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Coluccino G, Muraca VP, Corazza A, Lippe G. Cyclophilin D in Mitochondrial Dysfunction: A Key Player in Neurodegeneration? Biomolecules 2023; 13:1265. [PMID: 37627330 PMCID: PMC10452829 DOI: 10.3390/biom13081265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial dysfunction plays a pivotal role in numerous complex diseases. Understanding the molecular mechanisms by which the "powerhouse of the cell" turns into the "factory of death" is an exciting yet challenging task that can unveil new therapeutic targets. The mitochondrial matrix protein CyPD is a peptidylprolyl cis-trans isomerase involved in the regulation of the permeability transition pore (mPTP). The mPTP is a multi-conductance channel in the inner mitochondrial membrane whose dysregulated opening can ultimately lead to cell death and whose involvement in pathology has been extensively documented over the past few decades. Moreover, several mPTP-independent CyPD interactions have been identified, indicating that CyPD could be involved in the fine regulation of several biochemical pathways. To further enrich the picture, CyPD undergoes several post-translational modifications that regulate both its activity and interaction with its clients. Here, we will dissect what is currently known about CyPD and critically review the most recent literature about its involvement in neurodegenerative disorders, focusing on Alzheimer's Disease and Parkinson's Disease, supporting the notion that CyPD could serve as a promising therapeutic target for the treatment of such conditions. Notably, significant efforts have been made to develop CyPD-specific inhibitors, which hold promise for the treatment of such complex disorders.
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Affiliation(s)
- Gabriele Coluccino
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy; (V.P.M.); (A.C.)
| | | | | | - Giovanna Lippe
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy; (V.P.M.); (A.C.)
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2
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Gurung D, Danielson JA, Tasnim A, Zhang JT, Zou Y, Liu JY. Proline Isomerization: From the Chemistry and Biology to Therapeutic Opportunities. BIOLOGY 2023; 12:1008. [PMID: 37508437 PMCID: PMC10376262 DOI: 10.3390/biology12071008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
Proline isomerization, the process of interconversion between the cis- and trans-forms of proline, is an important and unique post-translational modification that can affect protein folding and conformations, and ultimately regulate protein functions and biological pathways. Although impactful, the importance and prevalence of proline isomerization as a regulation mechanism in biological systems have not been fully understood or recognized. Aiming to fill gaps and bring new awareness, we attempt to provide a wholistic review on proline isomerization that firstly covers what proline isomerization is and the basic chemistry behind it. In this section, we vividly show that the cause of the unique ability of proline to adopt both cis- and trans-conformations in significant abundance is rooted from the steric hindrance of these two forms being similar, which is different from that in linear residues. We then discuss how proline isomerization was discovered historically followed by an introduction to all three types of proline isomerases and how proline isomerization plays a role in various cellular responses, such as cell cycle regulation, DNA damage repair, T-cell activation, and ion channel gating. We then explore various human diseases that have been linked to the dysregulation of proline isomerization. Finally, we wrap up with the current stage of various inhibitors developed to target proline isomerases as a strategy for therapeutic development.
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Affiliation(s)
- Deepti Gurung
- Department of Medicine, University of Toledo College of Medicine, Toledo, OH 43614, USA
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Jacob A Danielson
- Department of Medicine, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Afsara Tasnim
- Department of Bioengineering, University of Toledo College of Engineering, Toledo, OH 43606, USA
| | - Jian-Ting Zhang
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Yue Zou
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Jing-Yuan Liu
- Department of Medicine, University of Toledo College of Medicine, Toledo, OH 43614, USA
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
- Department of Bioengineering, University of Toledo College of Engineering, Toledo, OH 43606, USA
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3
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Favretto F, Jiménez-Faraco E, Conter C, Dominici P, Hermoso JA, Astegno A. Structural Basis for Cyclosporin Isoform-Specific Inhibition of Cyclophilins from Toxoplasma gondii. ACS Infect Dis 2023; 9:365-377. [PMID: 36653744 PMCID: PMC9926490 DOI: 10.1021/acsinfecdis.2c00566] [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] [Indexed: 01/20/2023]
Abstract
Cyclosporin (CsA) has antiparasite activity against the human pathogen Toxoplasma gondii. A possible mechanism of action involves CsA binding to T. gondii cyclophilins, although much remains to be understood. Herein, we characterize the functional and structural properties of a conserved (TgCyp23) and a more divergent (TgCyp18.4) cyclophilin isoform from T. gondii. While TgCyp23 is a highly active cis-trans-prolyl isomerase (PPIase) and binds CsA with nanomolar affinity, TgCyp18.4 shows low PPIase activity and is significantly less sensitive to CsA inhibition. The crystal structure of the TgCyp23:CsA complex was solved at the atomic resolution showing the molecular details of CsA recognition by the protein. Computational and structural studies revealed relevant differences at the CsA-binding site between TgCyp18.4 and TgCyp23, suggesting that the two cyclophilins might have distinct functions in the parasite. These studies highlight the extensive diversification of TgCyps and pave the way for antiparasite interventions based on selective targeting of cyclophilins.
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Affiliation(s)
- Filippo Favretto
- Department
of Biotechnology, University of Verona, Strada Le Grazie 15, 37134Verona, Italy
| | - Eva Jiménez-Faraco
- Department
of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano (IQFR), CSIC, Serrano 119, 28006Madrid, Spain
| | - Carolina Conter
- Department
of Biotechnology, University of Verona, Strada Le Grazie 15, 37134Verona, Italy
| | - Paola Dominici
- Department
of Biotechnology, University of Verona, Strada Le Grazie 15, 37134Verona, Italy
| | - Juan A. Hermoso
- Department
of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano (IQFR), CSIC, Serrano 119, 28006Madrid, Spain,
| | - Alessandra Astegno
- Department
of Biotechnology, University of Verona, Strada Le Grazie 15, 37134Verona, Italy,
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4
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Wang L, Yang X, Zhou S, Lyu T, Shi L, Dong Y, Zhang H. Comparative transcriptome analysis revealed omnivorous adaptation of the small intestine of Melinae. Sci Rep 2021; 11:19162. [PMID: 34580368 PMCID: PMC8476558 DOI: 10.1038/s41598-021-98561-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023] Open
Abstract
As the main digestive organ, the small intestine plays a vital role in the digestion of animals. At present, most of the research on animal feeding habits focuses on carnivores and herbivores. However, the mechanism of feeding and digestion in omnivores remains unclear. This study aims to reveal the molecular basis of the omnivorous adaptive evolution of Melinae by comparing the transcriptome of the small intestines of Asian Badgers (Meles leucurus) and Northern Hog Badgers (Arctonyx albogularis). We obtained high-quality small intestinal transcriptome data from these two species. Key genes and signalling pathways were analysed through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and other databases. Research has mainly found that orthologous genes related to six enzymes have undergone adaptive evolution. In addition, the study also found three digestion-related pathways (cGMP-PKG, cAMP, and Hippo). They are related to the digestion and absorption of nutrients, the secretion of intestinal fluids, and the transport of food through the small intestine, which may help omnivorous animals adapt to an omnivorous diet. Our study provides insight into the adaptation of Melinae to omnivores and affords a valuable transcriptome resource for future research.
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Affiliation(s)
| | | | | | | | - Lupeng Shi
- Qufu Normal University, Qufu, 273165, China
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5
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Dujardin M, Bouckaert J, Rucktooa P, Hanoulle X. X-ray structure of alisporivir in complex with cyclophilin A at 1.5 Å resolution. Acta Crystallogr F Struct Biol Commun 2018; 74:583-592. [PMID: 30198892 PMCID: PMC6130424 DOI: 10.1107/s2053230x18010415] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 07/18/2018] [Indexed: 12/14/2022] Open
Abstract
Alisporivir (ALV) is an 11-amino-acid hydrophobic cyclic peptide with N-methyl-D-alanine and N-ethyl-L-valine (NEV) residues at positions 3 and 4, respectively. ALV is a non-immunosuppressive cyclosporin A (CsA) derivative. This inhibitor targets cyclophilins (Cyps), a family of proteins with peptidyl-prolyl cis/trans isomerase enzymatic activity. Cyps act as protein chaperones and are involved in numerous cellular functions. Moreover, Cyps have been shown to be an essential cofactor for the replication of many viruses, including Hepatitis C virus and Human immunodeficiency virus, and have also been shown to be involved in mitochondrial diseases. For these reasons, cyclophilins represent an attractive drug target. The structure of ALV in complex with cyclophilin A (CypA), the most abundant Cyp in humans, has been determined at 1.5 Å resolution. This first structure of the CypA-ALV complex shows that the binding of ALV is highly similar to that of CsA. The high resolution allowed the unambiguous determination of the conformations of residues 3 and 4 in ALV when bound to its target. In particular, the side-chain conformation of NEV4 precludes the interaction of the CypA-ALV complex with calcineurin, a cellular protein phosphatase involved in the immune response, which explains the non-immunosuppressive property of ALV. This study provides detailed molecular insights into the CypA-ALV interaction.
