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Begley M, Aragon M, Baker RW. A structure-based mechanism for initiation of AP-3 coated vesicle formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597630. [PMID: 38895279 PMCID: PMC11185636 DOI: 10.1101/2024.06.05.597630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Adaptor protein complex 3 (AP-3) mediates cargo sorting from endosomes to lysosomes and lysosome-related organelles. Recently, it was shown that AP-3 is in a constitutively open, active conformation compared to the related AP-1 and AP-2 coat complexes, which are inactive until undergoing large conformational changes upon membrane recruitment. How AP-3 is regulated is therefore an open question. To understand the mechanism of AP-3 membrane recruitment and activation, we reconstituted the core of human AP-3 and determined multiple structures in the soluble and membrane-bound states using electron cryo-microscopy (cryo-EM). Similar to yeast AP-3, human AP-3 is in a constitutively open conformation, with the cargo-binding domain of the μ3 subunit conformationally free. To reconstitute AP-3 activation by the small GTPase Arf1, we used lipid nanodiscs to build Arf1-AP-3 complexes on membranes and determined three structures that show the stepwise conformational changes required for formation of AP-3 coated vesicles. First, membrane-recruitment is driven by one of two predicted Arf1 binding sites on AP-3. In this conformation, AP-3 is flexibly tethered to the membrane and its cargo binding domain remains conformationally dynamic. Second, cargo binding causes AP-3 to adopt a fixed position and rigidifies the complex, which stabilizes binding for a second Arf1 molecule. Finally, binding of the second Arf1 molecule provides the template for AP-3 dimerization, providing a glimpse into the first step of coat polymerization. We propose coat polymerization only occurs after cargo engagement, thereby linking cargo sorting with assembly of higher order coat structures. Additionally, we provide evidence for two amphipathic helices in AP-3, suggesting that AP-3 contributes to membrane deformation during coat assembly. In total, these data provide evidence for the first stages of AP-3 mediated vesicle coat assembly.
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Affiliation(s)
- Matthew Begley
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine; Chapel Hill, NC 27516, USA
| | - Mahira Aragon
- New York Structural Biology Center; New York, NY 10027, USA
| | - Richard W. Baker
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine; Chapel Hill, NC 27516, USA
- UNC Lineberger Comprehensive Cancer Center. UNC Chapel Hill School of Medicine; Chapel Hill, NC 27516, USA
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Pasquarelli RR, Quan JJ, Cheng ES, Yang V, Britton TA, Sha J, Wohlschlegel JA, Bradley PJ. Characterization and functional analysis of Toxoplasma Golgi-associated proteins identified by proximity labelling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578703. [PMID: 38352341 PMCID: PMC10862792 DOI: 10.1101/2024.02.02.578703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Toxoplasma gondii possesses a highly polarized secretory pathway that contains both broadly conserved eukaryotic organelles and unique apicomplexan organelles which play essential roles in the parasite's lytic cycle. As in other eukaryotes, the T. gondii Golgi apparatus sorts and modifies proteins prior to their distribution to downstream organelles. Many of the typical trafficking factors found involved in these processes are missing from apicomplexan genomes, suggesting that these parasites have evolved unique proteins to fill these roles. Here we identify a novel Golgi-localizing protein (ULP1) which contains structural homology to the eukaryotic trafficking factor p115/Uso1. We demonstrate that depletion of ULP1 leads to a dramatic reduction in parasite fitness and replicative ability. Using ULP1 as bait for TurboID proximity labelling and immunoprecipitation, we identify eleven more novel Golgi-associated proteins and demonstrate that ULP1 interacts with the T. gondii COG complex. These proteins include both conserved trafficking factors and parasite-specific proteins. Using a conditional knockdown approach, we assess the effect of each of these eleven proteins on parasite fitness. Together, this work reveals a diverse set of novel T. gondii Golgi-associated proteins that play distinct roles in the secretory pathway. As several of these proteins are absent outside of the Apicomplexa, they represent potential targets for the development of novel therapeutics against these parasites. Importance Apicomplexan parasites such as Toxoplasma gondii infect a large percentage of the world's population and cause substantial human disease. These widespread pathogens use specialized secretory organelles to infect their host cells, modulate host cell functions, and cause disease. While the functions of the secretory organelles are now better understood, the Golgi apparatus of the parasite remains largely unexplored, particularly regarding parasite-specific innovations that may help direct traffic intracellularly. In this work, we characterize ULP1, a protein that is unique to parasites but shares structural similarity to the eukaryotic trafficking factor p115/Uso1. We show that ULP1 plays an important role in parasite replication and demonstrate that it interacts with the conserved oligomeric Golgi (COG) complex. We then use ULP1 proximity labelling to identify eleven additional Golgi-associated proteins which we functionally analyze via conditional knockdown. This work expands our knowledge of the Toxoplasma Golgi apparatus and identifies potential targets for therapeutic intervention.
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Wallace NS, Gadbery JE, Cohen CI, Kendall AK, Jackson LP. Tepsin binds LC3B to promote ATG9A trafficking and delivery. Mol Biol Cell 2024; 35:ar56. [PMID: 38381558 PMCID: PMC11064669 DOI: 10.1091/mbc.e23-09-0359-t] [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: 09/20/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024] Open
Abstract
Tepsin is an established accessory protein found in Adaptor Protein 4 (AP-4) coated vesicles, but the biological role of tepsin remains unknown. AP-4 vesicles originate at the trans-Golgi network (TGN) and target the delivery of ATG9A, a scramblase required for autophagosome biogenesis, to the cell periphery. Using in silico methods, we identified a putative LC3-Interacting Region (LIR) motif in tepsin. Biochemical experiments using purified recombinant proteins indicate tepsin directly binds LC3B preferentially over other members of the mammalian ATG8 family. Calorimetry and structural modeling data indicate this interaction occurs with micromolar affinity using the established LC3B LIR docking site. Loss of tepsin in cultured cells dysregulates ATG9A export from the TGN as well as ATG9A distribution at the cell periphery. Tepsin depletion in a mRFP-GFP-LC3B HeLa reporter cell line using siRNA knockdown increases autophagosome volume and number, but does not appear to affect flux through the autophagic pathway. Reintroduction of wild-type tepsin partially rescues ATG9A cargo trafficking defects. In contrast, reintroducing tepsin with a mutated LIR motif or missing N-terminus drives diffuse ATG9A subcellular distribution. Together, these data suggest roles for tepsin in cargo export from the TGN; ensuring delivery of ATG9A-positive vesicles; and in overall maintenance of autophagosome structure.
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Affiliation(s)
- Natalie S. Wallace
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - John E. Gadbery
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Cameron I. Cohen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
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Grisez T, Ravi NP, Froeyen M, Schols D, Van Meervelt L, De Jonghe S, Dehaen W. Synthesis of a 3,7-Disubstituted Isothiazolo[4,3- b]pyridine as a Potential Inhibitor of Cyclin G-Associated Kinase. Molecules 2024; 29:954. [PMID: 38474466 DOI: 10.3390/molecules29050954] [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: 01/15/2024] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Disubstituted isothiazolo[4,3-b]pyridines are known inhibitors of cyclin G-associated kinase. Since 3-substituted-7-aryl-isothiazolo[4,3-b]pyridines remain elusive, a strategy was established to prepare this chemotype, starting from 2,4-dichloro-3-nitropyridine. Selective C-4 arylation using ligand-free Suzuki-Miyaura coupling and palladium-catalyzed aminocarbonylation functioned as key steps in the synthesis. The 3-N-morpholinyl-7-(3,4-dimethoxyphenyl)-isothiazolo[4,3-b]pyridine was completely devoid of GAK affinity, in contrast to its 3,5- and 3,6-disubstituted congeners. Molecular modeling was applied to rationalize its inactivity as a GAK ligand.
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Affiliation(s)
- Tom Grisez
- Department of Chemistry, Sustainable Chemistry for Metals and Molecules, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Nitha Panikkassery Ravi
- Department of Chemistry, Sustainable Chemistry for Metals and Molecules, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Mathy Froeyen
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, P.O. Box 1041, B-3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, P.O. Box 1043, B-3000 Leuven, Belgium
| | - Luc Van Meervelt
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, P.O. Box 1043, B-3000 Leuven, Belgium
| | - Wim Dehaen
- Department of Chemistry, Sustainable Chemistry for Metals and Molecules, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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Yuan YH, Mao ND, Duan JL, Zhang H, Garrido C, Lirussi F, Gao Y, Xie T, Ye XY. Recent progress in discovery of novel AAK1 inhibitors: from pain therapy to potential anti-viral agents. J Enzyme Inhib Med Chem 2023; 38:2279906. [PMID: 37955299 PMCID: PMC10653628 DOI: 10.1080/14756366.2023.2279906] [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: 07/17/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023] Open
Abstract
Adaptor associated kinase 1 (AAK1), a member of the Ark1/Prk1 family of Ser/Thr kinases, is a specific key kinase regulating Thr156 phosphorylation at the μ2 subunit of the adapter complex-2 (AP-2) protein. Due to their important biological functions, AAK1 systems have been validated in clinics for neuropathic pain therapy, and are being explored as potential therapeutic targets for diseases caused by various viruses such as Hepatitis C (HCV), Dengue, Ebola, and COVID-19 viruses and for amyotrophic lateral sclerosis (ALS). Centreing on the advances of drug discovery programs in this field up to 2023, AAK1 inhibitors are discussed from the aspects of the structure-based rational molecular design, pharmacology, toxicology and synthetic routes for the compounds of interest in this review. The aim is to provide the medicinal chemistry community with up-to-date information and to accelerate the drug discovery programs in the field of AAK1 small molecule inhibitors.
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Affiliation(s)
- Ying-Hui Yuan
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Nian-Dong Mao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Ji-Long Duan
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Hang Zhang
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
- School of Basic Medical Science, Hangzhou Normal University, Hangzhou, China
| | - Carmen Garrido
- INSERM UMR 1231, Labex LipSTIC, University of Bourgogne, Dijon, France
- Cancer Center George François Leclerc, Dijon, France
- University of Bourgogne Franche-Comté, Besançon, France
| | - Frédéric Lirussi
- INSERM UMR 1231, Labex LipSTIC, University of Bourgogne, Dijon, France
- University of Franche-Comté & University Hospital of Besançon, Besancon, France
| | - Yuan Gao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xiang-Yang Ye
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
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Vuic B, Milos T, Tudor L, Nikolac Perkovic M, Konjevod M, Nedic Erjavec G, Farkas V, Uzun S, Mimica N, Svob Strac D. Pharmacogenomics of Dementia: Personalizing the Treatment of Cognitive and Neuropsychiatric Symptoms. Genes (Basel) 2023; 14:2048. [PMID: 38002991 PMCID: PMC10671071 DOI: 10.3390/genes14112048] [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: 10/10/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Dementia is a syndrome of global and progressive deterioration of cognitive skills, especially memory, learning, abstract thinking, and orientation, usually affecting the elderly. The most common forms are Alzheimer's disease, vascular dementia, and other (frontotemporal, Lewy body disease) dementias. The etiology of these multifactorial disorders involves complex interactions of various environmental and (epi)genetic factors and requires multiple forms of pharmacological intervention, including anti-dementia drugs for cognitive impairment, antidepressants, antipsychotics, anxiolytics and sedatives for behavioral and psychological symptoms of dementia, and other drugs for comorbid disorders. The pharmacotherapy of dementia patients has been characterized by a significant interindividual variability in drug response and the development of adverse drug effects. The therapeutic response to currently available drugs is partially effective in only some individuals, with side effects, drug interactions, intolerance, and non-compliance occurring in the majority of dementia patients. Therefore, understanding the genetic basis of a patient's response to pharmacotherapy might help clinicians select the most effective treatment for dementia while minimizing the likelihood of adverse reactions and drug interactions. Recent advances in pharmacogenomics may contribute to the individualization and optimization of dementia pharmacotherapy by increasing its efficacy and safety via a prediction of clinical outcomes. Thus, it can significantly improve the quality of life in dementia patients.
