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Ando T, Fukuda S, Ngo KX, Flechsig H. High-Speed Atomic Force Microscopy for Filming Protein Molecules in Dynamic Action. Annu Rev Biophys 2024; 53:19-39. [PMID: 38060998 DOI: 10.1146/annurev-biophys-030722-113353] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Structural biology is currently undergoing a transformation into dynamic structural biology, which reveals the dynamic structure of proteins during their functional activity to better elucidate how they function. Among the various approaches in dynamic structural biology, high-speed atomic force microscopy (HS-AFM) is unique in the ability to film individual molecules in dynamic action, although only topographical information is acquirable. This review provides a guide to the use of HS-AFM for biomolecular imaging and showcases several examples, as well as providing information on up-to-date progress in HS-AFM technology. Finally, we discuss the future prospects of HS-AFM in the context of dynamic structural biology in the upcoming era.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Shingo Fukuda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Kien X Ngo
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
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2
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Bidooki SH, Navarro MA, Fernandes SCM, Osada J. Thioredoxin Domain Containing 5 (TXNDC5): Friend or Foe? Curr Issues Mol Biol 2024; 46:3134-3163. [PMID: 38666927 PMCID: PMC11049379 DOI: 10.3390/cimb46040197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/25/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024] Open
Abstract
This review focuses on the thioredoxin domain containing 5 (TXNDC5), also known as endoplasmic reticulum protein 46 (ERp46), a member of the protein disulfide isomerase (PDI) family with a dual role in multiple diseases. TXNDC5 is highly expressed in endothelial cells, fibroblasts, pancreatic β-cells, liver cells, and hypoxic tissues, such as cancer endothelial cells and atherosclerotic plaques. TXNDC5 plays a crucial role in regulating cell proliferation, apoptosis, migration, and antioxidative stress. Its potential significance in cancer warrants further investigation, given the altered and highly adaptable metabolism of tumor cells. It has been reported that both high and low levels of TXNDC5 expression are associated with multiple diseases, such as arthritis, cancer, diabetes, brain diseases, and infections, as well as worse prognoses. TXNDC5 has been attributed to both oncogenic and tumor-suppressive features. It has been concluded that in cancer, TXNDC5 acts as a foe and responds to metabolic and cellular stress signals to promote the survival of tumor cells against apoptosis. Conversely, in normal cells, TXNDC5 acts as a friend to safeguard cells against oxidative and endoplasmic reticulum stress. Therefore, TXNDC5 could serve as a viable biomarker or even a potential pharmacological target.
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Affiliation(s)
- Seyed Hesamoddin Bidooki
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, E-50013 Zaragoza, Spain; (S.H.B.); (M.A.N.)
- Centre National de la Recherche Scientifique (CNRS), Institute of Analytical Sciences and Physico-Chemistry for Environment and Materials (IPREM), Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 000 Pau, France;
- MANTA—Marine Materials Research Group, Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 600 Anglet, France
| | - María A. Navarro
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, E-50013 Zaragoza, Spain; (S.H.B.); (M.A.N.)
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, E-50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, E-28029 Madrid, Spain
| | - Susana C. M. Fernandes
- Centre National de la Recherche Scientifique (CNRS), Institute of Analytical Sciences and Physico-Chemistry for Environment and Materials (IPREM), Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 000 Pau, France;
- MANTA—Marine Materials Research Group, Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 600 Anglet, France
| | - Jesus Osada
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, E-50013 Zaragoza, Spain; (S.H.B.); (M.A.N.)
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, E-50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, E-28029 Madrid, Spain
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Cai X, Ito S, Noi K, Inoue M, Ushioda R, Kato Y, Nagata K, Inaba K. Mechanistic characterization of disulfide bond reduction of an ERAD substrate mediated by cooperation between ERdj5 and BiP. J Biol Chem 2023; 299:105274. [PMID: 37739037 PMCID: PMC10591012 DOI: 10.1016/j.jbc.2023.105274] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/28/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023] Open
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) is a protein quality control process that eliminates misfolded proteins from the ER. DnaJ homolog subfamily C member 10 (ERdj5) is a protein disulfide isomerase family member that accelerates ERAD by reducing disulfide bonds of aberrant proteins with the help of an ER-resident chaperone BiP. However, the detailed mechanisms by which ERdj5 acts in concert with BiP are poorly understood. In this study, we reconstituted an in vitro system that monitors ERdj5-mediated reduction of disulfide-linked J-chain oligomers, known to be physiological ERAD substrates. Biochemical analyses using purified proteins revealed that J-chain oligomers were reduced to monomers by ERdj5 in a stepwise manner via trimeric and dimeric intermediates, and BiP synergistically enhanced this action in an ATP-dependent manner. Single-molecule observations of ERdj5-catalyzed J-chain disaggregation using high-speed atomic force microscopy, demonstrated the stochastic release of small J-chain oligomers through repeated actions of ERdj5 on peripheral and flexible regions of large J-chain aggregates. Using systematic mutational analyses, ERAD substrate disaggregation mediated by ERdj5 and BiP was dissected at the molecular level.