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Affiliation(s)
- Marie Dujardin
- UGSF–UMR8576, University of Lille, CNRS, F-59000 Lille, France
| | - Julie Bouckaert
- UGSF–UMR8576, University of Lille, CNRS, F-59000 Lille, France
| | | | - Xavier Hanoulle
- UGSF–UMR8576, University of Lille, CNRS, F-59000 Lille, France
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6
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Watashi K, Shimotohno K. Cyclophilin and Viruses: Cyclophilin as a Cofactor for Viral Infection and Possible Anti-Viral Target. Drug Target Insights 2017. [DOI: 10.1177/117739280700200017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Koichi Watashi
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Kunitada Shimotohno
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Kyoto, Japan
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7
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PPIA rs6850: A > G single-nucleotide polymorphism is associated with raised plasma cyclophilin A levels in patients with coronary artery disease. Mol Cell Biochem 2015; 412:259-68. [DOI: 10.1007/s11010-015-2632-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/15/2015] [Indexed: 12/20/2022]
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8
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Perrucci GL, Gowran A, Zanobini M, Capogrossi MC, Pompilio G, Nigro P. Peptidyl-prolyl isomerases: a full cast of critical actors in cardiovascular diseases. Cardiovasc Res 2015; 106:353-64. [DOI: 10.1093/cvr/cvv096] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/30/2015] [Indexed: 12/28/2022] Open
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9
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Blair LJ, Baker JD, Sabbagh JJ, Dickey CA. The emerging role of peptidyl-prolyl isomerase chaperones in tau oligomerization, amyloid processing, and Alzheimer's disease. J Neurochem 2015; 133:1-13. [PMID: 25628064 DOI: 10.1111/jnc.13033] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/12/2014] [Accepted: 01/05/2015] [Indexed: 12/20/2022]
Abstract
Peptidyl-prolyl cis/trans isomerases (PPIases), a unique family of molecular chaperones, regulate protein folding at proline residues. These residues are abundant within intrinsically disordered proteins, like the microtubule-associated protein tau. Tau has been shown to become hyperphosphorylated and accumulate as one of the two main pathological hallmarks in Alzheimer's disease, the other being amyloid beta (Ab). PPIases, including Pin1, FK506-binding protein (FKBP) 52, FKBP51, and FKBP12, have been shown to interact with and regulate tau biology. This interaction is particularly important given the numerous proline-directed phosphorylation sites found on tau and the role phosphorylation has been found to play in pathogenesis. This regulation then affects downstream aggregation and oligomerization of tau. However, many PPIases have yet to be explored for their effects on tau biology, despite the high likelihood of interaction based on proline content. Moreover, Pin1, FKBP12, FKBP52, cyclophilin (Cyp) A, CypB, and CypD have been shown to also regulate Ab production or the toxicity associated with Ab pathology. Therefore, PPIases directly and indirectly regulate pathogenic protein multimerization in Alzheimer's disease and represent a family rich in targets for modulating the accumulation and toxicity.
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Affiliation(s)
- Laura J Blair
- Department of Molecular Medicine, Byrd Alzheimer's Institute, University of South Florida, Tampa, Florida, USA
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10
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Valasani KR, Carlson EA, Battaile KP, Bisson A, Wang C, Lovell S, Yan SS. High-resolution crystal structures of two crystal forms of human cyclophilin D in complex with PEG 400 molecules. Acta Crystallogr F Struct Biol Commun 2014; 70:717-22. [PMID: 24915078 PMCID: PMC4051522 DOI: 10.1107/s2053230x14009480] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/28/2014] [Indexed: 11/10/2022] Open
Abstract
Cyclophilin D (CypD) is a key mitochondrial target for amyloid-β-induced mitochondrial and synaptic dysfunction and is considered a potential drug target for Alzheimer's disease. The high-resolution crystal structures of primitive orthorhombic (CypD-o) and primitive tetragonal (CypD-t) forms have been determined to 1.45 and 0.85 Å resolution, respectively, and are nearly identical structurally. Although an isomorphous structure of CypD-t has previously been reported, the structure reported here was determined at atomic resolution, while CypD-o represents a new crystal form for this protein. In addition, each crystal form contains a PEG 400 molecule bound to the same region along with a second PEG 400 site in CypD-t which occupies the cyclosporine A inhibitor binding site of CypD. Highly precise structural information for CypD should be extremely useful for discerning the detailed interaction of small molecules, particularly drugs and/or inhibitors, bound to CypD. The 0.85 Å resolution structure of CypD-t is the highest to date for any CypD structure.
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Affiliation(s)
- Koteswara Rao Valasani
- Department of Pharmacology and Toxicology and Higuchi Bioscience Center, University of Kansas, Lawrence, KS 66047, USA
| | - Emily A. Carlson
- Department of Pharmacology and Toxicology and Higuchi Bioscience Center, University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P. Battaile
- IMCA-CAT, Hauptman–Woodward Medical Research Institute, 9700 South Cass Avenue, Building 435A, Argonne, IL 60439, USA
| | - Andrea Bisson
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS 66047, USA
| | - Shirley ShiDu Yan
- Department of Pharmacology and Toxicology and Higuchi Bioscience Center, University of Kansas, Lawrence, KS 66047, USA
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11
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Murgiano L, D'Alessandro A, Zolla L, Valentini A, Pariset L. Comparison of Milk Fat Globule Membrane (MFGM) proteins in milk samples of Chianina and Holstein cattle breeds across three lactation phases through 2D IEF SDS PAGE — A preliminary study. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.10.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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12
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McGowan LC, Hamelberg D. Conformational plasticity of an enzyme during catalysis: intricate coupling between cyclophilin A dynamics and substrate turnover. Biophys J 2013; 104:216-26. [PMID: 23332074 DOI: 10.1016/j.bpj.2012.11.3815] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/25/2012] [Accepted: 11/27/2012] [Indexed: 01/15/2023] Open
Abstract
Enzyme catalysis is central to almost all biochemical processes, speeding up rates of reactions to biological relevant timescales. Enzymes make use of a large ensemble of conformations in recognizing their substrates and stabilizing the transition states, due to the inherent dynamical nature of biomolecules. The exact role of these diverse enzyme conformations and the interplay between enzyme conformational dynamics and catalysis is, according to the literature, not well understood. Here, we use molecular dynamics simulations to study human cyclophilin A (CypA), in order to understand the role of enzyme motions in the catalytic mechanism and recognition. Cyclophilin A is a tractable model system to study using classical simulation methods, because catalysis does not involve bond formation or breakage. We show that the conformational dynamics of active site residues of substrate-bound CypA is inherent in the substrate-free enzyme. CypA interacts with its substrate via conformational selection as the configurations of the substrate changes during catalysis. We also show that, in addition to tight intermolecular hydrophobic interactions between CypA and the substrate, an intricate enzyme-substrate intermolecular hydrogen-bonding network is extremely sensitive to the configuration of the substrate. These enzyme-substrate intermolecular interactions are loosely formed when the substrate is in the reactant and product states and become well formed and reluctant to break when the substrate is in the transition state. Our results clearly suggest coupling among enzyme-substrate intermolecular interactions, the dynamics of the enzyme, and the chemical step. This study provides further insights into the mechanism of peptidyl-prolyl cis/trans isomerases and the general interplay between enzyme conformational dynamics and catalysis.
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Affiliation(s)
- Lauren C McGowan
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, USA
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13
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Deleersnijder A, Van Rompuy AS, Desender L, Pottel H, Buée L, Debyser Z, Baekelandt V, Gerard M. Comparative analysis of different peptidyl-prolyl isomerases reveals FK506-binding protein 12 as the most potent enhancer of alpha-synuclein aggregation. J Biol Chem 2011; 286:26687-701. [PMID: 21652707 PMCID: PMC3143632 DOI: 10.1074/jbc.m110.182303] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 05/28/2011] [Indexed: 11/06/2022] Open
Abstract
FK506-binding proteins (FKBPs) are members of the immunophilins, enzymes that assist protein folding with their peptidyl-prolyl isomerase (PPIase) activity. Some non-immunosuppressive inhibitors of these enzymes have neuroregenerative and neuroprotective properties with an unknown mechanism of action. We have previously shown that FKBPs accelerate the aggregation of α-synuclein (α-SYN) in vitro and in a neuronal cell culture model for synucleinopathy. In this study we investigated whether acceleration of α-SYN aggregation is specific for the FKBP or even the PPIase family. Therefore, we studied the effect of several physiologically relevant PPIases, namely FKBP12, FKBP38, FKBP52, FKBP65, Pin1, and cyclophilin A, on α-SYN aggregation in vitro and in neuronal cell culture. Among all PPIases tested in vitro, FKBP12 accelerated α-SYN aggregation the most. Furthermore, only FKBP12 accelerated α-SYN fibril formation at subnanomolar concentrations, pointing toward an enzymatic effect. Although stable overexpression of various FKBPs enhanced the aggregation of α-SYN and cell death in cell culture, they were less potent than FKBP12. When FKBP38, FKBP52, and FKBP65 were overexpressed in a stable FKBP12 knockdown cell line, they could not fully restore the number of α-SYN inclusion-positive cells. Both in vitro and cell culture data provide strong evidence that FKBP12 is the most important PPIase modulating α-SYN aggregation and validate the protein as an interesting drug target for Parkinson disease.
