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Melo EP, El-Guendouz S, Correia C, Teodoro F, Lopes C, Martel PJ. A Conformational-Dependent Interdomain Redox Relay at the Core of Protein Disulfide Isomerase Activity. Antioxid Redox Signal 2024. [PMID: 38497737 DOI: 10.1089/ars.2023.0288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Aims: Protein disulfide isomerases (PDIs) are a family of chaperones resident in the endoplasmic reticulum (ER). In addition to holdase function, some members catalyze disulfide bond formation and isomerization, a crucial step for native folding and prevention of aggregation of misfolded proteins. PDIs are characterized by an arrangement of thioredoxin-like domains, with the canonical protein disulfide isomerase A1 (PDIA1) organized as four thioredoxin-like domains forming a horseshoe with two active sites, a and a', at the extremities. We aimed to clarify important aspects underlying the catalytic cycle of PDIA1 in the context of the full pathways of oxidative protein folding operating in the ER. Results: Using two fluorescent redox sensors, redox green fluorescent protein 2 (roGFP2) and HyPer (circularly permutated yellow fluorescent protein containing the regulatory domain of the H2O2-sensing protein OxyR), either unfolded or native, as client substrates, we identified the N-terminal a active site of PDIA1 as the main oxidant of thiols. From there, electrons can flow to the C-terminal a' active site, with the redox-dependent conformational flexibility of PDIA1 allowing the formation of an interdomain disulfide bond. The a' active site then acts as a crossing point to redirect electrons to ER downstream oxidases or back to client proteins to reduce scrambled disulfide bonds. Innovation and Conclusions: The two active sites of PDIA1 work cooperatively as an interdomain redox relay mechanism that explains PDIA1 oxidative activity to form native disulfides and PDIA1 reductase activity to resolve scrambled disulfides. This mechanism suggests a new rationale for shutting down oxidative protein folding under ER redox imbalance. Whether it applies to physiological substrates in cells remains to be shown.
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Affiliation(s)
- Eduardo P Melo
- Centro de Ciências do Mar (CCMAR), University of Algarve, Faro, Portugal
| | | | - Cátia Correia
- Centro de Ciências do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Fernando Teodoro
- Centro de Ciências do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Carlos Lopes
- Centro de Ciências do Mar (CCMAR), University of Algarve, Faro, Portugal
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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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Matsusaki M, Okada R, Tanikawa Y, Kanemura S, Ito D, Lin Y, Watabe M, Yamaguchi H, Saio T, Lee YH, Inaba K, Okumura M. Functional Interplay between P5 and PDI/ERp72 to Drive Protein Folding. BIOLOGY 2021; 10:biology10111112. [PMID: 34827105 PMCID: PMC8615271 DOI: 10.3390/biology10111112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/21/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
P5 is one of protein disulfide isomerase family proteins (PDIs) involved in endoplasmic reticulum (ER) protein quality control that assists oxidative folding, inhibits protein aggregation, and regulates the unfolded protein response. P5 reportedly interacts with other PDIs via intermolecular disulfide bonds in cultured cells, but it remains unclear whether complex formation between P5 and other PDIs is involved in regulating enzymatic and chaperone functions. Herein, we established the far-western blot method to detect non-covalent interactions between P5 and other PDIs and found that PDI and ERp72 are partner proteins of P5. The enzymatic activity of P5-mediated oxidative folding is up-regulated by PDI, while the chaperone activity of P5 is stimulated by ERp72. These findings shed light on the mechanism by which the complex formations among PDIs drive to synergistically accelerate protein folding and prevents aggregation. This knowledge has implications for understanding misfolding-related pathology.
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Affiliation(s)
- Motonori Matsusaki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3, Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan; (M.M.); (S.K.); (M.W.)
