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Sengül GF, Mishra R, Candiello E, Schu P. Hsc70 phosphorylation patterns and calmodulin regulate AP2 Clathrin-Coated-Vesicle life span for cell adhesion protein transport. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119611. [PMID: 37926156 DOI: 10.1016/j.bbamcr.2023.119611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023]
Abstract
AP2 forms AP2 CCV with clathrin and over 60 additional coat proteins. Due to this complexity, we have a limited understanding of CCV life cycle regulation. Synapses contain canonical AP2 CCV, canCCV, and more stable, thereby longer lived, AP2 CCV. The more stable AP2 CCV can be distinguished from canCCV due to the stable binding of Hsc70 to clathrin. The AP1/σ1B complex knockout leads to impaired synaptic vesicle recycling and altered endosomal protein sorting. This causes as a secondary phenotype the twofold upregulation of endocytosis by canCCV and by more stable AP2 CCV. These stable CCV are more stabilized than their wt counterpart, hence stCCV. They have less of the uncoating proteins synaptojanin1 and Hsc70, and more of the coat stabilizing AAK1. Hsc70 clathrin dissociation activity is regulated by complex phosphorylation patterns. Two major groups of hyper- and of hypo-phosphorylated Hsc70 proteins are formed. The latter are enriched in wt stable CCV and stabilized stCCV. Hsc70 T265 phosphorylation regulates binding of CaM/Ca2+. CaM/Ca2+ binding to the T265 domain blocks Hsc70 homodimerization and its concentration in stCCV required for clathrin disassembly. Kinases DYRK1A and CaMK-IIδ can phosphorylate T265 preventing CaM/Ca2+ binding. Their and the levels of STK38L and STK39/Cab39, which are able to phosphorylate additional Hsc70 residues are reduced in stCCV. The stCCV pathway sorts specifically the cell adhesion proteins CHL1 and Neurocan, supporting our model of that the stCCV pathway fulfills specific functions in synaptic plasticity.
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Affiliation(s)
- G F Sengül
- Georg-August-University Göttingen, University Medical Center, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Ankara Medipol University, Faculty of Medicine, Department of Medical Biochemistry, Turkey
| | - R Mishra
- Georg-August-University Göttingen, University Medical Center, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Dept. of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, England, United Kingdom
| | - E Candiello
- Georg-August-University Göttingen, University Medical Center, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; University of Turin, Tumor Immunology Laboratory, Torino, Italy
| | - P Schu
- Georg-August-University Göttingen, University Medical Center, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany.
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2
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Gusakova MS, Ivanov MV, Kashtanova DA, Taraskina AN, Erema VV, Mikova VM, Loshkarev RI, Ignatyeva OA, Akinshina AI, Mitrofanov SI, Snigir EA, Yudin VS, Makarov VV, Keskinov AA, Yudin SM. GWAS reveals genetic basis of a predisposition to severe COVID-19 through in silico modeling of the FYCO1 protein. Front Med (Lausanne) 2023; 10:1178939. [PMID: 37547597 PMCID: PMC10399629 DOI: 10.3389/fmed.2023.1178939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is heavily reliant on its natural ability to "hack" the host's genetic and biological pathways. The genetic susceptibility of the host is a key factor underlying the severity of the disease. Polygenic risk scores are essential for risk assessment, risk stratification, and the prevention of adverse outcomes. In this study, we aimed to assess and analyze the genetic predisposition to severe COVID-19 in a large representative sample of the Russian population as well as to build a reliable but simple polygenic risk score model with a lower margin of error. Another important goal was to learn more about the pathogenesis of severe COVID-19. We examined the tertiary structure of the FYCO1 protein, the only gene with mutations in its coding region and discovered changes in the coiled-coil domain. Our findings suggest that FYCO1 may accelerate viral intracellular replication and excessive exocytosis and may contribute to an increased risk of severe COVID-19. We found significant associations between COVID-19 and LZTFL1, FYCO1, XCR1, CCR9, TMLHE-AS1, and SCYL2 at 3p21.31. Our findings further demonstrate the polymorphic nature of the severe COVID-19 phenotype.
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Affiliation(s)
| | | | - Daria A. Kashtanova
- Federal State Budgetary Institution Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Moscow, Russia
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3
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Zhang C, Ma W, Xu M, Li T, Han G, Gu L, Chen M, Zhang M, Cheng B, Zhang X. Identification and Functional Characterization of ZmSCYL2 Involved in Phytosterol Accumulation in Plants. Int J Mol Sci 2023; 24:10411. [PMID: 37373558 DOI: 10.3390/ijms241210411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Phytosterols are natural active substances widely found in plants and play an important role in hypolipidemia, antioxidants, antitumor, immunomodulation, plant growth, and development. In this study, phytosterols were extracted and identified from the seed embryos of 244 maize inbred lines. Based on this, a genome-wide association study (GWAS) was used to predict the possible candidate genes responsible for phytosterol content; 9 SNPs and 32 candidate genes were detected, and ZmSCYL2 was identified to be associated with phytosterol accumulation. We initially confirmed its functions in transgenic Arabidopsis and found that mutation of ZmSCYL2 resulted in slow plant growth and a significant reduction in sterol content, while overexpression of ZmSCYL2 accelerated plant growth and significantly increased sterol content. These results were further confirmed in transgenic tobacco and suggest that ZmSCYL2 was closely related to plant growth; overexpression of ZmSCYL2 not only facilitated plant growth and development but also promoted the accumulation of phytosterols.