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Affiliation(s)
- Barbara Vuic
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Tina Milos
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Lucija Tudor
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Matea Nikolac Perkovic
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Marcela Konjevod
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Gordana Nedic Erjavec
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Vladimir Farkas
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Suzana Uzun
- Department for Biological Psychiatry and Psychogeriatry, University Hospital Vrapce, 10000 Zagreb, Croatia; (S.U.); (N.M.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Ninoslav Mimica
- Department for Biological Psychiatry and Psychogeriatry, University Hospital Vrapce, 10000 Zagreb, Croatia; (S.U.); (N.M.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Dubravka Svob Strac
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
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Siao W, Wang P, Zhao X, Vu LD, De Smet I, Russinova E. Phosphorylation of ADAPTOR PROTEIN-2 μ-adaptin by ADAPTOR-ASSOCIATED KINASE1 regulates the tropic growth of Arabidopsis roots. THE PLANT CELL 2023; 35:3504-3521. [PMID: 37440281 PMCID: PMC10473204 DOI: 10.1093/plcell/koad141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/21/2023] [Indexed: 07/14/2023]
Abstract
ADAPTOR-ASSOCIATED PROTEIN KINASE1 (AAK1) is a known regulator of clathrin-mediated endocytosis in mammals. Human AAK1 phosphorylates the μ2 subunit of the ADAPTOR PROTEIN-2 (AP-2) complex (AP2M) and plays important roles in cell differentiation and development. Previous interactome studies discovered the association of AAK1 with AP-2 in Arabidopsis (Arabidopsis thaliana), but its function was unclear. Here, genetic analysis revealed that the Arabidopsis aak1 and ap2m mutants both displayed altered root tropic growth, including impaired touch- and gravity-sensing responses. In Arabidopsis, AAK1-phosphorylated AP2M on Thr-163, and expression of the phospho-null version of AP2M in the ap2m mutant led to an aak1-like phenotype, whereas the phospho-mimic forms of AP2M rescued the aak1 mutant. In addition, we found that the AAK1-dependent phosphorylation state of AP2M modulates the frequency distribution of endocytosis. Our data indicate that the phosphorylation of AP2M on Thr-163 by AAK1 fine-tunes endocytosis in the Arabidopsis root to control its tropic growth.
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Affiliation(s)
- Wei Siao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Peng Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Xiuyang Zhao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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Wallace NS, Gadbery JE, Cohen CI, Kendall AK, Jackson LP. Tepsin binds LC3B to promote ATG9A export and delivery at the cell periphery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549521. [PMID: 37502979 PMCID: PMC10370099 DOI: 10.1101/2023.07.18.549521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tepsin is an established accessory protein found in Adaptor Protein 4 (AP-4) coated vesicles, but the biological role of tepsin remains unknown. AP-4 vesicles originate at the trans -Golgi network (TGN) and target the delivery of ATG9A, a scramblase required for autophagosome biogenesis, to the cell periphery. Using in silico methods, we identified a putative L C3-Interacting R egion (LIR) motif in tepsin. Biochemical experiments using purified recombinant proteins indicate tepsin directly binds LC3B, but not other members, of the mammalian ATG8 family. Calorimetry and structural modeling data indicate this interaction occurs with micromolar affinity using the established LC3B LIR docking site. Loss of tepsin in cultured cells dysregulates ATG9A export from the TGN as well as ATG9A distribution at the cell periphery. Tepsin depletion in a mRFP-GFP-LC3B HeLa reporter cell line using siRNA knockdown increases autophagosome volume and number, but does not appear to affect flux through the autophagic pathway. Re-introduction of wild-type tepsin partially rescues ATG9A cargo trafficking defects. In contrast, re-introducing tepsin with a mutated LIR motif or missing N-terminus does not fully rescue altered ATG9A subcellular distribution. Together, these data suggest roles for tepsin in cargo export from the TGN; delivery of ATG9A-positive vesicles at the cell periphery; and in overall maintenance of autophagosome structure.
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Huang C, Ji C, Wang J. Current thoughts on cellular functions of numb-associated kinases. Mol Biol Rep 2023; 50:4645-4652. [PMID: 37014568 PMCID: PMC10072014 DOI: 10.1007/s11033-023-08372-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/02/2023] [Indexed: 04/05/2023]
Abstract
Members of the Numb-associated kinase family of serine/threonine kinases play an essential role in many cellular processes, such as endocytosis, autophagy, dendrite morphogenesis, osteoblast differentiation, and the regulation of the Notch pathway. Numb-associated kinases have been relevant to diverse diseases, including neuropathic pain, Parkinson's disease, and prostate cancer. Therefore, they are considered potential therapeutic targets. In addition, it is reported that Numb-associated kinases have been involved in the life cycle of multiple viruses such as hepatitis C virus (HCV), Ebola virus (EBOV), and dengue virus (DENV). Recently, Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to threaten global health. Studies show that Numb-associated kinases are implicated in the infection of SARS-CoV-2 which can be suppressed by Numb-associated kinases inhibitors. Thus, Numb-associated kinases are proposed as potential host targets for broad-spectrum antiviral strategies. We will focus on the recent advances in Numb-associated kinases-related cellular functions and their potential as host targets for viral infections in this review. Questions that remained unknown on the cellular functions of Numb-associated kinases will also be discussed.
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Affiliation(s)
- Chenxi Huang
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, 100124, Beijing, China
| | - Cuicui Ji
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, 100124, Beijing, China.
| | - Juan Wang
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, 100124, Beijing, China.
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Lin HH, Kuo MW, Fan TC, Yu AL, Yu J. YULINK regulates vascular formation in zebrafish and HUVECs. Biol Res 2023; 56:7. [PMID: 36843032 PMCID: PMC9969694 DOI: 10.1186/s40659-023-00415-8] [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: 08/24/2022] [Accepted: 01/18/2023] [Indexed: 02/28/2023] Open
Abstract
BACKGROUND The distinct arterial and venous cell fates are dictated by a combination of various genetic factors which form diverse types of blood vessels such as arteries, veins, and capillaries. We report here that YULINK protein is involved in vasculogenesis, especially venous formation. METHODS In this manuscript, we employed gene knockdown, yeast two-hybrid, FLIM-FRET, immunoprecipitation, and various imaging technologies to investigate the role of YULINK gene in zebrafish and human umbilical vein endothelial cells (HUVECs). RESULTS Knockdown of YULINK during the arterial-venous developmental stage of zebrafish embryos led to the defective venous formation and abnormal vascular plexus formation. Knockdown of YULINK in HUVECs impaired their ability to undergo cell migration and differentiation into a capillary-like tube formation. In addition, the phosphorylated EPHB4 was decreased in YULINK knockdown HUVECs. Yeast two-hybrid, FLIM-FRET, immunoprecipitation, as well as imaging technologies showed that YULINK colocalized with endosome related proteins (EPS15, RAB33B or TICAM2) and markers (Clathrin and RHOB). VEGF-induced VEGFR2 internalization was also compromised in YULINK knockdown HUVECs, demonstrating to the involvement of YULINK. CONCLUSION This study suggests that YULINK regulates vasculogenesis, possibly through endocytosis in zebrafish and HUVECs.
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Affiliation(s)
- Hsin-Hung Lin
- grid.28665.3f0000 0001 2287 1366Chemical Biology and Molecular Biophysics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan ,grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Ming-Wei Kuo
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Tan-Chi Fan
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Alice L. Yu
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California, San Diego, CA USA
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333, Taoyuan, Taiwan. .,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
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11
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Zhang L, Liang X, Takáč T, Komis G, Li X, Zhang Y, Ovečka M, Chen Y, Šamaj J. Spatial proteomics of vesicular trafficking: coupling mass spectrometry and imaging approaches in membrane biology. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:250-269. [PMID: 36204821 PMCID: PMC9884029 DOI: 10.1111/pbi.13929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/14/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
In plants, membrane compartmentalization requires vesicle trafficking for communication among distinct organelles. Membrane proteins involved in vesicle trafficking are highly dynamic and can respond rapidly to changes in the environment and to cellular signals. Capturing their localization and dynamics is thus essential for understanding the mechanisms underlying vesicular trafficking pathways. Quantitative mass spectrometry and imaging approaches allow a system-wide dissection of the vesicular proteome, the characterization of ligand-receptor pairs and the determination of secretory, endocytic, recycling and vacuolar trafficking pathways. In this review, we highlight major proteomics and imaging methods employed to determine the location, distribution and abundance of proteins within given trafficking routes. We focus in particular on methodologies for the elucidation of vesicle protein dynamics and interactions and their connections to downstream signalling outputs. Finally, we assess their biological applications in exploring different cellular and subcellular processes.
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Affiliation(s)
- Liang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
- College of Life ScienceHenan Normal UniversityXinxiangChina
| | - Xinlin Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Tomáš Takáč
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - George Komis
- Department of Cell Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - Xiaojuan Li
- College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuan Zhang
- College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Miroslav Ovečka
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
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12
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Wang P, Siao W, Zhao X, Arora D, Wang R, Eeckhout D, Van Leene J, Kumar R, Houbaert A, De Winne N, Mylle E, Vandorpe M, Korver RA, Testerink C, Gevaert K, Vanneste S, De Jaeger G, Van Damme D, Russinova E. Adaptor protein complex interaction map in Arabidopsis identifies P34 as a common stability regulator. NATURE PLANTS 2023; 9:355-371. [PMID: 36635451 PMCID: PMC7615410 DOI: 10.1038/s41477-022-01328-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Adaptor protein (AP) complexes are evolutionarily conserved vesicle transport regulators that recruit coat proteins, membrane cargoes and coated vesicle accessory proteins. As in plants endocytic and post-Golgi trafficking intersect at the trans-Golgi network, unique mechanisms for sorting cargoes of overlapping vesicular routes are anticipated. The plant AP complexes are part of the sorting machinery, but despite some functional information, their cargoes, accessory proteins and regulation remain largely unknown. Here, by means of various proteomics approaches, we generated the overall interactome of the five AP and the TPLATE complexes in Arabidopsis thaliana. The interactome converged on a number of hub proteins, including the thus far unknown adaptin binding-like protein, designated P34. P34 interacted with the clathrin-associated AP complexes, controlled their stability and, subsequently, influenced clathrin-mediated endocytosis and various post-Golgi trafficking routes. Altogether, the AP interactome network offers substantial resources for further discoveries of unknown endomembrane trafficking regulators in plant cells.