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Affiliation(s)
- Angélique Deleersnijder
- From the Laboratory of Biochemistry and
- Laboratory for Neurobiology and Gene Therapy, K. U. Leuven, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Anne-Sophie Van Rompuy
- Laboratory for Neurobiology and Gene Therapy, K. U. Leuven, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | | | - Hans Pottel
- the Laboratory of Biophysics, K. U. Leuven-Kortrijk, Etienne Sabbelaan 53, B-8500 Kortrijk, Flanders, Belgium
| | - Luc Buée
- INSERM, U837, rue Polonovski, F-59000 Lille, France
- Université Lille-Nord de France, UDSL, Faculté de Médecine, Institut de Médecine Prédictive et Recherche Thérapeutique, Université Lille 2, Place de Verdun, F-59045 Lille, France, and
- CHRU, F-59037 Lille Cedex, France
| | - Zeger Debyser
- From the Laboratory of Biochemistry and
- the Laboratory for Molecular Virology and Gene Therapy and
| | - Veerle Baekelandt
- Laboratory for Neurobiology and Gene Therapy, K. U. Leuven, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Melanie Gerard
- From the Laboratory of Biochemistry and
- Laboratory for Neurobiology and Gene Therapy, K. U. Leuven, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
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14
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Koren J, Jinwal UK, Davey Z, Kiray J, Arulselvam K, Dickey CA. Bending tau into shape: the emerging role of peptidyl-prolyl isomerases in tauopathies. Mol Neurobiol 2011; 44:65-70. [PMID: 21523562 DOI: 10.1007/s12035-011-8182-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 04/12/2011] [Indexed: 01/21/2023]
Abstract
The Hsp90-associated cis-trans peptidyl-prolyl isomerase--FK506 binding protein 51 (FKBP51)--was recently found to co-localize with the microtubule (MT)-associated protein tau in neurons and physically interact with tau in brain tissues from humans who died from Alzheimer's disease (AD). Tau pathologically aggregates in neurons, a process that is closely linked with cognitive deficits in AD. Tau typically functions to stabilize and bundle MTs. Cellular events like calcium influx destabilize MTs, disengaging tau. This excess tau should be degraded, but sometimes it is stabilized and forms higher-order aggregates, a pathogenic hallmark of tauopathies. FKBP51 was also found to increase in forebrain neurons with age, further supporting a novel role for FKBP51 in tau processing. This, combined with compelling evidence that the prolyl isomerase Pin1 regulates tau stability and phosphorylation dynamics, suggests an emerging role for isomerization in tau pathogenesis.
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Affiliation(s)
- John Koren
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Tampa, FL 33613, USA
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15
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Park MS, Chu F, Xie J, Wang Y, Bhattacharya P, Chan WK. Identification of cyclophilin-40-interacting proteins reveals potential cellular function of cyclophilin-40. Anal Biochem 2011; 410:257-65. [PMID: 21146485 PMCID: PMC3034277 DOI: 10.1016/j.ab.2010.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Revised: 11/18/2010] [Accepted: 12/06/2010] [Indexed: 01/16/2023]
Abstract
Cyclophilin-40 (CyP40) is part of the immunophilin family and is found in Hsp90-containing protein complexes. We were interested in identifying proteins that interact with CyP40. CyP40-interacting proteins in HeLa cells were identified using the tandem affinity purification approach. Adenovirus expressing human CyP40 protein (Ad-CyP40), fused with streptavidin and calmodulin binding peptides at the N terminus, was generated. Proteins were separated on a sodium dodecyl sulfate-polyacrylamide gel electrophoresis gel after tandem affinity purification. Here 10 silver-stained protein bands that were enriched in the Ad-CyP40-infected lysate and the corresponding regions in the control lysate were excised, digested by trypsin, and identified by tandem mass spectrometric analysis. Of 11 interacting proteins that were identified, 4 (RACK1, Ku70, RPS3, and NF45) were expressed in rabbit reticulocyte lysate, bacteria, and MCF-7 cells. We confirmed that these proteins interact with CyP40. We observed that RACK1 suppressed the cobalt chloride-induced, hypoxia response element-dependent luciferase activity in MCF-7 cells but not in MCF-7 stable cells expressing approximately 10% of the cellular CyP40 content. In addition, RACK1 reduced the HIF-1α protein accumulation after cobalt chloride treatment, which was not observed when the CyP40 content was down-regulated. Collectively, we conclude that reduction of the HIF-1 α protein by RACK1 is CyP40-mediated.
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Affiliation(s)
- Miki Susanto Park
- Department of Pharmaceutics and Medicinal Chemistry, Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, CA 95211, USA.
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16
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Peptide Bond cis/trans Isomerases: A Biocatalysis Perspective of Conformational Dynamics in Proteins. Top Curr Chem (Cham) 2011; 328:35-67. [DOI: 10.1007/128_2011_151] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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LoGuidice A, Ramirez-Alcantara V, Proli A, Gavillet B, Boelsterli UA. Pharmacologic targeting or genetic deletion of mitochondrial cyclophilin D protects from NSAID-induced small intestinal ulceration in mice. Toxicol Sci 2010; 118:276-85. [PMID: 20668000 DOI: 10.1093/toxsci/kfq226] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Small intestinal ulceration is a frequent and potentially serious condition associated with nonselective cyclooxygenase 1/2 inhibitors (nonsteroidal anti-inflammatory drugs, NSAIDs) including diclofenac (DCF). An initial topical effect involving mitochondria has been implicated in the pathogenesis, but the exact mechanisms of NSAID-induced enteropathy are unknown. We aimed at investigating whether DCF caused enterocyte demise via the mitochondrial permeability transition (mPT) and whether inhibition of critical mPT regulators might protect the mucosa from DCF injury. Cultured enterocytes (IEC-6) exposed to DCF readily underwent mPT-mediated cell death. We then targeted mitochondrial cyclophilin D (CypD), a key regulator of the mPT, in a mouse model of NSAID enteropathy. C57BL/6J mice were treated with an ulcerogenic dose of DCF (60 mg/kg, ip), followed (+ 1 h) by a non-cholestatic dose (10 mg/kg, ip) of the CypD inhibitor, cyclosporin A (CsA). CsA greatly reduced the extent of small intestinal ulceration. To avoid potential calcineurin-mediated effects, we used the non-immunosuppressive cyclosporin analog, D-MeAla(3)-EtVal(4)-cyclosporin (Debio 025). Debio 025 similarly protected the mucosa from DCF injury. To exclude drug-drug interactions, we exposed mice genetically deficient in mitochondrial CypD (peptidyl-prolyl cis-trans isomerase F [Ppif(-/-)]) to DCF. Ppif-null mice were largely protected from the ulcerogenic effects of DCF, whereas their wild-type littermates developed typical enteropathy. Enterocyte injury was preceded by upregulation of the proapoptotic transcription factor C/EBP homologous protein (Chop). Chop-null mice were refractory to DCF enteropathy, suggesting a critical role of endoplasmic reticulum stress induced by DCF. In conclusion, mitochondrial CypD plays a key role in NSAID-induced enteropathy, lending itself as a potentially new therapeutic target for cytoprotective intervention.
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Affiliation(s)
- Amanda LoGuidice
- Department of Pharmaceutical Sciences, University of Connecticut School of Pharmacy, Storrs, Connecticut 06269, USA
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Abstract
Cyclophilin A (CyPA) has been studied as a multifunctional protein that is upregulated in a variety of inflammatory conditions, such as rheumatoid arthritis, autoimmune disease, and cancer. CyPA has been classified as an immunophilin and has a variety of intracellular functions, including intracellular signaling, protein trafficking, and the regulation of other proteins activity. Besides its intracellular functions, CyPA is a secreted molecule that has a physiological and pathological role in cardiovascular diseases, making it a potential biomarker and mediator in cardiovascular diseases, such as vascular stenosis, atherosclerosis, and abdominal aortic aneurysms.
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Affiliation(s)
- Kimio Satoh
- Aab Cardiovascular Research Institute and Department of Medicine, University of Rochester School of Medicine and Dentistry
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Pemberton TJ, Kay JE. Identification and comparative analysis of the peptidyl-prolyl cis/trans isomerase repertoires of H. sapiens, D. melanogaster, C. elegans, S. cerevisiae and Sz. pombe. Comp Funct Genomics 2010; 6:277-300. [PMID: 18629211 PMCID: PMC2447506 DOI: 10.1002/cfg.482] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 05/01/2005] [Accepted: 05/26/2005] [Indexed: 11/11/2022] Open
Abstract
The peptidyl-prolyl cis/trans isomerase (PPIase) class of proteins comprises three
member families that are found throughout nature and are present in all the major
compartments of the cell. Their numbers appear to be linked to the number of genes in
their respective genomes, although we have found the human repertoire to be smaller
than expected due to a reduced cyclophilin repertoire. We show here that whilst the
members of the cyclophilin family (which are predominantly found in the nucleus
and cytoplasm) and the parvulin family (which are predominantly nuclear) are
largely conserved between different repertoires, the FKBPs (which are predominantly
found in the cytoplasm and endoplasmic reticulum) are not. It therefore appears
that the cyclophilins and parvulins have evolved to perform conserved functions,
while the FKBPs have evolved to fill ever-changing niches within the constantly
evolving organisms. Many orthologous subgroups within the different PPIase families
appear to have evolved from a distinct common ancestor, whereas others, such as the
mitochondrial cyclophilins, appear to have evolved independently of one another. We
have also identified a novel parvulin within Drosophila melanogaster that is unique to
the fruit fly, indicating a recent evolutionary emergence. Interestingly, the fission yeast
repertoire, which contains no unique cyclophilins and parvulins, shares no PPIases
solely with the budding yeast but it does share a majority with the higher eukaryotes
in this study, unlike the budding yeast. It therefore appears that, in comparison with
Schizosaccharomyces pombe, Saccharomyces cerevisiae is a poor representation of the
higher eukaryotes for the study of PPIases.