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Affiliation(s)
- Chenchen Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Wanlu Ma
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Minyan Xu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Tao Li
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Guomin Han
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Longjiang Gu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Meng Chen
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Mengting Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Xin Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
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4
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Dahhan DA, Reynolds GD, Cárdenas JJ, Eeckhout D, Johnson A, Yperman K, Kaufmann WA, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek SY. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. THE PLANT CELL 2022; 34:2150-2173. [PMID: 35218346 PMCID: PMC9134090 DOI: 10.1093/plcell/koac071] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/22/2022] [Indexed: 05/26/2023]
Abstract
In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.
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Affiliation(s)
| | | | - Jessica J Cárdenas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Alexander Johnson
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | | | - Walter A Kaufmann
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | - Nou Vang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Xu Yan
- College Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science & Technology, Pohang 37673, Korea
| | - Antje Heese
- Division of Biochemistry, Interdisciplinary Plant Group, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Jiří Friml
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Jianwei Pan
- College Life Sciences, Lanzhou University, Lanzhou 730000, China
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5
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Dahhan DA, Reynolds GD, Cárdenas JJ, Eeckhout D, Johnson A, Yperman K, Kaufmann WA, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek SY. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. THE PLANT CELL 2022; 34:2150-2173. [PMID: 35218346 DOI: 10.1101/2021.09.16.460678] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/22/2022] [Indexed: 05/26/2023]
Abstract
In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.
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Affiliation(s)
- Dana A Dahhan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Gregory D Reynolds
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jessica J Cárdenas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Alexander Johnson
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | - Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Walter A Kaufmann
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | - Nou Vang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Xu Yan
- College Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science & Technology, Pohang 37673, Korea
| | - Antje Heese
- Division of Biochemistry, Interdisciplinary Plant Group, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Jiří Friml
- Institute of Science and Technology (IST Austria), Klosterneuburg 3400, Austria
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Jianwei Pan
- College Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Sebastian Y Bednarek
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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6
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Enkler L, Rinaldi B, de Craene JO, Hammann P, Nureki O, Senger B, Friant S, Becker HD. Cex1 is a component of the COPI intracellular trafficking machinery. Biol Open 2021; 10:bio.058528. [PMID: 33753324 PMCID: PMC8015235 DOI: 10.1242/bio.058528] [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] [Indexed: 11/20/2022] Open
Abstract
COPI (coatomer complex I) coated vesicles are involved in Golgi-to-ER and intra-Golgi trafficking pathways, and mediate retrieval of ER resident proteins. Functions and components of the COPI-mediated trafficking pathways, beyond the canonical set of Sec/Arf proteins, are constantly increasing in number and complexity. In mammalian cells, GORAB, SCYL1 and SCYL3 proteins regulate Golgi morphology and protein glycosylation in concert with the COPI machinery. Here, we show that Cex1, homologous to the mammalian SCYL proteins, is a component of the yeast COPI machinery, by interacting with Sec27, Sec28 and Sec33 (Ret1/Cop1) proteins of the COPI coat. Cex1 was initially reported to mediate channeling of aminoacylated tRNA outside of the nucleus. Our data show that Cex1 localizes at membrane compartments, on structures positive for the Sec33 α-COP subunit. Moreover, the Wbp1 protein required for N-glycosylation and interacting via its di-lysine motif with the Sec27 β′-COP subunit is mis-targeted in cex1Δ deletion mutant cells. Our data point to the possibility of developing Cex1 yeast-based models to study neurodegenerative disorders linked to pathogenic mutations of its human homologue SCYL1. Summary: Cex1, the yeast homologue of mammalian SCYL1, interacts with COPI coat components and is recruited to the Golgi to regulate retrograde vesicular trafficking and sorting
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Affiliation(s)
- Ludovic Enkler
- Génétique Moléculaire et Cellulaire, Université de Strasbourg, CNRS, GMGM UMR7156, F-67000 Strasbourg, France
| | - Bruno Rinaldi
- Génétique Moléculaire et Cellulaire, Université de Strasbourg, CNRS, GMGM UMR7156, F-67000 Strasbourg, France
| | - Johan Owen de Craene
- Génétique Moléculaire et Cellulaire, Université de Strasbourg, CNRS, GMGM UMR7156, F-67000 Strasbourg, France
| | - Philippe Hammann
- 'Architecture et Réactivité de l'ARN', Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, F-67000 Strasbourg, France
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Bruno Senger
- Génétique Moléculaire et Cellulaire, Université de Strasbourg, CNRS, GMGM UMR7156, F-67000 Strasbourg, France
| | - Sylvie Friant
- Génétique Moléculaire et Cellulaire, Université de Strasbourg, CNRS, GMGM UMR7156, F-67000 Strasbourg, France
| | - Hubert D Becker
- Génétique Moléculaire et Cellulaire, Université de Strasbourg, CNRS, GMGM UMR7156, F-67000 Strasbourg, France
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7
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Jiménez-Rojo N, Leonetti MD, Zoni V, Colom A, Feng S, Iyengar NR, Matile S, Roux A, Vanni S, Weissman JS, Riezman H. Conserved Functions of Ether Lipids and Sphingolipids in the Early Secretory Pathway. Curr Biol 2020; 30:3775-3787.e7. [DOI: 10.1016/j.cub.2020.07.059] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/05/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023]
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8
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Seidahmed MZ, Al-Kindi A, Alsaif HS, Miqdad A, Alabbad N, Alfifi A, Abdelbasit OB, Alhussein K, Alsamadi A, Ibrahim N, Al-Futaisi A, Al-Maawali A, Alkuraya FS. Recessive mutations in SCYL2 cause a novel syndromic form of arthrogryposis in humans. Hum Genet 2020; 139:513-519. [PMID: 31960134 DOI: 10.1007/s00439-020-02117-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/10/2020] [Indexed: 12/20/2022]
Abstract
Arthrogryposis multiplex congenita (AMC) is an important birth defect with a significant genetic contribution. Many syndromic forms of AMC have been described, but remain unsolved at the molecular level. In this report, we describe a novel syndromic form of AMC in two multiplex consanguineous families from Saudi Arabia and Oman. The phenotype is highly consistent, and comprises neurogenic arthrogryposis, microcephaly, brain malformation (absent corpus callosum), optic atrophy, limb fractures, profound global developmental delay, and early lethality. Whole-exome sequencing revealed a different homozygous truncating variant in SCYL2 in each of the two families. SCYL2 is a component of clathrin-coated vesicles, and deficiency of its mouse ortholog results in a severe neurological phenotype that largely recapitulates the phenotype observed in our patients. Our results suggest that severe neurogenic arthrogryposis with brain malformation is the human phenotypic consequence of SCYL2 loss of function mutations.
