1
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Wen JW, Zhang HL, Du PF. Vislocas: Vision transformers for identifying protein subcellular mis-localization signatures of different cancer subtypes from immunohistochemistry images. Comput Biol Med 2024; 174:108392. [PMID: 38608321 DOI: 10.1016/j.compbiomed.2024.108392] [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: 02/08/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Proteins must be sorted to specific subcellular compartments to perform their functions. Abnormal protein subcellular localizations are related to many diseases. Although many efforts have been made in predicting protein subcellular localization from various static information, including sequences, structures and interactions, such static information cannot predict protein mis-localization events in diseases. On the contrary, the IHC (immunohistochemistry) images, which have been widely applied in clinical diagnosis, contains information that can be used to find protein mis-localization events in disease states. In this study, we create the Vislocas method, which is capable of finding mis-localized proteins from IHC images as markers of cancer subtypes. By combining CNNs and vision transformer encoders, Vislocas can automatically extract image features at both global and local level. Vislocas can be trained with full-sized IHC images from scratch. It is the first attempt to create an end-to-end IHC image-based protein subcellular location predictor. Vislocas achieved comparable or better performances than state-of-the-art methods. We applied Vislocas to find significant protein mis-localization events in different subtypes of glioma, melanoma and skin cancer. The mis-localized proteins, which were found purely from IHC images by Vislocas, are in consistency with clinical or experimental results in literatures. All codes of Vislocas have been deposited in a Github repository (https://github.com/JingwenWen99/Vislocas). All datasets of Vislocas have been deposited in Zenodo (https://zenodo.org/records/10632698).
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Affiliation(s)
- Jing-Wen Wen
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
| | - Han-Lin Zhang
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
| | - Pu-Feng Du
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
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2
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Libberecht K, Vangansewinkel T, Van Den Bosch L, Lambrichts I, Wolfs E. Proteostasis plays an important role in demyelinating Charcot Marie Tooth disease. Biochem Pharmacol 2023; 216:115760. [PMID: 37604292 DOI: 10.1016/j.bcp.2023.115760] [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: 06/01/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Type 1 Charcot-Marie-Tooth disease (CMT1) is the most common demyelinating peripheral neuropathy. Patients suffer from progressive muscle weakness and sensory problems. The underlying disease mechanisms of CMT1 are still unclear and no therapy is currently available, hence patients completely rely on supportive care. Balancing protein levels is a complex multistep process fundamental to maintain cells in their healthy state and a disrupted proteostasis is a hallmark of several neurodegenerative diseases. When protein misfolding occurs, protein quality control systems are activated such as chaperones, the lysosomal-autophagy system and proteasomal degradation to ensure proper degradation. However, in pathological circumstances, these mechanisms are overloaded and thereby become inefficient to clear the load of misfolded proteins. Recent evidence strongly indicates that a disbalance in proteostasis plays an important role in several forms of CMT1. In this review, we present an overview of the protein quality control systems, their role in CMT1, and potential treatment strategies to restore proteostasis.
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Affiliation(s)
- Karen Libberecht
- UHasselt, Biomedical Research Institute (BIOMED), Lab for Functional Imaging & Research on Stem Cells (FIERCELab), Diepenbeek, Belgium; VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium.
| | - Tim Vangansewinkel
- UHasselt, Biomedical Research Institute (BIOMED), Lab for Functional Imaging & Research on Stem Cells (FIERCELab), Diepenbeek, Belgium; VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium; UHasselt, Biomedical Research Institute (BIOMED), Lab for Histology and Regeneration (HISTOREGEN Lab), Diepenbeek, Belgium
| | - Ludo Van Den Bosch
- KU Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), Leuven, Belgium; VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Ivo Lambrichts
- UHasselt, Biomedical Research Institute (BIOMED), Lab for Histology and Regeneration (HISTOREGEN Lab), Diepenbeek, Belgium
| | - Esther Wolfs
- UHasselt, Biomedical Research Institute (BIOMED), Lab for Functional Imaging & Research on Stem Cells (FIERCELab), Diepenbeek, Belgium.
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3
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Melnyk A, Lang S, Sicking M, Zimmermann R, Jung M. Co-chaperones of the Human Endoplasmic Reticulum: An Update. Subcell Biochem 2023; 101:247-291. [PMID: 36520310 DOI: 10.1007/978-3-031-14740-1_9] [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] [Indexed: 06/17/2023]
Abstract
In mammalian cells, the rough endoplasmic reticulum (ER) plays central roles in the biogenesis of extracellular plus organellar proteins and in various signal transduction pathways. For these reasons, the ER comprises molecular chaperones, which are involved in import, folding, assembly, export, plus degradation of polypeptides, and signal transduction components, such as calcium channels, calcium pumps, and UPR transducers plus adenine nucleotide carriers/exchangers in the ER membrane. The calcium- and ATP-dependent ER lumenal Hsp70, termed immunoglobulin heavy-chain-binding protein or BiP, is the central player in all these activities and involves up to nine different Hsp40-type co-chaperones, i.e., ER membrane integrated as well as ER lumenal J-domain proteins, termed ERj or ERdj proteins, two nucleotide exchange factors or NEFs (Grp170 and Sil1), and NEF-antagonists, such as MANF. Here we summarize the current knowledge on the ER-resident BiP/ERj chaperone network and focus on the interaction of BiP with the polypeptide-conducting and calcium-permeable Sec61 channel of the ER membrane as an example for BiP action and how its functional cycle is linked to ER protein import and various calcium-dependent signal transduction pathways.
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Affiliation(s)
- Armin Melnyk
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Sven Lang
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Mark Sicking
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Richard Zimmermann
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany.
| | - Martin Jung
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
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4
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Corona-Sanchez EG, Martínez-García EA, Lujano-Benítez AV, Pizano-Martinez O, Guerra-Durán IA, Chavarria-Avila E, Aguilar-Vazquez A, Martín-Márquez BT, Arellano-Arteaga KJ, Armendariz-Borunda J, Perez-Vazquez F, García-De la Torre I, Llamas-García A, Palacios-Zárate BL, Toriz-González G, Vazquez-Del Mercado M. Autoantibodies in the pathogenesis of idiopathic inflammatory myopathies: Does the endoplasmic reticulum stress response have a role? Front Immunol 2022; 13:940122. [PMID: 36189221 PMCID: PMC9520918 DOI: 10.3389/fimmu.2022.940122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/24/2022] [Indexed: 12/20/2022] Open
Abstract
Idiopathic inflammatory myopathies (IIMs) are a group of rare, acquired autoimmune diseases characterized by profound muscle weakness and immune cell invasion into non-necrotic muscle. They are related to the presence of antibodies known as myositis-specific antibodies and myositis-associated antibodies, which are associated with various IIM phenotypes and the clinical prognosis. The possibility of the participation of other pathological mechanisms involved in the inflammatory response in IIM has been proposed. Such mechanisms include the overexpression of major histocompatibility complex class I in myofibers, which correlates with the activation of stress responses of the endoplasmic reticulum (ER). Taking into account the importance of the ER for the maintenance of homeostasis of the musculoskeletal system in the regulation of proteins, there is probably a relationship between immunological and non-immunological processes and autoimmunity, and an example of this might be IIM. We propose that ER stress and its relief mechanisms could be related to inflammatory mechanisms triggering a humoral response in IIM, suggesting that ER stress might be related to the triggering of IIMs and their auto-antibodies’ production.
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Affiliation(s)
- Esther Guadalupe Corona-Sanchez
- Instituto de Investigación en Reumatología y del Sistema Músculo Esqueletico, Departamento de Biología Molecular, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Universidad de Guadalajara-Cuerpo Académico (UDG-CA)-703, Inmunología y Reumatología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Erika Aurora Martínez-García
- Instituto de Investigación en Reumatología y del Sistema Músculo Esqueletico, Departamento de Biología Molecular, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Universidad de Guadalajara-Cuerpo Académico (UDG-CA)-703, Inmunología y Reumatología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Andrea Verónica Lujano-Benítez
- Instituto de Investigación en Reumatología y del Sistema Músculo Esqueletico, Departamento de Biología Molecular, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Doctorado en Ciencias Biomedicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Oscar Pizano-Martinez
- Instituto de Investigación en Reumatología y del Sistema Músculo Esqueletico, Departamento de Biología Molecular, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Universidad de Guadalajara-Cuerpo Académico (UDG-CA)-703, Inmunología y Reumatología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Ivette Alejandra Guerra-Durán
- Instituto de Investigación en Reumatología y del Sistema Músculo Esqueletico, Departamento de Biología Molecular, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Efrain Chavarria-Avila
- Instituto de Investigación en Reumatología y del Sistema Músculo Esqueletico, Departamento de Biología Molecular, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Departamento de Disciplinas Filosófico Metodológicas e Instrumentales, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Andrea Aguilar-Vazquez
- Instituto de Investigación en Reumatología y del Sistema Músculo Esqueletico, Departamento de Biología Molecular, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Doctorado en Ciencias Biomedicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Beatriz Teresita Martín-Márquez
- Instituto de Investigación en Reumatología y del Sistema Músculo Esqueletico, Departamento de Biología Molecular, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Universidad de Guadalajara-Cuerpo Académico (UDG-CA)-703, Inmunología y Reumatología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Kevin Javier Arellano-Arteaga
- Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Especialidad de Medicina Interna, Padrón Nacional de Posgrados de Calidad (PNPC) Consejo Nacional de Ciencia y Tecnología (CONACyT), Guadalajara, Mexico
| | - Juan Armendariz-Borunda
- Instituto de Biología Molecular en Medicina, Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud, Guadalajara, Mexico
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Zapopan, Mexico
| | - Felipe Perez-Vazquez
- Departamento de Disciplinas Filosófico Metodológicas e Instrumentales, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Ignacio García-De la Torre
- Departamento de Inmunología y Reumatología, Hospital General de Occidente y Universidad de Guadalajara, Guadalajara, Mexico
| | - Arcelia Llamas-García
- Hospital Civil de Guadalajara “Dr. Juan I. Menchaca, ” Especialidad de Reumatología, Padrón Nacional de Posgrados de Calidad (PNPC) Consejo Nacional de Ciencia y Tecnología (CONACyT), Guadalajara, Mexico
| | - Brenda Lucía Palacios-Zárate
- Hospital Civil de Guadalajara “Dr. Juan I. Menchaca, ” Especialidad de Reumatología, Padrón Nacional de Posgrados de Calidad (PNPC) Consejo Nacional de Ciencia y Tecnología (CONACyT), Guadalajara, Mexico
| | - Guillermo Toriz-González
- Instituto Transdisciplinar de Investigación y Servicios (ITRANS), Universidad de Guadalajara, Zapopan, Mexico
| | - Monica Vazquez-Del Mercado
- Instituto de Investigación en Reumatología y del Sistema Músculo Esqueletico, Departamento de Biología Molecular, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Universidad de Guadalajara-Cuerpo Académico (UDG-CA)-703, Inmunología y Reumatología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Hospital Civil de Guadalajara “Dr. Juan I. Menchaca, ” Especialidad de Reumatología, Padrón Nacional de Posgrados de Calidad (PNPC) Consejo Nacional de Ciencia y Tecnología (CONACyT), Guadalajara, Mexico
- *Correspondence: Monica Vazquez-Del Mercado,
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5
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Farkas Á, Urlaub H, Bohnsack KE, Schwappach B. Regulated targeting of the monotopic hairpin membrane protein Erg1 requires the GET pathway. J Biophys Biochem Cytol 2022; 221:213228. [PMID: 35587358 PMCID: PMC9123286 DOI: 10.1083/jcb.202201036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/27/2022] [Accepted: 04/12/2022] [Indexed: 02/08/2023] Open
Abstract
The guided entry of tail-anchored proteins (GET) pathway targets C-terminally anchored transmembrane proteins and protects cells from lipotoxicity. Here, we reveal perturbed ergosterol production in ∆get3 cells and demonstrate the sensitivity of GET pathway mutants to the sterol synthesis inhibiting drug terbinafine. Our data uncover a key enzyme of sterol synthesis, the hairpin membrane protein squalene monooxygenase (Erg1), as a non-canonical GET pathway client, thus rationalizing the lipotoxicity phenotypes of GET pathway mutants. Get3 recognizes the hairpin targeting element of Erg1 via its classical client-binding pocket. Intriguingly, we find that the GET pathway is especially important for the acute upregulation of Erg1 induced by low sterol conditions. We further identify several other proteins anchored to the endoplasmic reticulum (ER) membrane exclusively via a hairpin as putative clients of the GET pathway. Our findings emphasize the necessity of dedicated targeting pathways for high-efficiency targeting of particular clients during dynamic cellular adaptation and highlight hairpin proteins as a potential novel class of GET clients.