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Affiliation(s)
- Trevor J Pemberton
- The Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton ,East Sussex BN1 9PX, United Kingdom.
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Satoh K, Nigro P, Berk BC. Oxidative stress and vascular smooth muscle cell growth: a mechanistic linkage by cyclophilin A. Antioxid Redox Signal 2010; 12:675-82. [PMID: 19747062 PMCID: PMC2861539 DOI: 10.1089/ars.2009.2875] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Inflammation and oxidative stress contribute to the pathology of many diseases, but specific therapeutic targets remain elusive. Oxidative stress, generated by excessive reactive oxygen species (ROS), promotes cardiovascular disease. However, the precise mechanism of how ROS deteriorate vascular function and promote vascular remodeling in vivo has not been clearly elucidated. Cyclophilin A (CyPA) is a 20 kD chaperone protein that is secreted from vascular smooth muscle cells (VSMC) in response to ROS, and stimulates VSMC proliferation and inflammatory cell migration in vitro and in vivo. CyPA (both intracellular and extracellular) contributes to inflammation and atherosclerosis by promoting endothelial cell (EC) apoptosis and EC expression of leukocyte adhesion molecules, stimulating leukocyte migration, enhancing T helper cell type 1 (Th1) responses, increasing proliferation of macrophages and vascular smooth muscle cells (VSMC), and increasing pro-inflammatory signal transduction in VSMC. We tested the hypothesis that CyPA contributes to cardiovascular diseases by analyzing several genetic interventions that include the CyPA knockout mouse and the CyPA overexpressing transgenic mouse (VSMC-Tg). CyPA plays a crucial role in VSMC proliferation/migration and inflammatory cell recruitment, resulting in cardiovascular diseases in vivo.
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Affiliation(s)
- Kimio Satoh
- Aab Cardiovascular Research Institute and Department of Medicine, University of Rochester School of Medicine and Dentistry, New York 14642, USA
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21
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Vaccine Therapy for Lung Cancer. Lung Cancer 2010. [DOI: 10.1007/978-1-60761-524-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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22
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Daum S, Schumann M, Mathea S, Aumüller T, Balsley MA, Constant SL, de Lacroix BF, Kruska F, Braun M, Schiene-Fischer C. Isoform-specific inhibition of cyclophilins. Biochemistry 2009; 48:6268-77. [PMID: 19480458 DOI: 10.1021/bi9007287] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cyclophilins belong to the enzyme class of peptidyl prolyl cis-trans isomerases which catalyze the cis-trans isomerization of prolyl bonds in peptides and proteins in different folding states. Cyclophilins have been shown to be involved in a multitude of cellular functions like cell growth, proliferation, and motility. Among the 20 human cyclophilin isoenzymes, the two most abundant members of the cyclophilin family, CypA and CypB, exhibit specific cellular functions in several inflammatory diseases, cancer development, and HCV replication. A small-molecule inhibitor on the basis of aryl 1-indanylketones has now been shown to discriminate between CypA and CypB in vitro. CypA binding of this inhibitor has been characterized by fluorescence anisotropy- and isothermal titration calorimetry-based cyclosporin competition assays. Inhibition of CypA- but not CypB-mediated chemotaxis of mouse CD4(+) T cells by the inhibitor provided biological proof of discrimination in vivo.
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Affiliation(s)
- Sebastian Daum
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
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Abstract
HCV (hepatitis C virus) infects nearly 3% of the population worldwide and has emerged as a major causative agent of liver disease, resulting in acute and chronic infections that can lead to fibrosis, cirrhosis and hepatocellular carcinoma. Hepatitis C represents the leading cause of liver transplantation in the United States and Europe. A positive-strand RNA virus of the Flaviviridae family, HCV contains a single-stranded RNA genome of approx. 9600 nucleotides. The genome RNA serves as both mRNA for translation of viral proteins and the template for RNA replication. Cis-acting RNA elements within the genome regulate RNA replication by forming secondary structures that interact with each other and trans-acting factors. Although structural proteins are clearly dispensable for RNA replication, recent evidence points to an important role of several non-structural proteins in particle assembly and release, turning their designation on its head. HCV enters host cells through receptor-mediated endocytosis, and the process requires the co-ordination of multiple cellular receptors and co-receptors. RNA replication takes place at specialized intracellular membrane structures called 'membranous webs' or 'membrane-associated foci', whereas viral assembly probably occurs on lipid droplets and endoplasmic reticulum. Liver inflammation plays a central role in the liver damage seen in hepatitis C, but many HCV proteins also directly contribute to HCV pathogenesis. In the present review, the molecular and cellular aspects of the HCV life cycle and the role of viral proteins in pathological liver conditions caused by HCV infection are described.
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Hanoulle X, Badillo A, Wieruszeski JM, Verdegem D, Landrieu I, Bartenschlager R, Penin F, Lippens G. Hepatitis C virus NS5A protein is a substrate for the peptidyl-prolyl cis/trans isomerase activity of cyclophilins A and B. J Biol Chem 2009; 284:13589-13601. [PMID: 19297321 DOI: 10.1074/jbc.m809244200] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We report here a biochemical and structural characterization of domain 2 of the nonstructural 5A protein (NS5A) from the JFH1 Hepatitis C virus strain and its interactions with cyclophilins A and B (CypA and CypB). Gel filtration chromatography, circular dichroism spectroscopy, and finally NMR spectroscopy all indicate the natively unfolded nature of this NS5A-D2 domain. Because mutations in this domain have been linked to cyclosporin A resistance, we used NMR spectroscopy to investigate potential interactions between NS5A-D2 and cellular CypA and CypB. We observed a direct molecular interaction between NS5A-D2 and both cyclophilins. The interaction surface on the cyclophilins corresponds to their active site, whereas on NS5A-D2, it proved to be distributed over the many proline residues of the domain. NMR heteronuclear exchange spectroscopy yielded direct evidence that many proline residues in NS5A-D2 form a valid substrate for the enzymatic peptidyl-prolyl cis/trans isomerase (PPIase) activity of CypA and CypB.
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Affiliation(s)
- Xavier Hanoulle
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, IFR 147, Université des Sciences et Technologies de Lille, F-59655 Villeneuve d'Ascq, France
| | - Aurélie Badillo
- Institut de Biologie et Chimie des Protéines, UMR 5086, CNRS, Université de Lyon, IFR 128, BioSciences Gerland-Lyon Sud, F-69397 Lyon, France
| | - Jean-Michel Wieruszeski
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, IFR 147, Université des Sciences et Technologies de Lille, F-59655 Villeneuve d'Ascq, France
| | - Dries Verdegem
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, IFR 147, Université des Sciences et Technologies de Lille, F-59655 Villeneuve d'Ascq, France
| | - Isabelle Landrieu
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, IFR 147, Université des Sciences et Technologies de Lille, F-59655 Villeneuve d'Ascq, France
| | - Ralf Bartenschlager
- Department of Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - François Penin
- Institut de Biologie et Chimie des Protéines, UMR 5086, CNRS, Université de Lyon, IFR 128, BioSciences Gerland-Lyon Sud, F-69397 Lyon, France
| | - Guy Lippens
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, IFR 147, Université des Sciences et Technologies de Lille, F-59655 Villeneuve d'Ascq, France.
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25
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He QL, Jiang H, Zhang F, Chen HB, Tang GL. Simultaneous identification of multiple receptors of natural product using an optimized cDNA phage display cloning. Bioorg Med Chem Lett 2008; 18:3995-8. [PMID: 18571405 DOI: 10.1016/j.bmcl.2008.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 06/03/2008] [Indexed: 10/22/2022]
Abstract
Simultaneously isolating more than one receptor of natural product remains a challenge to chemical genetics. Using cyclosporine A as an affinity probe and an optimized phage display cloning procedure, not only cyclophilin A, but also cyclophilin B was isolated as the full-length gene clone from a human brain cDNA library. This optimized protocol can be used to select protein targets of chemicals dependent on the binding affinity rather than on the relative abundance in cells.