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Affiliation(s)
| | - Adila Al-Kindi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abeer Miqdad
- Deparment of Pediatrics, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Nasser Alabbad
- Department of Obstetrics and Gynaecology, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Abdallah Alfifi
- Deparment of Pediatrics, Security Forces Hospital, Riyadh, Saudi Arabia
| | | | - Khalid Alhussein
- Deparment of Pediatrics, Security Forces Hospital, Riyadh, Saudi Arabia
| | | | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amna Al-Futaisi
- Department of Child Health, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Almundher Al-Maawali
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman.
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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9
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Witkos TM, Chan WL, Joensuu M, Rhiel M, Pallister E, Thomas-Oates J, Mould AP, Mironov AA, Biot C, Guerardel Y, Morelle W, Ungar D, Wieland FT, Jokitalo E, Tassabehji M, Kornak U, Lowe M. GORAB scaffolds COPI at the trans-Golgi for efficient enzyme recycling and correct protein glycosylation. Nat Commun 2019; 10:127. [PMID: 30631079 PMCID: PMC6328613 DOI: 10.1038/s41467-018-08044-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 12/06/2018] [Indexed: 01/08/2023] Open
Abstract
COPI is a key mediator of protein trafficking within the secretory pathway. COPI is recruited to the membrane primarily through binding to Arf GTPases, upon which it undergoes assembly to form coated transport intermediates responsible for trafficking numerous proteins, including Golgi-resident enzymes. Here, we identify GORAB, the protein mutated in the skin and bone disorder gerodermia osteodysplastica, as a component of the COPI machinery. GORAB forms stable domains at the trans-Golgi that, via interactions with the COPI-binding protein Scyl1, promote COPI recruitment to these domains. Pathogenic GORAB mutations perturb Scyl1 binding or GORAB assembly into domains, indicating the importance of these interactions. Loss of GORAB causes impairment of COPI-mediated retrieval of trans-Golgi enzymes, resulting in a deficit in glycosylation of secretory cargo proteins. Our results therefore identify GORAB as a COPI scaffolding factor, and support the view that defective protein glycosylation is a major disease mechanism in gerodermia osteodysplastica.
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Affiliation(s)
- Tomasz M Witkos
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Wing Lee Chan
- Berlin-Brandenburg Centre for Regenerative Therapies (BCRT), Institut fuer Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, 13353, Germany
- FG Development & Disease, Max Planck Institut fuer Molekulare Genetik, Berlin, 14195, Germany
| | - Merja Joensuu
- Cell and Molecular Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
- Clem Jones Centre of Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Brisbane, QLD 4072, Australia
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Manuel Rhiel
- Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, 69120, Germany
| | - Ed Pallister
- Department of Chemistry, University of York, York, YO10 5DG, UK
| | | | - A Paul Mould
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Alex A Mironov
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christophe Biot
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Yann Guerardel
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Willy Morelle
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Daniel Ungar
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Felix T Wieland
- Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, 69120, Germany
| | - Eija Jokitalo
- Cell and Molecular Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - May Tassabehji
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, M13 9WL, UK
| | - Uwe Kornak
- Berlin-Brandenburg Centre for Regenerative Therapies (BCRT), Institut fuer Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, 13353, Germany
- FG Development & Disease, Max Planck Institut fuer Molekulare Genetik, Berlin, 14195, Germany
| | - Martin Lowe
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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10
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Jung JY, Lee DW, Ryu SB, Hwang I, Schachtman DP. SCYL2 Genes Are Involved in Clathrin-Mediated Vesicle Trafficking and Essential for Plant Growth. PLANT PHYSIOLOGY 2017; 175:194-209. [PMID: 28751315 PMCID: PMC5580775 DOI: 10.1104/pp.17.00824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 07/24/2017] [Indexed: 05/10/2023]
Abstract
Protein transport between organelles is an essential process in all eukaryotic cells and is mediated by the regulation of processes such as vesicle formation, transport, docking, and fusion. In animals, SCY1-LIKE2 (SCYL2) binds to clathrin and has been shown to play roles in trans-Golgi network-mediated clathrin-coated vesicle trafficking. Here, we demonstrate that SCYL2A and SCYL2B, which are Arabidopsis (Arabidopsis thaliana) homologs of animal SCYL2, are vital for plant cell growth and root hair development. Studies of the SCYL2 isoforms using multiple single or double loss-of-function alleles show that SCYL2B is involved in root hair development and that SCYL2A and SCYL2B are essential for plant growth and development and act redundantly in those processes. Quantitative reverse transcription-polymerase chain reaction and a β-glucuronidase-aided promoter assay show that SCYL2A and SCYL2B are differentially expressed in various tissues. We also show that SCYL2 proteins localize to the Golgi, trans-Golgi network, and prevacuolar compartment and colocalize with Clathrin Heavy Chain1 (CHC1). Furthermore, bimolecular fluorescence complementation and coimmunoprecipitation data show that SCYL2B interacts with CHC1 and two Soluble NSF Attachment Protein Receptors (SNAREs): Vesicle Transport through t-SNARE Interaction11 (VTI11) and VTI12. Finally, we present evidence that the root hair tip localization of Cellulose Synthase-Like D3 is dependent on SCYL2B. These findings suggest the role of SCYL2 genes in plant cell developmental processes via clathrin-mediated vesicle membrane trafficking.