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Affiliation(s)
- Ákos Farkas
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytic Mass Spectrometry, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
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6
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Sicking M, Živná M, Bhadra P, Barešová V, Tirincsi A, Hadzibeganovic D, Hodaňová K, Vyleťal P, Sovová J, Jedličková I, Jung M, Bell T, Helms V, Bleyer AJ, Kmoch S, Cavalié A, Lang S. Phenylbutyrate rescues the transport defect of the Sec61α mutations V67G and T185A for renin. Life Sci Alliance 2022; 5:e202101150. [PMID: 35064074 PMCID: PMC8807872 DOI: 10.26508/lsa.202101150] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 11/24/2022] Open
Abstract
The human Sec61 complex is a widely distributed and abundant molecular machine. It resides in the membrane of the endoplasmic reticulum to channel two types of cargo: protein substrates and calcium ions. The SEC61A1 gene encodes for the pore-forming Sec61α subunit of the Sec61 complex. Despite their ubiquitous expression, the idiopathic SEC61A1 missense mutations p.V67G and p.T185A trigger a localized disease pattern diagnosed as autosomal dominant tubulointerstitial kidney disease (ADTKD-SEC61A1). Using cellular disease models for ADTKD-SEC61A1, we identified an impaired protein transport of the renal secretory protein renin and a reduced abundance of regulatory calcium transporters, including SERCA2. Treatment with the molecular chaperone phenylbutyrate reversed the defective protein transport of renin and the imbalanced calcium homeostasis. Signal peptide substitution experiments pointed at targeting sequences as the cause for the substrate-specific impairment of protein transport in the presence of the V67G or T185A mutations. Similarly, dominant mutations in the signal peptide of renin also cause ADTKD and point to impaired transport of this renal hormone as important pathogenic feature for ADTKD-SEC61A1 patients as well.
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Affiliation(s)
- Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Martina Živná
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pratiti Bhadra
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Veronika Barešová
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petr Vyleťal
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jana Sovová
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Jung
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Thomas Bell
- Department of Chemistry, University of Nevada, Reno, NV, USA
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Anthony J Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Adolfo Cavalié
- Experimental and Clinical Pharmacology and Toxicology, Pre-clinical Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
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7
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Reduced DNAJC3 Expression Affects Protein Translocation across the ER Membrane and Attenuates the Down-Modulating Effect of the Translocation Inhibitor Cyclotriazadisulfonamide. Int J Mol Sci 2022; 23:ijms23020584. [PMID: 35054769 PMCID: PMC8775681 DOI: 10.3390/ijms23020584] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 12/20/2022] Open
Abstract
One of the reported substrates for the endoplasmic reticulum (ER) translocation inhibitor cyclotriazadisulfonamide (CADA) is DNAJC3, a chaperone of the unfolded protein response during ER stress. In this study, we investigated the impact of altered DNAJC3 protein levels on the inhibitory activity of CADA. By comparing WT DNAJC3 with a CADA-resistant DNAJC3 mutant, we observed the enhanced sensitivity of human CD4, PTK7 and ERLEC1 for CADA when DNAJC3 was expressed at high levels. Combined treatment of CADA with a proteasome inhibitor resulted in synergistic inhibition of protein translocation and in the rescue of a small preprotein fraction, which presumably corresponds to the CADA affected protein fraction that is stalled at the Sec61 translocon. We demonstrate that DNAJC3 enhances the protein translation of a reporter protein that is expressed downstream of the CADA-stalled substrate, suggesting that DNAJC3 promotes the clearance of the clogged translocon. We propose a model in which a reduced DNAJC3 level by CADA slows down the clearance of CADA-stalled substrates. This results in higher residual translocation into the ER lumen due to the longer dwelling time of the temporarily stalled substrates in the translocon. Thus, by directly reducing DNAJC3 protein levels, CADA attenuates its net down-modulating effect on its substrates.
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8
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Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
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Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
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9
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Zimmermann R, Lang S, Lerner M, Förster F, Nguyen D, Helms V, Schrul B. Quantitative Proteomics and Differential Protein Abundance Analysis after the Depletion of PEX3 from Human Cells Identifies Additional Aspects of Protein Targeting to the ER. Int J Mol Sci 2021; 22:ijms222313028. [PMID: 34884833 PMCID: PMC8658024 DOI: 10.3390/ijms222313028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/19/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
Protein import into the endoplasmic reticulum (ER) is the first step in the biogenesis of around 10,000 different soluble and membrane proteins in humans. It involves the co- or post-translational targeting of precursor polypeptides to the ER, and their subsequent membrane insertion or translocation. So far, three pathways for the ER targeting of precursor polypeptides and four pathways for the ER targeting of mRNAs have been described. Typically, these pathways deliver their substrates to the Sec61 polypeptide-conducting channel in the ER membrane. Next, the precursor polypeptides are inserted into the ER membrane or translocated into the ER lumen, which may involve auxiliary translocation components, such as the TRAP and Sec62/Sec63 complexes, or auxiliary membrane protein insertases, such as EMC and the TMCO1 complex. Recently, the PEX19/PEX3-dependent pathway, which has a well-known function in targeting and inserting various peroxisomal membrane proteins into pre-existent peroxisomal membranes, was also found to act in the targeting and, putatively, insertion of monotopic hairpin proteins into the ER. These either remain in the ER as resident ER membrane proteins, or are pinched off from the ER as components of new lipid droplets. Therefore, the question arose as to whether this pathway may play a more general role in ER protein targeting, i.e., whether it represents a fourth pathway for the ER targeting of precursor polypeptides. Thus, we addressed the client spectrum of the PEX19/PEX3-dependent pathway in both PEX3-depleted HeLa cells and PEX3-deficient Zellweger patient fibroblasts by an established approach which involved the label-free quantitative mass spectrometry of the total proteome of depleted or deficient cells, as well as differential protein abundance analysis. The negatively affected proteins included twelve peroxisomal proteins and two hairpin proteins of the ER, thus confirming two previously identified classes of putative PEX19/PEX3 clients in human cells. Interestingly, fourteen collagen-related proteins with signal peptides or N-terminal transmembrane helices belonging to the secretory pathway were also negatively affected by PEX3 deficiency, which may suggest compromised collagen biogenesis as a hitherto-unknown contributor to organ failures in the respective Zellweger patients.
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Affiliation(s)
- Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
- Correspondence: (R.Z.); (B.S.)
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
| | - Monika Lerner
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Duy Nguyen
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (D.N.); (V.H.)
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (D.N.); (V.H.)
| | - Bianca Schrul
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
- Correspondence: (R.Z.); (B.S.)
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10
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Inhibitors of the Sec61 Complex and Novel High Throughput Screening Strategies to Target the Protein Translocation Pathway. Int J Mol Sci 2021; 22:ijms222112007. [PMID: 34769437 PMCID: PMC8585047 DOI: 10.3390/ijms222112007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/29/2021] [Indexed: 02/08/2023] Open
Abstract
Proteins targeted to the secretory pathway start their intracellular journey by being transported across biological membranes such as the endoplasmic reticulum (ER). A central component in this protein translocation process across the ER is the Sec61 translocon complex, which is only intracellularly expressed and does not have any enzymatic activity. In addition, Sec61 translocon complexes are difficult to purify and to reconstitute. Screening for small molecule inhibitors impairing its function has thus been notoriously difficult. However, such translocation inhibitors may not only be valuable tools for cell biology, but may also represent novel anticancer drugs, given that cancer cells heavily depend on efficient protein translocation into the ER to support their fast growth. In this review, different inhibitors of protein translocation will be discussed, and their specific mode of action will be compared. In addition, recently published screening strategies for small molecule inhibitors targeting the whole SRP-Sec61 targeting/translocation pathway will be summarized. Of note, slightly modified assays may be used in the future to screen for substances affecting SecYEG, the bacterial ortholog of the Sec61 complex, in order to identify novel antibiotic drugs.