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Affiliation(s)
- Peng Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Wei Siao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Xiuyang Zhao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Deepanksha Arora
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ren Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Rahul Kumar
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Anaxi Houbaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Michael Vandorpe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ruud A Korver
- Plant Physiology and Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Christa Testerink
- Plant Physiology and Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Laboratory of Plant Physiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
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13
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Rahmani S, Ahmed H, Ibazebo O, Fussner-Dupas E, Wakarchuk WW, Antonescu CN. O-GlcNAc transferase modulates the cellular endocytosis machinery by controlling the formation of clathrin-coated pits. J Biol Chem 2023; 299:102963. [PMID: 36731797 PMCID: PMC9999237 DOI: 10.1016/j.jbc.2023.102963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 02/01/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) controls the internalization and function of a wide range of cell surface proteins. CME occurs by the assembly of clathrin and many other proteins on the inner leaflet of the plasma membrane into clathrin-coated pits (CCPs). These structures recruit specific cargo destined for internalization, generate membrane curvature, and in many cases undergo scission from the plasma membrane to yield intracellular vesicles. The diversity of functions of cell surface proteins controlled via internalization by CME may suggest that regulation of CCP formation could be effective to allow cellular adaptation under different contexts. Of interest is how cues derived from cellular metabolism may regulate CME, given the reciprocal role of CME in controlling cellular metabolism. The modification of proteins with O-linked β-GlcNAc (O-GlcNAc) is sensitive to nutrient availability and may allow cellular adaptation to different metabolic conditions. Here, we examined how the modification of proteins with O-GlcNAc may control CCP formation and thus CME. We used perturbation of key enzymes responsible for protein O-GlcNAc modification, as well as specific mutants of the endocytic regulator AAK1 predicted to be impaired for O-GlcNAc modification. We identify that CCP initiation and the assembly of clathrin and other proteins within CCPs are controlled by O-GlcNAc protein modification. This reveals a new dimension of regulation of CME and highlights the important reciprocal regulation of cellular metabolism and endocytosis.
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Affiliation(s)
- Sadia Rahmani
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada; Graduate Program in Molecular Science, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Hafsa Ahmed
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Osemudiamen Ibazebo
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Eden Fussner-Dupas
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada; Graduate Program in Molecular Science, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
| | - Costin N Antonescu
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada; Graduate Program in Molecular Science, Toronto Metropolitan University, Toronto, Ontario, Canada.
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14
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Pembridge OG, Wallace NS, Clements TP, Jackson LP. AP-4 loss in CRISPR-edited zebrafish affects early embryo development. Adv Biol Regul 2023; 87:100945. [PMID: 36642642 PMCID: PMC9992121 DOI: 10.1016/j.jbior.2022.100945] [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: 11/11/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Mutations in the heterotetrametric adaptor protein 4 (AP-4; ε/β4/μ4/σ4 subunits) membrane trafficking coat complex lead to complex neurological disorders characterized by spastic paraplegia, microcephaly, and intellectual disabilities. Understanding molecular mechanisms underlying these disorders continues to emerge with recent identification of an essential autophagy protein, ATG9A, as an AP-4 cargo. Significant progress has been made uncovering AP-4 function in cell culture and patient-derived cell lines, and ATG9A trafficking by AP-4 is considered a potential target for gene therapy approaches. In contrast, understanding how AP-4 trafficking affects development and function at the organismal level has long been hindered by loss of conserved AP-4 genes in key model systems (S. cerevisiae, C. elegans, D. melanogaster). However, zebrafish (Danio rerio) have retained AP-4 and can serve as an important model system for studying both the nervous system and overall development. We undertook gene editing in zebrafish using a CRISPR-ExoCas9 knockout system to determine how loss of single AP-4, or its accessory protein tepsin, genes affect embryo development 24 h post-fertilization (hpf). Single gene-edited embryos display abnormal head morphology and neural necrosis. We further conducted the first exploration of how AP-4 single gene knockouts in zebrafish embryos affect expression levels and patterns of two autophagy genes, atg9a and map1lc3b. This work suggests zebrafish may be further adapted and developed as a tool to uncover AP-4 function in membrane trafficking and autophagy in the context of a model organism.
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Affiliation(s)
- Olivia G Pembridge
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Natalie S Wallace
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Thomas P Clements
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
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15
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Buser DP, Spang A. Protein sorting from endosomes to the TGN. Front Cell Dev Biol 2023; 11:1140605. [PMID: 36895788 PMCID: PMC9988951 DOI: 10.3389/fcell.2023.1140605] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/09/2023] [Indexed: 02/23/2023] Open
Abstract
Retrograde transport from endosomes to the trans-Golgi network is essential for recycling of protein and lipid cargoes to counterbalance anterograde membrane traffic. Protein cargo subjected to retrograde traffic include lysosomal acid-hydrolase receptors, SNARE proteins, processing enzymes, nutrient transporters, a variety of other transmembrane proteins, and some extracellular non-host proteins such as viral, plant, and bacterial toxins. Efficient delivery of these protein cargo molecules depends on sorting machineries selectively recognizing and concentrating them for their directed retrograde transport from endosomal compartments. In this review, we outline the different retrograde transport pathways governed by various sorting machineries involved in endosome-to-TGN transport. In addition, we discuss how this transport route can be analyzed experimentally.
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Affiliation(s)
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland
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16
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Mattera R, De Pace R, Bonifacino JS. The adaptor protein chaperone AAGAB stabilizes AP-4 complex subunits. Mol Biol Cell 2022; 33:ar109. [PMID: 35976721 DOI: 10.1091/mbc.e22-05-0177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Adaptor protein 4 (AP-4) is a heterotetrameric complex composed of ε, β4, μ4 and σ4 subunits that mediates export of a subset of transmembrane cargos, including autophagy protein 9A (ATG9A), from the trans-Golgi network (TGN). AP-4 has received particular attention in recent years because mutations in any of its subunits cause a complicated form of hereditary spastic paraplegia (HSP or SPG) referred to as "AP-4-deficiency syndrome." The identification of proteins that interact with AP-4 has shed light on the mechanisms of AP-4-dependent cargo sorting and distribution within the cell. However, the mechanisms by which the AP-4 complex itself is assembled have remained unknown. Herein, we report that the alpha- and gamma-adaptin-binding protein (AAGAB, also known as p34) binds to and stabilizes the AP-4 ε-and σ4 subunits, thus promoting complex assembly. The importance of this binding is underscored by the observation that AAGAB-knockout cells exhibit reduced levels of AP-4 subunits and accumulation of ATG9A at the TGN like those in cells, mice, or patients with mutations in AP-4-subunit genes. These findings demonstrate that AP-4 assembly is not spontaneous but AAGAB-assisted, thus contributing to the understanding of an adaptor protein complex that is critically involved in development of the central nervous system.
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Affiliation(s)
- Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Raffaella De Pace
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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17
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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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18
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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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19
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Gorelova V. A roadmap of plant clathrin-mediated vesicle trafficking. THE PLANT CELL 2022; 34:2106-2107. [PMID: 35348757 PMCID: PMC9134048 DOI: 10.1093/plcell/koac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
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20
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Zaccai NR, Kadlecova Z, Dickson VK, Korobchevskaya K, Kamenicky J, Kovtun O, Umasankar PK, Wrobel AG, Kaufman JGG, Gray SR, Qu K, Evans PR, Fritzsche M, Sroubek F, Höning S, Briggs JAG, Kelly BT, Owen DJ, Traub LM. FCHO controls AP2's initiating role in endocytosis through a PtdIns(4,5)P 2-dependent switch. SCIENCE ADVANCES 2022; 8:eabn2018. [PMID: 35486718 PMCID: PMC9054013 DOI: 10.1126/sciadv.abn2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Clathrin-mediated endocytosis (CME) is the main mechanism by which mammalian cells control their cell surface proteome. Proper operation of the pivotal CME cargo adaptor AP2 requires membrane-localized Fer/Cip4 homology domain-only proteins (FCHO). Here, live-cell enhanced total internal reflection fluorescence-structured illumination microscopy shows that FCHO marks sites of clathrin-coated pit (CCP) initiation, which mature into uniform-sized CCPs comprising a central patch of AP2 and clathrin corralled by an FCHO/Epidermal growth factor potential receptor substrate number 15 (Eps15) ring. We dissect the network of interactions between the FCHO interdomain linker and AP2, which concentrates, orients, tethers, and partially destabilizes closed AP2 at the plasma membrane. AP2's subsequent membrane deposition drives its opening, which triggers FCHO displacement through steric competition with phosphatidylinositol 4,5-bisphosphate, clathrin, cargo, and CME accessory factors. FCHO can now relocate toward a CCP's outer edge to engage and activate further AP2s to drive CCP growth/maturation.
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Affiliation(s)
- Nathan R. Zaccai
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Zuzana Kadlecova
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | | | - Kseniya Korobchevskaya
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, UK
| | - Jan Kamenicky
- Czech Academy of Sciences, Institute of Information Theory and Automation, Pod Vodarenskou vezi 4, 182 08 Prague 8, Czech Republic
| | - Oleksiy Kovtun
- MRC LMB Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Perunthottathu K. Umasankar
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Antoni G. Wrobel
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | | | - Sally R. Gray
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Kun Qu
- MRC LMB Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | | | - Marco Fritzsche
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, UK
- Rosalind Franklin Institute, Harwell Campus, Didcot, UK
| | - Filip Sroubek
- Czech Academy of Sciences, Institute of Information Theory and Automation, Pod Vodarenskou vezi 4, 182 08 Prague 8, Czech Republic
| | - Stefan Höning
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Joseph-Stelzmann-Straße 52, 50931 Cologne, Germany
| | - John A. G. Briggs
- MRC LMB Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Bernard T. Kelly
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - David J. Owen
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Linton M. Traub
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, Pittsburgh, PA, USA
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21
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Duan D, Hanson M, Holland DO, Johnson ME. Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis. Sci Rep 2022; 12:5413. [PMID: 35354856 PMCID: PMC8967901 DOI: 10.1038/s41598-022-09259-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/21/2022] [Indexed: 11/25/2022] Open
Abstract
Proteins that drive processes like clathrin-mediated endocytosis (CME) are expressed at copy numbers within a cell and across cell types varying from hundreds (e.g. auxilin) to millions (e.g. clathrin). These variations contain important information about function, but without integration with the interaction network, they cannot capture how supply and demand for each protein depends on binding to shared and distinct partners. Here we construct the interface-resolved network of 82 proteins involved in CME and establish a metric, a stoichiometric balance ratio (SBR), that quantifies whether each protein in the network has an abundance that is sub- or super-stoichiometric dependent on the global competition for binding. We find that highly abundant proteins (like clathrin) are super-stoichiometric, but that not all super-stoichiometric proteins are highly abundant, across three cell populations (HeLa, fibroblast, and neuronal synaptosomes). Most strikingly, within all cells there is significant competition to bind shared sites on clathrin and the central AP-2 adaptor by other adaptor proteins, resulting in most being in excess supply. Our network and systematic analysis, including response to perturbations of network components, show how competition for shared binding sites results in functionally similar proteins having widely varying stoichiometries, due to variations in both abundance and their unique network of binding partners.