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Affiliation(s)
- Qing-Li He
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Road, Shanghai 200032, China
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26
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Cyclophilin A is an essential cofactor for hepatitis C virus infection and the principal mediator of cyclosporine resistance in vitro. J Virol 2008; 82:5269-78. [PMID: 18385230 DOI: 10.1128/jvi.02614-07] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cyclosporine (CsA) and its derivatives potently suppress hepatitis C virus (HCV) replication. Recently, CsA-resistant HCV replicons have been identified in vitro. We examined the dependence of the wild-type and CsA-resistant replicons on various cyclophilins for replication. A strong correlation between CsA resistance and reduced dependency on cyclophilin A (CyPA) for replication was identified. Silencing of CyPB or CyPC expression had no significant effect on replication, whereas various forms of small interfering RNA (siRNA) directed at CyPA inhibited HCV replication of wild-type but not CsA-resistant replicons. The efficiency of a particular siRNA in suppressing CyPA expression was correlated with its potency in inhibiting HCV replication, and expression of an siRNA-resistant CyPA cDNA rescued replication. In addition, an anti-CyPA antibody blocked replication of the wild-type but not the resistant replicon in an in vitro replication assay. Depletion of CyPA alone in the CsA-resistant replicon cells eliminated CsA resistance, indicating that CyPA is the chief mediator of the observed CsA resistance. The dependency on CyPA for replication was observed for both genotype (GT) 1a and 1b replicons as well as a GT 2a infectious virus. An interaction between CyPA and HCV RNA as well as the viral polymerase that is sensitive to CsA treatment in wild-type but not in resistant replicons was detected. These findings reveal the molecular mechanism of CsA resistance and identify CyPA as a critical cellular cofactor for HCV replication and infection.
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27
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Yeh HY, Klesius PH. Channel catfish, Ictalurus punctatus, cyclophilin A and B cDNA characterization and expression analysis. Vet Immunol Immunopathol 2008; 121:370-7. [DOI: 10.1016/j.vetimm.2007.09.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 09/10/2007] [Accepted: 09/26/2007] [Indexed: 11/16/2022]
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28
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Ikura T, Ito N. Requirements for peptidyl-prolyl isomerization activity: a comprehensive mutational analysis of the substrate-binding cavity of FK506-binding protein 12. Protein Sci 2007; 16:2618-25. [PMID: 18029417 PMCID: PMC2222811 DOI: 10.1110/ps.073203707] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 09/18/2007] [Accepted: 09/18/2007] [Indexed: 10/22/2022]
Abstract
Peptidyl-prolyl isomerase (PPIase) activity is exhibited by many proteins belonging to the PPIase family. However, the catalytic mechanism of this activity remains to be completely elucidated. Here, we selected human FK506-binding protein 12 (FKBP12) as the model PPIase and investigated the nature of amino acid residues essential for the activity. The crystal structures of several complexes of PPIase with short peptides revealed that the residues Asp37, Arg42, Phe46, Val55, Trp59, and Tyr82 in the substrate-binding cavity of FKBP12 appear to play key roles in the PPIase activity. Each of these six residues was substituted by 20 common amino acid residues. The activity of each mutant protein was measured using a peptide analog by the chymotrypsin digestion assay and then compared with wild-type FKBP12. It was found that site-specific interactions by the side chains of amino acid residues constituting the substrate-binding cavity were not essential for the PPIase activity, although the 37th, 55th, and 82nd amino acid residues significantly contributed to the activity. This suggests that the PPIase activity requires only the hydrophobic cavity that captures the Pro-containing peptide.
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Affiliation(s)
- Teikichi Ikura
- Laboratory of Structural Biology, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.
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29
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Eliseev RA, Filippov G, Velos J, VanWinkle B, Goldman A, Rosier RN, Gunter TE. Role of cyclophilin D in the resistance of brain mitochondria to the permeability transition. Neurobiol Aging 2007; 28:1532-42. [PMID: 16876914 DOI: 10.1016/j.neurobiolaging.2006.06.022] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Revised: 05/12/2006] [Accepted: 06/23/2006] [Indexed: 11/26/2022]
Abstract
The mitochondrial permeability transition (MPT) is involved in both necrosis and apoptosis. Cyclophilin D (CypD) is an important component of the MPT. Brain mitochondria are more resistant to the MPT when compared to heart or liver mitochondria. We found that this increased resistance correlates with low expression of CypD in brain when compared to heart or liver. In newborn rats, sensitivity of brain mitochondria to the MPT and CypD expression are significantly higher than in mature animals. In an in vitro model of neuronal development, mitochondria in differentiated neuronal-like cells exert a higher calcium threshold toward MPT induction and express significantly less CypD when compared to undifferentiated precursor cells. Gain and loss of function experiments confirm the role of CypD in sensitivity to the MPT. Together our data indicate that the increased calcium threshold of brain mitochondria to the MPT correlates with low expression of CypD in brain; and that neuronal cells lose CypD during differentiation and become less sensitive to the MPT induction. This may be a protection mechanism that raises the threshold of brain tissue against injuries.
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Affiliation(s)
- Roman A Eliseev
- Musculoskeletal Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States. roman
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Sen B, Venugopal V, Chakraborty A, Datta R, Dolai S, Banerjee R, Datta AK. Amino acid residues of Leishmania donovani cyclophilin key to interaction with its adenosine kinase: biological implications. Biochemistry 2007; 46:7832-43. [PMID: 17552497 DOI: 10.1021/bi602625h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclophilins (CyPs), by interacting with a variety of proteins, often modulate their biological activities and thus have been implicated in several cellular functions. However, mechanisms that determine such interactions are poorly understood. We earlier reported that an endoplasmic reticulum (ER)-located cyclophilin (LdCyP) from the purine auxotrophic parasitic protozoan Leishmania donovani reactivated its adenosine kinase (AdK). The AdK-reactivating property of LdCyP was however abolished at high ionic strength but not by nonionic detergents. Modeling of LdCyP, based on its crystal structure solved at 1.97 A resolution, revealed several solvent-exposed hydrophobic and charged residues. Mutagenesis of several of such solvent-exposed residues was performed and their corresponding activities with regard to their (i) AdK reactivation property, (ii) ability to form complex with the enzyme, (iii) capacity to induce red shift in the intrinsic tryptophan fluorescence maxima of AdK, and (iv) efficiency to withdraw the ADP inhibition from the AdK-mediated reaction were compared to the wild-type protein. Results indicated that while the replacement of R147 with either A or D severely impaired all of the above characteristics displayed by the wild-type LdCyP, the effect of mutating K114 and K153 was although relatively less but nevertheless noticeable. Alteration of other exposed hydrophobic and charged residues apparently did not have any discernible effect. Under the condition of cellular stress, the ER-located LdCyP is released into the cytoplasm with concomitant increase both in the specific activity of the cytosol-resident AdK and the uptake of radiolabeled Ado into the cells. These experiments, besides demonstrating the importance of the positive charge, identified R147 as the most crucial residue in the LdCyP-AdK interaction and provide evidence for the stress-induced retrograde translocation of LdCyP from the ER to the cytoplasm. A possible implication of this interaction in the life cycle of the parasite is proposed.
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Affiliation(s)
- Banibrata Sen
- The Division of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata-700032, India
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Golbik R, Yu C, Weyher-Stingl E, Huber R, Moroder L, Budisa N, Schiene-Fischer C. Peptidyl Prolylcis/trans-Isomerases: Comparative Reactivities of Cyclophilins, FK506-Binding Proteins, and Parvulins with Fluorinated Oligopeptide and Protein Substrates. Biochemistry 2005; 44:16026-34. [PMID: 16331962 DOI: 10.1021/bi051442w] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Peptidyl prolyl cis/trans-isomerases catalyze the cis-trans isomerization of prolyl bonds in oligopeptides and various folding states of proteins. The proline residue in PPIase substrates at the P1' subsite, which follows the isomerizing peptide bond, appears to be the common recognition element for all subfamilies of this enzyme class. The molecular principles that govern substrate specificity at the P1' subsite were analyzed using 4-fluoroproline-containing tetrapeptide 4-nitroanilides and barstar Cys40Ala/Cys82Ala/Pro27Ala/Pro48-->4-fluoroproline quadruple variants. Generally, PPIase catalysis demonstrated stereospecificity for monofluoro substitutions at the 4-position of the pyrrolidine ring. However, the replacement of hydrogens with fluoro atoms did not impair productive interactions for the majority of PPIase-substrate complexes. Comparison of specificity constants for oligopeptide and protein substrates revealed striking differences in the 4-fluoroproline substituent effects between members of the PPIase families. Introduction of 4(R)-fluoroproline resulted in an oligopeptide substrate completely resistant to catalytic effects of FKBP-like PPIases. By contrast, the 4(R)-fluoroproline barstar variant demonstrated only slightly reduced or even better catalytic susceptibility when compared to the parent barstar Cys40Ala/Cys82Ala/Pro27Ala/Pro48 substrate. On the other hand, Suc-Ala-Ser-4(S)-FPro-Phe-pNA exhibits a discriminating specificity toward the prototypic parvulin, the Escherichia coli Par10. The E. coli trigger factor, in the extreme, catalyzes Cys40Ala/Cys82Ala/Pro27Ala/4-F(2)Pro48 with a more than 20-fold higher efficiency when compared to the proline-containing congener. These findings support the combined subsite concept for PPIase catalysis in which the positioning of a substrate in the active cleft must activate a still unknown number of remote subsites in the transition state of the reaction. The number of critical subsites was shown to vary between the PPIase families.