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15, Kuramoto-cho, Tokushima 770-8503, Japan;
| | - Rina Okada
- School of Science and Technology, Kwansei Gakuin University, 2-1, Gakuen, Sanda 669-1337, Japan; (R.O.); (Y.T.); (H.Y.)
| | - Yuya Tanikawa
- School of Science and Technology, Kwansei Gakuin University, 2-1, Gakuen, Sanda 669-1337, Japan; (R.O.); (Y.T.); (H.Y.)
| | - Shingo Kanemura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3, Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan; (M.M.); (S.K.); (M.W.)
- School of Science and Technology, Kwansei Gakuin University, 2-1, Gakuen, Sanda 669-1337, Japan; (R.O.); (Y.T.); (H.Y.)
| | - Dai Ito
- Department of Brain and Cognitive Science, Daegu Gyeongbuk Institute of Science and Technology, 333, Techno Jungang Daero, Daegu 42988, Korea;
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si 28119, Korea; (Y.L.); (Y.-H.L.)
| | - Mai Watabe
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3, Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan; (M.M.); (S.K.); (M.W.)
| | - Hiroshi Yamaguchi
- School of Science and Technology, Kwansei Gakuin University, 2-1, Gakuen, Sanda 669-1337, Japan; (R.O.); (Y.T.); (H.Y.)
| | - Tomohide Saio
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15, Kuramoto-cho, Tokushima 770-8503, Japan;
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si 28119, Korea; (Y.L.); (Y.-H.L.)
- Bio-Analytical Science, University of Science and Technology, 217, Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
- Research Headquarters, Korea Brain Research Institute, 61, Cheomdan-ro, Dong-gu, Daegu 41068, Korea
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan;
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3, Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan; (M.M.); (S.K.); (M.W.)
- Correspondence: ; Tel.: +81-22-795-5764
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Kanemura S, Matsusaki M, Inaba K, Okumura M. PDI Family Members as Guides for Client Folding and Assembly. Int J Mol Sci 2020; 21:ijms21249351. [PMID: 33302492 PMCID: PMC7763558 DOI: 10.3390/ijms21249351] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/06/2020] [Accepted: 12/06/2020] [Indexed: 12/27/2022] Open
Abstract
Complicated and sophisticated protein homeostasis (proteostasis) networks in the endoplasmic reticulum (ER), comprising disulfide catalysts, molecular chaperones, and their regulators, help to maintain cell viability. Newly synthesized proteins inserted into the ER need to fold and assemble into unique native structures to fulfill their physiological functions, and this is assisted by protein disulfide isomerase (PDI) family. Herein, we focus on recent advances in understanding the detailed mechanisms of PDI family members as guides for client folding and assembly to ensure the efficient production of secretory proteins.
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Affiliation(s)
- Shingo Kanemura
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan;
| | - Motonori Matsusaki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; (M.M.); (K.I.)
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramakiaza Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; (M.M.); (K.I.)
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramakiaza Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
- Correspondence: ; Tel.: +81-22-217-5628
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Kanemura S, Sofia EF, Hirai N, Okumura M, Kadokura H, Inaba K. Characterization of the endoplasmic reticulum-resident peroxidases GPx7 and GPx8 shows the higher oxidative activity of GPx7 and its linkage to oxidative protein folding. J Biol Chem 2020; 295:12772-12785. [PMID: 32719007 DOI: 10.1074/jbc.ra120.013607] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/17/2020] [Indexed: 12/13/2022] Open
Abstract
Oxidative protein folding occurs primarily in the mammalian endoplasmic reticulum, enabled by a diverse network comprising more than 20 members of the protein disulfide isomerase (PDI) family and more than five PDI oxidases. Although the canonical disulfide bond formation pathway involving Ero1α and PDI has been well-studied so far, the physiological roles of the newly identified PDI oxidases, glutathione peroxidase-7 (GPx7) and -8 (GPx8), are only poorly understood. We here demonstrated that human GPx7 has much higher reactivity with H2O2 and hence greater PDI oxidation activity than human GPx8. The high reactivity of GPx7 is due to the presence of a catalytic tetrad at the redox-active site, which stabilizes the sulfenylated species generated upon the reaction with H2O2 Although it was previously postulated that GPx7 catalysis involved a highly reactive peroxidatic cysteine that can be sulfenylated by H2O2, we revealed that a resolving cysteine instead regulates the PDI oxidation activity of GPx7. We also determined that GPx7 formed complexes preferentially with PDI and P5 in H2O2-treated cells. Altogether, these results suggest that human GPx7 functions as an H2O2-dependent PDI oxidase in cells, whereas PDI oxidation may not be the central physiological role of human GPx8.