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Affiliation(s)
- Ji-Yul Jung
- Department of Plant Molecular Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Dong Wook Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Stephen Beungtae Ryu
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Inhwan Hwang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
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11
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The secret life of kinases: insights into non-catalytic signalling functions from pseudokinases. Biochem Soc Trans 2017; 45:665-681. [PMID: 28620028 DOI: 10.1042/bst20160331] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 12/31/2022]
Abstract
Over the past decade, our understanding of the mechanisms by which pseudokinases, which comprise ∼10% of the human and mouse kinomes, mediate signal transduction has advanced rapidly with increasing structural, biochemical, cellular and genetic studies. Pseudokinases are the catalytically defective counterparts of conventional, active protein kinases and have been attributed functions as protein interaction domains acting variously as allosteric modulators of conventional protein kinases and other enzymes, as regulators of protein trafficking or localisation, as hubs to nucleate assembly of signalling complexes, and as transmembrane effectors of such functions. Here, by categorising mammalian pseudokinases based on their known functions, we illustrate the mechanistic diversity among these proteins, which can be viewed as a window into understanding the non-catalytic functions that can be exerted by conventional protein kinases.
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12
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Haugsten EM, Sørensen V, Kunova Bosakova M, de Souza GA, Krejci P, Wiedlocha A, Wesche J. Proximity Labeling Reveals Molecular Determinants of FGFR4 Endosomal Transport. J Proteome Res 2016; 15:3841-3855. [DOI: 10.1021/acs.jproteome.6b00652] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ellen Margrethe Haugsten
- Department
of Molecular Cell Biology, Institute for Cancer Research, The Norwegian
Radium Hospital, Oslo University Hospital, Montebello, 0379 Oslo, Norway
- Centre
for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Montebello, 0379 Oslo, Norway
| | - Vigdis Sørensen
- Department
of Molecular Cell Biology, Institute for Cancer Research, The Norwegian
Radium Hospital, Oslo University Hospital, Montebello, 0379 Oslo, Norway
- Centre
for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Montebello, 0379 Oslo, Norway
- Department
of Core Facilities, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379 Oslo, Norway
| | - Michaela Kunova Bosakova
- Department
of Biology, Faculty of Medicine, Masaryk University, Kamenice
5, 625 00 Brno-Bohunice, Czech Republic
| | - Gustavo Antonio de Souza
- Department
of Immunology, Oslo University Hospital−Rikshospitalet and University of Oslo, 0027 Oslo, Norway
- The
Brain Institute, Universidade Federal do Rio Grande do Norte, UFRN, Natal, RN 59078, Brazil
| | - Pavel Krejci
- Department
of Biology, Faculty of Medicine, Masaryk University, Kamenice
5, 625 00 Brno-Bohunice, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, 656
91 Brno, Czech Republic
| | - Antoni Wiedlocha
- Department
of Molecular Cell Biology, Institute for Cancer Research, The Norwegian
Radium Hospital, Oslo University Hospital, Montebello, 0379 Oslo, Norway
- Centre
for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Montebello, 0379 Oslo, Norway
| | - Jørgen Wesche
- Department
of Molecular Cell Biology, Institute for Cancer Research, The Norwegian
Radium Hospital, Oslo University Hospital, Montebello, 0379 Oslo, Norway
- Centre
for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Montebello, 0379 Oslo, Norway
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13
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Kowalczyk KM, Petersen J. Fission Yeast SCYL1/2 Homologue Ppk32: A Novel Regulator of TOR Signalling That Governs Survival during Brefeldin A Induced Stress to Protein Trafficking. PLoS Genet 2016; 12:e1006041. [PMID: 27191590 PMCID: PMC4871519 DOI: 10.1371/journal.pgen.1006041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/19/2016] [Indexed: 12/02/2022] Open
Abstract
Target of Rapamycin (TOR) signalling allows eukaryotic cells to adjust cell growth in response to changes in their nutritional and environmental context. The two distinct TOR complexes (TORC1/2) localise to the cell’s internal membrane compartments; the endoplasmic reticulum (ER), Golgi apparatus and lysosomes/vacuoles. Here, we show that Ppk32, a SCYL family pseudo-kinase, is a novel regulator of TOR signalling. The absence of ppk32 expression confers resistance to TOR inhibition. Ppk32 inhibition of TORC1 is critical for cell survival following Brefeldin A (BFA) induced stress. Treatment of wild type cells with either the TORC1 specific inhibitor rapamycin or the general TOR inhibitor Torin1 confirmed that a reduction in TORC1 activity promoted recovery from BFA induced stress. Phosphorylation of Ppk32 on two residues that are conserved within the SCYL pseudo-kinase family are required for this TOR inhibition. Phosphorylation on these sites controls Ppk32 protein levels and sensitivity to BFA. BFA induced ER stress does not account for the response to BFA that we report here, however BFA is also known to induce Golgi stress and impair traffic to lysosomes. In summary, Ppk32 reduce TOR signalling in response to BFA induced stress to support cell survival. The Target of Rapamycin (TOR) pathway plays a central role coordinating cell growth and cell division in response to the different cellular environments. This is achieved by TOR controlling various metabolic processes, cell growth and cell division, and in part by the localisation of TOR protein complexes to specific internal endomembranes and compartments. Here, we report a novel role for the SCYL family pseudo-kinase, Ppk32 in restraining TOR signalling when cells experience stresses, which specifically affect endomembranes and compartments where TOR complexes are localised. Cells exposed to endomembrane stress (induced by Brefeldin A), displayed increased cell survival when simultaneously treated with the TOR complex 1 (TORC1) inhibitor, rapamycin, presumably because the reduction in TORC1 signalling slows cellular processes to allow cells sufficient time to recover and adapt to this stress. Importantly cancer, neuro-degeneration and neurological diseases are all associated with stress to the endomembrane protein trafficking system. Our findings suggest that therapeutic rapamycin treatment to reduce TOR signalling and block proliferation of cancer cells, which are inherently experiencing such stress, may have the unintended consequence of enhancing cell survival. It is notable, therefore, that our reported mechanisms to reduce Ppk32 protein levels, likely to be conserved in humans, may represent a way to increase TOR signalling and thus increase cell death of cancer types with inherent stress to these internal membrane systems.