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Affiliation(s)
- Ralph Golbik
- Institute of Biochemistry, Department of Enzymology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany
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Yao Q, Li M, Yang H, Chai H, Fisher W, Chen C. Roles of cyclophilins in cancers and other organ systems. World J Surg 2005; 29:276-80. [PMID: 15706440 DOI: 10.1007/s00268-004-7812-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Cyclophilins are originally identified as cellular binding proteins for the immunosuppressive drug cyclosporin A. Many cyclophilins, including CypA, CypB, CypC, CypD, and Cyp40, have been discovered and shown to be ubiquitously distributed in many types of cells and organ systems. Recent investigations have uncovered many important properties and functions for cyclophilins including peptidyle-prolyl-isomerase activity and protein folding/repair; maintaining mitochondrial functions and involvement in apoptosis; roles in regulation of T-cell function and inflammation; interaction with CD147; and pathogenesis of vascular disease, human immunodeficiency virus infection, and rheumatoid arthritis. Furthermore, the expression and functions of cyclophilins may be correlated with tumor biology of several types of cancers including pancreatic carcinoma. Molecular mechanisms of cyclophilin-mediated biologic events and future directions of research are discussed in this review. Understanding the roles of cyclophilins in cancers and other organ systems will be crucial in determining clinical applications for the treatment or diagnosis of human diseases.
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Affiliation(s)
- Qizhi Yao
- Molecular Surgeon Research Center, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, USA.
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Basso E, Fante L, Fowlkes J, Petronilli V, Forte MA, Bernardi P. Properties of the permeability transition pore in mitochondria devoid of Cyclophilin D. J Biol Chem 2005; 280:18558-61. [PMID: 15792954 DOI: 10.1074/jbc.c500089200] [Citation(s) in RCA: 628] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We have studied the properties of the permeability transition pore (PTP) in mitochondria from the liver of mice where the Ppif gene encoding for mitochondrial Cyclophilin D (CyP-D) had been inactivated. Mitochondria from Ppif-/- mice had no CyP-D and displayed a striking desensitization of the PTP to Ca2+, in that pore opening required about twice the Ca2+ load necessary to open the pore in strain-matched, wild-type mitochondria. Mitochondria lacking CyP-D were insensitive to Cyclosporin A (CsA), which increased the Ca2+ retention capacity only in mitochondria from wild-type mice. The PTP response to ubiquinone 0, depolarization, pH, adenine nucleotides, and thiol oxidants was similar in mitochondria from wild-type and Ppif-/- mice. These experiments demonstrate that (i) the PTP can form and open in the absence of CyP-D, (ii) that CyP-D represents the target for PTP inhibition by CsA, and (iii) that CyP-D modulates the sensitivity of the PTP to Ca2+ but not its regulation by the proton electrochemical gradient, adenine nucleotides, and oxidative stress. These results have major implications for our current understanding of the PTP and its modulation in vitro and in vivo.
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Affiliation(s)
- Emy Basso
- Department of Biomedical Sciences and Consiglio Nazionale delle Ricerche Institute of Neuroscience, University of Padova, Viale Giuseppe Colombo 3, I-35121 Padova, Italy
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Yang H, Li M, Chai H, Yan S, Lin P, Lumsden AB, Yao Q, Chen C. Effects of cyclophilin A on cell proliferation and gene expressions in human vascular smooth muscle cells and endothelial cells. J Surg Res 2005; 123:312-9. [PMID: 15680395 DOI: 10.1016/j.jss.2004.08.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Indexed: 12/13/2022]
Abstract
BACKGROUND Cyclophilin A (CypA) is a cytosolic protein which involves many biological functions including immune modulation, cell growth, tumorigenesis, and vascular disease. The objective of this study was to determine the effect of CypA on cell proliferation and several gene expressions in human endothelial cells and vascular smooth muscle cells. METHODS Human coronary artery endothelial cells (HCAEC), human lung microvascular endothelial cells (HMVEC-L), and human aorta smooth muscle cells (HAoSMC) were used in this study. Cells were treated with 10 nM CypA for 24 h. The cell proliferation was determined by [3H]thymidine incorporation. The mRNA levels of 13 genes including CD147 (receptor for CypA), PDGF-BB, endothelin-1 (ET-1), vascular endothelial growth factor receptor-1 (VEGFR-1), VEGFR-2, VEGFR-3, neuropilin-1 (NRP-1), NRP-2, eNOS, iNOS, nNOS, ICAM-1, and PECAM-1 were semiquantitatively determined by real time RT-PCR as standardized with a house keeping gene beta-actin. RESULTS CypA significantly increased cell proliferation of HAoSMC and HMVEC-L by 31% and 45%, respectively, as compared to controls, but had no effect on HCAEC. Blocking CD147 did not affect the mitogenic action of CypA. In addition, CypA also significantly increased the mRNA expression of CD147 by 43% and VEGFR-2 by 65% in HAoSMCs (P < 0.05, t test). HAoSMCs expressed much higher CD147 and neuropilin-1 (NRP-1) mRNA than HMVECs-L and HCAECs (P < 0.017, ANOVA). Furthermore, CypA increased ET-1 mRNA by 22% and VEGFR-1 mRNA by 23% in HMVECs-L, but had limited effects on HCAECs. HMVECs-L had much higher expressions of PDGF-BB, ET-1, VEGFR-2, VEGFR-1, VEGFR-3, and NRP-2 than HAoSMCs and HCAECs (P < 0.017, ANOVA). By contrast, HCAECs had much higher ICAM-1 mRNA levels than HMVECs-L and HAoSMCs (P < 0.017, ANOVA). CONCLUSIONS These data demonstrate that CypA has a mitogenic effect on HAoSMCs and HMVECs-L, but not HCAECs. CD147 may not mediate the action of CypA. In addition, CypA substantially alters the mRNA levels of several key genes in human vascular cells, indicating potential multifunctional roles of CypA in vascular system. Furthermore, this study provides several new aspects of gene expressions in vascular cells.
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MESH Headings
- Aorta/cytology
- Capillaries/cytology
- Cell Division/drug effects
- Cells, Cultured
- Coronary Vessels/cytology
- Cyclophilin A/pharmacology
- Cyclophilin A/physiology
- Endothelium, Vascular/cytology
- Endothelium, Vascular/drug effects
- Endothelium, Vascular/physiology
- Gene Expression/drug effects
- Humans
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/physiology
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Affiliation(s)
- Hui Yang
- Molecular Surgeon Research Center, Division of Vascular Surgery and Endovascular Therapy, Michael E. DeBakey Department of Surgery, Baylor College of Medicine and the Methodist Hospital, Houston, Texas 77030, USA
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Li Y, Johnson N, Capano M, Edwards M, Crompton M. Cyclophilin-D promotes the mitochondrial permeability transition but has opposite effects on apoptosis and necrosis. Biochem J 2004; 383:101-9. [PMID: 15233627 PMCID: PMC1134048 DOI: 10.1042/bj20040669] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2004] [Revised: 06/25/2004] [Accepted: 07/02/2004] [Indexed: 11/17/2022]
Abstract
Cyclophilin-D is a peptidylprolyl cis-trans isomerase of the mitochondrial matrix. It is involved in mitochondrial permeability transition, in which the adenine nucleotide translocase of the inner membrane is transformed from an antiporter to a non-selective pore. The permeability transition has been widely considered as a mechanism in both apoptosis and necrosis. The present study examines the effects of cyclophilin-D on the permeability transition and lethal cell injury, using a neuronal (B50) cell line stably overexpressing cyclophilin-D in mitochondria. Cyclophilin-D overexpression rendered isolated mitochondria far more susceptible to the permeability transition induced by Ca2+ and oxidative stress. Similarly, cyclophilin-D overexpression brought forward the onset of the permeability transition in intact cells subjected to oxidative stress. In addition, in the absence of stress, the mitochondria of cells overexpressing cyclophilin-D maintained a lower inner-membrane potential than those of normal cells. All these effects of cyclophilin-D overexpression were abolished by cyclosporin A. It is concluded that cyclophilin-D promotes the permeability transition in B50 cells. However, cyclophilin-D overexpression had opposite effects on apoptosis and necrosis; whereas NO-induced necrosis was promoted, NO- and staurosporine-induced apoptosis were inhibited. These findings indicate that the permeability transition leads to cell necrosis, but argue against its involvement in apoptosis.
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Key Words
- apoptosis
- cyclophilin-d
- mitochondria
- necrosis
- permeability transition
- afc, 7-amino-4-trifluoromethylcoumarin
- ant, adenine nucleotide translocase
- cccp, carbonyl cyanide m-chlorophenylhydrazone
- csa, cyclosporin a
- cyp, cyclophilin
- cyp-d(+) cells, stable cell line overexpressing cyp-d
- gst, glutathione s-transferase
- mcyp-d, mature cyp-d
- pcyp-d, precursor cyp-d
- ppiase, peptidylprolyl cis–trans isomerase
- pt, permeability transition
- tmre, tetramethylrhodamine ethylester
- tpp+, tetraphenylphosphonium ion
- vdac, voltage-dependent anion channel
- δψm, mitochondrial inner-membrane potential
- h95q etc., his95→gln substitution etc
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Affiliation(s)
- Yanmin Li
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
| | - Nicholas Johnson
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
| | - Michela Capano
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
| | - Mina Edwards
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
| | - Martin Crompton
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
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Johnson J, Bhave M. Characterisation and physical mapping of cyclophilin A genes and identification of new classes of cyclophilins in wheat. J Cereal Sci 2004. [DOI: 10.1016/j.jcs.2004.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
The 18 kDa archetypal cyclosporin-A binding protein, cyclophilin-A, has multiple paralogues in the human genome. Only 18 of those paralogues have been detected as mRNAs or proteins whose masses vary from 18 to 354 kDa, whereas the functional significance of the open reading frames (ORFs) encoding other paralogues of cyclophilin-A remains unknown. The genomes of Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Schizosaccharomyces pombe, and Saccharomyces cerevisiae encode different numbers of the cyclophilin paralogues, some of which are orthologous to the human cyclophilins. A library of novel algorithms was developed and used for computation of the conservation levels for hydrophobicity and bulkiness profiles, and amino acid compositions (AACs) of 303 aligned sequences of cyclophilins. The majority of the paralogues and orthologues encoded in these 6 genomes differ considerably from each other. Some of the orthologues and paralogues have high correlation coefficients (CCFs) for pairwise compared hydrophobicity and bulkiness profiles, and whose AACs differ to a low degree. Convergence of these three properties of the polypeptide chain and apparent conservation of the typical sequence hallmarks and parameters allowed for the clustering of the functionally related orthologues and paralogues of the cyclophilins. The clustering method allowed for sorting out the cyclophilins into several distinct classes. Analyses of the overlapping clusters of sequences permitted delineation of some hypothetical pathways that might have led to the creation of certain paralogues of cyclophilins in the eukaryotic genomes.
