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Wang G, Qin J, Verderosa AD, Hor L, Santos-Martin C, Paxman JJ, Martin JL, Totsika M, Heras B. A Buried Water Network Modulates the Activity of the Escherichia coli Disulphide Catalyst DsbA. Antioxidants (Basel) 2023; 12:antiox12020380. [PMID: 36829940 PMCID: PMC9952396 DOI: 10.3390/antiox12020380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
The formation of disulphide bonds is an essential step in the folding of many proteins that enter the secretory pathway; therefore, it is not surprising that eukaryotic and prokaryotic organisms have dedicated enzymatic systems to catalyse this process. In bacteria, one such enzyme is disulphide bond-forming protein A (DsbA), a thioredoxin-like thiol oxidase that catalyses the oxidative folding of proteins required for virulence and fitness. A large body of work on DsbA proteins, particularly Escherichia coli DsbA (EcDsbA), has demonstrated the key role that the Cys30-XX-Cys33 catalytic motif and its unique redox properties play in the thiol oxidase activity of this enzyme. Using mutational and functional analyses, here we identify that a set of charged residues, which form an acidic groove on the non-catalytic face of the enzyme, further modulate the activity of EcDsbA. Our high-resolution structures indicate that these residues form a water-mediated proton wire that can transfer protons from the bulk solvent to the active site. Our results support the view that proton shuffling may facilitate the stabilisation of the buried Cys33 thiolate formed during the redox reaction and promote the correct direction of the EcDsbA-substrate thiol-disulphide exchange. Comparison with other proteins of the same class and proteins of the thioredoxin-superfamily in general suggest that a proton relay system appears to be a conserved catalytic feature among this widespread superfamily of proteins. Furthermore, this study also indicates that the acidic groove of DsbA could be a promising allosteric site to develop novel DsbA inhibitors as antibacterial therapeutics.
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Affiliation(s)
- Geqing Wang
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Correspondence: (G.W.); (B.H.)
| | - Jilong Qin
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Anthony D. Verderosa
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Lilian Hor
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Carlos Santos-Martin
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Jason J. Paxman
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Jennifer L. Martin
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Begoña Heras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Correspondence: (G.W.); (B.H.)
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Venturelli S, Leischner C, Helling T, Renner O, Burkard M, Marongiu L. Minerals and Cancer: Overview of the Possible Diagnostic Value. Cancers (Basel) 2022; 14:1256. [PMID: 35267564 PMCID: PMC8909570 DOI: 10.3390/cancers14051256] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 12/16/2022] Open
Abstract
Cancer is the second leading cause of death worldwide and is expected to increase by one-third over the next two decades, in parallel with the growing proportion of the elderly population. Treatment and control of cancer incidence is a global issue. Since there is no clear way to prevent or cure this deadly malignancy, diagnostic, predictive, and prognostic markers for oncological diseases are of great therapeutic value. Minerals and trace elements are important micronutrients for normal physiological function of the body. They are abundant in natural food sources and are regularly included in dietary supplements whereas highly processed industrial food often contains reduced or altered amounts of them. In modern society, the daily intake, storage pools, and homeostasis of these micronutrients are dependent on certain dietary habits and can be thrown out of balance by malignancies. The current work summarizes the data on minerals and trace elements associated with abnormal accumulation or depletion states in tumor patients and discusses their value as potential tumor-associated biomarkers that could be introduced into cancer therapy.
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Affiliation(s)
- Sascha Venturelli
- Department of Nutritional Biochemistry, Institute of Nutritional Sciences, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany; (S.V.); (C.L.); (T.H.); (O.R.)