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Affiliation(s)
- Shingo Kanemura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan.,School of Science and Technology, Kwansei Gakuin University, Gakuen, Sanda, Hyogo, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramaki, Aza, Aoba-ku, Sendai, Miyagi, Japan
| | - Elza Firdiani Sofia
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Naoya Hirai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Masaki Okumura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramaki, Aza, Aoba-ku, Sendai, Miyagi, Japan
| | - Hiroshi Kadokura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
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Matsusaki M, Okuda A, Matsuo K, Gekko K, Masuda T, Naruo Y, Hirose A, Kono K, Tsuchi Y, Urade R. Regulation of plant ER oxidoreductin 1 (ERO1) activity for efficient oxidative protein folding. J Biol Chem 2019; 294:18820-18835. [PMID: 31685660 DOI: 10.1074/jbc.ra119.010917] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/27/2019] [Indexed: 12/14/2022] Open
Abstract
In the endoplasmic reticulum (ER), ER oxidoreductin 1 (ERO1) catalyzes intramolecular disulfide-bond formation within its substrates in coordination with protein-disulfide isomerase (PDI) and related enzymes. However, the molecular mechanisms that regulate the ERO1-PDI system in plants are unknown. Reduction of the regulatory disulfide bonds of the ERO1 from soybean, GmERO1a, is catalyzed by enzymes in five classes of PDI family proteins. Here, using recombinant proteins, vacuum-ultraviolet circular dichroism spectroscopy, biochemical and protein refolding assays, and quantitative immunoblotting, we found that GmERO1a activity is regulated by reduction of intramolecular disulfide bonds involving Cys-121 and Cys-146, which are located in a disordered region, similarly to their locations in human ERO1. Moreover, a GmERO1a variant in which Cys-121 and Cys-146 were replaced with Ala residues exhibited hyperactive oxidation. Soybean PDI family proteins differed in their ability to regulate GmERO1a. Unlike yeast and human ERO1s, for which PDI is the preferred substrate, GmERO1a directly transferred disulfide bonds to the specific active center of members of five classes of PDI family proteins. Of these proteins, GmPDIS-1, GmPDIS-2, GmPDIM, and GmPDIL7 (which are group II PDI family proteins) failed to catalyze effective oxidative folding of substrate RNase A when there was an unregulated supply of disulfide bonds from the C121A/C146A hyperactive mutant GmERO1a, because of its low disulfide-bond isomerization activity. We conclude that regulation of plant ERO1 activity is particularly important for effective oxidative protein folding by group II PDI family proteins.
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Affiliation(s)
- Motonori Matsusaki
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Aya Okuda
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Kagamiyama, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Kunihiko Gekko
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Kagamiyama, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Taro Masuda
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yurika Naruo
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Akiho Hirose
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Keiichi Kono
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yuichiro Tsuchi
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Reiko Urade
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.
