evolutionarily conserved hetero-octameric protein complex that has been proposed to organize vesicle tethering at the Golgi apparatus. Defects in seven of the eight COG subunits are linked to Congenital Disorders of Glycosylation (CDG)-type II, a family of rare diseases involving misregulation of protein glycosylation, alterations in Golgi structure, variations in retrograde trafficking through the Golgi and system-wide clinical pathologies. A troublesome aspect of these diseases are the neurological pathologies such as low IQ, microcephaly, and cerebellar atrophy. The essential function of the COG complex is dependent upon interactions with other components of trafficking machinery, such as Rab-GTPases and SNAREs. COG-interacting Rabs and SNAREs have been implicated in neurodegenerative diseases like Alzheimer's disease and Parkinson's disease. Defects in Golgi maintenance disrupts trafficking and processing of essential proteins, frequently associated with and contributing to compromised neuron function and human disease. Despite the recent advances in molecular neuroscience, the subcellular bases for most neurodegenerative diseases are poorly understood. This article gives an overview of the potential contributions of the COG complex and its Rab and SNARE partners in the pathogenesis of different neurodegenerative disorders.
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Affiliation(s)
- Leslie K Climer
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Maxim Dobretsov
- Department of Anesthesiology, College of Medicine, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Vladimir Lupashin
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences Little Rock, AR, USA
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36
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Dubuke ML, Maniatis S, Shaffer SA, Munson M. The Exocyst Subunit Sec6 Interacts with Assembled Exocytic SNARE Complexes. J Biol Chem 2015; 290:28245-28256. [PMID: 26446795 DOI: 10.1074/jbc.m115.673806] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Indexed: 11/06/2022] Open
Abstract
In eukaryotic cells, membrane-bound vesicles carry cargo between intracellular compartments, to and from the cell surface, and into the extracellular environment. Many conserved families of proteins are required for properly localized vesicle fusion, including the multisubunit tethering complexes and the SNARE complexes. These protein complexes work together to promote proper vesicle fusion in intracellular trafficking pathways. However, the mechanism by which the exocyst, the exocytosis-specific multisubunit tethering complex, interacts with the exocytic SNAREs to mediate vesicle targeting and fusion is currently unknown. We have demonstrated previously that the Saccharomyces cerevisiae exocyst subunit Sec6 directly bound the plasma membrane SNARE protein Sec9 in vitro and that Sec6 inhibited the assembly of the binary Sso1-Sec9 SNARE complex. Therefore, we hypothesized that the interaction between Sec6 and Sec9 prevented the assembly of premature SNARE complexes at sites of exocytosis. To map the determinants of this interaction, we used cross-linking and mass spectrometry analyses to identify residues required for binding. Mutation of residues identified by this approach resulted in a growth defect when introduced into yeast. Contrary to our previous hypothesis, we discovered that Sec6 does not change the rate of SNARE assembly but, rather, binds both the binary Sec9-Sso1 and ternary Sec9-Sso1-Snc2 SNARE complexes. Together, these results suggest a new model in which Sec6 promotes SNARE complex assembly, similar to the role proposed for other tether subunit-SNARE interactions.
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Affiliation(s)
- Michelle L Dubuke
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Stephanie Maniatis
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605; Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545
| | - Scott A Shaffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605; Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545
| | - Mary Munson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.
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37
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Hierro A, Gershlick DC, Rojas AL, Bonifacino JS. Formation of Tubulovesicular Carriers from Endosomes and Their Fusion to the trans-Golgi Network. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 318:159-202. [PMID: 26315886 DOI: 10.1016/bs.ircmb.2015.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Endosomes undergo extensive spatiotemporal rearrangements as proteins and lipids flux through them in a series of fusion and fission events. These controlled changes enable the concentration of cargo for eventual degradation while ensuring the proper recycling of other components. A growing body of studies has now defined multiple recycling pathways from endosomes to the trans-Golgi network (TGN) which differ in their molecular machineries. The recycling process requires specific sets of lipids, coats, adaptors, and accessory proteins that coordinate cargo selection with membrane deformation and its association with the cytoskeleton. Specific tethering factors and SNARE (SNAP (Soluble NSF Attachment Protein) Receptor) complexes are then required for the docking and fusion with the acceptor membrane. Herein, we summarize some of the current knowledge of the machineries that govern the retrograde transport from endosomes to the TGN.