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Affiliation(s)
- Daisy Duan
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Meretta Hanson
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | | | - Margaret E Johnson
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA.
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22
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Davies AK, Alecu JE, Ziegler M, Vasilopoulou CG, Merciai F, Jumo H, Afshar-Saber W, Sahin M, Ebrahimi-Fakhari D, Borner GHH. AP-4-mediated axonal transport controls endocannabinoid production in neurons. Nat Commun 2022; 13:1058. [PMID: 35217685 PMCID: PMC8881493 DOI: 10.1038/s41467-022-28609-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 01/08/2022] [Indexed: 01/20/2023] Open
Abstract
The adaptor protein complex AP-4 mediates anterograde axonal transport and is essential for axon health. AP-4-deficient patients suffer from a severe neurodevelopmental and neurodegenerative disorder. Here we identify DAGLB (diacylglycerol lipase-beta), a key enzyme for generation of the endocannabinoid 2-AG (2-arachidonoylglycerol), as a cargo of AP-4 vesicles. During normal development, DAGLB is targeted to the axon, where 2-AG signalling drives axonal growth. We show that DAGLB accumulates at the trans-Golgi network of AP-4-deficient cells, that axonal DAGLB levels are reduced in neurons from a patient with AP-4 deficiency, and that 2-AG levels are reduced in the brains of AP-4 knockout mice. Importantly, we demonstrate that neurite growth defects of AP-4-deficient neurons are rescued by inhibition of MGLL (monoacylglycerol lipase), the enzyme responsible for 2-AG hydrolysis. Our study supports a new model for AP-4 deficiency syndrome in which axon growth defects arise through spatial dysregulation of endocannabinoid signalling. Davies et al. identify a putative mechanism underlying the childhood neurological disorder AP-4 deficiency syndrome. In the absence of AP-4, an enzyme that makes 2-AG is not transported to the axon, leading to axonal growth defects, which can be rescued by inhibition of 2-AG breakdown.
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Affiliation(s)
- Alexandra K Davies
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.
| | - Julian E Alecu
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marvin Ziegler
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Department of Functional Neuroanatomy, Institute of Anatomy and Cell Biology, Heidelberg University, INF 307, Heidelberg, 69120, Germany
| | - Catherine G Vasilopoulou
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Fabrizio Merciai
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.,Department of Pharmacy and PhD Program in Drug Discovery and Development, University of Salerno, 84084, Fisciano, SA, Italy
| | - Hellen Jumo
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Wardiya Afshar-Saber
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mustafa Sahin
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Darius Ebrahimi-Fakhari
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.
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23
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Shin J, Nile A, Oh JW. Role of adaptin protein complexes in intracellular trafficking and their impact on diseases. Bioengineered 2021; 12:8259-8278. [PMID: 34565296 PMCID: PMC8806629 DOI: 10.1080/21655979.2021.1982846] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023] Open
Abstract
Adaptin proteins (APs) play a crucial role in intracellular cell trafficking. The 'classical' role of APs is carried out by AP1‒3, which bind to clathrin, cargo, and accessory proteins. Accordingly, AP1-3 are crucial for both vesicle formation and sorting. All APs consist of four subunits that are indispensable for their functions. In fact, based on studies using cells, model organism knockdown/knock-out, and human variants, each subunit plays crucial roles and contributes to the specificity of each AP. These studies also revealed that the sorting and intracellular trafficking function of AP can exert varying effects on pathology by controlling features such as cell development, signal transduction related to the apoptosis and proliferation pathways in cancer cells, organelle integrity, receptor presentation, and viral infection. Although the roles and functions of AP1‒3 are relatively well studied, the functions of the less abundant and more recently identified APs, AP4 and AP5, are still to be investigated. Further studies on these APs may enable a better understanding and targeting of specific diseases.APs known or suggested locations and functions.
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Affiliation(s)
- Juhyun Shin
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
| | - Arti Nile
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
| | - Jae-Wook Oh
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
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24
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Willy NM, Ferguson JP, Akatay A, Huber S, Djakbarova U, Silahli S, Cakez C, Hasan F, Chang HC, Travesset A, Li S, Zandi R, Li D, Betzig E, Cocucci E, Kural C. De novo endocytic clathrin coats develop curvature at early stages of their formation. Dev Cell 2021; 56:3146-3159.e5. [PMID: 34774130 DOI: 10.1016/j.devcel.2021.10.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/14/2021] [Accepted: 10/22/2021] [Indexed: 01/09/2023]
Abstract
Sculpting a flat patch of membrane into an endocytic vesicle requires curvature generation on the cell surface, which is the primary function of the endocytosis machinery. Using super-resolved live cell fluorescence imaging, we demonstrate that curvature generation by individual clathrin-coated pits can be detected in real time within cultured cells and tissues of developing organisms. Our analyses demonstrate that the footprint of clathrin coats increases monotonically during the formation of pits at different levels of plasma membrane tension. These findings are only compatible with models that predict curvature generation at the early stages of endocytic clathrin pit formation. We also found that CALM adaptors associated with clathrin plaques form clusters, whereas AP2 distribution is more homogenous. Considering the curvature sensing and driving roles of CALM, we propose that CALM clusters may increase the strain on clathrin lattices locally, eventually giving rise to rupture and subsequent pit completion at the edges of plaques.
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Affiliation(s)
- Nathan M Willy
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Joshua P Ferguson
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Ata Akatay
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Scott Huber
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | | | - Salih Silahli
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Cemal Cakez
- Department of Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - Farah Hasan
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Henry C Chang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Alex Travesset
- Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA; Ames Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Siyu Li
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA
| | - Dong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Eric Betzig
- Departments of Physics and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Emanuele Cocucci
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
| | - Comert Kural
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA; Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.
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25
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Involvement of adaptor proteins in clathrin-mediated endocytosis of virus entry. Microb Pathog 2021; 161:105278. [PMID: 34740810 DOI: 10.1016/j.micpath.2021.105278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022]
Abstract
The first step in the initiation of effective viral infection is breaking through the cytomembrane to enter the cell. Clathrin-mediated endocytosis is a key vesicular trafficking process in which a variety of cargo molecules are transported from the outside to the inside of the cell. This process is hijacked by numerous families of enveloped or non-enveloped viruses, which use it to enter host cells, followed by trafficking to their replicating sites. Various adaptor proteins that assist in cargo selection, coat assembly, and clathrin-coated bud maturation are important in this process. Research data documented on the involvement of adaptor proteins, such as AP-2, Eps-15, Epsin1, and AP180/CALM, in the invasion of viruses via the clathrin-mediated endocytosis have provided novel insights into understanding the viral life cycle and have led to the development of novel therapeutics. Here, we summarize the latest discoveries on the role of these adaptor proteins in clathrin-mediated endocytosis of virus entry and also discuss the future trends in this field.
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26
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Ramesh ST, Navyasree KV, Sah S, Ashok AB, Qathoon N, Mohanty S, Swain RK, Umasankar PK. BMP2K phosphorylates AP-2 and regulates clathrin-mediated endocytosis. Traffic 2021; 22:377-396. [PMID: 34480404 DOI: 10.1111/tra.12814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 01/29/2023]
Abstract
Phosphorylation of the central adaptor protein complex, AP-2 is pivotal for clathrin-mediated endocytosis (CME). Here, we uncover the role of an uncharacterized kinase (BMP-2 inducible kinase-BMP2K) in AP-2 phosphorylation. We demonstrate that BMP2K can phosphorylate AP-2 in vitro and in vivo. Functional impairment of BMP2K impedes AP-2 phosphorylation leading to defects in clathrin-coated pit (CCP) morphology and cargo internalization. BMP2K engages AP-2 via its extended C-terminus and this interaction is important for its CCP localization and function. Notably, endogenous BMP2K levels decline upon functional impairment of AP-2 indicating AP-2 dependent BMP2K stabilization in cells. Further, functional inactivation of BMP2K in zebrafish embryos yields gastrulation phenotypes which mirror AP-2 loss-of-function suggesting physiological relevance of BMP2K in vertebrates. Together, our findings propose involvement of a novel kinase in AP-2 phosphorylation and in the operation of CME.
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Affiliation(s)
- Shikha T Ramesh
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.,Centre for Doctoral Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Kolaparamba V Navyasree
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.,Centre for Doctoral Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sneha Sah
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Anjitha B Ashok
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Nishada Qathoon
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | | | | | - Perunthottathu K Umasankar
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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27
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An in vitro vesicle formation assay reveals cargo clients and factors that mediate vesicular trafficking. Proc Natl Acad Sci U S A 2021; 118:2101287118. [PMID: 34433667 PMCID: PMC8536394 DOI: 10.1073/pnas.2101287118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein sorting in the secretory pathway is a fundamentally important cellular process, but the clients of a specific cargo sorting machinery remains largely underinvestigated. Here, utilizing a vesicle formation assay to profile proteins associated with vesicles, we identified cytosolic proteins that are associated with vesicle membranes in a GTP-dependent manner or that interact with GTP-bound Sar1A. We found that two of them, FAM84B and PRRC1, regulate anterograde trafficking. Moreover, we revealed specific clients of two export adaptors, SURF4 and ERGIC53. These analyses demonstrate that our approach is powerful to identify factors that regulate vesicular trafficking and to uncover clients of specific cargo receptors, providing a robust method to reveal insights into the secretory pathway. The fidelity of protein transport in the secretory pathway relies on the accurate sorting of proteins to their correct destinations. To deepen our understanding of the underlying molecular mechanisms, it is important to develop a robust approach to systematically reveal cargo proteins that depend on specific sorting machinery to be enriched into transport vesicles. Here, we used an in vitro assay that reconstitutes packaging of human cargo proteins into vesicles to quantify cargo capture. Quantitative mass spectrometry (MS) analyses of the isolated vesicles revealed cytosolic proteins that are associated with vesicle membranes in a GTP-dependent manner. We found that two of them, FAM84B (also known as LRAT domain containing 2 or LRATD2) and PRRC1, contain proline-rich domains and regulate anterograde trafficking. Further analyses revealed that PRRC1 is recruited to endoplasmic reticulum (ER) exit sites, interacts with the inner COPII coat, and its absence increases membrane association of COPII. In addition, we uncovered cargo proteins that depend on GTP hydrolysis to be captured into vesicles. Comparing control cells with cells depleted of the cargo receptors, SURF4 or ERGIC53, we revealed specific clients of each of these two export adaptors. Our results indicate that the vesicle formation assay in combination with quantitative MS analysis is a robust and powerful tool to uncover novel factors that mediate vesicular trafficking and to uncover cargo clients of specific cellular factors.