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Affiliation(s)
| | - Janni Petersen
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- Flinders Centre for Innovation in Cancer, School of Medicine, Flinders University, Adelaide, Australia
- South Australia Health and Medical Research Institute, Adelaide, Australia
- * E-mail:
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14
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Abstract
The generation of mice lacking SCYL1 or SCYL2 and the identification of Scyl1 as the causative gene in the motor neuron disease mouse model muscle deficient (Scyl1mdf/mdf) demonstrated the importance of the SCY1-like family of protein pseudokinases in neuronal function and survival. Several essential cellular processes such as intracellular trafficking and nuclear tRNA export are thought to be regulated by SCYL proteins. However, whether deregulation of these processes contributes to the neurodegenerative processes associated with the loss of SCYL proteins is still unclear. Here, I briefly review the evidence supporting that SCYL proteins play a role in these processes and discuss their possible involvement in the neuronal functions of SCYL proteins. I also propose ways to determine the importance of these pathways for the functions of SCYL proteins in vivo.
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Affiliation(s)
- Stephane Pelletier
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
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15
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SCYL2 Protects CA3 Pyramidal Neurons from Excitotoxicity during Functional Maturation of the Mouse Hippocampus. J Neurosci 2015. [PMID: 26203146 DOI: 10.1523/jneurosci.2056-14.2015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Neuronal death caused by excessive excitatory signaling, excitotoxicity, plays a central role in neurodegenerative disorders. The mechanisms regulating this process, however, are still incompletely understood. Here we show that the coated vesicle-associated kinase SCYL2/CVAK104 plays a critical role for the normal functioning of the nervous system and for suppressing excitotoxicity in the developing hippocampus. Targeted disruption of Scyl2 in mice caused perinatal lethality in the vast majority of newborn mice and severe sensory-motor deficits in mice that survived to adulthood. Consistent with a neurogenic origin of these phenotypes, neuron-specific deletion of Scyl2 also caused perinatal lethality in the majority of newborn mice and severe neurological defects in adult mice. The neurological deficits in these mice were associated with the degeneration of several neuronal populations, most notably CA3 pyramidal neurons of the hippocampus, which we analyzed in more detail. The loss of CA3 neurons occurred during the functional maturation of the hippocampus and was the result of a BAX-dependent apoptotic process. Excessive excitatory signaling was present at the onset of degeneration, and inhibition of excitatory signaling prevented the degeneration of CA3 neurons. Biochemical fractionation reveals that Scyl2-deficient mice have an altered composition of excitatory receptors at synapses. Our findings demonstrate an essential role for SCYL2 in regulating neuronal function and survival and suggest a role for SCYL2 in regulating excitatory signaling in the developing brain. Significance statement: Here we examine the in vivo function of SCYL2, an evolutionarily conserved and ubiquitously expressed protein pseudokinase thought to regulate protein trafficking along the secretory pathway, and demonstrate its importance for the normal functioning of the nervous system and for suppressing excitatory signaling in the developing brain. Together with recent studies demonstrating a role of SCYL1 in preventing motor neuron degeneration, our findings clearly establish the SCY1-like family of protein pseudokinases as key regulators of neuronal function and survival.
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16
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Agarwal D, Qi Y, Jiang T, Liu X, Shi W, Wali VB, Turk B, Ross JS, Fraser Symmans W, Pusztai L, Hatzis C. Characterization of DNA variants in the human kinome in breast cancer. Sci Rep 2015; 5:14736. [PMID: 26420498 PMCID: PMC4588561 DOI: 10.1038/srep14736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/07/2015] [Indexed: 02/04/2023] Open
Abstract
Kinases play a key role in cancer biology, and serve as potential clinically useful targets for designing cancer therapies. We examined nucleic acid variations in the human kinome and several known cancer-related genes in breast cancer. DNA was extracted from fine needle biopsies of 73 primary breast cancers and 19 metastatic lesions. Targeted sequencing of 518 kinases and 68 additional cancer related genes was performed using the SOLiD sequencing platform. We detected 1561 unique, non-synonymous variants in kinase genes in the 92 cases, and 74 unique variants in 43 kinases that were predicted to have major functional impact on the protein. Three kinase groups—CMGC, STE and TKL—showed greater mutational load in metastatic compared to primary cancer samples, however, after correction for multiple testing the difference was significant only for the TKL group (P = 0.04). We also observed that a higher proportion of histologic grade 1 and 2 cases had high functional impact variants in the SCYL2 gene compared with grade 3 cases. Our findings indicate that individual breast cancers harbor a substantial number of potentially functionally important nucleotide variations in kinase genes, most of which are present in unique combinations and include both somatic and germline functional variants.