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Affiliation(s)
- Aitor Hierro
- Structural Biology Unit, CIC bioGUNE, Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - David C Gershlick
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | - Juan S Bonifacino
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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38
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Kuhlee A, Raunser S, Ungermann C. Functional homologies in vesicle tethering. FEBS Lett 2015; 589:2487-97. [PMID: 26072291 DOI: 10.1016/j.febslet.2015.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 05/30/2015] [Accepted: 06/01/2015] [Indexed: 11/24/2022]
Abstract
The HOPS multisubunit tethering factor (MTC) is a macromolecular protein complex composed of six different subunits. It is one of the key components in the perception and subsequent fusion of multivesicular bodies and vacuoles. Electron microscopy studies indicate structural flexibility of the purified HOPS complex. Inducing higher rigidity into HOPS by biochemically modifying the complex declines the potential to mediate SNARE-driven membrane fusion. Thus, we propose that integral flexibility seems to be not only a feature, but of essential need for the function of HOPS. This review focuses on the general features of membrane tethering and fusion. For this purpose, we compare the structure and mode of action of different tethering factors to highlight their common central features and mechanisms.
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Affiliation(s)
- Anne Kuhlee
- Department of Structural Biochemistry, Max-Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max-Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Christian Ungermann
- Department of Biology, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany
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39
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Lecat S, Matthes HWD, Pepperkok R, Simpson JC, Galzi JL. A Fluorescent Live Imaging Screening Assay Based on Translocation Criteria Identifies Novel Cytoplasmic Proteins Implicated in G Protein-coupled Receptor Signaling Pathways. Mol Cell Proteomics 2015; 14:1385-99. [PMID: 25759509 PMCID: PMC4424407 DOI: 10.1074/mcp.m114.046698] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/20/2015] [Indexed: 12/13/2022] Open
Abstract
Several cytoplasmic proteins that are involved in G protein-coupled receptor signaling cascades are known to translocate to the plasma membrane upon receptor activation, such as beta-arrestin2. Based on this example and in order to identify new cytoplasmic proteins implicated in the ON-and-OFF cycle of G protein-coupled receptor, a live-imaging screen of fluorescently labeled cytoplasmic proteins was performed using translocation criteria. The screening of 193 fluorescently tagged human proteins identified eight proteins that responded to activation of the tachykinin NK2 receptor by a change in their intracellular localization. Previously we have presented the functional characterization of one of these proteins, REDD1, that translocates to the plasma membrane. Here we report the results of the entire screening. The process of cell activation was recorded on videos at different time points and all the videos can be visualized on a dedicated website. The proteins BAIAP3 and BIN1, partially translocated to the plasma membrane upon activation of NK2 receptors. Proteins ARHGAP12 and PKM2 translocated toward membrane blebs. Three proteins that associate with the cytoskeleton were of particular interest : PLEKHH2 rearranged from individual dots located near the cell-substrate adhesion surface into lines of dots. The speriolin-like protein, SPATC1L, redistributed to cell-cell junctions. The Chloride intracellular Channel protein, CLIC2, translocated from actin-enriched plasma membrane bundles to cell-cell junctions upon activation of NK2 receptors. CLIC2, and one of its close paralogs, CLIC4, were further shown to respond with the same translocation pattern to muscarinic M3 and lysophosphatidic LPA receptors. This screen allowed us to identify potential actors in signaling pathways downstream of G protein-coupled receptors and could be scaled-up for high-content screening.