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11
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Nakamura S, Yamashita R, Miyauchi Y, Tanaka Y, Ishii Y. Adenine-related compounds modulate UDP-glucuronosyltransferase (UGT) activity in mouse liver microsomes. Xenobiotica 2021; 51:1247-1254. [PMID: 34727004 DOI: 10.1080/00498254.2021.2001075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Adenine-related compounds are allosteric inhibitors of UDP-glucuronosyltransferase (UGT) in rat liver microsomes (RLM) and human UGT isoforms treated with detergent or pore-forming peptide, alamethicin.To clarify whether the same is true beyond species, the effects of adenine-related compounds on 4-methylumbelliferone (4-MU) glucuronidation were examined using detergent-treated mouse liver microsomes (MLM).Brij-58 treatment of MLM increased the Vmax and the Michaelis constant, Km, of 4-MU. This study was performed using Brij-58-treated MLM as an enzyme source. ATP- and ADP-inhibited 4-MU glucuronidation. In contrast, AMP caused a 1.5-fold increase in glucuronidation. Oxidised forms, NAD+ and NADP+, potently inhibited 4-MU glucuronidation, whereas the reduced forms, NADH and NADPH, did not. Furthermore, the IC50 values of ATP, ADP, NAD+, and NADP+ were approximately 15 μM.In our previous study, ATP was the strongest inhibitor of UGT activity in RLM. However, in this study, the above-mentioned compounds inhibited 4-MU UGT in a comparable and non-competitive manner. Furthermore, AMP antagonised the inhibitory effects of ATP and ADP.These results suggest that ATP, ADP, NAD+, and NADP+ are common endogenous inhibitors of UGT beyond species.
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Affiliation(s)
- Shoji Nakamura
- Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryohei Yamashita
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuu Miyauchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.,Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| | - Yoshitaka Tanaka
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuji Ishii
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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12
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Davis MM, Lamichhane R, Bruce BD. Elucidating Protein Translocon Dynamics with Single-Molecule Precision. Trends Cell Biol 2021; 31:569-583. [PMID: 33865650 DOI: 10.1016/j.tcb.2021.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/28/2023]
Abstract
Translocons are protein assemblies that facilitate the targeting and transport of proteins into and across biological membranes. Our understanding of these systems has been advanced using genetics, biochemistry, and structural biology. Despite these classic advances, until recently we have still largely lacked a detailed understanding of how translocons recognize and facilitate protein translocation. With the advent and improvements of cryogenic electron microscopy (cryo-EM) single-particle analysis and single-molecule fluorescence microscopy, the details of how translocons function are finally emerging. Here, we introduce these methods and evaluate their importance in understanding translocon structure, function, and dynamics.
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Affiliation(s)
- Madeline M Davis
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Rajan Lamichhane
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Barry D Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Graduate Program in Genome Science and Technology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, Knoxville, TN 37996, USA.
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13
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Sicking M, Lang S, Bochen F, Roos A, Drenth JPH, Zakaria M, Zimmermann R, Linxweiler M. Complexity and Specificity of Sec61-Channelopathies: Human Diseases Affecting Gating of the Sec61 Complex. Cells 2021; 10:1036. [PMID: 33925740 PMCID: PMC8147068 DOI: 10.3390/cells10051036] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 12/14/2022] Open
Abstract
The rough endoplasmic reticulum (ER) of nucleated human cells has crucial functions in protein biogenesis, calcium (Ca2+) homeostasis, and signal transduction. Among the roughly one hundred components, which are involved in protein import and protein folding or assembly, two components stand out: The Sec61 complex and BiP. The Sec61 complex in the ER membrane represents the major entry point for precursor polypeptides into the membrane or lumen of the ER and provides a conduit for Ca2+ ions from the ER lumen to the cytosol. The second component, the Hsp70-type molecular chaperone immunoglobulin heavy chain binding protein, short BiP, plays central roles in protein folding and assembly (hence its name), protein import, cellular Ca2+ homeostasis, and various intracellular signal transduction pathways. For the purpose of this review, we focus on these two components, their relevant allosteric effectors and on the question of how their respective functional cycles are linked in order to reconcile the apparently contradictory features of the ER membrane, selective permeability for precursor polypeptides, and impermeability for Ca2+. The key issues are that the Sec61 complex exists in two conformations: An open and a closed state that are in a dynamic equilibrium with each other, and that BiP contributes to its gating in both directions in cooperation with different co-chaperones. While the open Sec61 complex forms an aqueous polypeptide-conducting- and transiently Ca2+-permeable channel, the closed complex is impermeable even to Ca2+. Therefore, we discuss the human hereditary and tumor diseases that are linked to Sec61 channel gating, termed Sec61-channelopathies, as disturbances of selective polypeptide-impermeability and/or aberrant Ca2+-permeability.
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Affiliation(s)
- Mark Sicking
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Sven Lang
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Florian Bochen
- Department of Otorhinolaryngology, Head and Neck Surgery, Saarland University Medical Center, D-66421 Homburg, Germany; (F.B.); (M.L.)
| | - Andreas Roos
- Department of Neuropediatrics, Essen University Hospital, D-45147 Essen, Germany;
| | - Joost P. H. Drenth
- Department of Molecular Gastroenterology and Hepatology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Muhammad Zakaria
- Department of Genetics, Hazara University, Mansehra 21300, Pakistan;
| | - Richard Zimmermann
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Maximilian Linxweiler
- Department of Otorhinolaryngology, Head and Neck Surgery, Saarland University Medical Center, D-66421 Homburg, Germany; (F.B.); (M.L.)
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14
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Targeting of HER/ErbB family proteins using broad spectrum Sec61 inhibitors coibamide A and apratoxin A. Biochem Pharmacol 2020; 183:114317. [PMID: 33152346 DOI: 10.1016/j.bcp.2020.114317] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/17/2023]
Abstract
Coibamide A is a potent cancer cell toxin and one of a select group of natural products that inhibit protein entry into the secretory pathway via a direct inhibition of the Sec61 protein translocon. Many Sec61 client proteins are clinically relevant drug targets once trafficked to their final destination in or outside the cell, however the use of Sec61 inhibitors to block early biosynthesis of specific proteins is at a pre-clinical stage. In the present study we evaluated the action of coibamide A against human epidermal growth factor receptor (HER, ErbB) proteins in representative breast and lung cancer cell types. HERs were selected for this study as they represent a family of Sec61 clients that is frequently dysregulated in human cancers, including coibamide-sensitive cell types. Although coibamide A inhibits biogenesis of a broad range of Sec61 substrate proteins in a presumed substrate-nonselective manner, endogenous HER3 (ErbB-3) and EGFR (ErbB-1) proteins were more sensitive to coibamide A, and the related Sec61 inhibitor apratoxin A, than HER2 (ErbB-2). Despite this rank order of sensitivity (HER3 > EGFR > HER2), Sec61-dependent inhibition by coibamide A was sufficient to decrease cell surface expression of HER2. We report that coibamide A- or apratoxin A-mediated block of HER3 entry into the secretory pathway is unlikely to be mediated by the HER3 signal peptide alone. HER3 (G11L/S15L), that is fully resistant to the highly substrate-selective cotransin analogue CT8, was more resistant than wild-type HER3 but only at low coibamide A (3 nM) concentrations; HER3 (G11L/S15L) expression was inhibited by higher concentrations of either natural product. Time- and concentration-dependent decreases in HER protein expression induced a commensurate reduction in AKT/MAPK signaling in breast and lung cancer cell types and loss in cell viability. Coibamide A potentiated the cytotoxic efficacy of small molecule kinase inhibitors lapatinib and erlotinib in breast and lung cancer cell types, respectively. These data indicate that natural product modulators of Sec61 function have value as chemical probes to interrogate HER/ErbB signaling in treatment-resistant human cancers.
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15
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Lu L, Xu X, Du X, Zeng T, Yang T, Chen Y, Tao Z, Zhong S, Wen J, Zhou C. Transcriptome analyses to reveal the dynamic change mechanism of pigeon magnum during one egg-laying cycle. Mol Reprod Dev 2020; 87:1141-1151. [PMID: 33084116 DOI: 10.1002/mrd.23428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/29/2020] [Accepted: 09/12/2020] [Indexed: 12/14/2022]
Abstract
We analyzed the transcriptome of pigeon magnum in three stages (C1: pre-ovulation, C2: post-ovulation, C3: 5-6 days after ovulation) to elucidate the molecular and cellular events associated with morphological changes during the laying cycle. We observed that C1 was highly developed, apoptosis rate was highest in C2, and C3 attained the smallest size. Through RNA-sequencing, we obtained 54,764,938 (97.2%) high-quality clean reads that aligned to 20,767 genes. Gene expression profile analysis showed the greatest difference between C1 and C3; 3966 differentially expressed genes (DEGs) were identified, of which 2250 genes were upregulated and 1716 genes were downregulated in C1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that protein processing and transport activities were prominent in C1, and upregulated genes included those related to signal recognition particle (SRP), signal recognition particle receptor (SRPR), translocon, GRP78, RRBP1, TRAP, TRAM1, and OST. Egg white protein-related gene expression was highest, with OVALY being the most highly expressed. In C2, apoptosis-related gene expression was higher than in C1, and fatty acid metabolism was active, which may be correlated with magnum tissue regression. Collagen- and laminin-related gene expression was prominent in C1 and C3, indicating roles in egg white protein generation and magnum reconstruction. PR gene expression was highest and exhibited drastic change in the three groups, indicating that PR and its regulation may be involved in changes in magnum morphology and function. Through the identification and functional analysis of DEGs and other crucial genes, this may contribute to understand the egg white protein production, magnum tissue regression, and magnum regeneration mechanisms.
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Affiliation(s)
- Lizhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang, China
| | - Xiaoqin Xu
- Institute of Ecology, China West Normal University, Nanchong, Sichuan, China
| | - Xue Du
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang, China
| | - Tao Zeng
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang, China
| | - Tingbang Yang
- Institute of Ecology, China West Normal University, Nanchong, Sichuan, China
| | - Yao Chen
- Institute of Ecology, China West Normal University, Nanchong, Sichuan, China
| | - Zhengrong Tao
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang, China
| | - Shengliang Zhong
- PingYang XingLiang Pigeon Farming Co. Ltd., Wenzhou, Zhejiang, China
| | - Jihui Wen
- PingYang AoFeng Pigeon Farming Co. Ltd., Wenzhou, Zhejiang, China
| | - Caiquan Zhou
- Institute of Ecology, China West Normal University, Nanchong, Sichuan, China
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16
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Lu KY, Pasaje CFA, Srivastava T, Loiselle DR, Niles JC, Derbyshire E. Phosphatidylinositol 3-phosphate and Hsp70 protect Plasmodium falciparum from heat-induced cell death. eLife 2020; 9:e56773. [PMID: 32975513 PMCID: PMC7518890 DOI: 10.7554/elife.56773] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022] Open
Abstract
Phosphatidylinositol 3-phosphate (PI(3)P) levels in Plasmodium falciparum correlate with tolerance to cellular stresses caused by artemisinin and environmental factors. However, PI(3)P function during the Plasmodium stress response was unknown. Here, we used PI3K inhibitors and antimalarial agents to examine the importance of PI(3)P under thermal conditions recapitulating malarial fever. Live cell microscopy using chemical and genetic reporters revealed that PI(3)P stabilizes the digestive vacuole (DV) under heat stress. We demonstrate that heat-induced DV destabilization in PI(3)P-deficient P. falciparum precedes cell death and is reversible after withdrawal of the stress condition and the PI3K inhibitor. A chemoproteomic approach identified PfHsp70-1 as a PI(3)P-binding protein. An Hsp70 inhibitor and knockdown of PfHsp70-1 phenocopy PI(3)P-deficient parasites under heat shock. Furthermore, PfHsp70-1 downregulation hypersensitizes parasites to heat shock and PI3K inhibitors. Our findings underscore a mechanistic link between PI(3)P and PfHsp70-1 and present a novel PI(3)P function in DV stabilization during heat stress.