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Beal DM, Bastow EL, Staniforth GL, von der Haar T, Freedman RB, Tuite MF. Quantitative Analyses of the Yeast Oxidative Protein Folding Pathway In Vitro and In Vivo. Antioxid Redox Signal 2019; 31:261-274. [PMID: 30880408 PMCID: PMC6602113 DOI: 10.1089/ars.2018.7615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 12/11/2022]
Abstract
Aims: Efficient oxidative protein folding (OPF) in the endoplasmic reticulum (ER) is a key requirement of the eukaryotic secretory pathway. In particular, protein folding linked to the formation of disulfide bonds, an activity dependent on the enzyme protein disulfide isomerase (PDI), is crucial. For the de novo formation of disulfide bonds, reduced PDI must be reoxidized by an ER-located oxidase (ERO1). Despite some knowledge of this pathway, the kinetic parameters with which these components act and the importance of specific parameters, such as PDI reoxidation by Ero1, for the overall performance of OPF in vivo remain poorly understood. Results: We established an in vitro system using purified yeast (Saccharomyces cerevisiae) PDI (Pdi1p) and ERO1 (Ero1p) to investigate OPF. This necessitated the development of a novel reduction/oxidation processing strategy to generate homogenously oxidized recombinant yeast Ero1p. This new methodology enabled the quantitative assessment of the interaction of Pdi1p and Ero1p in vitro by measuring oxygen consumption and reoxidation of reduced RNase A. The resulting quantitative data were then used to generate a simple model that can describe the oxidizing capacity of Pdi1p and Ero1p in vitro and predict the in vivo effect of modulation of the levels of these proteins. Innovation: We describe a model that can be used to explore the OPF pathway and its control in a quantitative way. Conclusion: Our study informs and provides new insights into how OPF works at a molecular level and provides a platform for the design of more efficient heterologous protein expression systems in yeast.
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Affiliation(s)
- Dave M. Beal
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Emma L. Bastow
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Gemma L. Staniforth
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Robert B. Freedman
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Mick F. Tuite
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
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Passam FJ, Chiu J. Allosteric disulphide bonds as reversible mechano-sensitive switches that control protein functions in the vasculature. Biophys Rev 2019; 11:419-430. [PMID: 31090016 DOI: 10.1007/s12551-019-00543-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/29/2019] [Indexed: 01/02/2023] Open
Abstract
Disulphide bonds are covalent linkages of two cysteine residues (R-S-S-R') in proteins. Unlike peptide bonds, disulphide bonds are reversible in nature allowing cleaved bonds to reform. Disulphide bonds are important structural elements that stabilise protein conformation. They can be of catalytic function found in enzymes that facilitate redox reactions in the cleavage/formation of disulphide bonds in their substrates. Emerging evidence also indicates that disulphide bonds can be of regulatory function which alter protein activity when they are cleaved or formed. This class of regulatory disulphide bonds is known as allosteric disulphide bonds. Allosteric disulphide bonds are mechano-sensitive, and stretching or twisting the sulphur-sulphur bond by mechanical force can make it easier or harder to be cleaved. This makes allosteric disulphide bonds an ideal type of mechano-sensitive switches for regulating protein functions in the vasculature where cells are continuously subjected to fluid shear force. This review will discuss the chemistry and biophysical properties of allosteric disulphide bonds and how they emerge to be mechano-sensitive switches in regulating platelet function and clot formation.
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Affiliation(s)
- Freda J Passam
- Heart Research Institute and Charles Perkins centre, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Joyce Chiu
- The Centenary Institute, NHMRC Clinical Trial Centre, Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia.
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Dynamic assembly of protein disulfide isomerase in catalysis of oxidative folding. Nat Chem Biol 2019; 15:499-509. [PMID: 30992562 DOI: 10.1038/s41589-019-0268-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 03/07/2019] [Indexed: 11/08/2022]
Abstract
Time-resolved direct observations of proteins in action provide essential mechanistic insights into biological processes. Here, we present mechanisms of action of protein disulfide isomerase (PDI)-the most versatile disulfide-introducing enzyme in the endoplasmic reticulum-during the catalysis of oxidative protein folding. Single-molecule analysis by high-speed atomic force microscopy revealed that oxidized PDI is in rapid equilibrium between open and closed conformations, whereas reduced PDI is maintained in the closed state. In the presence of unfolded substrates, oxidized PDI, but not reduced PDI, assembles to form a face-to-face dimer, creating a central hydrophobic cavity with multiple redox-active sites, where substrates are likely accommodated to undergo accelerated oxidative folding. Such PDI dimers are diverse in shape and have different lifetimes depending on substrates. To effectively guide proper oxidative protein folding, PDI regulates conformational dynamics and oligomeric states in accordance with its own redox state and the configurations or folding states of substrates.