- Department of Vegetative and Clinical Physiology, Institute of Physiology, University of Tuebingen, Wilhelmstraße 56, 72074 Tuebingen, Germany
| | - Christian Leischner
- Department of Nutritional Biochemistry, Institute of Nutritional Sciences, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany; (S.V.); (C.L.); (T.H.); (O.R.)
| | - Thomas Helling
- Department of Nutritional Biochemistry, Institute of Nutritional Sciences, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany; (S.V.); (C.L.); (T.H.); (O.R.)
| | - Olga Renner
- Department of Nutritional Biochemistry, Institute of Nutritional Sciences, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany; (S.V.); (C.L.); (T.H.); (O.R.)
| | - Markus Burkard
- Department of Nutritional Biochemistry, Institute of Nutritional Sciences, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany; (S.V.); (C.L.); (T.H.); (O.R.)
| | - Luigi Marongiu
- Department of Nutritional Biochemistry, Institute of Nutritional Sciences, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany; (S.V.); (C.L.); (T.H.); (O.R.)
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3
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Vascular thiol isomerases: Structures, regulatory mechanisms, and inhibitor development. Drug Discov Today 2021; 27:626-635. [PMID: 34757205 DOI: 10.1016/j.drudis.2021.10.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/15/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Vascular thiol isomerases (VTIs), including PDI, ERp5, ERp57, ERp72, and thioredoxin-related transmembrane protein 1 (TMX1), have important roles in platelet aggregation and thrombosis. Research on VTIs, their substrates in thrombosis, their regulatory mechanisms, and inhibitor development is an emerging and rapidly evolving area in vascular biology. Here, we describe the structures and functions of VTIs, summarize the relationship between the vascular TIs and thrombosis, and focus on the development of VTI inhibitors for antithrombotic applications.
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Brahimi F, Galan A, Jmaeff S, Barcelona PF, De Jay N, Dejgaard K, Young JC, Kleinman CL, Thomas DY, Saragovi HU. Alternative Splicing of a Receptor Intracellular Domain Yields Different Ectodomain Conformations, Enabling Isoform-Selective Functional Ligands. iScience 2020; 23:101447. [PMID: 32829283 PMCID: PMC7452315 DOI: 10.1016/j.isci.2020.101447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/13/2020] [Accepted: 08/06/2020] [Indexed: 01/04/2023] Open
Abstract
Events at a receptor ectodomain affect the intracellular domain conformation, activating signal transduction (out-to-in conformational effects). We investigated the reverse direction (in-to-out) where the intracellular domain may impact on ectodomain conformation. The primary sequences of naturally occurring TrkC receptor isoforms (TrkC-FL and TrkC.T1) only differ at the intracellular domain. However, owing to their differential association with Protein Disulfide Isomerase the isoforms have different disulfide bonding and conformations at the ectodomain. Conformations were exploited to develop artificial ligands, mAbs, and small molecules, with isoform-specific binding and biased activation. Consistent, the physiological ligands NT-3 and PTP-sigma bind both isoforms, but NT-3 activates all signaling pathways, whereas PTP-sigma activates biased signals. Our data support an "in-to-out" model controlling receptor ectodomain conformation, a strategy that enables heterogeneity in receptors, ligands, and bioactivity. These concepts may be extended to the many wild-type or oncogenic receptors with known isoforms.