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Affiliation(s)
- Kuan-Yi Lu
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke UniversityDurhamUnited States
- Department of Chemistry, Duke UniversityDurhamUnited States
| | | | | | - David R Loiselle
- Department of Pharmacology and Cancer Biology, School of Medicine, Duke UniversityDurhamUnited States
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Emily Derbyshire
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke UniversityDurhamUnited States
- Department of Chemistry, Duke UniversityDurhamUnited States
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17
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Hosomi A, Iida K, Cho T, Iida H, Kaneko M, Suzuki T. The ER-associated protease Ste24 prevents N-terminal signal peptide-independent translocation into the endoplasmic reticulum in Saccharomyces cerevisiae. J Biol Chem 2020; 295:10406-10419. [PMID: 32513868 DOI: 10.1074/jbc.ra120.012575] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
Soluble proteins destined for the secretory pathway contain an N-terminal signal peptide that induces their translocation into the endoplasmic reticulum (ER). The importance of N-terminal signal peptides for ER translocation has been extensively examined over the past few decades. However, in the budding yeast Saccharomyces cerevisiae, a few proteins devoid of a signal peptide are still translocated into the ER and then N-glycosyl-ated. Using signal peptide-truncated reporter proteins, here we report the detection of significant translocation of N-terminal signal peptide-truncated proteins in a yeast mutant strain (ste24Δ) that lacks the endopeptidase Ste24 at the ER membrane. Furthermore, several ER/cytosolic proteins, including Sec61, Sec66, and Sec72, were identified as being involved in the translocation process. On the basis of screening for 20 soluble proteins that may be N-glycosylated in the ER in the ste24Δ strain, we identified the transcription factor Rme1 as a protein that is partially N-glycosylated despite the lack of a signal peptide. These results clearly indicate that some proteins lacking a signal peptide can be translocated into the ER and that Ste24 typically suppresses this process.
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Affiliation(s)
- Akira Hosomi
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Kamiina, Nagano, Japan
| | - Kazuko Iida
- Laboratory of Biomembrane, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Toshihiko Cho
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Hidetoshi Iida
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Masashi Kaneko
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Kamiina, Nagano, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
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18
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Lumangtad LA, Bell TW. The signal peptide as a new target for drug design. Bioorg Med Chem Lett 2020; 30:127115. [PMID: 32209293 PMCID: PMC7138182 DOI: 10.1016/j.bmcl.2020.127115] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/06/2020] [Accepted: 03/15/2020] [Indexed: 01/16/2023]
Abstract
Many current and potential drug targets are membrane-bound or secreted proteins that are expressed and transported via the Sec61 secretory pathway. They are targeted to translocon channels across the membrane of the endoplasmic reticulum (ER) by signal peptides (SPs), which are temporary structures on the N-termini of their nascent chains. During translation, such proteins enter the lumen and membrane of the ER by a process known as co-translational translocation. Small molecules have been found that interfere with this process, decreasing protein expression by recognizing the unique structures of the SPs of particular proteins. The SP may thus become a validated target for designing drugs for numerous disorders, including certain hereditary diseases.
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Affiliation(s)
| | - Thomas W Bell
- Department of Chemistry, University of Nevada, Reno, NV 89557-0216, USA.
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19
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Florentin A, Cobb DW, Kudyba HM, Muralidharan V. Directing traffic: Chaperone-mediated protein transport in malaria parasites. Cell Microbiol 2020; 22:e13215. [PMID: 32388921 PMCID: PMC7282954 DOI: 10.1111/cmi.13215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 12/16/2022]
Abstract
The ability of eukaryotic parasites from the phylum Apicomplexa to cause devastating diseases is predicated upon their ability to maintain faithful and precise protein trafficking mechanisms. Their parasitic life cycle depends on the trafficking of effector proteins to the infected host cell, transport of proteins to several critical organelles required for survival, as well as transport of parasite and host proteins to the digestive organelles to generate the building blocks for parasite growth. Several recent studies have shed light on the molecular mechanisms parasites utilise to transform the infected host cells, transport proteins to essential metabolic organelles and for biogenesis of organelles required for continuation of their life cycle. Here, we review key pathways of protein transport originating and branching from the endoplasmic reticulum, focusing on the essential roles of chaperones in these processes. Further, we highlight key gaps in our knowledge that prevents us from building a holistic view of protein trafficking in these deadly human pathogens.
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Affiliation(s)
- Anat Florentin
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - David W Cobb
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Heather M Kudyba
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Vasant Muralidharan
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
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20
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Abstract
In eukaryotic cells, about one-third of the synthesized proteins are translocated into the endoplasmic reticulum; they are membrane or lumen resident proteins and proteins direct to the Golgi apparatus. The co-translational translocation takes place through the heterotrimeric protein-conducting channel Sec61 which is associated with the ribosome and many accessory components, such as the heterotetrameric translocon-associated protein (TRAP) complex. Recently, microscopic techniques, such as cryo-electron microscopy and cryo-electron tomography, have enabled the determination of the translocation machinery structure. However, at present, there is a lack of understanding regarding the roles of some of its components; indeed, the TRAP complex function during co-translational translocation needs to be established. In addition, TRAP may play a role during unfolded protein response, endoplasmic-reticulum-associated protein degradation and congenital disorder of glycosylation (ssr4 CDG). In this article, I describe the current understanding of the TRAP complex in the light of its possible function(s).
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Affiliation(s)
- Antonietta Russo
- Medical Biochemistry and Molecular Biology, UKS, University of Saarland, Homburg, Germany
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21
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Karamyshev AL, Tikhonova EB, Karamysheva ZN. Translational Control of Secretory Proteins in Health and Disease. Int J Mol Sci 2020; 21:ijms21072538. [PMID: 32268488 PMCID: PMC7177344 DOI: 10.3390/ijms21072538] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
Secretory proteins are synthesized in a form of precursors with additional sequences at their N-terminal ends called signal peptides. The signal peptides are recognized co-translationally by signal recognition particle (SRP). This interaction leads to targeting to the endoplasmic reticulum (ER) membrane and translocation of the nascent chains into the ER lumen. It was demonstrated recently that in addition to a targeting function, SRP has a novel role in protection of secretory protein mRNAs from degradation. It was also found that the quality of secretory proteins is controlled by the recently discovered Regulation of Aberrant Protein Production (RAPP) pathway. RAPP monitors interactions of polypeptide nascent chains during their synthesis on the ribosomes and specifically degrades their mRNAs if these interactions are abolished due to mutations in the nascent chains or defects in the targeting factor. It was demonstrated that pathological RAPP activation is one of the molecular mechanisms of human diseases associated with defects in the secretory proteins. In this review, we discuss recent progress in understanding of translational control of secretory protein biogenesis on the ribosome and pathological consequences of its dysregulation in human diseases.
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Affiliation(s)
- Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
- Correspondence: (A.L.K.); (Z.N.K.); Tel.: +1-806-743-4102 (A.L.K.); +1-806-834-5075 (Z.N.K.)
| | - Elena B. Tikhonova
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
| | - Zemfira N. Karamysheva
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
- Correspondence: (A.L.K.); (Z.N.K.); Tel.: +1-806-743-4102 (A.L.K.); +1-806-834-5075 (Z.N.K.)
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22
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Hsu HM, Huang YH, Aryal S, Liu HW, Chen C, Chen SH, Chu CH, Tai JH. Endomembrane Protein Trafficking Regulated by a TvCyP2 Cyclophilin in the Protozoan Parasite, Trichomonas vaginalis. Sci Rep 2020; 10:1275. [PMID: 31988345 PMCID: PMC6985235 DOI: 10.1038/s41598-020-58270-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/10/2020] [Indexed: 01/08/2023] Open
Abstract
In Trichomonas vaginalis, the TvCyP1-catalyzed conformational switches of two glycinyl-prolyl imide bonds in Myb3 were previously shown to regulate the trafficking of Myb3 from cytoplasmic membrane compartments towards the nucleus. In this study, TvCyP2 was identified as a second cyclophilin that binds to Myb3 at the same dipeptide motifs. The enzymatic proficiency of TvCyP2, but not its binding to Myb3, was aborted by a mutation of Arg75 in the catalytic domain. TvCyP2 was localized to the endoplasmic reticulum with a weak signal that extensively extends into the cytoplasm as well as to the plasma membrane according to an immunofluorescence assay. Moreover, TvCyP2 was co-enriched with TvCyP1 and Myb3 in various membrane fractions purified by differential and gradient centrifugation. TvCyP2 was found to proficiently enzymatically regulate the distribution of TvCyP1 and Myb3 among purified membrane fractions, and to localize TvCyP1 in hydrogenosomes and on plasma membranes. Protein complexes immunoprecipitated from lysates of cells overexpressing TvCyP1 and TvCyP2 were found to share some common components, like TvCyP1, TvCyP2, TvBip, Myb3, TvHSP72, and the hydrogenosomal heat shock protein 70 (HSP70). Direct interaction between TvCyP1 and TvCyP2 was confirmed by a GST pull-down assay. Fusion of vesicles with hydrogenosomes was observed by transmission electron microscopy, whereas TvCyP1, TvCyP2, and Myb3 were each detected at the fusion junction by immunoelectron microscopy. These observations suggest that T. vaginalis may have evolved a novel protein trafficking pathway to deliver proteins among the endomembrane compartments, hydrogenosomes and plasma membranes.