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Affiliation(s)
- Divyansh Agarwal
- Department of Breast Medical Oncology of Yale University, New Haven, CT, USA.,Molecular, Cellular and Developmental Biology of Yale University, New Haven, CT, USA
| | - Yuan Qi
- Department of Quantitative Sciences of the University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Tingting Jiang
- Department of Breast Medical Oncology of Yale University, New Haven, CT, USA
| | - Xiuping Liu
- Experimental Therapeutics of the University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Weiwei Shi
- Department of Breast Medical Oncology of Yale University, New Haven, CT, USA
| | - Vikram B Wali
- Department of Breast Medical Oncology of Yale University, New Haven, CT, USA
| | - Benjamin Turk
- Department of Pharmacology of Yale University, New Haven, CT, USA
| | - Jeffrey S Ross
- Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA.,Foundation Medicine, Cambridge, MA, USA
| | - W Fraser Symmans
- Pathology of the University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Lajos Pusztai
- Department of Breast Medical Oncology of Yale University, New Haven, CT, USA
| | - Christos Hatzis
- Department of Breast Medical Oncology of Yale University, New Haven, CT, USA
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17
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Makiyama T, Nakamura H, Nagasaka N, Yamashita H, Honda T, Yamaguchi N, Nishida A, Murayama T. Trafficking of Acetyl-C16-Ceramide-NBD with Long-Term Stability and No Cytotoxicity into the Golgi Complex. Traffic 2015; 16:476-92. [DOI: 10.1111/tra.12265] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 01/20/2015] [Accepted: 01/20/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Tomohiko Makiyama
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences; Chiba University; Chiba 260-8675 Japan
| | - Hiroyuki Nakamura
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences; Chiba University; Chiba 260-8675 Japan
| | - Nobuo Nagasaka
- Laboratory of Organic Chemistry, Graduate School of Pharmaceutical Sciences; Chiba University; Chiba 260-8675 Japan
| | - Hisahiro Yamashita
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences; Chiba University; Chiba 260-8675 Japan
| | - Takuya Honda
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences; Chiba University; Chiba 260-8675 Japan
| | - Naoto Yamaguchi
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences; Chiba University; Chiba 260-8675 Japan
| | - Atsushi Nishida
- Laboratory of Organic Chemistry, Graduate School of Pharmaceutical Sciences; Chiba University; Chiba 260-8675 Japan
| | - Toshihiko Murayama
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences; Chiba University; Chiba 260-8675 Japan
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18
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RNAi screening reveals a large signaling network controlling the Golgi apparatus in human cells. Mol Syst Biol 2013; 8:629. [PMID: 23212246 PMCID: PMC3542528 DOI: 10.1038/msb.2012.59] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 10/11/2012] [Indexed: 12/11/2022] Open
Abstract
RNAi screening and automated image analysis reveal 180 kinases and phosphatases regulating the organization of the Golgi apparatus. Most of these genes also control the expression of specific glycans, pointing to a web of interactions between signaling cascades and glycosylation at the Golgi. ![]()
Golgi organization was probed with three markers of different Golgi compartments and quantitative morphological analysis. Knockdowns of ∼20% of all known kinases and phosphatases affected the Golgi globally or in a compartment-specific manner, and were comparable in degree to the depletion of known membrane traffic regulators such as SNAREs. Several cell surface receptors, their cognate ligands and downstream effectors regulate Golgi organization, suggesting a large regulatory network. Most signaling genes affected both Golgi morphology and the expression of specific glycans.
The Golgi apparatus has many important physiological functions, including sorting of secretory cargo and biosynthesis of complex glycans. These functions depend on the intricate and compartmentalized organization of the Golgi apparatus. To investigate the mechanisms that regulate Golgi architecture, we developed a quantitative morphological assay using three different Golgi compartment markers and quantitative image analysis, and performed a kinome- and phosphatome-wide RNAi screen in HeLa cells. Depletion of 159 signaling genes, nearly 20% of genes assayed, induced strong and varied perturbations in Golgi morphology. Using bioinformatics data, a large regulatory network could be constructed. Specific subnetworks are involved in phosphoinositides regulation, acto-myosin dynamics and mitogen activated protein kinase signaling. Most gene depletion also affected Golgi functions, in particular glycan biosynthesis, suggesting that signaling cascades can control glycosylation directly at the Golgi level. Our results provide a genetic overview of the signaling pathways that control the Golgi apparatus in human cells.
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19
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Cancino J, Luini A. Signaling Circuits on the Golgi Complex. Traffic 2012; 14:121-34. [DOI: 10.1111/tra.12022] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/12/2012] [Accepted: 10/12/2012] [Indexed: 01/21/2023]
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20
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Miyakawa K, Sawasaki T, Matsunaga S, Tokarev A, Quinn G, Kimura H, Nomaguchi M, Adachi A, Yamamoto N, Guatelli J, Ryo A. Interferon-Induced SCYL2 Limits Release of HIV-1 by Triggering PP2A-Mediated Dephosphorylation of the Viral Protein Vpu. Sci Signal 2012; 5:ra73. [PMID: 23047923 DOI: 10.1126/scisignal.2003212] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kei Miyakawa
- Department of Microbiology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
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21
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Abstract
Clathrin is considered the prototype vesicle coat protein whose self-assembly mediates sorting of membrane cargo and recruitment of lipid modifiers. Detailed knowledge of clathrin biochemistry, structure, and interacting proteins has accumulated since the first observation, almost 50 years ago, of its role in receptor-mediated endocytosis of yolk protein. This review summarizes that knowledge, and focuses on properties of the clathrin heavy and light chain subunits and interaction of the latter with Hip proteins, to address the diversity of clathrin function beyond conventional receptor-mediated endocytosis. The distinct functions of the two human clathrin isoforms (CHC17 and CHC22) are discussed, highlighting CHC22's specialized involvement in traffic of the GLUT4 glucose transporter and consequent role in human glucose metabolism. Analysis of clathrin light chain function and interaction with the actin-binding Hip proteins during bacterial infection defines a novel actin-organizing function for CHC17 clathrin. By considering these diverse clathrin functions, along with intracellular sorting roles and influences on mitosis, further relevance of clathrin function to human health and disease is established.