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Affiliation(s)
- Andrzej Galat
- Département d'Ingénierie et d'Etudes des Protéines, DSV/CEA, Gif-sur-Yvette Cedex, France.
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Hong F, Lee J, Piao YJ, Jae YK, Kim YJ, Oh C, Seo JS, Yun YS, Yang CW, Ha J, Kim SS. Transgenic mice overexpressing cyclophilin A are resistant to cyclosporin A-induced nephrotoxicity via peptidyl-prolyl cis–trans isomerase activity. Biochem Biophys Res Commun 2004; 316:1073-80. [PMID: 15044094 DOI: 10.1016/j.bbrc.2004.02.160] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Indexed: 10/26/2022]
Abstract
Cyclosporin A (CsA) suppresses immune reaction by inhibiting calcineurin activity after forming complex with cyclophilins and is currently widely used as an immunosuppressive drug. Cyclophilin A (CypA) is the most abundantly and ubiquitously expressed family member of cyclophilins. We previously showed that CsA toxicity is mediated by ROS generation as well as by inhibition of peptidyl-prolyl cis-trans isomerase (PPIase) activity of CypA in CsA-treated myoblasts [FASEB J. 16 (2002) 1633]. Since CsA-induced nephrotoxicity is the most significant adverse effect in its clinical utilization, we here investigated the role of CsA inhibition of CypA PPIase activity in its nephrotoxicity using transgenic mouse models. Transgenic mice of either wild type (CypA/wt) or R55A PPIase mutant type (CypA/R55A), a dominant negative mutant of CypA PPIase activity, showed normal growth without any apparent abnormalities. However, CsA-induced nephrotoxicity was virtually suppressed in CypA/wt mice, but exacerbated in CypA/R55A mice, compared to that of littermates. Also, life expectancy was extended in CypA/wt mice and shortened in CypA/R55A mice during CsA administration. Besides, CsA-induced nephrotoxicity was inversely related to the levels of catalase expression and activity. In conclusion, our data provide in vivo evidence that supplement of CypA PPIase activity allows animal's resistance toward CsA-induced nephrotoxicity.
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Affiliation(s)
- Feng Hong
- Department of Molecular Biology, Medical Science and Engineering Research Center for Bioreaction to Reactive Oxygen Species, School of Medicine, Kyung Hee University, Seoul 130-701, Republic of Korea
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Stamnes MA, Rutherford SL, Zuker CS. Cyclophilins: a new family of proteins involved in intracellular folding. Trends Cell Biol 2004; 2:272-6. [PMID: 14731520 DOI: 10.1016/0962-8924(92)90200-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proteins of the cyclophilin family display two intriguing properties. On the one hand, they are the intracellular receptors for the immunosuppressive drug cyclosporin A (CsA); on the other hand, they function in vitro as enzymes that catalyse slow steps in protein folding. A dissection of the role of CsA in mediating immunosuppression, together with recent studies on the biology of cyclophilins in the absence of this ligand, is providing fundamental insight into the cellular function of this protein family.
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Affiliation(s)
- M A Stamnes
- Howard Hughes Medical Institute and Departments of Biology and Neuroscience, University of California at San Diego, La Jolla, CA 92093-0649, USA
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40
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Manzoni C, Duranti M, Eberini I, Scharnag H, März W, Castiglioni S, Lovati MR. Subcellular localization of soybean 7S globulin in HepG2 cells and LDL receptor up-regulation by its alpha' constituent subunit. J Nutr 2003; 133:2149-55. [PMID: 12840170 DOI: 10.1093/jn/133.7.2149] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The aims of this work were to monitor the subcellular localization of soybean 7S globulin in HepG2 cells and determine its interaction with cell protein components, by using laser-induced fluorescence capillary electrophoresis (LIF-CE). Furthermore, we evaluated in the same cell line the involvement of the alpha' constituent subunit from 7S globulin in the modulation of LDL catabolism. The results indicated a main fluorescein isothiocyanate-tagged 7S globulin (FITC-7S) component in the cytosolic fraction, that was not present in the nuclear compartment. The electrophoretic mobility of this tagged component suggested either a dissociation of the 7S oligomer or its partial intracellular degradation. Interactions of soybean 7S globulin with FITC-thioredoxin 1 and FITC-cyclophilin B, HepG2 cell membrane proteins, were demonstrated in in vitro assays. In a separate experiment with HepG2 cells, the ability of the alpha' subunit purified from soybean 7S globulin to modulate the activity of the LDL receptors was evaluated by tracking the uptake and degradation of labeled LDL. The up-regulation of LDL receptors by the alpha' subunit, as further confirmed by a LDL receptor promoter assay, was significantly greater than that found in the control cells. In conclusion, this study, while confirming our previous indirect evidence of the key role of alpha' subunit on the cell cholesterol homeostasis, reveals a potentially interesting association of soybean 7S globulin with proteins, such as thioredoxin 1 and cyclophilin B, that are involved in cell protection against oxidative stress.
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Affiliation(s)
- Cristina Manzoni
- Department of Pharmacological Sciences, University of Milan, 20133 Milan, Italy
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41
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Schmid H, Cohen CD, Henger A, Irrgang S, Schlöndorff D, Kretzler M. Validation of endogenous controls for gene expression analysis in microdissected human renal biopsies. Kidney Int 2003; 64:356-60. [PMID: 12787429 DOI: 10.1046/j.1523-1755.2003.00074.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The appropriate choice of an internal reference is critical for quantitative RNA analysis. However, no comparison of frequently used "housekeeping" genes is available for renal biopsy studies. METHODS Microdissected biopsies from 165 patients, including a wide range of histopathologic diagnoses, were analyzed [immunoglobulin A (IgA) nephritis, membranous glomerulopathy, rapid progressive glomerulonephritis, minimal change disease, focal segmental glomerulosclerosis (FSGS), nephrosclerosis, diabetic nephropathy, interstitial nephritis, and controls]. Expression of three frequently used housekeeping genes [glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S rRNA, and cyclophilin A] was examined by real-time reverse transcription-polymerase chain reaction (RT-PCR). RESULTS Absolute expression values of reference genes obtained from the renal biopsies were related to each other. In tubulointerstitial compartment, a positive correlation coefficient (r) of 0.96 was observed between 18S rRNA and cyclophilin A. However, a subset of samples showed lower expression levels for GAPDH in relation to 18S rRNA or cyclophilin A, resulting in a decrease to r = 0.77 and r = 0.73, respectively, consistent with considerable mRNA regulation of GAPDH. In glomerular samples, a comparable low correlation between GAPDH versus 18S rRNA (r = 0.75) was obtained. CONCLUSION Using a single housekeeper gene as reference for renal biopsy studies, differences in gene expression ratios may reflect regulation of the internal control rather than the mRNA under investigation. Relating the gene expression to several housekeepers in parallel (i.e., 18S rRNA and cyclophilin A) should result in robust expression data.
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Affiliation(s)
- Holger Schmid
- Medizinische Poliklinik, Ludwig-Maximilians-University of Munich, Munich, Germany
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42
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Briscoe CP, Tadayyon M, Andrews JL, Benson WG, Chambers JK, Eilert MM, Ellis C, Elshourbagy NA, Goetz AS, Minnick DT, Murdock PR, Sauls HR, Shabon U, Spinage LD, Strum JC, Szekeres PG, Tan KB, Way JM, Ignar DM, Wilson S, Muir AI. The orphan G protein-coupled receptor GPR40 is activated by medium and long chain fatty acids. J Biol Chem 2003; 278:11303-11. [PMID: 12496284 DOI: 10.1074/jbc.m211495200] [Citation(s) in RCA: 862] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
GPR40 is a member of a subfamily of homologous G protein-coupled receptors that include GPR41 and GPR43 and that have no current function or ligand ascribed. Ligand fishing experiments in HEK293 cells expressing human GPR40 revealed that a range of saturated and unsaturated carboxylic acids with carbon chain lengths greater than six were able to induce an elevation of [Ca(2+)](i), measured using a fluorometric imaging plate reader. 5,8,11-Eicosatriynoic acid was the most potent fatty acid tested, with a pEC(50) of 5.7. G protein coupling of GPR40 was examined in Chinese hamster ovary cells expressing the G alpha(q/i)-responsive Gal4-Elk1 reporter system. Expression of human GPR40 led to a constitutive induction of luciferase activity, which was further increased by exposure of the cells to eicosatriynoic acid. Neither the constitutive nor ligand-mediated luciferase induction was inhibited by pertussis toxin treatment, suggesting that GPR40 was coupled to G alpha(q/11.) Expression analysis by quantitative reverse transcription-PCR showed that GPR40 was specifically expressed in brain and pancreas, with expression in rodent pancreas being localized to insulin-producing beta-cells. These data suggest that some of the physiological effects of fatty acids in pancreatic islets and brain may be mediated through a cell-surface receptor.