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Affiliation(s)
- Hong-Ming Hsu
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Hsin Huang
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Sarita Aryal
- Structural Biology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsing-Wei Liu
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chinpan Chen
- Structural Biology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Hsin Chu
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| | - Jung-Hsiang Tai
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei, Taiwan. .,Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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Milani A, Basirnejad M, Bolhassani A. Heat-shock proteins in diagnosis and treatment: an overview of different biochemical and immunological functions. Immunotherapy 2020; 11:215-239. [PMID: 30730280 DOI: 10.2217/imt-2018-0105] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Heat-shock proteins (HSPs) have been involved in different functions including chaperone activity, protein folding, apoptosis, autophagy and immunity. The HSP families have powerful effects on the stimulation of innate immune responses through Toll-like receptors and scavenger receptors. Moreover, HSP-mediated phagocytosis directly enhances the processing and presentation of internalized antigens via the endocytic pathway in adaptive immune system. These properties of HSPs have been used for development of prophylactic and therapeutic vaccines against infectious and noninfectious diseases. Several studies also demonstrated the relationship between HSPs and drug resistance as well as their use as a novel biomarker for detecting tumors in patients. The present review describes different roles of HSPs in biology and medicine especially biochemical and immunological aspects.
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Affiliation(s)
- Alireza Milani
- Department of Hepatitis & AIDS, Pasteur Institute of Iran, Tehran, Iran.,Iranian Comprehensive Hemophilia Care Center, Tehran, Iran
| | | | - Azam Bolhassani
- Department of Hepatitis & AIDS, Pasteur Institute of Iran, Tehran, Iran
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24
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Abstract
Endoplasmic reticulum-associated degradation (ERAD) is an essential process that removes misfolded proteins from the ER, preventing cellular dysfunction and disease. While most of the key components of ERAD are known, their specific localization remains a mystery. This study uses in situ cryo-electron tomography to directly visualize the ERAD machinery within the native cellular environment. Proteasomes and Cdc48, the complexes that extract and degrade ER proteins, cluster together in non–membrane-bound cytosolic microcompartments that contact ribosome-free patches on the ER membrane. This discrete molecular organization may facilitate efficient ERAD. Structural analysis reveals that proteasomes directly engage ER-localized substrates, providing evidence for a noncanonical “direct ERAD” pathway. In addition, live-cell fluorescence microscopy suggests that these ER-associated proteasome clusters form by liquid–liquid phase separation. To promote the biochemical reactions of life, cells can compartmentalize molecular interaction partners together within separated non–membrane-bound regions. It is unknown whether this strategy is used to facilitate protein degradation at specific locations within the cell. Leveraging in situ cryo-electron tomography to image the native molecular landscape of the unicellular alga Chlamydomonas reinhardtii, we discovered that the cytosolic protein degradation machinery is concentrated within ∼200-nm foci that contact specialized patches of endoplasmic reticulum (ER) membrane away from the ER–Golgi interface. These non–membrane-bound microcompartments exclude ribosomes and consist of a core of densely clustered 26S proteasomes surrounded by a loose cloud of Cdc48. Active proteasomes in the microcompartments directly engage with putative substrate at the ER membrane, a function canonically assigned to Cdc48. Live-cell fluorescence microscopy revealed that the proteasome clusters are dynamic, with frequent assembly and fusion events. We propose that the microcompartments perform ER-associated degradation, colocalizing the degradation machinery at specific ER hot spots to enable efficient protein quality control.
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Haßdenteufel S, Johnson N, Paton AW, Paton JC, High S, Zimmermann R. Chaperone-Mediated Sec61 Channel Gating during ER Import of Small Precursor Proteins Overcomes Sec61 Inhibitor-Reinforced Energy Barrier. Cell Rep 2019; 23:1373-1386. [PMID: 29719251 PMCID: PMC5946456 DOI: 10.1016/j.celrep.2018.03.122] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 02/15/2018] [Accepted: 03/27/2018] [Indexed: 11/24/2022] Open
Abstract
Protein transport into the mammalian endoplasmic reticulum (ER) is mediated by the heterotrimeric Sec61 channel. The signal recognition particle (SRP) and TRC systems and Sec62 have all been characterized as membrane-targeting components for small presecretory proteins, whereas Sec63 and the lumenal chaperone BiP act as auxiliary translocation components. Here, we report the transport requirements of two natural, small presecretory proteins and engineered variants using semipermeabilized human cells after the depletion of specific ER components. Our results suggest that hSnd2, Sec62, and SRP and TRC receptor each provide alternative targeting pathways for short secretory proteins and define rules of engagement for the actions of Sec63 and BiP during their membrane translocation. We find that the Sec62/Sec63 complex plus BiP can facilitate Sec61 channel opening, thereby allowing precursors that have weak signal peptides or other inhibitory features to translocate. A Sec61 inhibitor can mimic the effect of BiP depletion on Sec61 gating, suggesting that they both act at the same essential membrane translocation step. Small human presecretory proteins use all known targeting routes to the Sec61 complex Their insertion into Sec61 is selectively facilitated by BiP, Sec62, and Sec63 Selectivity is driven by weak signal peptides plus downstream inhibitory features Cyclic heptadepsipeptides phenocopy the effect of BiP depletion on Sec61 gating
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Affiliation(s)
- Sarah Haßdenteufel
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany.
| | - Nicholas Johnson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Adrienne W Paton
- Research Centre for Infectious Disease, University of Adelaide, Adelaide, SA 5005, Australia
| | - James C Paton
- Research Centre for Infectious Disease, University of Adelaide, Adelaide, SA 5005, Australia
| | - Stephen High
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany.
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Tsukazaki T. Structure-based working model of SecDF, a proton-driven bacterial protein translocation factor. FEMS Microbiol Lett 2019; 365:4987937. [PMID: 29718185 PMCID: PMC5974789 DOI: 10.1093/femsle/fny112] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/26/2018] [Indexed: 01/17/2023] Open
Abstract
The bacterial membrane protein SecDF enhances protein translocation across the membrane driven by the complex of SecA ATPase and SecYEG. Many newly synthesized proteins in the cytoplasm are programmed to be translocated to the periplasm via the narrow channel that is formed in the center of SecYEG. During the protein-translocation process, SecDF is proposed to undergo repeated conformational transitions to pull out the precursor protein from the SecYEG channel into the periplasm. Once SecDF captures the precursor protein on the periplasmic surface, SecDF can complete protein translocation even if SecA function is inactivated by ATP depletion, implying that SecDF is a protein-translocation motor that works independent of SecA. Structural and functional analyses of SecDF in 2011 suggested that SecDF utilizes the proton gradient and interacts with precursor protein in the flexible periplasmic region. The crystal structures of SecDF in different states at more than 3Å resolution were reported in 2017 and 2018, which further improved our understanding of the dynamic molecular mechanisms of SecDF. This review summarizes recent structural studies of SecDF.
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Affiliation(s)
- Tomoya Tsukazaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
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27
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Khan HA, Margulies CE. The Role of Mammalian Creb3-Like Transcription Factors in Response to Nutrients. Front Genet 2019; 10:591. [PMID: 31293620 PMCID: PMC6598459 DOI: 10.3389/fgene.2019.00591] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 06/04/2019] [Indexed: 12/18/2022] Open
Abstract
Our ability to overcome the challenges behind metabolic disorders will require a detailed understanding of the regulation of responses to nutrition. The Creb3 transcription factor family appears to have a unique regulatory role that links cellular secretory capacity with development, nutritional state, infection, and other stresses. This role in regulating individual secretory capacity genes could place this family of transcription factors at an important regulatory intersection mediating an animal’s responses to nutrients and other environmental challenges. Interestingly, in both humans and mice, individuals with mutations in Creb3L3/CrebH, one of the Creb3 family members, exhibit hypertriglyceridemia (HTG) thus linking this transcription factor to lipid metabolism. We are beginning to understand how Creb3L3 and related family members are regulated and to dissect the potential redundancy and cross talk between distinct family members, thereby mediating both healthy and pathological responses to the environment. Here, we review the current knowledge on the regulation of Creb3 family transcription factor activity, their target genes, and their role in metabolic disease.
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Affiliation(s)
- Haris A Khan
- Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Carla E Margulies
- Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany
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28
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Garbuz DG, Zatsepina OG, Evgen’ev MB. The Major Human Stress Protein Hsp70 as a Factor of Protein Homeostasis and a Cytokine-Like Regulator. Mol Biol 2019. [DOI: 10.1134/s0026893319020055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Silencing of Aberrant Secretory Protein Expression by Disease-Associated Mutations. J Mol Biol 2019; 431:2567-2580. [PMID: 31100385 DOI: 10.1016/j.jmb.2019.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/04/2019] [Accepted: 05/07/2019] [Indexed: 11/23/2022]
Abstract
Signal recognition particle (SRP) recognizes signal sequences of secretory proteins and targets them to the endoplasmic reticulum membrane for translocation. Many human diseases are connected with defects in signal sequences. The current dogma states that the molecular basis of the disease-associated mutations in the secretory proteins is connected with defects in their transport. Here, we demonstrate for several secretory proteins with disease-associated mutations that the molecular mechanism is different from the dogma. Positively charged or helix-breaking mutations in the signal sequence hydrophobic core prevent synthesis of the aberrant proteins and lead to degradation of their mRNAs. The degree of mRNA depletion depends on the location and severity of the mutation in the signal sequence and correlates with inhibition of SRP interaction. Thus, SRP protects secretory protein mRNAs from degradation. The data demonstrate that if disease-associated mutations obstruct SRP interaction, they lead to silencing of the mutated protein expression.