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Meyer AJ, Riemer J, Rouhier N. Oxidative protein folding: state-of-the-art and current avenues of research in plants. THE NEW PHYTOLOGIST 2019; 221:1230-1246. [PMID: 30230547 DOI: 10.1111/nph.15436] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/01/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 1230 I. Introduction 1230 II. Formation and isomerization of disulfides in the ER and the Golgi apparatus 1231 III. The disulfide relay in the mitochondrial intermembrane space: why are plants different? 1236 IV. Disulfide bond formation on luminal proteins in thylakoids 1240 V. Conclusion 1242 Acknowledgements 1242 References 1242 SUMMARY: Disulfide bonds are post-translational modifications crucial for the structure and function of thousands of proteins. Their formation and isomerization, referred to as oxidative folding, require specific protein machineries found in oxidizing subcellular compartments, namely the endoplasmic reticulum and the associated endomembrane system, the intermembrane space of mitochondria and the thylakoid lumen of chloroplasts. At least one protein component is required for transferring electrons from substrate proteins to an acceptor that is usually molecular oxygen. For oxidation reactions, incoming reduced substrates are oxidized by thiol-oxidoreductase proteins (or domains in case of chimeric proteins), which are usually themselves oxidized by a single thiol oxidase, the enzyme generating disulfide bonds de novo. By contrast, the description of the molecular actors and pathways involved in proofreading and isomerization of misfolded proteins, which require a tightly controlled redox balance, lags behind. Herein we provide a general overview of the knowledge acquired on the systems responsible for oxidative protein folding in photosynthetic organisms, highlighting their particularities compared to other eukaryotes. Current research challenges are discussed including the importance and specificity of these oxidation systems in the context of the existence of reducing systems in the same compartments.
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Affiliation(s)
- Andreas J Meyer
- INRES-Chemical Signalling, University of Bonn, 53113, Bonn, Germany
| | - Jan Riemer
- Institute of Biochemistry, University of Cologne, 50674, Cologne, Germany
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O'Brien H, Kanemura S, Okumura M, Baskin RP, Bandyopadhyay PK, Olivera BM, Ellgaard L, Inaba K, Safavi-Hemami H. Ero1-Mediated Reoxidation of Protein Disulfide Isomerase Accelerates the Folding of Cone Snail Toxins. Int J Mol Sci 2018; 19:ijms19113418. [PMID: 30384459 PMCID: PMC6275033 DOI: 10.3390/ijms19113418] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 01/09/2023] Open
Abstract
Disulfide-rich peptides are highly abundant in nature and their study has provided fascinating insight into protein folding, structure and function. Venomous cone snails belong to a group of organisms that express one of the largest sets of disulfide-rich peptides (conotoxins) found in nature. The diversity of structural scaffolds found for conotoxins suggests that specialized molecular adaptations have evolved to ensure their efficient folding and secretion. We recently showed that canonical protein disulfide isomerase (PDI) and a conotoxin-specific PDI (csPDI) are ubiquitously expressed in the venom gland of cone snails and play a major role in conotoxin folding. Here, we identify cone snail endoplasmic reticulum oxidoreductin-1 (Conus Ero1) and investigate its role in the oxidative folding of conotoxins through reoxidation of cone snail PDI and csPDI. We show that Conus Ero1 preferentially reoxidizes PDI over csPDI, suggesting that the reoxidation of csPDI may rely on an Ero1-independent molecular pathway. Despite the preferential reoxidation of PDI over csPDI, the combinatorial effect of Ero1 and csPDI provides higher folding yields than Ero1 and PDI. We further demonstrate that the highest in vitro folding rates of two model conotoxins are achieved when all three enzymes are present, indicating that these enzymes may act synergistically. Our findings provide new insight into the generation of one of the most diverse classes of disulfide-rich peptides and may improve current in vitro approaches for the production of venom peptides for pharmacological studies.