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Affiliation(s)
- Fouad Brahimi
- Lady Davis Institute-Jewish General Hospital, McGill University, 3755 Côte St. Catherine, E-535, Montreal, QC H3T 1E2, Canada
| | - Alba Galan
- Lady Davis Institute-Jewish General Hospital, McGill University, 3755 Côte St. Catherine, E-535, Montreal, QC H3T 1E2, Canada
| | - Sean Jmaeff
- Lady Davis Institute-Jewish General Hospital, McGill University, 3755 Côte St. Catherine, E-535, Montreal, QC H3T 1E2, Canada
- Department of Pharmacology, McGill University, Montreal, QC, Canada
| | - Pablo F. Barcelona
- Lady Davis Institute-Jewish General Hospital, McGill University, 3755 Côte St. Catherine, E-535, Montreal, QC H3T 1E2, Canada
| | - Nicolas De Jay
- Lady Davis Institute-Jewish General Hospital, McGill University, 3755 Côte St. Catherine, E-535, Montreal, QC H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kurt Dejgaard
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Jason C. Young
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Claudia L. Kleinman
- Lady Davis Institute-Jewish General Hospital, McGill University, 3755 Côte St. Catherine, E-535, Montreal, QC H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - David Y. Thomas
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - H. Uri Saragovi
- Lady Davis Institute-Jewish General Hospital, McGill University, 3755 Côte St. Catherine, E-535, Montreal, QC H3T 1E2, Canada
- Department of Pharmacology, McGill University, Montreal, QC, Canada
- Department of Ophthalmology and Visual Science, McGill University, Montreal, QC, Canada
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Komatsu K, Kumon K, Arita M, Onitsuka M, Omasa T, Yohda M. Effect of the disulfide isomerase PDIa4 on the antibody production of Chinese hamster ovary cells. J Biosci Bioeng 2020; 130:637-643. [PMID: 32878739 DOI: 10.1016/j.jbiosc.2020.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/22/2020] [Accepted: 08/02/2020] [Indexed: 12/30/2022]
Abstract
Therapeutic monoclonal antibodies recognize and bind specific molecules on the surface of target cells, stimulating the immune system, which can attack these targeted cells. These antibodies are produced by mammalian cells, including Chinese hamster ovary (CHO) cells, because the formation of antibodies requires complicated posttranslational modifications, including peptidyl-prolyl cis/trans isomerization, disulfide bond formation, and glycosylation. Currently, it is thought that the efficient production of secretory proteins is limited by posttranslational processes. The ER is the biosynthesis site of all secreted and membrane proteins. The accumulation of unfolded proteins in the ER causes the ER stress response. During the ER stress state, various molecular chaperones are expressed to prevent proteins from the aggregate formation. The molecular chaperone involved in ER stress likely plays an essential role in the production of secretory proteins. The purpose of this study was to improve the production of monoclonal antibodies by cells. We elucidated the function of ER chaperones in the production of a monoclonal antibody. First, we quantitatively measured the mRNA expression levels of protein disulfide-isomerase family members. In CHO HcD6 cells treated with tunicamycin, the expression level of pdia4 was significantly increased. Second, we investigated the relationship between PDIa4 and antibody productivity in pdia4-knockdown cells. Both a decrease in the amount of secreted antibody and the accumulation of immature antibodies inside the cells were observed. Recombinant PDIa4 was able to refold the antibodies and Fabs. These results indicate that PDIa4 affects the production of monoclonal antibodies by catalyzing disulfide bond formation in these antibodies in CHO cells.
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Affiliation(s)
- Kei Komatsu
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kento Kumon
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Mayuno Arita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Masayoshi Onitsuka
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima 770-8513, Japan
| | - Takeshi Omasa
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
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6
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Chiu J, Hogg PJ. Allosteric disulfides: Sophisticated molecular structures enabling flexible protein regulation. J Biol Chem 2019; 294:2949-2960. [PMID: 30635401 DOI: 10.1074/jbc.rev118.005604] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein disulfide bonds link pairs of cysteine residues in polypeptide chains. Many of these bonds serve a purely structural or energetic role, but a growing subset of cleavable disulfide bonds has been shown to control the function of the mature protein in which they reside. These allosteric disulfides and the factors that cleave these bonds are being identified across biological systems and life forms and have been shown to control hemostasis, the immune response, and viral infection in mammals. The discovery of these functional disulfides and a rationale for their facile nature has been aided by the emergence of a conformational signature for allosteric bonds. This post-translational modification mostly occurs extracellularly, making these chemical events prime drug targets. Indeed, a membrane-impermeable inhibitor of one of the cleaving factors is currently being trialed as an antithrombotic agent in cancer patients. Allosteric disulfides are firmly established as a sophisticated means by which a protein's shape and function can be altered; however, the full scope of this biological regulation will not be realized without new tools and techniques to study this regulation and innovative ways of targeting it.