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30
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Eeyarestatin Compounds Selectively Enhance Sec61-Mediated Ca 2+ Leakage from the Endoplasmic Reticulum. Cell Chem Biol 2019; 26:571-583.e6. [PMID: 30799222 PMCID: PMC6483976 DOI: 10.1016/j.chembiol.2019.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/06/2018] [Accepted: 01/24/2019] [Indexed: 01/01/2023]
Abstract
Eeyarestatin 1 (ES1) inhibits p97-dependent protein degradation, Sec61-dependent protein translocation into the endoplasmic reticulum (ER), and vesicular transport within the endomembrane system. Here, we show that ES1 impairs Ca2+ homeostasis by enhancing the Ca2+ leakage from mammalian ER. A comparison of various ES1 analogs suggested that the 5-nitrofuran (5-NF) ring of ES1 is crucial for this effect. Accordingly, the analog ES24, which conserves the 5-NF domain of ES1, selectively inhibited protein translocation into the ER, displayed the highest potency on ER Ca2+ leakage of ES1 analogs studied and induced Ca2+-dependent cell death. Using small interfering RNA-mediated knockdown of Sec61α, we identified Sec61 complexes as the targets that mediate the gain of Ca2+ leakage induced by ES1 and ES24. By interacting with the lateral gate of Sec61α, ES1 and ES24 likely capture Sec61 complexes in a Ca2+-permeable, open state, in which Sec61 complexes allow Ca2+ leakage but are translocation incompetent. ES1, ES2, and ES24 deplete Ca2+ in ER ESR35 and ES47 do not affect cellular Ca2+ homeostasis The most potent eeyarestatin, ES24, comprises only the 5-nitrofuran domain ES1 and ES24 target Sec61 complexes in ER
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31
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Coelho JPL, Stahl M, Bloemeke N, Meighen-Berger K, Alvira CP, Zhang ZR, Sieber SA, Feige MJ. A network of chaperones prevents and detects failures in membrane protein lipid bilayer integration. Nat Commun 2019; 10:672. [PMID: 30737405 PMCID: PMC6368539 DOI: 10.1038/s41467-019-08632-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
A fundamental step in membrane protein biogenesis is their integration into the lipid bilayer with a defined orientation of each transmembrane segment. Despite this, it remains unclear how cells detect and handle failures in this process. Here we show that single point mutations in the membrane protein connexin 32 (Cx32), which cause Charcot-Marie-Tooth disease, can cause failures in membrane integration. This leads to Cx32 transport defects and rapid degradation. Our data show that multiple chaperones detect and remedy this aberrant behavior: the ER-membrane complex (EMC) aids in membrane integration of low-hydrophobicity transmembrane segments. If they fail to integrate, these are recognized by the ER-lumenal chaperone BiP. Ultimately, the E3 ligase gp78 ubiquitinates Cx32 proteins, targeting them for degradation. Thus, cells use a coordinated system of chaperones for the complex task of membrane protein biogenesis, which can be compromised by single point mutations, causing human disease.
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Affiliation(s)
- João P L Coelho
- Center for Integrated Protein Science at the Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Matthias Stahl
- Center for Integrated Protein Science at the Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
- SciLifeLab, Department of Oncology-Pathology, Karolinska Institutet, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Nicolas Bloemeke
- Center for Integrated Protein Science at the Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Kevin Meighen-Berger
- Center for Integrated Protein Science at the Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Carlos Piedrafita Alvira
- Center for Integrated Protein Science at the Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Zai-Rong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Stephan A Sieber
- Center for Integrated Protein Science at the Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Matthias J Feige
- Center for Integrated Protein Science at the Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany.
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstr. 2a, 85748, Garching, Germany.
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32
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Cardon F, Pallisse R, Bardor M, Caron A, Vanier J, Ele Ekouna JP, Lerouge P, Boitel‐Conti M, Guillet M. Brassica rapa hairy root based expression system leads to the production of highly homogenous and reproducible profiles of recombinant human alpha-L-iduronidase. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:505-516. [PMID: 30058762 PMCID: PMC6335068 DOI: 10.1111/pbi.12994] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/02/2018] [Accepted: 07/22/2018] [Indexed: 05/28/2023]
Abstract
The Brassica rapa hairy root based expression platform, a turnip hairy root based expression system, is able to produce human complex glycoproteins such as the alpha-L-iduronidase (IDUA) with an activity similar to the one produced by Chinese Hamster Ovary (CHO) cells. In this article, a particular attention has been paid to the N- and O-glycosylation that characterize the alpha-L-iduronidase produced using this hairy root based system. This analysis showed that the recombinant protein is characterized by highly homogeneous post translational profiles enabling a strong batch to batch reproducibility. Indeed, on each of the 6 N-glycosylation sites of the IDUA, a single N-glycan composed of a core Man3 GlcNAc2 carrying one beta(1,2)-xylose and one alpha(1,3)-fucose epitope (M3XFGN2) was identified, highlighting the high homogeneity of the production system. Hydroxylation of proline residues and arabinosylation were identified during O-glycosylation analysis, still with a remarkable reproducibility. This platform is thus positioned as an effective and consistent expression system for the production of human complex therapeutic proteins.
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Affiliation(s)
| | | | - Muriel Bardor
- Laboratoire Glyco‐MEV EA4358UNIROUENNormandie UniversitéRouenFrance
- Institut Universitaire de France (I.U.F.)Paris Cedex 05France
| | | | - Jessica Vanier
- Laboratoire Glyco‐MEV EA4358UNIROUENNormandie UniversitéRouenFrance
| | - Jean Pierre Ele Ekouna
- Biologie des Plantes et Innovation (BIOPI)Université de Picardie Jules VerneAmiensFrance
| | - Patrice Lerouge
- Laboratoire Glyco‐MEV EA4358UNIROUENNormandie UniversitéRouenFrance
| | - Michèle Boitel‐Conti
- Biologie des Plantes et Innovation (BIOPI)Université de Picardie Jules VerneAmiensFrance
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Sun LZ, Wang CH, Luo MB, Li H. Trapped and non-trapped polymer translocations through a spherical pore. J Chem Phys 2019; 150:024904. [PMID: 30646715 DOI: 10.1063/1.5063331] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The polymer translocation through a spherical pore is studied using the Langevin dynamics simulation. The translocation events are classified into two types: one is the trapped translocation in which the entire polymer is trapped in the pore and the other is the non-trapped translocation where the pore cannot hold the whole polymer. We find that the trapped translocation is favored at large spheres and small external voltages. However, the monomer-pore attraction would lead to the non-monotonic behavior of the trapped translocation possibility out of all translocation events. Moreover, both the trapped and non-trapped translocation times are dependent on the polymer length, pore size, external voltage, and the monomer-pore attraction. There exist two pathways for the polymer in the trapped translocation: an actively trapped pathway for the polymer trapped in the pore before the head monomer arrives at the pore exit, and a passively trapped pathway for the polymer trapped in the pore while the head monomer is struggling to move out of the pore. The studies of trapped pathways can provide a deep understanding of the polymer translocation behavior.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Chang-Hui Wang
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Haibin Li
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
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Lang S, Nguyen D, Pfeffer S, Förster F, Helms V, Zimmermann R. Functions and Mechanisms of the Human Ribosome-Translocon Complex. Subcell Biochem 2019; 93:83-141. [PMID: 31939150 DOI: 10.1007/978-3-030-28151-9_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The membrane of the endoplasmic reticulum (ER) in human cells harbors the protein translocon, which facilitates membrane insertion and translocation of almost every newly synthesized polypeptide targeted to organelles of the secretory pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins, which are associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, Sec61 channel opening and closing, and modification of precursor polypeptides in transit through the Sec61 complex. Recently, cryoelectron tomography of translocons in native ER membranes has given unprecedented insights into the architecture and dynamics of the native, ribosome-associated translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion or translocation of newly synthesized polypeptides as well as the possible roles of the Sec61 channel as a passive ER calcium leak channel and regulator of ATP/ADP exchange between cytosol and ER.
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Affiliation(s)
- Sven Lang
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany.
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- ZMBH, 69120, Heidelberg, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Richard Zimmermann
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany
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35
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Klein W, Rutz C, Eckhard J, Provinciael B, Specker E, Neuenschwander M, Kleinau G, Scheerer P, von Kries JP, Nazaré M, Vermeire K, Schülein R. Use of a sequential high throughput screening assay to identify novel inhibitors of the eukaryotic SRP-Sec61 targeting/translocation pathway. PLoS One 2018; 13:e0208641. [PMID: 30543669 PMCID: PMC6292634 DOI: 10.1371/journal.pone.0208641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/20/2018] [Indexed: 11/22/2022] Open
Abstract
The SRP-Sec61 targeting/translocation pathway of eukaryotic cells targets nascent protein chains to the membrane of the endoplasmic reticulum. Using this machinery, secretory proteins are translocated across this membrane whereas membrane proteins are integrated into the lipid bilayer. One of the key players of the pathway is the protein-conducting Sec61 (translocon) complex of the endoplasmic reticulum. The Sec61 complex has no enzymatic activity, is expressed only intracellularly and is difficult to purify and to reconstitute. Screening for small molecule inhibitors impairing its functions is thus notoriously difficult. Such inhibitors may not only be valuable tools for cell biology, they may also represent novel anti-tumor drugs. Here we have developed a two-step, sequential screening assay for inhibitors of the whole SRP-Sec61 targeting/translocation pathway which might include molecules affecting Sec61 complex functions. The resulting hit compounds were analyzed using a whole cell biosynthesis assay and a cell free transcription/translation/translocation assay. Using this methodology, we identified novel compounds inhibiting this pathway. Following structure-based back screening, one of these substances was analyzed in more detail and we could show that it indeed impairs translocation at the level of the Sec61 complex. A slightly modified methodology may be used in the future to screen for substances affecting SecYEG, the bacterial ortholog of the Sec61 complex in order to derive novel antibiotic drugs.
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Affiliation(s)
- Wolfgang Klein
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Claudia Rutz
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Jamina Eckhard
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Becky Provinciael
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Edgar Specker
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | | | - Gunnar Kleinau
- Charité—Universitätsmedizin Berlin, Campus Charité Mitte, Charité Centrum Grundlagenmedizin CC2, Institut für Medizinische Physik und Biophysik, Group Protein X-ray Crystallography & Signal Transduction, Berlin, Germany
| | - Patrick Scheerer
- Charité—Universitätsmedizin Berlin, Campus Charité Mitte, Charité Centrum Grundlagenmedizin CC2, Institut für Medizinische Physik und Biophysik, Group Protein X-ray Crystallography & Signal Transduction, Berlin, Germany
| | | | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Kurt Vermeire
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Ralf Schülein
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- * E-mail:
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36
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Depaoli MR, Hay JC, Graier WF, Malli R. The enigmatic ATP supply of the endoplasmic reticulum. Biol Rev Camb Philos Soc 2018; 94:610-628. [PMID: 30338910 PMCID: PMC6446729 DOI: 10.1111/brv.12469] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/20/2018] [Accepted: 08/30/2018] [Indexed: 12/11/2022]
Abstract
The endoplasmic reticulum (ER) is a functionally and morphologically complex cellular organelle largely responsible for a variety of crucial functions, including protein folding, maturation and degradation. Furthermore, the ER plays an essential role in lipid biosynthesis, dynamic Ca2+ storage, and detoxification. Malfunctions in ER‐related processes are responsible for the genesis and progression of many diseases, such as heart failure, cancer, neurodegeneration and metabolic disorders. To fulfill many of its vital functions, the ER relies on a sufficient energy supply in the form of adenosine‐5′‐triphosphate (ATP), the main cellular energy source. Despite landmark discoveries and clarification of the functional principles of ER‐resident proteins and key ER‐related processes, the mechanism underlying ER ATP transport remains somewhat enigmatic. Here we summarize ER‐related ATP‐consuming processes and outline our knowledge about the nature and function of the ER energy supply.