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Affiliation(s)
- Sandra Lecat
- From the ‡GPCRs, Pain and Inflammation Team, UMR7242, CNRS-University of Strasbourg, LabEx Medalis, 300 Bvd Sébastien Brant, 67412 Illkirch, France;
| | - Hans W D Matthes
- From the ‡GPCRs, Pain and Inflammation Team, UMR7242, CNRS-University of Strasbourg, LabEx Medalis, 300 Bvd Sébastien Brant, 67412 Illkirch, France
| | - Rainer Pepperkok
- §European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Meyerhofstr 1, 69117 Heidelberg, Germany
| | - Jeremy C Simpson
- ¶¶School of Biology and Environmental Science and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jean-Luc Galzi
- From the ‡GPCRs, Pain and Inflammation Team, UMR7242, CNRS-University of Strasbourg, LabEx Medalis, 300 Bvd Sébastien Brant, 67412 Illkirch, France
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40
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Cog5-Cog7 crystal structure reveals interactions essential for the function of a multisubunit tethering complex. Proc Natl Acad Sci U S A 2014; 111:15762-7. [PMID: 25331899 DOI: 10.1073/pnas.1414829111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The conserved oligomeric Golgi (COG) complex is required, along with SNARE and Sec1/Munc18 (SM) proteins, for vesicle docking and fusion at the Golgi. COG, like other multisubunit tethering complexes (MTCs), is thought to function as a scaffold and/or chaperone to direct the assembly of productive SNARE complexes at the sites of membrane fusion. Reflecting this essential role, mutations in the COG complex can cause congenital disorders of glycosylation. A deeper understanding of COG function and dysfunction will likely depend on elucidating its molecular structure. Despite some progress toward this goal, including EM studies of COG lobe A (subunits 1-4) and higher-resolution structures of portions of Cog2 and Cog4, the structures of COG's eight subunits and the principles governing their assembly are mostly unknown. Here, we report the crystal structure of a complex between two lobe B subunits, Cog5 and Cog7. The structure reveals that Cog5 is a member of the complexes associated with tethering containing helical rods (CATCHR) fold family, with homology to subunits of other MTCs including the Dsl1, exocyst, and Golgi-associated retrograde protein (GARP) complexes. The Cog5-Cog7 interaction is analyzed in relation to the Dsl1 complex, the only other CATCHR-family MTC for which subunit interactions have been characterized in detail. Biochemical and functional studies validate the physiological relevance of the observed Cog5-Cog7 interface, indicate that it is conserved from yeast to humans, and demonstrate that its disruption in human cells causes defects in trafficking and glycosylation.
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Tagaya M, Arasaki K, Inoue H, Kimura H. Moonlighting functions of the NRZ (mammalian Dsl1) complex. Front Cell Dev Biol 2014; 2:25. [PMID: 25364732 PMCID: PMC4206994 DOI: 10.3389/fcell.2014.00025] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/20/2014] [Indexed: 12/31/2022] Open
Abstract
The yeast Dsl1 complex, which comprises Dsl1, Tip20, and Sec39/Dsl3, has been shown to participate, as a vesicle-tethering complex, in retrograde trafficking from the Golgi apparatus to the endoplasmic reticulum. Its metazoan counterpart NRZ complex, which comprises NAG, RINT1, and ZW10, is also involved in Golgi-to-ER retrograde transport, but each component of the complex has diverse cellular functions including endosome-to-Golgi transport, cytokinesis, cell cycle checkpoint, autophagy, and mRNA decay. In this review, we summarize the current knowledge of the metazoan NRZ complex and discuss the "moonlighting" functions and intercorrelation of their subunits.
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Affiliation(s)
- Mitsuo Tagaya
- Department of Molecular Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences Hachioji, Japan
| | - Kohei Arasaki
- Department of Molecular Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences Hachioji, Japan
| | - Hiroki Inoue
- Department of Molecular Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences Hachioji, Japan
| | - Hana Kimura
- Department of Molecular Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences Hachioji, Japan
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Nogueira C, Erlmann P, Villeneuve J, Santos AJ, Martínez-Alonso E, Martínez-Menárguez JÁ, Malhotra V. SLY1 and Syntaxin 18 specify a distinct pathway for procollagen VII export from the endoplasmic reticulum. eLife 2014. [PMID: 24842878 DOI: 10.7554/elife.02784.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
TANGO1 binds and exports Procollagen VII from the endoplasmic reticulum (ER). In this study, we report a connection between the cytoplasmic domain of TANGO1 and SLY1, a protein that is required for membrane fusion. Knockdown of SLY1 by siRNA arrested Procollagen VII in the ER without affecting the recruitment of COPII components, general protein secretion, and retrograde transport of the KDEL-containing protein BIP, and ERGIC53. SLY1 is known to interact with the ER-specific SNARE proteins Syntaxin 17 and 18, however only Syntaxin 18 was required for Procollagen VII export. Neither SLY1 nor Syntaxin 18 was required for the export of the equally bulky Procollagen I from the ER. Altogether, these findings reveal the sorting of bulky collagen family members by TANGO1 at the ER and highlight the existence of different export pathways for secretory cargoes one of which is mediated by the specific SNARE complex containing SLY1 and Syntaxin 18.DOI: http://dx.doi.org/10.7554/eLife.02784.001.