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Affiliation(s)
- Joyce Chiu
- From the Centenary Institute, National Health and Medical Research Council Clinical Trials Centre, Sydney Medical School, University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Philip J Hogg
- From the Centenary Institute, National Health and Medical Research Council Clinical Trials Centre, Sydney Medical School, University of Sydney, Camperdown, New South Wales 2006, Australia
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7
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Tsachaki M, Mladenovic N, Štambergová H, Birk J, Odermatt A. Hexose-6-phosphate dehydrogenase controls cancer cell proliferation and migration through pleiotropic effects on the unfolded-protein response, calcium homeostasis, and redox balance. FASEB J 2018; 32:2690-2705. [PMID: 29295867 PMCID: PMC5901385 DOI: 10.1096/fj.201700870rr] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hexose-6-phosphate dehydrogenase (H6PD) produces reduced NADPH in the endoplasmic reticulum (ER) lumen. NADPH constitutes a cofactor for many reducing enzymes, and its inability to traverse biologic membranes makes in situ synthesis of NADPH in the ER lumen indispensable. The H6PD gene is amplified in several types of malignancies, and earlier work pointed toward a potential involvement of the enzyme in cancer cell growth. In the present study, we demonstrated a pivotal role of H6PD in proliferation and migratory potential of 3 human breast cancer cell lines. Knockdown of H6PD decreased proliferation and migration in SUM159, MCF7, and MDA-MB-453 cells. To understand the mechanism through which H6PD exerts its effects, we investigated the cellular changes after H6PD silencing in SUM159 cells. Knockdown of H6PD resulted in an increase in ER lumen oxidation, and down-regulation of many components of the unfolded protein response, including the transcription factors activating transcription factor-4, activating transcription factor-6, split X-box binding protein-1, and CCAAT/enhancer binding protein homologous protein. This effect was accompanied by an increase in sarco/endoplasmic reticulum Ca2+-ATPase-2 pump expression and an decrease in inositol trisphosphate receptor-III, which led to augmented levels of calcium in the ER. Further characterization of the molecular pathways involving H6PD could greatly broaden our understanding of how the ER microenvironment sustains malignant cell growth.-Tsachaki, M., Mladenovic, N., Štambergová, H., Birk, J., Odermatt, A. Hexose-6-phosphate dehydrogenase controls cancer cell proliferation and migration through pleiotropic effects on the unfolded protein response, calcium homeostasis, and redox balance.
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Affiliation(s)
- Maria Tsachaki
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Natasa Mladenovic
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Hana Štambergová
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Julia Birk
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Alex Odermatt
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
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8
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The disulfide isomerase ERp72 supports arterial thrombosis in mice. Blood 2017; 130:817-828. [PMID: 28576878 DOI: 10.1182/blood-2016-12-755587] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/30/2017] [Indexed: 01/01/2023] Open
Abstract
Several CGHC motif-containing disulfide isomerases support thrombosis. We here report that endoplasmic reticulum protein 72 (ERp72), with 3 CGHC redox-active sites (ao, a, and a'), supports thrombosis. We generated a new conditional knockout mouse model and found that Tie2-Cre/ERp72fl/fl mice with blood and endothelial cells lacking ERp72 had prolonged tail bleeding times and decreased platelet accumulation in laser-induced cremaster arteriole injury and FeCl3-induced mesenteric arterial injury. Fibrin deposition was decreased in the laser injury model. Both platelet and fibrin accumulation defects were fully rescued by infusion of recombinant ERp72 containing functional a and a' CGHC motifs (ERp72(oo-ss-ss)). Infusion of ERp72 containing inactivated a and a' CGHC motifs (ERp72(ss-oo-oo)) inhibited platelet accumulation and fibrin deposition in wild-type mice. Infusion of ERp72(oo-ss-ss) into β3-null mice increased fibrin deposition in the absence of platelets. ERp72-null platelets had defective aggregation, JON/A binding, P-selectin expression, and adenosine triphosphate (ATP) secretion. The aggregation and ATP secretion defects were fully rescued by ERp72(oo-ss-ss) but partially rescued by ERp72(ss-oo-ss) and ERp72(ss-ss-oo). Aggregation and ATP secretion of human platelets was potentiated by ERp72(oo-ss-ss) but inhibited by ERp72(ss-oo-ss) and ERp72(ss-ss-oo). These data suggest that both the a and a' active sites are required for platelet function. ERp72 bound poorly to β3-null mouse platelets, and the addition of ERp72(oo-ss-ss) to human platelets generated thiols in αIIbβ3, suggesting a direct interaction of ERp72 with αIIbβ3. Defective aggregation of ERp72-null platelets was recovered by ERp72, but not other thiol isomerases. In summary, ERp72 plays a critical role in platelet function and coagulation through the a and a' CGHC motifs.