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Affiliation(s)
- Maria R Depaoli
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Jesse C Hay
- Division of Biological Sciences and Center for Structural and Functional Neuroscience, The University of Montana, 32 Campus Drive, HS410, Missoula, MT 59812-4824, U.S.A
| | - Wolfgang F Graier
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria.,BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Roland Malli
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria.,BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
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37
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Karamyshev AL, Karamysheva ZN. Lost in Translation: Ribosome-Associated mRNA and Protein Quality Controls. Front Genet 2018; 9:431. [PMID: 30337940 PMCID: PMC6180196 DOI: 10.3389/fgene.2018.00431] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/11/2018] [Indexed: 12/15/2022] Open
Abstract
Aberrant, misfolded, and mislocalized proteins are often toxic to cells and result in many human diseases. All proteins and their mRNA templates are subject to quality control. There are several distinct mechanisms that control the quality of mRNAs and proteins during translation at the ribosome. mRNA quality control systems, nonsense-mediated decay, non-stop decay, and no-go decay detect premature stop codons, the absence of a natural stop codon, and stalled ribosomes in translation, respectively, and degrade their mRNAs. Defective truncated polypeptide nascent chains generated from faulty mRNAs are degraded by ribosome-associated protein quality control pathways. Regulation of aberrant protein production, a novel pathway, senses aberrant proteins by monitoring the status of nascent chain interactions during translation and triggers degradation of their mRNA. Here, we review the current progress in understanding of the molecular mechanisms of mRNA and protein quality controls at the ribosome during translation.
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Affiliation(s)
- Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Zemfira N Karamysheva
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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38
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Nguyen D, Stutz R, Schorr S, Lang S, Pfeffer S, Freeze HH, Förster F, Helms V, Dudek J, Zimmermann R. Proteomics reveals signal peptide features determining the client specificity in human TRAP-dependent ER protein import. Nat Commun 2018; 9:3765. [PMID: 30217974 PMCID: PMC6138672 DOI: 10.1038/s41467-018-06188-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 08/23/2018] [Indexed: 12/22/2022] Open
Abstract
In mammalian cells, one-third of all polypeptides are transported into or across the ER membrane via the Sec61 channel. While the Sec61 complex facilitates translocation of all polypeptides with amino-terminal signal peptides (SP) or transmembrane helices, the Sec61-auxiliary translocon-associated protein (TRAP) complex supports translocation of only a subset of precursors. To characterize determinants of TRAP substrate specificity, we here systematically identify TRAP-dependent precursors by analyzing cellular protein abundance changes upon TRAP depletion using quantitative label-free proteomics. The results are validated in independent experiments by western blotting, quantitative RT-PCR, and complementation analysis. The SPs of TRAP clients exhibit above-average glycine-plus-proline content and below-average hydrophobicity as distinguishing features. Thus, TRAP may act as SP receptor on the ER membrane’s cytosolic face, recognizing precursor polypeptides with SPs of high glycine-plus-proline content and/or low hydrophobicity, and triggering substrate-specific opening of the Sec61 channel through interactions with the ER-lumenal hinge of Sec61α. While Sec61 enables ER import of all polypeptides with N-terminal signal peptides, only selected clients are accepted for TRAP-assisted ER import. Here, the authors use a proteomics approach to characterize TRAP-dependent clients, identifying signal peptide features that govern recognition by TRAP.
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Affiliation(s)
- Duy Nguyen
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Regine Stutz
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany
| | - Stefan Schorr
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany
| | - Stefan Pfeffer
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, 82152, Martinsried, Germany
| | - Hudson H Freeze
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany.
| | - Johanna Dudek
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany.
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany.
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39
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Mavylutov T, Chen X, Guo L, Yang J. APEX2- tagging of Sigma 1-receptor indicates subcellular protein topology with cytosolic N-terminus and ER luminal C-terminus. Protein Cell 2018; 9:733-737. [PMID: 28929457 PMCID: PMC6053353 DOI: 10.1007/s13238-017-0468-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Timur Mavylutov
- Department of Anesthesiology, University of Wisconsin SMPH, Madison, WI, 53705, USA
| | - Xi Chen
- Department of Anesthesiology, University of Wisconsin SMPH, Madison, WI, 53705, USA
| | - Lianwang Guo
- Department of Surgery and Physiology & Cell Biology, Ohio State University, Columbus, OH, 43210, USA
| | - Jay Yang
- Department of Anesthesiology, University of Wisconsin SMPH, Madison, WI, 53705, USA.
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40
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Van Puyenbroeck V, Vermeire K. Inhibitors of protein translocation across membranes of the secretory pathway: novel antimicrobial and anticancer agents. Cell Mol Life Sci 2018; 75:1541-1558. [PMID: 29305616 PMCID: PMC5897483 DOI: 10.1007/s00018-017-2743-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/15/2017] [Accepted: 12/27/2017] [Indexed: 12/22/2022]
Abstract
Proteins routed to the secretory pathway start their journey by being transported across biological membranes, such as the endoplasmic reticulum. The essential nature of this protein translocation process has led to the evolution of several factors that specifically target the translocon and block translocation. In this review, various translocation pathways are discussed together with known inhibitors of translocation. Properties of signal peptide-specific systems are highlighted for the development of new therapeutic and antimicrobial applications, as compounds can target signal peptides from either host cells or pathogens and thereby selectively prevent translocation of those specific proteins. Broad inhibition of translocation is also an interesting target for the development of new anticancer drugs because cancer cells heavily depend on efficient protein translocation into the endoplasmic reticulum to support their fast growth.
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Affiliation(s)
- Victor Van Puyenbroeck
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000, Leuven, Belgium
| | - Kurt Vermeire
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000, Leuven, Belgium.
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41
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Kim MJ, Min SH, Shin SY, Kim MN, Lee H, Jang JY, Kim SW, Park KS, Jung HS. Attenuation of PERK enhances glucose-stimulated insulin secretion in islets. J Endocrinol 2018; 236:125-136. [PMID: 29273589 DOI: 10.1530/joe-17-0497] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/22/2017] [Indexed: 01/18/2023]
Abstract
PERK is a pancreatic endoplasmic reticulum (ER) kinase. Its complete deletion in pancreatic β cells induces insulin deficiency; however, the effects of partial Perk suppression are unclear. We investigated the effect of partial PERK suppression using the specific PERK inhibitors GSK2606414 and GSK2656157. Low-dose GSK2606414 treatment for 24 h enhanced glucose-stimulated insulin secretion (GSIS), islet insulin content and calcium transit in mouse (at 40 nM) and human (at 50-100 nM) pancreatic islets. GSK2606414 also induced the expression of the ER chaperone BiP and the release of calcium from the ER. When Bip expression was inhibited using a Bip siRNA, the GSK2606414-induced augmentation of the ER calcium level, islet insulin contents, glucose-stimulated cytosolic calcium transit and GSIS were abrogated. In both wild-type and insulin-deficient Atg7-knockout mice, 8 weeks of GSK2656157 treatment enhanced GSIS and improved hyperglycemia without affecting body weight. In conclusion, partial PERK inhibition induced BiP expression in islets, increased glucose-stimulated calcium transit and islet insulin contents and enhanced GSIS, suggesting that low-dose PERK inhibitors could potentially be used to treat insulin deficiency.
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Affiliation(s)
- Min Joo Kim
- Department of Internal MedicineSeoul National University College of Medicine, Seoul, Republic of Korea
| | - Se Hee Min
- Department of Internal MedicineSeoul National University College of Medicine, Seoul, Republic of Korea
| | - Seon Young Shin
- Innovative Research Institute for Cell TherapySeoul, Republic of Korea
| | - Mi Na Kim
- Innovative Research Institute for Cell TherapySeoul, Republic of Korea
| | - Hakmo Lee
- Innovative Research Institute for Cell TherapySeoul, Republic of Korea
| | - Jin Young Jang
- Department of SurgerySeoul National University College of Medicine, Seoul, Republic of Korea
| | - Sun-Whe Kim
- Department of SurgerySeoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyong Soo Park
- Department of Internal MedicineSeoul National University College of Medicine, Seoul, Republic of Korea
- Innovative Research Institute for Cell TherapySeoul, Republic of Korea
| | - Hye Seung Jung
- Department of Internal MedicineSeoul National University College of Medicine, Seoul, Republic of Korea
- Innovative Research Institute for Cell TherapySeoul, Republic of Korea
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42
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Lang S, Pfeffer S, Lee PH, Cavalié A, Helms V, Förster F, Zimmermann R. An Update on Sec61 Channel Functions, Mechanisms, and Related Diseases. Front Physiol 2017; 8:887. [PMID: 29163222 PMCID: PMC5672155 DOI: 10.3389/fphys.2017.00887] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/19/2017] [Indexed: 12/18/2022] Open
Abstract
The membrane of the endoplasmic reticulum (ER) of nucleated human cells harbors the protein translocon, which facilitates membrane integration or translocation of almost every newly synthesized polypeptide targeted to organelles of the endo- and exocytotic pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins and complexes that are permanently or transiently associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, modification of precursor polypeptides in transit through the Sec61 complex, and Sec61 channel gating, i.e., dynamic regulation of the pore forming subunit to mediate precursor transport and calcium efflux. Recently, cryoelectron tomography of translocons in native ER membrane vesicles, derived from human cell lines or patient fibroblasts, and even intact cells has given unprecedented insights into the architecture and dynamics of the native translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion, and translocation of newly synthesized polypeptides as well as the putative physiological roles of the Sec61 channel as a passive ER calcium leak channel. Furthermore, the structural insights into the Sec61 channel are incorporated into an overview and update on Sec61 channel-related diseases—the Sec61 channelopathies—and novel therapeutic concepts for their treatment.
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Affiliation(s)
- Sven Lang
- Competence Center for Molecular Medicine, Saarland University Medical School, Homburg, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Po-Hsien Lee
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Adolfo Cavalié
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, Homburg, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Richard Zimmermann
- Competence Center for Molecular Medicine, Saarland University Medical School, Homburg, Germany
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43
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Kuhn A, Haase M, Leptihn S. Assisted and Unassisted Protein Insertion into Liposomes. Biophys J 2017; 113:1187-1193. [PMID: 28454841 PMCID: PMC5607036 DOI: 10.1016/j.bpj.2017.03.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/30/2017] [Accepted: 03/31/2017] [Indexed: 02/04/2023] Open
Abstract
The insertion of newly synthesized membrane proteins is a well-regulated and fascinating process occurring in every living cell. Several translocases and insertases have been found in prokaryotic and eukaryotic cells, the Sec61 complex and the Get complex in the endoplasmic reticulum and the SecYEG complex and YidC in bacteria and archaea. In mitochondria, TOM and TIM complexes transport nuclear-encoded proteins, whereas the Oxa1 is required for the insertion of mitochondria-encoded membrane proteins. Related to the bacterial YidC and the mitochondrial Oxa1 are the Alb3 and Alb4 proteins in chloroplasts. These membrane insertases are comparably simple and can be studied in vitro, after their biochemical purification and reconstitution in artificial lipid bilayers such as liposomes or nanodiscs. Here, we describe the recent progress to study the molecular mechanism of YidC-dependent and unassisted membrane insertion at the single molecule level.