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28
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CALM supports clathrin-coated vesicle completion upon membrane tension increase. Proc Natl Acad Sci U S A 2021; 118:2010438118. [PMID: 34155137 DOI: 10.1073/pnas.2010438118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The most represented components of clathrin-coated vesicles (CCVs) are clathrin triskelia and the adaptors clathrin assembly lymphoid myeloid leukemia protein (CALM) and the heterotetrameric complex AP2. Investigation of the dynamics of AP180-amino-terminal-homology (ANTH) recruitment during CCV formation has been hampered by CALM toxicity upon overexpression. We used knock-in gene editing to express a C-terminal-attached fluorescent version of CALM, while preserving its endogenous expression levels, and cutting-edge live-cell microscopy approaches to study CALM recruitment at forming CCVs. Our results demonstrate that CALM promotes vesicle completion upon membrane tension increase as a function of the amount of this adaptor present. Since the expression of adaptors, including CALM, differs among cells, our data support a model in which the efficiency of clathrin-mediated endocytosis is tissue specific and explain why CALM is essential during embryogenesis and red blood cell development.
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29
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Djakbarova U, Madraki Y, Chan ET, Kural C. Dynamic interplay between cell membrane tension and clathrin-mediated endocytosis. Biol Cell 2021; 113:344-373. [PMID: 33788963 DOI: 10.1111/boc.202000110] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022]
Abstract
Deformability of the plasma membrane, the outermost surface of metazoan cells, allows cells to be dynamic, mobile and flexible. Factors that affect this deformability, such as tension on the membrane, can regulate a myriad of cellular functions, including membrane resealing, cell motility, polarisation, shape maintenance, membrane area control and endocytic vesicle trafficking. This review focuses on mechanoregulation of clathrin-mediated endocytosis (CME). We first delineate the origins of cell membrane tension and the factors that yield to its spatial and temporal fluctuations within cells. We then review the recent literature demonstrating that tension on the membrane is a fast-acting and reversible regulator of CME. Finally, we discuss tension-based regulation of endocytic clathrin coat formation during physiological processes.
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Affiliation(s)
| | - Yasaman Madraki
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Emily T Chan
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA.,Molecular Biophysics Training Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Cömert Kural
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA.,Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
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30
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Clague MJ, Urbé S. Data mining for traffic information. Traffic 2021; 21:162-168. [PMID: 31596015 DOI: 10.1111/tra.12702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/23/2022]
Abstract
Modern cell biology is now rich with data acquired at the whole genome and proteome level. We can add value to this data through integration and application of specialist knowledge. To illustrate, we will focus on the SNARE and RAB proteins; key regulators of intracellular fusion specificity and organelle identity. We examine published mass spectrometry data to gain an estimate of protein copy number and organelle distribution in HeLa cells for each family member. We also survey recent global CRISPR/Cas9 screens for essential genes from these families. We highlight instances of co-essentiality with other genes across a large panel of cell lines that allows for the identification of functionally coherent clusters. Examples of such correlations include RAB10 with the SNARE protein Syntaxin4 (STX4) and RAB7/RAB21 with the WASH and the CCC (COMMD/CCDC22/CCDC93) complexes, both of which are linked to endosomal recycling pathways.
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Affiliation(s)
- Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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31
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Lee CT, Akamatsu M, Rangamani P. Value of models for membrane budding. Curr Opin Cell Biol 2021; 71:38-45. [PMID: 33706232 DOI: 10.1016/j.ceb.2021.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/16/2022]
Abstract
The budding of membranes and curvature generation is common to many forms of trafficking in cells. Clathrin-mediated endocytosis, as a prototypical example of trafficking, has been studied in great detail using a variety of experimental systems and methods. Recently, advances in experimental methods have led to great strides in insights on the molecular mechanisms and the spatiotemporal dynamics of the protein machinery associated with membrane curvature generation. These advances have been ably supported by computational models, which have given us insights into the underlying mechanical principles of clathrin-mediated endocytosis. On the other hand, targeted experimental perturbation of membranes has lagged behind that of proteins in cells. In this area, modeling is especially critical to interpret experimental measurements in a mechanistic context. Here, we discuss the contributions made by these models to our understanding of endocytosis and identify opportunities to strengthen the connections between models and experiments.
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Affiliation(s)
- Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego Jacobs School of Engineering, 9500 Gilman Drive #0411, La Jolla, CA, 92093, USA
| | - Matthew Akamatsu
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego Jacobs School of Engineering, 9500 Gilman Drive #0411, La Jolla, CA, 92093, USA.
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32
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Jia J, Yue X, Zhu L, Jing S, Wang Y, Gim B, Qian Y, Lee I. KDEL receptor is a cell surface receptor that cycles between the plasma membrane and the Golgi via clathrin-mediated transport carriers. Cell Mol Life Sci 2021; 78:1085-1100. [PMID: 32562023 PMCID: PMC11072833 DOI: 10.1007/s00018-020-03570-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022]
Abstract
KDEL receptor cycles between the ER and the Golgi to retrieve ER-resident chaperones that get leaked to the secretory pathway during protein export from the ER. Recent studies have shown that a fraction of KDEL receptor may reside in the plasma membrane and function as a putative cell surface receptor. However, the trafficking itinerary and mechanism of cell surface expressed KDEL receptor remains largely unknown. In this study, we used N-terminally Halo-tagged KDEL receptor to investigate its endocytosis from the plasma membrane and trafficking itinerary of the endocytosed receptor through the endolysosomal compartments. Our results indicate that surface-expressed KDEL receptor undergoes highly complex recycling pathways via the Golgi and peri-nuclear recycling endosomes that are positive for Rab11 and Rab14, respectively. Unexpectedly, KDEL receptor appears to preferentially utilize clathrin-mediated endocytic pathway as well as clathrin-dependent transport carriers for export from the trans-Golgi network. Taken together, we suggest that KDEL receptor may be a bona fide cell surface receptor with a complex, yet well-defined trafficking itinerary through the endolysosomal compartments.
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Affiliation(s)
- Jie Jia
- School of Life Science and Technology, ShanghaiTech University, Pudong, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xihua Yue
- School of Life Science and Technology, ShanghaiTech University, Pudong, Shanghai, China
| | - Lianhui Zhu
- School of Life Science and Technology, ShanghaiTech University, Pudong, Shanghai, China
| | - Shuaiyang Jing
- School of Life Science and Technology, ShanghaiTech University, Pudong, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yijing Wang
- School of Life Science and Technology, ShanghaiTech University, Pudong, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bopil Gim
- School of Physical Science and Technology, ShanghaiTech University, Pudong, Shanghai, China
| | - Yi Qian
- School of Life Science and Technology, ShanghaiTech University, Pudong, Shanghai, China.
| | - Intaek Lee
- School of Life Science and Technology, ShanghaiTech University, Pudong, Shanghai, China.
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33
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Tobys D, Kowalski LM, Cziudaj E, Müller S, Zentis P, Pach E, Zigrino P, Blaeske T, Höning S. Inhibition of clathrin-mediated endocytosis by knockdown of AP-2 leads to alterations in the plasma membrane proteome. Traffic 2020; 22:6-22. [PMID: 33225555 DOI: 10.1111/tra.12770] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 01/05/2023]
Abstract
In eukaryotic cells, clathrin-mediated endocytosis (CME) is a central pathway for the internalization of proteins from the cell surface, thereby contributing to the maintenance of the plasma membrane protein composition. A key component for the formation of endocytic clathrin-coated vesicles (CCVs) is AP-2, as it sequesters cargo membrane proteins, recruits a multitude of other endocytic factors and initiates clathrin polymerization. Here, we inhibited CME by depletion of AP-2 and explored the consequences for the plasma membrane proteome. Quantitative analysis revealed accumulation of major constituents of the endosomal-lysosomal system reflecting a block in retrieval by compensatory CME. The noticeable enrichment of integrins and blockage of their turnover resulted in severely impaired cell migration. Rare proteins such as the anti-cancer drug target CA9 and tumor markers (CD73, CD164, CD302) were significantly enriched. The AP-2 knockdown attenuated the global endocytic capacity, but clathrin-independent entry pathways were still operating, as indicated by persistent internalization of specific membrane-spanning and GPI-anchored receptors (PVR, IGF1R, CD55, TNAP). We hypothesize that blocking AP-2 function and thus inhibiting CME may be a novel approach to identify new druggable targets, or to increase their residence time at the plasma membrane, thereby increasing the probability for efficient therapeutic intervention.
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Affiliation(s)
- David Tobys
- Institute for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Lisa Maria Kowalski
- Institute for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Eva Cziudaj
- Institute for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Stefan Müller
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Peter Zentis
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
| | - Elke Pach
- Department of Dermatology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Paola Zigrino
- Department of Dermatology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Tobias Blaeske
- Department of Plant Physiology and Biochemistry, University of Constance, Constance, Germany
| | - Stefan Höning
- Institute for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
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The role of AP-4 in cargo export from the trans-Golgi network and hereditary spastic paraplegia. Biochem Soc Trans 2020; 48:1877-1888. [PMID: 33084855 DOI: 10.1042/bst20190664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 01/02/2023]
Abstract
Heterotetrameric adaptor protein (AP) complexes play key roles in protein sorting and transport vesicle formation in the endomembrane system of eukaryotic cells. One of these complexes, AP-4, was identified over 20 years ago but, up until recently, its function remained unclear. AP-4 associates with the trans-Golgi network (TGN) through interaction with small GTPases of the ARF family and recognizes transmembrane proteins (i.e. cargos) having specific sorting signals in their cytosolic domains. Recent studies identified accessory proteins (tepsin, RUSC2 and the FHF complex) that co-operate with AP-4, and cargos (amyloid precursor protein, ATG9A and SERINC3/5) that are exported from the TGN in an AP-4-dependent manner. Defective export of ATG9A from the TGN in AP-4-deficient cells was shown to reduce ATG9A delivery to pre-autophagosomal structures, impairing autophagosome formation and/or maturation. In addition, mutations in AP-4-subunit genes were found to cause neurological dysfunction in mice and a form of complicated hereditary spastic paraplegia referred to as 'AP-4-deficiency syndrome' in humans. These findings demonstrated that mammalian AP-4 is required for the development and function of the central nervous system, possibly through its role in the sorting of ATG9A for the maintenance of autophagic homeostasis. In this article, we review the properties and functions of AP-4, and discuss how they might explain the clinical features of AP-4 deficiency.