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Affiliation(s)
- Henrik O'Brien
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
| | - Shingo Kanemura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, Sendai 980-8577, Japan.
| | - Masaki Okumura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, Sendai 980-8577, Japan.
| | - Robert P Baskin
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
| | | | | | - Lars Ellgaard
- Department of Biology, University of Copenhagen, 2200 Copenhagen N., Denmark.
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, Sendai 980-8577, Japan.
| | - Helena Safavi-Hemami
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA.
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Moilanen A, Korhonen K, Saaranen MJ, Ruddock LW. Molecular analysis of human Ero1 reveals novel regulatory mechanisms for oxidative protein folding. Life Sci Alliance 2018; 1:e201800090. [PMID: 30456358 PMCID: PMC6238587 DOI: 10.26508/lsa.201800090] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/18/2018] [Accepted: 06/18/2018] [Indexed: 11/24/2022] Open
Abstract
Oxidative protein folding in the ER is driven mainly by oxidases of the endoplasmic reticulum oxidoreductin 1 (Ero1) family. Their action is regulated to avoid cell stress, including hyperoxidation. Previously published regulatory mechanisms are based on the rearrangement of active site and regulatory disulfides. In this study, we identify two novel regulatory mechanisms. First, both human Ero1 isoforms exist in a dynamic mixed disulfide complex with protein disulfide isomerase, which involves cysteines (Cys166 in Ero1α and Cys165 in Ero1β) that have previously been regarded as being nonfunctional. Second, our kinetic studies reveal that Ero1 not only has a high affinity for molecular oxygen as the terminal acceptor of electrons but also that there is a high cooperativity of binding (Hill coefficient >3). This allows Ero1 to maintain high activity under hypoxic conditions, without compromising cellular viability under hyper-hypoxic conditions. These data, together with novel mechanistic details of differences in activation between the two human Ero1 isoforms, provide important new insights into the catalytic cycle of human Ero1 and how they have been fine-tuned to operate at low oxygen concentrations.
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Affiliation(s)
- Antti Moilanen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Kati Korhonen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Mirva J Saaranen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Lloyd W Ruddock
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
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Maegawa KI, Watanabe S, Noi K, Okumura M, Amagai Y, Inoue M, Ushioda R, Nagata K, Ogura T, Inaba K. The Highly Dynamic Nature of ERdj5 Is Key to Efficient Elimination of Aberrant Protein Oligomers through ER-Associated Degradation. Structure 2017; 25:846-857.e4. [PMID: 28479060 DOI: 10.1016/j.str.2017.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/08/2017] [Accepted: 04/10/2017] [Indexed: 12/12/2022]
Abstract
ERdj5, composed of an N-terminal J domain followed by six thioredoxin-like domains, is the largest protein disulfide isomerase family member and functions as an ER-localized disulfide reductase that enhances ER-associated degradation (ERAD). Our previous studies indicated that ERdj5 comprises two regions, the N- and C-terminal clusters, separated by a linker loop and with distinct functional roles in ERAD. We here present a new crystal structure of ERdj5 with a largely different cluster arrangement relative to that in the original crystal structure. Single-molecule observation by high-speed atomic force microscopy visualized rapid cluster movement around the flexible linker loop, indicating the highly dynamic nature of ERdj5 in solution. ERdj5 mutants with a fixed-cluster orientation compromised the ERAD enhancement activity, likely because of less-efficient reduction of aberrantly formed disulfide bonds and prevented substrate transfer in the ERdj5-mediated ERAD pathway. We propose a significant role of ERdj5 conformational dynamics in ERAD of disulfide-linked oligomers.
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Affiliation(s)
- Ken-Ichi Maegawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; CREST, JST, Japan
| | - Satoshi Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; CREST, JST, Japan
| | - Kentaro Noi
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan; CREST, JST, Japan
| | - Masaki Okumura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yuta Amagai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Michio Inoue
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; CREST, JST, Japan
| | - Ryo Ushioda
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto 603-8455, Japan; CREST, JST, Japan
| | - Kazuhiro Nagata
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto 603-8455, Japan; CREST, JST, Japan
| | - Teru Ogura
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan; CREST, JST, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; CREST, JST, Japan.
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