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Structure-based functional annotation of hypothetical proteins from Candida dubliniensis: a quest for potential drug targets. 3 Biotech 2015; 5:561-576. [PMID: 28324558 PMCID: PMC4522726 DOI: 10.1007/s13205-014-0256-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 09/30/2014] [Indexed: 12/24/2022] Open
Abstract
Candida dubliniensis is an emerging pathogenic yeast in humans and infections are usually restricted to mucosal parts of the body. However, its presence in specimens of immunocompromised individuals, especially in HIV-positive patients, is of major medical concern. There is a large fraction of genomes of C. dubliniensis in the database which are uncharacterized for their biochemical, biophysical, and/or cellular functions, and are identified as hypothetical proteins (HPs). Function annotation of Candida genome is, therefore, essentially required to facilitate the understanding of mechanisms of pathogenesis and biochemical pathways important for selecting novel therapeutic target. Here, we carried out an extensive analysis to explain the functional properties of genome, using available protein structure and function analysis tools. We successfully modeled the structures of eight HPs for which a template with moderate sequence similarity was available in the protein data bank. All modeled structures were analyzed and we found that these proteins may act as transporter, kinase, transferase, ketosteroid, isomerase, hydrolase, oxidoreductase, and binding targets for DNA and RNA. Since these unique HPs of Candida showed no homologs in humans, these proteins are expected to be a potential target for future antifungal therapy.
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Peng L, Rasmussen MI, Chailyan A, Houen G, Højrup P. Probing the structure of human protein disulfide isomerase by chemical cross-linking combined with mass spectrometry. J Proteomics 2014; 108:1-16. [PMID: 24792702 DOI: 10.1016/j.jprot.2014.04.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/07/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022]
Abstract
UNLABELLED Protein disulfide-isomerase (PDI) is a four-domain flexible protein that catalyzes the formation of disulfide bonds in the endoplasmic reticulum. Here we have analyzed native PDI purified from human placenta by chemical cross-linking followed by mass spectrometry (CXMS). In addition to PDI the sample contained soluble calnexin and ERp72. Extensive cross-linking was observed within the PDI molecule, both intra- and inter-domain, as well as between the different components in the mixture. The high sensitivity of the analysis in the current experiments, combined with a likely promiscuous interaction pattern of the involved proteins, revealed relatively densely populated cross-link heat maps. The established X-ray structure of the monomeric PDI could be confirmed; however, the dimer as presented in the existing models does not seem to be prevalent in solution as modeling on the observed cross-links revealed new models of dimeric PDI. The observed inter-protein cross-links confirmed the existence of a peptide binding area on calnexin that binds strongly both PDI and ERp72. On the other hand, interaction sites on PDI and ERp72 could not be uniquely identified, indicating a more non-specific interaction pattern. BIOLOGICAL SIGNIFICANCE The present work demonstrates the use of chemical cross-linking and mass spectrometry (CXMS) for the determination of a solution structure of natural human PDI and its interaction with the chaperones ERp72 and calnexin. The data shows that the dimeric structure of PDI may be more diverse than indicated by present models. We further observe that the temperature influences the cross-linking pattern of PDI, but this does not influence the overall folding pattern of the molecule.