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Affiliation(s)
- Frances M Brodsky
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143-0552, USA.
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22
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Schrimpe-Rutledge AC, Fontès G, Gritsenko MA, Norbeck AD, Anderson DJ, Waters KM, Adkins JN, Smith RD, Poitout V, Metz TO. Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics. J Proteome Res 2012; 11:3520-32. [PMID: 22578083 DOI: 10.1021/pr3002996] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The prevalence of diabetes mellitus is increasing dramatically throughout the world, and the disease has become a major public health issue. The most common form of the disease, type 2 diabetes, is characterized by insulin resistance and insufficient insulin production from the pancreatic beta-cell. Since glucose is the most potent regulator of beta-cell function under physiological conditions, identification of the insulin secretory defect underlying type 2 diabetes requires a better understanding of glucose regulation of human beta-cell function. To this aim, a bottom-up LC-MS/MS-based proteomics approach was used to profile pooled islets from multiple donors under basal (5 mM) or high (15 mM) glucose conditions. Our analysis discovered 256 differentially abundant proteins (∼p < 0.05) after 24 h of high glucose exposure from more than 4500 identified in total. Several novel glucose-regulated proteins were elevated under high glucose conditions, including regulators of mRNA splicing (pleiotropic regulator 1), processing (retinoblastoma binding protein 6), and function (nuclear RNA export factor 1), in addition to neuron navigator 1 and plasminogen activator inhibitor 1. Proteins whose abundances markedly decreased during incubation at 15 mM glucose included Bax inhibitor 1 and synaptotagmin-17. Up-regulation of dicer 1 and SLC27A2 and down-regulation of phospholipase Cβ4 were confirmed by Western blots. Many proteins found to be differentially abundant after high glucose stimulation are annotated as uncharacterized or hypothetical. These findings expand our knowledge of glucose regulation of the human islet proteome and suggest many hitherto unknown responses to glucose that require additional studies to explore novel functional roles.
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23
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Yien YY, Bieker JJ. Functional interactions between erythroid Krüppel-like factor (EKLF/KLF1) and protein phosphatase PPM1B/PP2Cβ. J Biol Chem 2012; 287:15193-204. [PMID: 22393050 DOI: 10.1074/jbc.m112.350496] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Erythroid Krüppel-like factor (EKLF; KLF1) is an erythroid-specific transcription factor required for the transcription of genes that regulate erythropoiesis. In this paper, we describe the identification of a novel EKLF interactor, Ppm1b, a serine-threonine protein phosphatase that has been implicated in the attenuation of NFκB signaling and the regulation of Cdk9 phosphorylation status. We show that Ppm1b interacts with EKLF via its PEST1 sequence. However, its genetic regulatory role is complex. Using a promoter-reporter assay in an erythroid cell line, we show that Ppm1b superactivates EKLF at the β-globin and BKLF promoters, dependent on intact Ppm1b phosphatase activity. Conversely, depletion of Ppm1b in CD34(+) cells leads to a higher level of endogenous β-globin gene activation after differentiation. We also observe that Ppm1b likely has an indirect role in regulating EKLF turnover via its zinc finger domain. Together, these studies show that Ppm1b plays a multilayered role in regulating the availability and optimal activity of the EKLF protein in erythroid cells.
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Affiliation(s)
- Yvette Y Yien
- Department of Developmental and Regenerative Biology, The Mount Sinai School of Medicine, New York, New York 10029, USA
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25
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Hoffmann A, Dannhauser PN, Groos S, Hinrichsen L, Curth U, Ungewickell EJ. A Comparison of GFP-Tagged Clathrin Light Chains with Fluorochromated Light Chains In Vivo and In Vitro. Traffic 2010; 11:1129-40. [DOI: 10.1111/j.1600-0854.2010.01084.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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26
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Katoh Y, Ritter B, Gaffry T, Blondeau F, Höning S, McPherson PS. The clavesin family, neuron-specific lipid- and clathrin-binding Sec14 proteins regulating lysosomal morphology. J Biol Chem 2009; 284:27646-54. [PMID: 19651769 PMCID: PMC2785693 DOI: 10.1074/jbc.m109.034884] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 07/20/2009] [Indexed: 11/06/2022] Open
Abstract
Clathrin-coated vesicles (CCVs) originating from the trans-Golgi network (TGN) provide a major transport pathway from the secretory system to endosomes/lysosomes. Herein we describe paralogous Sec14 domain-bearing proteins, clavesin 1/CRALBPL and clavesin 2, identified through a proteomic analysis of CCVs. Clavesins are enriched on CCVs and form a complex with clathrin heavy chain (CHC) and adaptor protein-1, major coat components of TGN-derived CCVs. The proteins co-localize with markers of endosomes and the TGN as well as with CHC and adaptor protein-1. A membrane mimic assay using the Sec14 domain of clavesin 1 reveals phosphatidylinositol 3,5-bisphosphate as a specific lipid partner. Phosphatidylinositol 3,5-bisphosphate is localized to late endosomes/lysosomes, and interestingly, isoform-specific knockdown of clavesins in neurons using lentiviral delivery of interfering RNA leads to enlargement of a lysosome-associated membrane protein 1-positive membrane compartment with no obvious influence on the CCV machinery at the TGN. Since clavesins are expressed exclusively in neurons, this new protein family appears to provide a unique neuron-specific regulation of late endosome/lysosome morphology.