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Affiliation(s)
- Cristina Nogueira
- Cell and Developmental Biology Program, Center for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Patrik Erlmann
- Cell and Developmental Biology Program, Center for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Julien Villeneuve
- Cell and Developmental Biology Program, Center for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - António Jm Santos
- Cell and Developmental Biology Program, Center for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Emma Martínez-Alonso
- Department of Cellular Biology and Histology, Faculty of Medicine, University of Murcia, Murcia, Spain
| | | | - Vivek Malhotra
- Cell and Developmental Biology Program, Center for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Nogueira C, Erlmann P, Villeneuve J, Santos AJ, Martínez-Alonso E, Martínez-Menárguez JÁ, Malhotra V. SLY1 and Syntaxin 18 specify a distinct pathway for procollagen VII export from the endoplasmic reticulum. eLife 2014; 3:e02784. [PMID: 24842878 PMCID: PMC4054776 DOI: 10.7554/elife.02784] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
TANGO1 binds and exports Procollagen VII from the endoplasmic reticulum (ER). In this study, we report a connection between the cytoplasmic domain of TANGO1 and SLY1, a protein that is required for membrane fusion. Knockdown of SLY1 by siRNA arrested Procollagen VII in the ER without affecting the recruitment of COPII components, general protein secretion, and retrograde transport of the KDEL-containing protein BIP, and ERGIC53. SLY1 is known to interact with the ER-specific SNARE proteins Syntaxin 17 and 18, however only Syntaxin 18 was required for Procollagen VII export. Neither SLY1 nor Syntaxin 18 was required for the export of the equally bulky Procollagen I from the ER. Altogether, these findings reveal the sorting of bulky collagen family members by TANGO1 at the ER and highlight the existence of different export pathways for secretory cargoes one of which is mediated by the specific SNARE complex containing SLY1 and Syntaxin 18.DOI: http://dx.doi.org/10.7554/eLife.02784.001.
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Affiliation(s)
- Cristina Nogueira
- Cell and Developmental Biology Program, Center for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Patrik Erlmann
- Cell and Developmental Biology Program, Center for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Julien Villeneuve
- Cell and Developmental Biology Program, Center for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - António Jm Santos
- Cell and Developmental Biology Program, Center for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Emma Martínez-Alonso
- Department of Cellular Biology and Histology, Faculty of Medicine, University of Murcia, Murcia, Spain
| | | | - Vivek Malhotra
- Cell and Developmental Biology Program, Center for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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44
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Ong YS, Tran THT, Gounko NV, Hong W. TMEM115 is an integral membrane protein of the Golgi complex involved in retrograde transport. J Cell Sci 2014; 127:2825-39. [PMID: 24806965 PMCID: PMC4077589 DOI: 10.1242/jcs.136754] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Searching and evaluating the Human Protein Atlas for transmembrane proteins enabled us to identify an integral membrane protein, TMEM115, that is enriched in the Golgi complex. Biochemical and cell biological analysis suggested that TMEM115 has four candidate transmembrane domains located in the N-terminal region. Both the N- and C-terminal domains are oriented towards the cytoplasm. Immunofluorescence analysis supports that TMEM115 is enriched in the Golgi cisternae. Functionally, TMEM115 knockdown or overexpression delays Brefeldin-A-induced Golgi-to-ER retrograde transport, phenocopying cells with mutations or silencing of the conserved oligomeric Golgi (COG) complex. Co-immunoprecipitation and in vitro binding experiments reveals that TMEM115 interacts with the COG complex, and might self-interact to form dimers or oligomers. A short region (residues 206–229) immediately to the C-terminal side of the fourth transmembrane domain is both necessary and sufficient for Golgi targeting. Knockdown of TMEM115 also reduces the binding of the lectins peanut agglutinin (PNA) and Helix pomatia agglutinin (HPA), suggesting an altered O-linked glycosylation profile. These results establish that TMEM115 is an integral membrane protein of the Golgi stack regulating Golgi-to-ER retrograde transport and is likely to be part of the machinery of the COG complex.