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He K, Song E, Upadhyayula S, Dang S, Gaudin R, Skillern W, Bu K, Capraro BR, Rapoport I, Kusters I, Ma M, Kirchhausen T. Dynamics of Auxilin 1 and GAK in clathrin-mediated traffic. J Cell Biol 2020; 219:133624. [PMID: 31962345 PMCID: PMC7054993 DOI: 10.1083/jcb.201908142] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/28/2019] [Accepted: 12/15/2019] [Indexed: 01/08/2023] Open
Abstract
Clathrin-coated vesicles lose their clathrin lattice within seconds of pinching off, through the action of the Hsc70 “uncoating ATPase.” The J- and PTEN-like domain–containing proteins, auxilin 1 (Aux1) and auxilin 2 (GAK), recruit Hsc70. The PTEN-like domain has no phosphatase activity, but it can recognize phosphatidylinositol phosphate head groups. Aux1 and GAK appear on coated vesicles in successive transient bursts, immediately after dynamin-mediated membrane scission has released the vesicle from the plasma membrane. These bursts contain a very small number of auxilins, and even four to six molecules are sufficient to mediate uncoating. In contrast, we could not detect auxilins in abortive pits or at any time during coated pit assembly. We previously showed that clathrin-coated vesicles have a dynamic phosphoinositide landscape, and we have proposed that lipid head group recognition might determine the timing of Aux1 and GAK appearance. The differential recruitment of Aux1 and GAK correlates with temporal variations in phosphoinositide composition, consistent with a lipid-switch timing mechanism.
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Affiliation(s)
- Kangmin He
- Department of Cell Biology, Harvard Medical School, Boston, MA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA.,Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Eli Song
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - Srigokul Upadhyayula
- Department of Cell Biology, Harvard Medical School, Boston, MA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA.,Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Song Dang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - Raphael Gaudin
- Department of Cell Biology, Harvard Medical School, Boston, MA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - Wesley Skillern
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - Kevin Bu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | | | - Iris Rapoport
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Ilja Kusters
- Department of Cell Biology, Harvard Medical School, Boston, MA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - Minghe Ma
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - Tom Kirchhausen
- Department of Cell Biology, Harvard Medical School, Boston, MA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA.,Department of Pediatrics, Harvard Medical School, Boston, MA
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36
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EPSIN1 and MTV1 define functionally overlapping but molecularly distinct trans-Golgi network subdomains in Arabidopsis. Proc Natl Acad Sci U S A 2020; 117:25880-25889. [PMID: 32989160 DOI: 10.1073/pnas.2004822117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The plant trans-Golgi network (TGN) is a central trafficking hub where secretory, vacuolar, recycling, and endocytic pathways merge. Among currently known molecular players involved in TGN transport, three different adaptor protein (AP) complexes promote vesicle generation at the TGN with different cargo specificity and destination. Yet, it remains unresolved how sorting into diverging vesicular routes is spatially organized. Here, we study the family of Arabidopsis thaliana Epsin-like proteins, which are accessory proteins to APs facilitating vesicle biogenesis. By comprehensive molecular, cellular, and genetic analysis of the EPSIN gene family, we identify EPSIN1 and MODIFIED TRANSPORT TO THE VACUOLE1 (MTV1) as its only TGN-associated members. Despite their large phylogenetic distance, they perform overlapping functions in vacuolar and secretory transport. By probing their relationship with AP complexes, we find that they define two molecularly independent pathways: While EPSIN1 associates with AP-1, MTV1 interacts with AP-4, whose function is required for MTV1 recruitment. Although both EPSIN1/AP-1 and MTV1/AP-4 pairs reside at the TGN, high-resolution microscopy reveals them as spatially separate entities. Our results strongly support the hypothesis of molecularly, functionally, and spatially distinct subdomains of the plant TGN and suggest that functional redundancy can be achieved through parallelization of molecularly distinct but functionally overlapping pathways.
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37
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Cendrowski J, Kaczmarek M, Mazur M, Kuzmicz-Kowalska K, Jastrzebski K, Brewinska-Olchowik M, Kominek A, Piwocka K, Miaczynska M. Splicing variation of BMP2K balances abundance of COPII assemblies and autophagic degradation in erythroid cells. eLife 2020; 9:e58504. [PMID: 32795391 PMCID: PMC7473771 DOI: 10.7554/elife.58504] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/13/2020] [Indexed: 12/26/2022] Open
Abstract
Intracellular transport undergoes remodeling upon cell differentiation, which involves cell type-specific regulators. Bone morphogenetic protein 2-inducible kinase (BMP2K) has been potentially implicated in endocytosis and cell differentiation but its molecular functions remained unknown. We discovered that its longer (L) and shorter (S) splicing variants regulate erythroid differentiation in a manner unexplainable by their involvement in AP-2 adaptor phosphorylation and endocytosis. However, both variants interact with SEC16A and could localize to the juxtanuclear secretory compartment. Variant-specific depletion approach showed that BMP2K isoforms constitute a BMP2K-L/S regulatory system that controls the distribution of SEC16A and SEC24B as well as SEC31A abundance at COPII assemblies. Finally, we found L to promote and S to restrict autophagic degradation and erythroid differentiation. Hence, we propose that BMP2K-L and BMP2K-S differentially regulate abundance and distribution of COPII assemblies as well as autophagy, possibly thereby fine-tuning erythroid differentiation.
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Affiliation(s)
- Jaroslaw Cendrowski
- Laboratory of Cell Biology, International Institute of Molecular and Cell BiologyWarsawPoland
| | - Marta Kaczmarek
- Laboratory of Cell Biology, International Institute of Molecular and Cell BiologyWarsawPoland
| | - Michał Mazur
- Laboratory of Cell Biology, International Institute of Molecular and Cell BiologyWarsawPoland
| | | | - Kamil Jastrzebski
- Laboratory of Cell Biology, International Institute of Molecular and Cell BiologyWarsawPoland
| | | | - Agata Kominek
- Laboratory of Cytometry, Nencki Institute of Experimental BiologyWarsawPoland
| | - Katarzyna Piwocka
- Laboratory of Cytometry, Nencki Institute of Experimental BiologyWarsawPoland
| | - Marta Miaczynska
- Laboratory of Cell Biology, International Institute of Molecular and Cell BiologyWarsawPoland
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Kovtun O, Dickson VK, Kelly BT, Owen DJ, Briggs JAG. Architecture of the AP2/clathrin coat on the membranes of clathrin-coated vesicles. SCIENCE ADVANCES 2020; 6:eaba8381. [PMID: 32743075 PMCID: PMC7375805 DOI: 10.1126/sciadv.aba8381] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/17/2020] [Indexed: 05/19/2023]
Abstract
Clathrin-mediated endocytosis (CME) is crucial for modulating the protein composition of a cell's plasma membrane. Clathrin forms a cage-like, polyhedral outer scaffold around a vesicle, to which cargo-selecting clathrin adaptors are attached. Adaptor protein complex (AP2) is the key adaptor in CME. Crystallography has shown AP2 to adopt a range of conformations. Here, we used cryo-electron microscopy, tomography, and subtomogram averaging to determine structures, interactions, and arrangements of clathrin and AP2 at the key steps of coat assembly, from AP2 in solution to membrane-assembled clathrin-coated vesicles (CCVs). AP2 binds cargo and PtdIns(4,5)P 2 (phosphatidylinositol 4,5-bisphosphate)-containing membranes via multiple interfaces, undergoing conformational rearrangement from its cytosolic state. The binding mode of AP2 β2 appendage into the clathrin lattice in CCVs and buds implies how the adaptor structurally modulates coat curvature and coat disassembly.
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Affiliation(s)
- Oleksiy Kovtun
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg , Germany
| | - Veronica Kane Dickson
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Bernard T. Kelly
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Corresponding author. (B.T.K.); (D.J.O.); (J.A.G.B.)
| | - David J. Owen
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Corresponding author. (B.T.K.); (D.J.O.); (J.A.G.B.)
| | - John A. G. Briggs
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg , Germany
- Corresponding author. (B.T.K.); (D.J.O.); (J.A.G.B.)
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Groener M, Wang Y, Cross E, Tian X, Ebenezer K, Baik E, Pedigo C, Schiffer M, Inoue K, Ishibe S. Identification of Podocyte Cargo Proteins by Proteomic Analysis of Clathrin-Coated Vesicles. KIDNEY360 2020; 1:480-490. [PMID: 35368594 PMCID: PMC8809311 DOI: 10.34067/kid.0000212020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/13/2020] [Indexed: 04/20/2023]
Abstract
Background Clathrin-mediated endocytosis (CME) plays a fundamental role in podocyte health. Genetic ablation of genes implicated in CME has been shown to cause severe proteinuria and foot process effacement in mice. However, little is known about the cargo of clathrin-coated vesicles (CCVs) in podocytes. The goal of this study was to isolate CCVs from podocytes and identify their cargo by proteomic analysis. Methods Glomeruli isolated from Podocin-Cre Rosa-DTRflox mouse kidneys were seeded and treated with diphtheria toxin to obtain pure primary podocyte cultures. CCVs were isolated by differential gradient ultracentrifugation, and enrichment of CCVs was assessed by immunoblotting and electron microscopy (EM). Liquid chromatography-mass spectrometry (LC-MS) was performed for proteomic analysis. Proteins with higher abundance than transferrin receptor protein 1 were evaluated for CCV cargo potential against previously published literature. Immunofluorescence staining of identified cargo proteins and CCVs was performed in podocytes for further verification. Results Immunoblotting for multiple protein markers of CME revealed enrichment in the CCV fraction. Enrichment of CCVs among other small vesicles was observed via EM. Proteomics yielded a total of >1200 significant proteins. Multiple-step data analysis revealed 36 CCV-associated proteins, of which 10 represent novel, highly abundant cargo proteins in podocytes. Colocalization of cargo proteins and CCVs on immunostaining was observed. Conclusions Our identification of podocyte CCV cargo proteins helps to elucidate the importance of endocytic trafficking for podocyte health and maintenance of the glomerular environment.
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Affiliation(s)
- Marwin Groener
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
- Department of Nephrology and Hypertension, University Hospital Erlangen, Erlangen, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ying Wang
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Elizabeth Cross
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Xuefei Tian
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Karen Ebenezer
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Eunice Baik
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Christopher Pedigo
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Mario Schiffer
- Department of Nephrology and Hypertension, University Hospital Erlangen, Erlangen, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Mount Desert Island Biological Laboratories, Salisbury Cove, Maine
| | - Kazunori Inoue
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Shuta Ishibe
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
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40
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Gadbery JE, Abraham A, Needle CD, Moth C, Sheehan J, Capra JA, Jackson LP. Integrating structural and evolutionary data to interpret variation and pathogenicity in adapter protein complex 4. Protein Sci 2020; 29:1535-1549. [PMID: 32285480 PMCID: PMC7255511 DOI: 10.1002/pro.3870] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/01/2020] [Accepted: 04/10/2020] [Indexed: 12/13/2022]
Abstract
Genetic variation in the membrane trafficking adapter protein complex 4 (AP-4) can result in pathogenic neurological phenotypes including microencephaly, spastic paraplegias, epilepsy, and other developmental defects. We lack molecular mechanisms responsible for impaired AP-4 function arising from genetic variation, because AP-4 remains poorly understood structurally. Here, we analyze patterns of AP-4 genetic evolution and conservation to identify regions that are likely important for function and thus more susceptible to pathogenic variation. We map known variants onto an AP-4 homology model and predict the likelihood of pathogenic variation at a given location on the structure of AP-4. We find significant clustering of likely pathogenic variants located at the interface between the β4 and N-μ4 subunits, as well as throughout the C-μ4 subunit. Our work offers an integrated perspective on how genetic and evolutionary forces affect AP-4 structure and function. As more individuals with uncharacterized AP-4 variants are identified, our work provides a foundation upon which their functional effects and disease relevance can be interpreted.