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Affiliation(s)
- Yohei Katoh
- From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada and
| | - Brigitte Ritter
- From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada and
| | - Thomas Gaffry
- the Institute of Biochemistry I and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Francois Blondeau
- From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada and
| | - Stefan Höning
- the Institute of Biochemistry I and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Peter S. McPherson
- From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada and
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27
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Terabayashi T, Funato Y, Fukuda M, Miki H. A coated vesicle-associated kinase of 104 kDa (CVAK104) induces lysosomal degradation of frizzled 5 (Fzd5). J Biol Chem 2009; 284:26716-24. [PMID: 19643732 DOI: 10.1074/jbc.m109.039313] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Receptor internalization is recognized as an important mechanism for controlling numerous cell surface receptors. This event contributes not only to regulate signal transduction but also to adjust the amount of cell surface receptors. Frizzleds (Fzds) are seven-pass transmembrane receptor family proteins for Wnt ligands. Recent studies indicated that Fzd5 is internalized in response to Wnt stimulation to activate downstream signaling pathways. After internalization, it appears that Fzd5 is recycled back to the plasma membrane. However, whether internalized Fzd5 is sorted to lysosomes for protein degradation remains unclear. We here report that a coated vesicle-associated kinase of 104 kDa (CVAK104) selectively induces lysosomal degradation of Fzd5. We identify CVAK104 as a novel binding partner of Dishevelled (Dvl), a scaffold protein in the Wnt signaling pathway. Interestingly, we find that CVAK104 also interacts with Fzd5 but not with Fzd1 or Fzd4. CVAK104 selectively induces intracellular accumulation of Fzd5 via the clathrin-mediated pathway, which is suppressed by coexpression of a dominant negative form of Rab5. Fzd5 is subsequently degraded by a lysosomal pathway. Indeed, knockdown of endogenous CVAK104 by RNA interference results in an increase in the amount of Fzd5. In contrast, Wnt treatment induces Fzd5 internalization but does not stimulate its degradation. Overexpression or knockdown of CVAK104 results in a significant suppression or activation of the Wnt/beta-catenin pathway, respectively. These results suggest that CVAK104 regulates the amount of Fzd5 by inducing lysosomal degradation, which probably contributes to the suppression of the Wnt signaling pathway.
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Affiliation(s)
- Takeshi Terabayashi
- Laboratory of Intracellular Signaling, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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Burman JL, Bourbonniere L, Philie J, Stroh T, Dejgaard SY, Presley JF, McPherson PS. Scyl1, mutated in a recessive form of spinocerebellar neurodegeneration, regulates COPI-mediated retrograde traffic. J Biol Chem 2008; 283:22774-86. [PMID: 18556652 DOI: 10.1074/jbc.m801869200] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Scy1-like 1 (Scyl1), a member of the Scy1-like family of catalytically inactive protein kinases, was recently identified as the gene product altered in muscle-deficient mice, which suffer from motor neuron degeneration and cerebellar atrophy. To determine the function of Scyl1, we have now used a mass spectrometry-based screen to search for Scyl1-binding partners and identified components of coatomer I (COPI) coats. The interaction was confirmed in pull-down assays, and Scyl1 co-immunoprecipitates with betaCOP from brain lysates. Interestingly, and unique for a non-transmembrane domain protein, Scyl1 binds COPI coats using a C-terminal RKLD-COO(-) sequence, similar to the KKXX-COO(-) COPI-binding motif found in transmembrane endoplasmic reticulum (ER) proteins. Scyl1 co-localizes with betaCOP and is localized, in an Arf1-independent manner, to the ER-Golgi intermediate compartment and the cis-Golgi, sites of COPI-mediated membrane budding. The localization and binding properties of Scyl1 strongly suggest a function in COPI transport, and inhibitory RNA-mediated knock down of the protein disrupts COPI-mediated retrograde traffic of the KDEL receptor to the ER without affecting anterograde traffic from the ER. Our data demonstrate a function for Scyl1 as an accessory factor in COPI trafficking and suggest for the first time that alterations in the COPI pathway result in neurodegenerative disease.
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Affiliation(s)
- Jonathon L Burman
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
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Borner GHH, Rana AA, Forster R, Harbour M, Smith JC, Robinson MS. CVAK104 is a novel regulator of clathrin-mediated SNARE sorting. Traffic 2007; 8:893-903. [PMID: 17587408 PMCID: PMC2239300 DOI: 10.1111/j.1600-0854.2007.00576.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Clathrin-coated vesicles (CCVs) mediate transport between the plasma membrane, endosomes and the trans Golgi network. Using comparative proteomics, we have identified coated-vesicle-associated kinase of 104 kDa (CVAK104) as a candidate accessory protein for CCV-mediated trafficking. Here, we demonstrate that the protein colocalizes with clathrin and adaptor protein-1 (AP-1), and that it is associated with a transferrin-positive endosomal compartment. Consistent with these observations, clathrin as well as the cargo adaptors AP-1 and epsinR can be coimmunoprecipitated with CVAK104. Small interfering RNA (siRNA) knockdown of CVAK104 in HeLa cells results in selective loss of the SNARE proteins syntaxin 8 and vti1b from CCVs. Morpholino-mediated knockdown of CVAK104 in Xenopus tropicalis causes severe developmental defects, including a bent body axis and ventral oedema. Thus, CVAK104 is an evolutionarily conserved protein involved in SNARE sorting that is essential for normal embryonic development.
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Affiliation(s)
| | - Amer A Rana
- Gurdon Institute, University of CambridgeCambridge CB2 1QN, UK
| | | | | | - James C Smith
- Gurdon Institute, University of CambridgeCambridge CB2 1QN, UK
| | - Margaret S Robinson
- CIMR, University of CambridgeCambridge CB2 0XY, UK
- Corresponding author: Margaret S. Robinson,
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