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Affiliation(s)
- Yan Shan Ong
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Ton Hoai Thi Tran
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Natalia V Gounko
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore IMB-IMCB Joint Electron Microscopy Suite, 20 Biopolis Street, Singapore 138671, Singapore
| | - Wanjin Hong
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore Department of Biochemistry, National University of Singapore, Singapore 117599, Singapore
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Multiple and distinct strategies of yeast SNAREs to confer the specificity of membrane fusion. Sci Rep 2014; 4:4277. [PMID: 24589832 PMCID: PMC3940976 DOI: 10.1038/srep04277] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 02/17/2014] [Indexed: 01/04/2023] Open
Abstract
Trans-QabcR-SNARE pairing on opposing membranes is crucial for eukaryotic membrane fusion, but how selective pairs of Qabc- and R-SNARE proteins regulate membrane fusion specificity remains elusive. Here, we studied 14 purified full-length SNAREs that function in yeast endoplasmic reticulum (ER)-Golgi, intra-Golgi, endosomal, and vacuolar transport by comprehensively testing cis-QabcR-SNARE assembly and fusogenicity of reconstituted SNARE proteoliposomes. Strikingly, the cognate ER-Golgi and intra-Golgi SNARE-complex assemblies were highly stringent, whereas endosomal and vacuolar SNAREs assembled rather promiscuously into the non-cognate mixed complexes. However, these patterns of cis-SNARE assemblies cannot solely explain their potency to be fusogenic via trans-SNARE pairing: Only the vacuolar 3Q-SNARE combination is fusogenic in the absence of additional components; endosomal SNARE-dependent fusogenicity requires membrane-tethering factors; and ER-Golgi SNAREs can be fusogenic by synergistic actions of tethering factors and the cognate Sec1/Munc18-family protein Sly1p. Thus, our findings uncover multiple and distinct strategies of SNAREs to directly mediate fusion specificity.
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Hong W, Lev S. Tethering the assembly of SNARE complexes. Trends Cell Biol 2014; 24:35-43. [DOI: 10.1016/j.tcb.2013.09.006] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 12/11/2022]
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Balderhaar HJK, Ungermann C. CORVET and HOPS tethering complexes - coordinators of endosome and lysosome fusion. J Cell Sci 2013; 126:1307-16. [PMID: 23645161 DOI: 10.1242/jcs.107805] [Citation(s) in RCA: 370] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Protein and lipid transport along the endolysosomal system of eukaryotic cells depends on multiple fusion and fission events. Over the past few years, the molecular constituents of both fission and fusion machineries have been identified. Here, we focus on the mechanism of membrane fusion at endosomes, vacuoles and lysosomes, and in particular on the role of the two homologous tethering complexes called CORVET and HOPS. Both complexes are heterohexamers; they share four subunits, interact with Rab GTPases and soluble NSF attachment protein receptors (SNAREs) and can tether membranes. Owing to the presence of specific subunits, CORVET is a Rab5 effector complex, whereas HOPS can bind efficiently to late endosomes and lysosomes through Rab7. Based on the recently described overall structure of the HOPS complex and a number of in vivo and in vitro analyses, important insights into their function have been obtained. Here, we discuss the general function of both complexes in yeast and in metazoan cells in the context of endosomal biogenesis and maturation.