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Affiliation(s)
- John E. Gadbery
- Department of Biological SciencesVanderbilt UniversityNashvilleTennesseeUSA
| | - Abin Abraham
- Vanderbilt Genetics InstituteVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - Carli D. Needle
- Department of Biological SciencesVanderbilt UniversityNashvilleTennesseeUSA
| | - Christopher Moth
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
| | - Jonathan Sheehan
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
- Department of BiochemistryVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - John A. Capra
- Department of Biological SciencesVanderbilt UniversityNashvilleTennesseeUSA
- Vanderbilt Genetics InstituteVanderbilt University School of MedicineNashvilleTennesseeUSA
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
- Department of Biomedical InformaticsVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - Lauren P. Jackson
- Department of Biological SciencesVanderbilt UniversityNashvilleTennesseeUSA
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
- Department of BiochemistryVanderbilt University School of MedicineNashvilleTennesseeUSA
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41
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Brod J, Hellwig A, Wieland FT. Epsin but not AP-2 supports reconstitution of endocytic clathrin-coated vesicles. FEBS Lett 2020; 594:2227-2239. [PMID: 32337703 DOI: 10.1002/1873-3468.13801] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/05/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022]
Abstract
Formation of clathrin-coated vesicles (CCVs) in receptor-mediated endocytosis is a mechanistically well-established process, in which clathrin, the adaptor protein complex AP-2, and the large GTPase dynamin play crucial roles. In order to obtain more mechanistic insight into this process, here we established a giant unilamellar vesicle (GUV)-based in vitro CCV reconstitution system with chemically defined components and the full-length recombinant proteins clathrin, AP-2, epsin-1, and dynamin-2. Our results support the predominant model in which hydrolysis of GTP by dynamin is a prerequisite to generate CCVs. Strikingly, in this system at near physiological concentrations of reagents, epsin-1 alone does not have the propensity for scission but is required for bud formation, whereas AP-2 and clathrin are not sufficient. Thus, our study reveals that epsin-1 is an important factor for the maturation of clathrin coated buds, a prerequisite for vesicle generation.
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Affiliation(s)
- Jan Brod
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Germany
| | - Andrea Hellwig
- Interdisciplinary Center for Neurosciences (IZN), University of Heidelberg, Germany
| | - Felix T Wieland
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Germany
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42
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A New Pathway Promotes Adaptation of Human Glioblastoma Cells to Glucose Starvation. Cells 2020; 9:cells9051249. [PMID: 32443613 PMCID: PMC7290719 DOI: 10.3390/cells9051249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptation of glioblastoma to caloric restriction induces compensatory changes in tumor metabolism that are incompletely known. Here we show that in human glioblastoma cells maintained in exhausted medium, SHC adaptor protein 3 (SHC3) increases due to down-regulation of SHC3 protein degradation. This effect is reversed by glucose addition and is not present in normal astrocytes. Increased SHC3 levels are associated to increased glucose uptake mediated by changes in membrane trafficking of glucose transporters of the solute carrier 2A superfamily (GLUT/SLC2A). We found that the effects on vesicle trafficking are mediated by SHC3 interactions with adaptor protein complex 1 and 2 (AP), BMP-2-inducible protein kinase and a fraction of poly ADP-ribose polymerase 1 (PARP1) associated to vesicles containing GLUT/SLC2As. In glioblastoma cells, PARP1 inhibitor veliparib mimics glucose starvation in enhancing glucose uptake. Furthermore, cytosol extracted from glioblastoma cells inhibits PARP1 enzymatic activity in vitro while immunodepletion of SHC3 from the cytosol significantly relieves this inhibition. The identification of a new pathway controlling glucose uptake in high grade gliomas represents an opportunity for repositioning existing drugs and designing new ones.
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43
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Mattera R, Williamson CD, Ren X, Bonifacino JS. The FTS-Hook-FHIP (FHF) complex interacts with AP-4 to mediate perinuclear distribution of AP-4 and its cargo ATG9A. Mol Biol Cell 2020; 31:963-979. [PMID: 32073997 PMCID: PMC7185972 DOI: 10.1091/mbc.e19-11-0658] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/05/2020] [Accepted: 02/12/2020] [Indexed: 01/08/2023] Open
Abstract
The heterotetrameric adaptor protein complex 4 (AP-4) is a component of a protein coat associated with the trans-Golgi network (TGN). Mutations in AP-4 subunits cause a complicated form of autosomal-recessive hereditary spastic paraplegia termed AP-4-deficiency syndrome. Recent studies showed that AP-4 mediates export of the transmembrane autophagy protein ATG9A from the TGN to preautophagosomal structures. To identify additional proteins that cooperate with AP-4 in ATG9A trafficking, we performed affinity purification-mass spectrometry followed by validation of the hits by biochemical and functional analyses. This approach resulted in the identification of the fused toes homolog-Hook-FHIP (FHF) complex as a novel AP-4 accessory factor. We found that the AP-4-FHF interaction is mediated by direct binding of the AP-4 μ4 subunit to coiled-coil domains in the Hook1 and Hook2 subunits of FHF. Knockdown of FHF subunits resulted in dispersal of AP-4 and ATG9A from the perinuclear region of the cell, consistent with the previously demonstrated role of the FHF complex in coupling organelles to the microtubule (MT) retrograde motor dynein-dynactin. These findings thus uncover an additional mechanism for the distribution of ATG9A within cells and provide further evidence for a role of protein coats in coupling transport vesicles to MT motors.
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Affiliation(s)
- Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Chad D. Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Xuefeng Ren
- Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Juan S. Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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Birnbaum J, Scharf S, Schmidt S, Jonscher E, Hoeijmakers WAM, Flemming S, Toenhake CG, Schmitt M, Sabitzki R, Bergmann B, Fröhlke U, Mesén-Ramírez P, Blancke Soares A, Herrmann H, Bártfai R, Spielmann T. A Kelch13-defined endocytosis pathway mediates artemisinin resistance in malaria parasites. Science 2020; 367:51-59. [PMID: 31896710 DOI: 10.1126/science.aax4735] [Citation(s) in RCA: 224] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 09/19/2019] [Accepted: 10/30/2019] [Indexed: 01/20/2023]
Abstract
Artemisinin and its derivatives (ARTs) are the frontline drugs against malaria, but resistance is jeopardizing their effectiveness. ART resistance is mediated by mutations in the parasite's Kelch13 protein, but Kelch13 function and its role in resistance remain unclear. In this study, we identified proteins located at a Kelch13-defined compartment. Inactivation of eight of these proteins, including Kelch13, rendered parasites resistant to ART, revealing a pathway critical for resistance. Functional analysis showed that these proteins are required for endocytosis of hemoglobin from the host cell. Parasites with inactivated Kelch13 or a resistance-conferring Kelch13 mutation displayed reduced hemoglobin endocytosis. ARTs are activated by degradation products of hemoglobin. Hence, reduced activity of Kelch13 and its interactors diminishes hemoglobin endocytosis and thereby ART activation, resulting in parasite resistance.
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Affiliation(s)
- Jakob Birnbaum
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Sarah Scharf
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Sabine Schmidt
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Ernst Jonscher
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | | | - Sven Flemming
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Christa Geeke Toenhake
- Department of Molecular Biology, Radboud University, Geert Grooteplein 26-28, 6525 GA Nijmegen, Netherlands
| | - Marius Schmitt
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Ricarda Sabitzki
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Bärbel Bergmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Ulrike Fröhlke
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Paolo Mesén-Ramírez
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | | | - Hendrik Herrmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Richárd Bártfai
- Department of Molecular Biology, Radboud University, Geert Grooteplein 26-28, 6525 GA Nijmegen, Netherlands
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
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45
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Wells C, Couñago RM, Limas JC, Almeida TL, Cook JG, Drewry DH, Elkins JM, Gileadi O, Kapadia NR, Lorente-Macias A, Pickett JE, Riemen A, Ruela-de-Sousa RR, Willson TM, Zhang C, Zuercher WJ, Zutshi R, Axtman AD. SGC-AAK1-1: A Chemical Probe Targeting AAK1 and BMP2K. ACS Med Chem Lett 2020; 11:340-345. [PMID: 32184967 DOI: 10.1021/acsmedchemlett.9b00399] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/23/2019] [Indexed: 12/12/2022] Open
Abstract
Inhibitors based on a 3-acylaminoindazole scaffold were synthesized to yield potent dual AAK1/BMP2K inhibitors. Optimization furnished a small molecule chemical probe (SGC-AAK1-1, 25) that is potent and selective for AAK1/BMP2K over other NAK family members, demonstrates narrow activity in a kinome-wide screen, and is functionally active in cells. This inhibitor represents one of the best available small molecule tools to study the functions of AAK1 and BMP2K.
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Affiliation(s)
- Carrow Wells
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Rafael M. Couñago
- SGC, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-886, Brazil
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, UNICAMP, Campinas, SP 13083-875, Brazil
| | - Juanita C. Limas
- Department of Pharmacology, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Tuanny L. Almeida
- SGC, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-886, Brazil
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, UNICAMP, Campinas, SP 13083-875, Brazil
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - David H. Drewry
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Jonathan M. Elkins
- SGC, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-886, Brazil
- SGC, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, U.K
| | - Opher Gileadi
- SGC, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-886, Brazil
- SGC, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, U.K
| | - Nirav R. Kapadia
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Alvaro Lorente-Macias
- Departamento de Química Farmacéutica y Orgánica, University of Granada, Granada, 18071, Spain
| | - Julie E. Pickett
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Alexander Riemen
- Luceome Biotechnologies, LLC, Tucson, Arizona 85719, United States
| | - Roberta R. Ruela-de-Sousa
- SGC, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-886, Brazil
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, UNICAMP, Campinas, SP 13083-875, Brazil
| | - Timothy M. Willson
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Cunyu Zhang
- Platform Technology Sciences, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - William J. Zuercher
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center (LCCC), UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Reena Zutshi
- Luceome Biotechnologies, LLC, Tucson, Arizona 85719, United States
| | - Alison D. Axtman
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
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46
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Lundberg E, Borner GHH. Spatial proteomics: a powerful discovery tool for cell biology. Nat Rev Mol Cell Biol 2020; 20:285-302. [PMID: 30659282 DOI: 10.1038/s41580-018-0094-y] [Citation(s) in RCA: 264] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein subcellular localization is tightly controlled and intimately linked to protein function in health and disease. Capturing the spatial proteome - that is, the localizations of proteins and their dynamics at the subcellular level - is therefore essential for a complete understanding of cell biology. Owing to substantial advances in microscopy, mass spectrometry and machine learning applications for data analysis, the field is now mature for proteome-wide investigations of spatial cellular regulation. Studies of the human proteome have begun to reveal a complex architecture, including single-cell variations, dynamic protein translocations, changing interaction networks and proteins localizing to multiple compartments. Furthermore, several studies have successfully harnessed the power of comparative spatial proteomics as a discovery tool to unravel disease mechanisms. We are at the beginning of an era in which spatial proteomics finally integrates with cell biology and medical research, thereby paving the way for unbiased systems-level insights into cellular processes. Here, we discuss current methods for spatial proteomics using imaging or mass spectrometry and specifically highlight global comparative applications. The aim of this Review is to survey the state of the field and also to encourage more cell biologists to apply spatial proteomics approaches.