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Affiliation(s)
- Li Peng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Morten Ib Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Anna Chailyan
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Gunnar Houen
- Department of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Copenhagen, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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Tang CH, Lai YR, Chen YC, Li CH, Lu YF, Chen HY, Lien HW, Yang CH, Huang CJ, Wang CY, Kao CF, Hwang SPL. Expression of zebrafish anterior gradient 2 in the semicircular canals and supporting cells of otic vesicle sensory patches is regulated by Sox10. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:425-37. [PMID: 24768923 DOI: 10.1016/j.bbagrm.2014.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/17/2014] [Accepted: 04/15/2014] [Indexed: 11/16/2022]
Abstract
AGR2 is a member of the protein disulfide isomerase (PDI) family, which is implicated in cancer cell growth and metastasis, asthma, and inflammatory bowel disease. Despite the contributions of this protein to several biological processes, the regulatory mechanisms controlling expression of the AGR2 gene in different organs remain unclear. Zebrafish anterior gradient 2 (agr2) is expressed in several organs, including the otic vesicles that contain mucus-secreting cells. To elucidate the regulatory mechanisms controlling agr2 expression in otic vesicles, we generated a Tg(-6.0 k agr2:EGFP) transgenic fish line that expressed EGFP in a pattern recapitulating that of agr2. Double immunofluorescence studies were used to demonstrate that Agr2 and GFP colocalize in the semicircular canals and supporting cells of all sensory patches in the otic vesicles of Tg(-6.0 k agr2:EGFP) embryos. Transient/stable transgenic analyses coupled with 5'-end deletion revealed that a 100 bp sequence within the -2.6 to -2.5 kbp region upstream of agr2 directs EGFP expression specifically in the otic vesicles. Two HMG-binding motifs were detected in this region. Mutation of these motifs prevented EGFP expression. Furthermore, EGFP expression in the otic vesicles was prevented by knockdown of the sox10 gene. This corresponded with decreased agr2 expression in the otic vesicles of sox10 morphants during different developmental stages. Electrophoretic mobility shift assays were used to show that Sox10 binds to HMG-binding motifs located within the -2.6 to -2.5 kbp region upstream of agr2. These results demonstrate that agr2 expression in the otic vesicles of zebrafish embryos is regulated by Sox10.
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Affiliation(s)
- Chih-Hao Tang
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Yun-Ren Lai
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Yi-Chung Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chen-Hsiu Li
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Yu-Fen Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hung-Yen Chen
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Huang-Wei Lien
- Institute of Fisheries Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chung-Hsiang Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chang-Jen Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chen-Yi Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Sheng-Ping L Hwang
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
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12
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Funkner A, Parthier C, Schutkowski M, Zerweck J, Lilie H, Gyrych N, Fischer G, Stubbs MT, Ferrari DM. Peptide binding by catalytic domains of the protein disulfide isomerase-related protein ERp46. J Mol Biol 2013; 425:1340-62. [PMID: 23376096 DOI: 10.1016/j.jmb.2013.01.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 01/09/2013] [Accepted: 01/23/2013] [Indexed: 11/18/2022]
Abstract
The protein disulfide isomerase (PDI) family member ERp46/endoPDI/thioredoxin domain-containing protein 5 is preferentially expressed in a limited number of tissues, where it may function as a survival factor for nitrosative stress in vivo. It is involved in insulin production as well as in adiponectin signaling and interacts specifically with the redox-regulatory endoplasmic reticulum proteins endoplasmic oxidoreductin 1α (Ero1α) and peroxiredoxin-4. Here, we show that ERp46, although lacking a PDI-like redox-inactive b'-thioredoxin domain with its hydrophobic substrate binding site, is able to bind to a large pool of peptides containing aromatic and basic residues via all three of its catalytic domains (a(0), a and a'), though the a(0) domain may contain the primary binding site. ERp46, which shows relatively higher activity as a disulfide-reductase than as an oxidase/isomerase in vitro compared to PDI and ERp57, possesses chaperone activity in vivo, a property also shared by the C-terminal a' domain. A crystal structure of the a' domain is also presented, offering a view of possible substrate binding sites within catalytic domains of PDI proteins.