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Affiliation(s)
- Xiaohan Cai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan; Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Shogo Ito
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan; Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kentaro Noi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Michio Inoue
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
| | - Ryo Ushioda
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Yukinari Kato
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kazuhiro Nagata
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan; Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan; Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
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Robinson PJ, Pringle MA, Fleming B, Bulleid NJ. Distinct role of ERp57 and ERdj5 as a disulfide isomerase and reductase during ER protein folding. J Cell Sci 2023; 136:286707. [PMID: 36655611 PMCID: PMC10022741 DOI: 10.1242/jcs.260656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/13/2022] [Indexed: 01/20/2023] Open
Abstract
Proteins entering the secretory pathway need to attain native disulfide pairings to fold correctly. For proteins with complex disulfides, this process requires the reduction and isomerisation of non-native disulfides. Two key members of the protein disulfide isomerase (PDI) family, ERp57 and ERdj5 (also known as PDIA3 and DNAJC10, respectively), are thought to be required for correct disulfide formation but it is unknown whether they act as a reductase, an isomerase or both. In addition, it is unclear how reducing equivalents are channelled through PDI family members to substrate proteins. Here, we show that neither enzyme is required for disulfide formation, but ERp57 is required for isomerisation of non-native disulfides within glycoproteins. In addition, alternative PDIs compensate for the absence of ERp57 to isomerise glycoprotein disulfides, but only in the presence of a robust reductive pathway. ERdj5 is required for this alternative pathway to function efficiently indicating its role as a reductase. Our results define the essential cellular functions of two PDIs, highlighting a distinction between formation, reduction and isomerisation of disulfide bonds.
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Affiliation(s)
- Philip John Robinson
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Marie Anne Pringle
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Bethany Fleming
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Neil John Bulleid
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK
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Mideksa YG, Aschenbrenner I, Fux A, Kaylani D, Weiß CA, Nguyen TA, Bach NC, Lang K, Sieber SA, Feige MJ. A comprehensive set of ER protein disulfide isomerase family members supports the biogenesis of proinflammatory interleukin 12 family cytokines. J Biol Chem 2022; 298:102677. [PMID: 36336075 PMCID: PMC9731863 DOI: 10.1016/j.jbc.2022.102677] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/06/2022] Open
Abstract
Cytokines of the interleukin 12 (IL-12) family are assembled combinatorially from shared α and β subunits. A common theme is that human IL-12 family α subunits remain incompletely structured in isolation until they pair with a designate β subunit. Accordingly, chaperones need to support and control specific assembly processes. It remains incompletely understood, which chaperones are involved in IL-12 family biogenesis. Here, we site-specifically introduce photocrosslinking amino acids into the IL-12 and IL-23 α subunits (IL-12α and IL-23α) for stabilization of transient chaperone-client complexes for mass spectrometry. Our analysis reveals that a large set of endoplasmic reticulum chaperones interacts with IL-12α and IL-23α. Among these chaperones, we focus on protein disulfide isomerase (PDI) family members and reveal IL-12 family subunits to be clients of several incompletely characterized PDIs. We find that different PDIs show selectivity for different cysteines in IL-12α and IL-23α. Despite this, PDI binding generally stabilizes unassembled IL-12α and IL-23α against degradation. In contrast, α:β assembly appears robust, and only multiple simultaneous PDI depletions reduce IL-12 secretion. Our comprehensive analysis of the IL-12/IL-23 chaperone machinery reveals a hitherto uncharacterized role for several PDIs in this process. This extends our understanding of how cells accomplish the task of specific protein assembly reactions for signaling processes. Furthermore, our findings show that cytokine secretion can be modulated by targeting specific endoplasmic reticulum chaperones.
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Affiliation(s)
- Yonatan G. Mideksa
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Isabel Aschenbrenner
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Anja Fux
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Dinah Kaylani
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Caroline A.M. Weiß
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Tuan-Anh Nguyen
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Nina C. Bach
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Kathrin Lang
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany,Laboratory of Organic Chemistry, ETH Zürich, Zurich, Switzerland
| | - Stephan A. Sieber
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Matthias J. Feige
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany,For correspondence: Matthias J. Feige
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