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Affiliation(s)
- Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
| | - Maximilian Haase
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
| | - Sebastian Leptihn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany.
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44
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Haßdenteufel S, Sicking M, Schorr S, Aviram N, Fecher-Trost C, Schuldiner M, Jung M, Zimmermann R, Lang S. hSnd2 protein represents an alternative targeting factor to the endoplasmic reticulum in human cells. FEBS Lett 2017; 591:3211-3224. [PMID: 28862756 DOI: 10.1002/1873-3468.12831] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022]
Abstract
Recently, understanding of protein targeting to the endoplasmic reticulum (ER) was expanded by the discovery of multiple pathways that function in parallel to the signal recognition particle (SRP). Guided entry of tail-anchored proteins and SRP independent (SND) are two such targeting pathways described in yeast. So far, no human SND component is functionally characterized. Here, we report hSnd2 as the first constituent of the human SND pathway able to support substrate-specific protein targeting to the ER. Similar to its yeast counterpart, hSnd2 is assumed to function as a membrane-bound receptor preferentially targeting precursors carrying C-terminal transmembrane domains. Our genetic and physical interaction studies show that hSnd2 is part of a complex network of targeting and translocation that is dynamically regulated.
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Affiliation(s)
- Sarah Haßdenteufel
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Stefan Schorr
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Naama Aviram
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Claudia Fecher-Trost
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Saarland University, Homburg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Martin Jung
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Richard Zimmermann
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
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45
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The complex co-translational processing of glycoprotein GP5 of type 1 porcine reproductive and respiratory syndrome virus. Virus Res 2017; 240:112-120. [PMID: 28807563 DOI: 10.1016/j.virusres.2017.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 11/20/2022]
Abstract
GP5 and M, the major membrane proteins of porcine reproductive and respiratory syndrome virus (PRRSV), are the driving force for virus budding and a target for antibodies. We studied co-translational processing of GP5 from an European PRRSV-1 strain. Using mass spectrometry, we show that in virus particles of a Lelystad variant, the signal peptide of GP5 was absent due to cleavage between glycine-34 and asparagine-35. This cleavage site removes an epitope for a neutralizing monoclonal antibody, but leaves intact another epitope recognized by neutralizing pig sera. Upon ectopic expression of this GP5 in cells, signal peptide cleavage was however inefficient. Complete cleavage occurred when cysteine-24 was changed to proline or an unused glycosylation site involving asparagine-35 was mutated. Insertion of proline at position 24 also caused carbohydrate attachment to asparagine-35. Glycosylation sites introduced downstream of residue 35 were used, but did not inhibit signal peptide processing. Co-expression of the M protein rescued this processing defect in GP5, suggesting a novel function of M towards GP5. We speculate that a complex interplay of the co-translational modifications of GP5 affect the N-terminal structure of the mature proteins and hence its antigenicity.
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46
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Chaperone families and interactions in metazoa. Essays Biochem 2017; 60:237-253. [PMID: 27744339 DOI: 10.1042/ebc20160004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/04/2016] [Indexed: 01/31/2023]
Abstract
Quality control is an essential aspect of cellular function, with protein folding quality control being carried out by molecular chaperones, a diverse group of highly conserved proteins that specifically identify misfolded conformations. Molecular chaperones are thus required to support proteins affected by expressed polymorphisms, mutations, intrinsic errors in gene expression, chronic insult or the acute effects of the environment, all of which contribute to a flux of metastable proteins. In this article, we review the four main chaperone families in metazoans, namely Hsp60 (where Hsp is heat-shock protein), Hsp70, Hsp90 and sHsps (small heat-shock proteins), as well as their co-chaperones. Specifically, we consider the structural and functional characteristics of each family and discuss current models that attempt to explain how chaperones recognize and act together to protect or recover aberrant proteins.
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47
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Craig EA, Marszalek J. How Do J-Proteins Get Hsp70 to Do So Many Different Things? Trends Biochem Sci 2017; 42:355-368. [PMID: 28314505 DOI: 10.1016/j.tibs.2017.02.007] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/09/2017] [Accepted: 02/16/2017] [Indexed: 01/07/2023]
Abstract
Hsp70 chaperone machineries have pivotal roles in an array of fundamental biological processes through their facilitation of protein folding, disaggregation, and remodeling. The obligate J-protein co-chaperones of Hsp70s drive much of this remarkable multifunctionality, with most Hsp70s having multiple J-protein partners. Recent data suggest that J-protein-driven versatility is substantially due to precise localization within the cell and the specificity of substrate protein binding. However, this relatively simple view belies the intricacy of J-protein function. Examples are emerging of J-protein interactions with Hsp70s and other chaperones, as well as integration into broader cellular networks. These interactions fine-tune, in critical ways, the ability of Hsp70s to participate in diverse cellular processes.
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Affiliation(s)
- Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
| | - Jaroslaw Marszalek
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA; Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland.
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48
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Tribensky A, Graf AW, Diehl M, Fleck W, Przyborski JM. Trafficking of PfExp1 to the parasitophorous vacuolar membrane of Plasmodium falciparum is independent of protein folding and the PTEX translocon. Cell Microbiol 2017; 19. [PMID: 27892646 DOI: 10.1111/cmi.12710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/19/2016] [Accepted: 11/24/2016] [Indexed: 12/13/2022]
Abstract
Having entered the mature human erythrocyte, the malaria parasite survives and propagates within a parasitophorous vacuole, a membrane-bound compartment separating the parasite from the host cell cytosol. The bounding membrane of this vacuole, referred to as the parasitophorous vacuolar membrane (PVM), contains parasite-encoded proteins, but how these membrane proteins are trafficked to the PVM remains unknown. Here, we have studied the trafficking of PfExp1 to the PVM. We find that trafficking of PfExp1 to the PVM is independent of the folding state of the protein and also continues unabated upon inactivation of the PVM translocon Plasmodium Translocon of Exported proteins (PTEX). Our data strongly suggest that the trafficking of membrane proteins to the PVM occurs by as yet unknown mechanism, potentially unique to Plasmodium.
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Affiliation(s)
- Anke Tribensky
- Department of Parasitology, University of Marburg, Marburg, Germany
| | - Andreas W Graf
- Department of Parasitology, University of Marburg, Marburg, Germany
| | - Mathias Diehl
- Department of Parasitology, University of Marburg, Marburg, Germany
| | - Wiebke Fleck
- Department of Parasitology, University of Marburg, Marburg, Germany
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49
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Pendin D, Greotti E, Lefkimmiatis K, Pozzan T. Exploring cells with targeted biosensors. J Gen Physiol 2016; 149:1-36. [PMID: 28028123 PMCID: PMC5217087 DOI: 10.1085/jgp.201611654] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/26/2016] [Accepted: 12/01/2016] [Indexed: 01/10/2023] Open
Abstract
Cellular signaling networks are composed of multiple pathways, often interconnected, that form complex networks with great potential for cross-talk. Signal decoding depends on the nature of the message as well as its amplitude, temporal pattern, and spatial distribution. In addition, the existence of membrane-bound organelles, which are both targets and generators of messages, add further complexity to the system. The availability of sensors that can localize to specific compartments in live cells and monitor their targets with high spatial and temporal resolution is thus crucial for a better understanding of cell pathophysiology. For this reason, over the last four decades, a variety of strategies have been developed, not only to generate novel and more sensitive probes for ions, metabolites, and enzymatic activity, but also to selectively deliver these sensors to specific intracellular compartments. In this review, we summarize the principles that have been used to target organic or protein sensors to different cellular compartments and their application to cellular signaling.
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Affiliation(s)
- Diana Pendin
- Neuroscience Institute, National Research Council, Padua Section, 35121 Padua, Italy.,Department of Biomedical Sciences, University of Padua, 35121 Padua, Italy
| | - Elisa Greotti
- Neuroscience Institute, National Research Council, Padua Section, 35121 Padua, Italy.,Department of Biomedical Sciences, University of Padua, 35121 Padua, Italy
| | - Konstantinos Lefkimmiatis
- Neuroscience Institute, National Research Council, Padua Section, 35121 Padua, Italy.,Venetian Institute of Molecular Medicine, 35129 Padua, Italy
| | - Tullio Pozzan
- Neuroscience Institute, National Research Council, Padua Section, 35121 Padua, Italy.,Venetian Institute of Molecular Medicine, 35129 Padua, Italy.,Department of Biomedical Sciences, University of Padua, 35121 Padua, Italy
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50
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Liu X, Zhang W, Zhao Z, Dai X, Yang Y, Bai Z. Protein secretion in Corynebacterium glutamicum. Crit Rev Biotechnol 2016; 37:541-551. [PMID: 27737570 DOI: 10.1080/07388551.2016.1206059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Corynebacterium glutamicum, a Gram-positive bacterium, has been widely used for the industrial production of amino acids, such as glutamate and lysine, for decades. Due to several characteristics - its ability to secrete properly folded and functional target proteins into culture broth, its low levels of endogenous extracellular proteins and its lack of detectable extracellular hydrolytic enzyme activity - C. glutamicum is also a very favorable host cell for the secretory production of heterologous proteins, important enzymes, and pharmaceutical proteins. The target proteins are secreted into the culture medium, which has attractive advantages over the manufacturing process for inclusion of body expression - the simplified downstream purification process. The secretory process of proteins is complicated and energy consuming. There are two major secretory pathways in C. glutamicum, the Sec pathway and the Tat pathway, both have specific signal peptides that mediate the secretion of the target proteins. In the present review, we critically discuss recent progress in the secretory production of heterologous proteins and examine in depth the mechanisms of the protein translocation process in C. glutamicum. Some successful case studies of actual applications of this secretory expression host are also evaluated. Finally, the existing issues and solutions in using C. glutamicum as a host of secretory proteins are specifically addressed.
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Affiliation(s)
- Xiuxia Liu
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Wei Zhang
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Zihao Zhao
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Xiaofeng Dai
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Yankun Yang
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Zhonghu Bai
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
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