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Affiliation(s)
- Andreas Funkner
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle (Saale), Germany
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Progranulin, a glycoprotein deficient in frontotemporal dementia, is a novel substrate of several protein disulfide isomerase family proteins. PLoS One 2011; 6:e26454. [PMID: 22028881 PMCID: PMC3196579 DOI: 10.1371/journal.pone.0026454] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 09/27/2011] [Indexed: 12/30/2022] Open
Abstract
The reduced production or activity of the cysteine-rich glycoprotein progranulin is responsible for about 20% of cases of familial frontotemporal dementia. However, little is known about the molecular mechanisms that govern the level and secretion of progranulin. Here we show that progranulin is expressed in mouse cortical neurons and more prominently in mouse microglia in culture and is abundant in the endoplasmic reticulum (ER) and Golgi. Using chemical crosslinking, immunoprecipitation, and mass spectrometry, we found that progranulin is bound to a network of ER Ca(2+)-binding chaperones including BiP, calreticulin, GRP94, and four members of the protein disulfide isomerase (PDI) family. Loss of ERp57 inhibits progranulin secretion. Thus, progranulin is a novel substrate of several PDI family proteins and modulation of the ER chaperone network may be a therapeutic target for controlling progranulin secretion.
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14
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CrossWork: software-assisted identification of cross-linked peptides. J Proteomics 2011; 74:1871-83. [PMID: 21600323 DOI: 10.1016/j.jprot.2011.04.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 04/19/2011] [Accepted: 04/22/2011] [Indexed: 11/23/2022]
Abstract
The increased interest in chemical cross-linking for probing protein structure and interaction has led to a large increase in literature describing new cross-linkers and search programs. However, this has not led to a corresponding increase in the analysis of large and complex proteins. A major obstacle is that the new cross-linkers are either not readily available and/or have a low reactivity. In combination with aging search programs that are slow and have low sensitivity, or new search programs that are described but not released, these efforts do little to advance the field of cross-linking. Here we present a method pipeline for chemical cross-linking, using two standard cross-linkers, BS3 and BS2G, combined with our freely available CrossWork search program. By this approach we generate cross-link data sufficient to derive structural information for large and complex proteins. CrossWork searches batches of tandem mass-spectrometric data, and identifies cross-linked and non-cross-linked peptides using a standard PC. We tested CrossWork by searching mass-spectrometric datasets of cross-linked complement factor C3 against small (1 protein) and large (1000 proteins) search spaces, and show that the resulting distance constraints agree with the established structures. We further investigated the structure of the multi-domain ERp72, and combined the individual domains of ERp72 into a single structure.
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15
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Comparative genomic study of protein disulfide isomerases from photosynthetic organisms. Genomics 2011; 97:37-50. [DOI: 10.1016/j.ygeno.2010.10.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 09/15/2010] [Accepted: 10/07/2010] [Indexed: 11/19/2022]
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Participation of lectin chaperones and thiol oxidoreductases in protein folding within the endoplasmic reticulum. Curr Opin Cell Biol 2010; 23:157-66. [PMID: 21094034 DOI: 10.1016/j.ceb.2010.10.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 10/05/2010] [Accepted: 10/21/2010] [Indexed: 01/21/2023]
Abstract
Protein folding within the endoplasmic reticulum occurs in conjunction with a complex array of molecular chaperones and folding catalysts that assist the folding process as well as function in quality control processes to monitor the outcome. In this review, we summarize recent advances in the calnexin/calreticulin chaperone system that is directed primarily toward Asn-linked glycoproteins, as well as the protein disulfide isomerase family of enzymes that catalyze disulfide formation, reduction, and isomerization. We highlight issues related to function and substrate specificity as well as the functional interplay between the two systems.
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Kozlov G, Määttänen P, Thomas DY, Gehring K. A structural overview of the PDI family of proteins. FEBS J 2010; 277:3924-36. [DOI: 10.1111/j.1742-4658.2010.07793.x] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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