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Affiliation(s)
- Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden. .,Department of Genetics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Georg H H Borner
- Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany.
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47
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Behne R, Teinert J, Wimmer M, D’Amore A, Davies AK, Scarrott JM, Eberhardt K, Brechmann B, Chen IPF, Buttermore ED, Barrett L, Dwyer S, Chen T, Hirst J, Wiesener A, Segal D, Martinuzzi A, Duarte ST, Bennett JT, Bourinaris T, Houlden H, Roubertie A, Santorelli FM, Robinson M, Azzouz M, Lipton JO, Borner GHH, Sahin M, Ebrahimi-Fakhari D. Adaptor protein complex 4 deficiency: a paradigm of childhood-onset hereditary spastic paraplegia caused by defective protein trafficking. Hum Mol Genet 2020; 29:320-334. [PMID: 31915823 PMCID: PMC7001721 DOI: 10.1093/hmg/ddz310] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/22/2019] [Accepted: 12/05/2019] [Indexed: 12/25/2022] Open
Abstract
Deficiency of the adaptor protein complex 4 (AP-4) leads to childhood-onset hereditary spastic paraplegia (AP-4-HSP): SPG47 (AP4B1), SPG50 (AP4M1), SPG51 (AP4E1) and SPG52 (AP4S1). This study aims to evaluate the impact of loss-of-function variants in AP-4 subunits on intracellular protein trafficking using patient-derived cells. We investigated 15 patient-derived fibroblast lines and generated six lines of induced pluripotent stem cell (iPSC)-derived neurons covering a wide range of AP-4 variants. All patient-derived fibroblasts showed reduced levels of the AP4E1 subunit, a surrogate for levels of the AP-4 complex. The autophagy protein ATG9A accumulated in the trans-Golgi network and was depleted from peripheral compartments. Western blot analysis demonstrated a 3-5-fold increase in ATG9A expression in patient lines. ATG9A was redistributed upon re-expression of AP4B1 arguing that mistrafficking of ATG9A is AP-4-dependent. Examining the downstream effects of ATG9A mislocalization, we found that autophagic flux was intact in patient-derived fibroblasts both under nutrient-rich conditions and when autophagy is stimulated. Mitochondrial metabolism and intracellular iron content remained unchanged. In iPSC-derived cortical neurons from patients with AP4B1-associated SPG47, AP-4 subunit levels were reduced while ATG9A accumulated in the trans-Golgi network. Levels of the autophagy marker LC3-II were reduced, suggesting a neuron-specific alteration in autophagosome turnover. Neurite outgrowth and branching were reduced in AP-4-HSP neurons pointing to a role of AP-4-mediated protein trafficking in neuronal development. Collectively, our results establish ATG9A mislocalization as a key marker of AP-4 deficiency in patient-derived cells, including the first human neuron model of AP-4-HSP, which will aid diagnostic and therapeutic studies.
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Affiliation(s)
- Robert Behne
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Julian Teinert
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Pediatric Neurology and Metabolic Medicine, Center for Child and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Miriam Wimmer
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Angelica D’Amore
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Molecular Medicine, IRCCS Fondazione Stella Maris, 56018 Pisa, Italy
| | - Alexandra K Davies
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Joseph M Scarrott
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Kathrin Eberhardt
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Barbara Brechmann
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ivy Pin-Fang Chen
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth D Buttermore
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lee Barrett
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sean Dwyer
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Teresa Chen
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Antje Wiesener
- Institute of Human Genetics, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Devorah Segal
- Division of Pediatric Neurology, Department of Pediatrics, Weill Cornell Medicine, New York City, NY 10021, USA
| | - Andrea Martinuzzi
- Scientific Institute, IRCCS E. Medea, Unità Operativa Conegliano, 31015 Treviso, Italy
| | - Sofia T Duarte
- Department of Pediatric Neurology, Centro Hospitalar de Lisboa Central, 1169-050 Lisbon, Portugal
| | - James T Bennett
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Thomas Bourinaris
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1E 6BT, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1E 6BT, UK
| | | | | | - Margaret Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Mimoun Azzouz
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Jonathan O Lipton
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Mustafa Sahin
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Darius Ebrahimi-Fakhari
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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48
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Gutierrez JM, Feizi A, Li S, Kallehauge TB, Hefzi H, Grav LM, Ley D, Baycin Hizal D, Betenbaugh MJ, Voldborg B, Faustrup Kildegaard H, Min Lee G, Palsson BO, Nielsen J, Lewis NE. Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion. Nat Commun 2020; 11:68. [PMID: 31896772 PMCID: PMC6940358 DOI: 10.1038/s41467-019-13867-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/22/2019] [Indexed: 01/08/2023] Open
Abstract
In mammalian cells, >25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion of different proteins. Unraveling its impact on diverse proteins is particularly important for biopharmaceutical production. Here we delineate the core secretory pathway functions and integrate them with genome-scale metabolic reconstructions of human, mouse, and Chinese hamster ovary cells. The resulting reconstructions enable the computation of energetic costs and machinery demands of each secreted protein. By integrating additional omics data, we find that highly secretory cells have adapted to reduce expression and secretion of other expensive host cell proteins. Furthermore, we predict metabolic costs and maximum productivities of biotherapeutic proteins and identify protein features that most significantly impact protein secretion. Finally, the model successfully predicts the increase in secretion of a monoclonal antibody after silencing a highly expressed selection marker. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology.
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Affiliation(s)
- Jahir M Gutierrez
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Amir Feizi
- Department of Biology and Biological Engineering, Kemivägen 10, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Shangzhong Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Thomas B Kallehauge
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Hooman Hefzi
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Lise M Grav
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Daniel Ley
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Michael J Betenbaugh
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218-2686, USA
| | - Bjorn Voldborg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Helene Faustrup Kildegaard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Gyun Min Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Kemivägen 10, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA.
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA.
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA.
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49
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Kustatscher G, Grabowski P, Schrader TA, Passmore JB, Schrader M, Rappsilber J. Co-regulation map of the human proteome enables identification of protein functions. Nat Biotechnol 2019; 37:1361-1371. [PMID: 31690884 DOI: 10.1038/s41587-019-0298-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 09/27/2019] [Indexed: 01/07/2023]
Abstract
Assigning functions to the vast array of proteins present in eukaryotic cells remains challenging. To identify relationships between proteins, and thereby enable functional annotation of proteins, we determined changes in abundance of 10,323 human proteins in response to 294 biological perturbations using isotope-labeling mass spectrometry. We applied the machine learning algorithm treeClust to reveal functional associations between co-regulated human proteins from ProteomeHD, a compilation of our own data and datasets from the Proteomics Identifications database. This produced a co-regulation map of the human proteome. Co-regulation was able to capture relationships between proteins that do not physically interact or colocalize. For example, co-regulation of the peroxisomal membrane protein PEX11β with mitochondrial respiration factors led us to discover an organelle interface between peroxisomes and mitochondria in mammalian cells. We also predicted the functions of microproteins that are difficult to study with traditional methods. The co-regulation map can be explored at www.proteomeHD.net .
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Affiliation(s)
- Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Piotr Grabowski
- Division of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Data Sciences and Artificial Intelligence, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | | | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK. .,Division of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.
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50
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Wrobel AG, Kadlecova Z, Kamenicky J, Yang JC, Herrmann T, Kelly BT, McCoy AJ, Evans PR, Martin S, Müller S, Salomon S, Sroubek F, Neuhaus D, Höning S, Owen DJ. Temporal Ordering in Endocytic Clathrin-Coated Vesicle Formation via AP2 Phosphorylation. Dev Cell 2019; 50:494-508.e11. [PMID: 31430451 PMCID: PMC6706699 DOI: 10.1016/j.devcel.2019.07.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/18/2019] [Accepted: 07/15/2019] [Indexed: 11/23/2022]
Abstract
Clathrin-mediated endocytosis (CME) is key to maintaining the transmembrane protein composition of cells' limiting membranes. During mammalian CME, a reversible phosphorylation event occurs on Thr156 of the μ2 subunit of the main endocytic clathrin adaptor, AP2. We show that this phosphorylation event starts during clathrin-coated pit (CCP) initiation and increases throughout CCP lifetime. μ2Thr156 phosphorylation favors a new, cargo-bound conformation of AP2 and simultaneously creates a binding platform for the endocytic NECAP proteins but without significantly altering AP2's cargo affinity in vitro. We describe the structural bases of both. NECAP arrival at CCPs parallels that of clathrin and increases with μ2Thr156 phosphorylation. In turn, NECAP recruits drivers of late stages of CCP formation, including SNX9, via a site distinct from where NECAP binds AP2. Disruption of the different modules of this phosphorylation-based temporal regulatory system results in CCP maturation being delayed and/or stalled, hence impairing global rates of CME.
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Affiliation(s)
| | | | - Jan Kamenicky
- Czech Academy of Sciences, Institute of Information Theory and Automation, Pod Vodarenskou vezi 4, 182 08 Prague 8, Czech Republic
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Torsten Herrmann
- University of Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | | | - Airlie J McCoy
- CIMR, WT/MRC Building, Hills Road, Cambridge CB2 0QQ, UK
| | - Philip R Evans
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephen Martin
- The Francis Crick Institute, 1 Midland Road, London NW1 1ST, UK
| | - Stefan Müller
- Center for Molecular Medicine (CMMC), University of Cologne, Robert-Koch-Straße 21, 50931 Cologne, Germany
| | - Susanne Salomon
- Institute for Biochemistry I, Medical Faulty, University of Cologne, Joseph-Stelzmann-Straße 52, 50931 Cologne, Germany
| | - Filip Sroubek
- Czech Academy of Sciences, Institute of Information Theory and Automation, Pod Vodarenskou vezi 4, 182 08 Prague 8, Czech Republic
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stefan Höning
- Institute for Biochemistry I, Medical Faulty, University of Cologne, Joseph-Stelzmann-Straße 52, 50931 Cologne, Germany.
| | - David J Owen
- CIMR, WT/MRC Building, Hills Road, Cambridge CB2 0QQ, UK
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