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Affiliation(s)
- Henning J kleine Balderhaar
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry Section, Barbarastrasse 13, 49076 Osnabrück, Germany
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Comparative genomic analysis of multi-subunit tethering complexes demonstrates an ancient pan-eukaryotic complement and sculpting in Apicomplexa. PLoS One 2013; 8:e76278. [PMID: 24086721 PMCID: PMC3785458 DOI: 10.1371/journal.pone.0076278] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/22/2013] [Indexed: 11/19/2022] Open
Abstract
Apicomplexa are obligate intracellular parasites that cause tremendous disease burden world-wide. They utilize a set of specialized secretory organelles in their invasive process that require delivery of components for their biogenesis and function, yet the precise mechanisms underpinning such processes remain unclear. One set of potentially important components is the multi-subunit tethering complexes (MTCs), factors increasingly implicated in all aspects of vesicle-target interactions. Prompted by the results of previous studies indicating a loss of membrane trafficking factors in Apicomplexa, we undertook a bioinformatic analysis of MTC conservation. Building on knowledge of the ancient presence of most MTC proteins, we demonstrate the near complete retention of MTCs in the newly available genomes for Guillardiatheta and Bigelowiellanatans. The latter is a key taxonomic sampling point as a basal sister taxa to the group including Apicomplexa. We also demonstrate an ancient origin of the CORVET complex subunits Vps8 and Vps3, as well as the TRAPPII subunit Tca17. Having established that the lineage leading to Apicomplexa did at one point possess the complete eukaryotic complement of MTC components, we undertook a deeper taxonomic investigation in twelve apicomplexan genomes. We observed excellent conservation of the VpsC core of the HOPS and CORVET complexes, as well as the core TRAPP subunits, but sparse conservation of TRAPPII, COG, Dsl1, and HOPS/CORVET-specific subunits. However, those subunits that we did identify appear to be expressed with similar patterns to the fully conserved MTC proteins, suggesting that they may function as minimal complexes or with analogous partners. Strikingly, we failed to identify any subunits of the exocyst complex in all twelve apicomplexan genomes, as well as the dinoflagellate Perkinsus marinus. Overall, we demonstrate reduction of MTCs in Apicomplexa and their ancestors, consistent with modification during, and possibly pre-dating, the move from free-living marine algae to deadly human parasites.
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Laufman O, Freeze HH, Hong W, Lev S. Deficiency of the Cog8 subunit in normal and CDG-derived cells impairs the assembly of the COG and Golgi SNARE complexes. Traffic 2013; 14:1065-77. [PMID: 23865579 DOI: 10.1111/tra.12093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 07/16/2013] [Accepted: 07/19/2013] [Indexed: 12/14/2022]
Abstract
Multiple mutations in different subunits of the tethering complex Conserved Oligomeric Golgi (COG) have been identified as a cause for Congenital Disorders of Glycosylation (CDG) in humans. Yet, the mechanisms by which COG mutations induce the pleiotropic CDG defects have not been fully defined. By detailed analysis of Cog8 deficiency in either HeLa cells or CDG-derived fibroblasts, we show that Cog8 is required for the assembly of both the COG complex and the Golgi Stx5-GS28-Ykt6-GS15 and Stx6-Stx16-Vti1a-VAMP4 SNARE complexes. The assembly of these SNARE complexes is also impaired in cells derived from a Cog7-deficient CDG patient. Likewise, the integrity of the COG complex is also impaired in Cog1-, Cog4- and Cog6-depleted cells. Significantly, deficiency of Cog1, Cog4, Cog6 or Cog8 distinctly influences the production of COG subcomplexes and their Golgi targeting. These results shed light on the structural organization of the COG complex and its subcellular localization, and suggest that its integrity is required for both tethering of transport vesicles to the Golgi apparatus and the assembly of Golgi SNARE complexes. We propose that these two key functions are generally and mechanistically impaired in COG-associated CDG patients, thereby exerting severe pleiotropic defects.
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Affiliation(s)
- Orly Laufman
- Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, 76100, Israel
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Structural basis of Vps33A recruitment to the human HOPS complex by Vps16. Proc Natl Acad Sci U S A 2013; 110:13345-50. [PMID: 23901104 DOI: 10.1073/pnas.1307074110] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The multisubunit homotypic fusion and vacuole protein sorting (HOPS) membrane-tethering complex is required for late endosome-lysosome and autophagosome-lysosome fusion in mammals. We have determined the crystal structure of the human HOPS subunit Vps33A, confirming its identity as a Sec1/Munc18 family member. We show that HOPS subunit Vps16 recruits Vps33A to the human HOPS complex and that residues 642-736 are necessary and sufficient for this interaction, and we present the crystal structure of Vps33A in complex with Vps16(642-736). Mutations at the binding interface disrupt the Vps33A-Vps16 interaction both in vitro and in cells, preventing recruitment of Vps33A to the HOPS complex. The Vps33A-Vps16 complex provides a structural framework for studying the association between Sec1/Munc18 proteins and tethering complexes.
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