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Affiliation(s)
- Celia P Briscoe
- Department of Metabolic Diseases, GlaxoSmithKline, Research Triangle Park, North Carolina 27709, USA.
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43
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Pulkkinen MA, Spencer-Dene B, Dickson C, Otonkoski T. The IIIb isoform of fibroblast growth factor receptor 2 is required for proper growth and branching of pancreatic ductal epithelium but not for differentiation of exocrine or endocrine cells. Mech Dev 2003; 120:167-75. [PMID: 12559489 DOI: 10.1016/s0925-4773(02)00440-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Fibroblast growth factors (Fgfs) and their receptors have been implicated in embryonic pancreas development. Recently it was shown that Fgf10, a major ligand for the IIIb isoform of fibroblast growth factor receptor 2 (Fgfr2b), has an important regulatory role in early pancreas development. The aim of our study was to define the role of Fgfr2b in pancreas development by analyzing the phenotype of Fgfr2b (-/-) mice. Pancreases of Fgfr2b (-/-) embryos were noticeably smaller than the wild type littermates during embryogenesis, and pancreatic ductal branching as well as duct cell proliferation was significantly reduced. However, both exocrine and endocrine pancreatic differentiation occurred relatively normally. Exogenous addition of Fgfr2b ligands (Fgf7 and Fgf10) stimulated duct cell proliferation and inhibited endocrine cell differentiation in the ex vivo embryonic organ cultures of wild type pancreas. Our results thus suggest that Fgfr2b-mediated signaling plays a major role in pancreatic ductal proliferation and branching morphogenesis, but has little effect on endocrine and exocrine differentiation.
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Affiliation(s)
- Mari-Anne Pulkkinen
- Biomedicum Helsinki, Program for Developmental and Reproductive Biology and Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland.
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Yu HS, Kong HH, Chung DI. Cloning and characterization of Giardia intestinalis cyclophilin. THE KOREAN JOURNAL OF PARASITOLOGY 2002; 40:131-8. [PMID: 12325442 PMCID: PMC2721039 DOI: 10.3347/kjp.2002.40.3.131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The cyclophilins (Cyps) are family members of proteins that exhibit peptidylprolyl cis-trans isomerase (PPIase, EC 5.2.1.8) activity and bind the immunosuppressive agent cyclosprin A (CsA) in varying degrees. During the process of random sequencing of a cDNA library made from Giardia intestinalis WB strain, the cyclophilin gene (gicyp 1) was isolated. An open reading frame of gicyp 1 gene was 576 nucleotides, which corresponded to a translation product of 176 amino acids (Gicyp 1). The identity with other Cyps was about 58-71%. The 13 residues that constituted the CsA binding site of human cyclophilin were also detected in the amino acid sequence of Gicyp 1, including tryptophan residue essential for the drug binding. The single copy of the gicyp 1 gene was detected in the G. intestinalis chromosome by southern hybridization analysis. Recombinant Gicyp 1 protein clearly accelerated the rate of cis-->trans isomerization of the peptide substrate and the catalysis was completely inhibited by the addition of 0.5 microM CsA.
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Affiliation(s)
- Hak-Sun Yu
- Department of Parasitology, College of Medicine, Kyungpook National University, Daegu 700-422, Korea
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Newby LJ, Streets AJ, Zhao Y, Harris PC, Ward CJ, Ong ACM. Identification, characterization, and localization of a novel kidney polycystin-1-polycystin-2 complex. J Biol Chem 2002; 277:20763-73. [PMID: 11901144 DOI: 10.1074/jbc.m107788200] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The functions of the two proteins defective in autosomal dominant polycystic kidney disease, polycystin-1 and polycystin-2, have not been fully clarified, but it has been hypothesized that they may heterodimerize to form a "polycystin complex" involved in cell adhesion. In this paper, we demonstrate for the first time the existence of a native polycystin complex in mouse kidney tubular cells transgenic for PKD1, non-transgenic kidney cells, and normal adult human kidney. Polycystin-1 is heavily N-glycosylated, and several glycosylated forms of polycystin-1 differing in their sensitivity to endoglycosidase H (Endo H) were found; in contrast, native polycystin-2 was fully Endo H-sensitive. Using highly specific antibodies to both proteins, we show that polycystin-2 associates selectively with two species of full-length polycystin-1, one Endo H-sensitive and the other Endo H-resistant; importantly, the latter could be further enriched in plasma membrane fractions and co-immunoprecipitated with polycystin-2. Finally, a subpopulation of this complex co-localized to the lateral cell borders of PKD1 transgenic kidney cells. These results demonstrate that polycystin-1 and polycystin-2 interact in vivo to form a stable heterodimeric complex and suggest that disruption of this complex is likely to be of primary relevance to the pathogenesis of cyst formation in autosomal dominant polycystic kidney disease.
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Affiliation(s)
- Linda J Newby
- Sheffield Kidney Institute, University Section of Medicine, Division of Clinical Sciences, University of Sheffield, Sheffield S5 7AU, United Kingdom
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Abstract
Mitochondria play a critical role in initiating both apoptotic and necrotic cell death. A major player in this process is the mitochondrial permeability transition pore (MPTP), a non-specific pore, permeant to any molecule of < 1.5 kDa, that opens in the inner mitochondrial membrane under conditions of elevated matrix [Ca(2+)], especially when this is accompanied by oxidative stress and depleted adenine nucleotides. Opening of the MPTP causes massive swelling of mitochondria, rupture of the outer membrane and release of intermembrane components that induce apoptosis. In addition mitochondria become depolarised causing inhibition of oxidative phosphorylation and stimulation of ATP hydrolysis. Pore opening is inhibited by cyclosporin A analogues with the same affinity as they inhibit the peptidyl-prolyl cis-trans isomerase activity of mitochondrial cyclophilin (CyP-D). These data and the observation that different ligands of the adenine nucleotide translocase (ANT) can either stimulate or inhibit pore opening led to the proposal that the MPTP is formed by a Ca-triggered conformational change of the ANT that is facilitated by the binding of CyP-D. Our model is able to explain the mode of action of a wide range of known modulators of the MPTP that exert their effects by changing the binding affinity of the ANT for CyP-D, Ca(2+) or adenine nucleotides. The extensive evidence for this model from our own and other laboratories is presented, including reconstitution studies that demonstrate the minimum configuration of the MPTP to require neither the voltage activated anion channel (VDAC or porin) nor any other outer membrane protein. However, other proteins including Bcl-2, BAX and virus-derived proteins may interact with the ANT to regulate the MPTP. Recent data suggest that oxidative cross-linking of two matrix facing cysteine residues on the ANT (Cys(56) and Cys(159)) plays a key role in regulating the MPTP. Adenine nucleotide binding to the ANT is inhibited by Cys(159) modification whilst oxidation of Cys(56) increases CyP-D binding to the ANT, probably at Pro(61).
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Hursting SD, Shen JC, Sun XY, Wang TTY, Phang JM, Perkins SN. Modulation of cyclophilin gene expression by N-4-(hydroxyphenyl)retinamide: association with reactive oxygen species generation and apoptosis. Mol Carcinog 2002; 33:16-24. [PMID: 11807954 DOI: 10.1002/mc.10020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
To explore the mechanisms underlying the pro-apoptotic effects of the synthetic retinoid N-4-(hydroxyphenyl)retinamide (4-HPR) on LNCaP human prostate cancer cells, we used the differential display-polymerase chain reaction (DD-PCR) technique to identify 4-HPR-responsive genes. RNA extracted from LNCaP cells that had been treated for 24 h with 4-HPR at a dose (2.5 microM) optimal for apoptosis induction was used for DD-PCR analysis using random primers. A differentially expressed 115 bp fragment was cloned and sequenced and then identified in GenBank as having a high degree of homology with several members of the cyclophilin gene family. Northern blot analyses using specific probes for cyclophilin A, cyclophilin D, and the cloned 115-bp fragment were performed on RNA extracted from LNCaP cells and MCF-7 human breast cancer cells treated with 4-HPR, N-acetylcysteine (NAC, an anti-oxidant), 4-HPR plus NAC, cyclosporin A, R-1881 (a synthetic androgen), dehydroepiandrosterone, all-trans retinoic acid, or prednisone. 4-HPR downregulated the transcript detected by the 115-bp fragment. Expression patterns detected by the 115-bp fragment and cyclophilin D probes were identical in response to each treatment; none of these treatments affected cyclophilin A expression. Furthermore, expression of mRNA transcripts detected by the 115-bp fragment and cyclophilin D probes correlated with the generation of reactive oxygen species (ROS), as detected by measurement of 2,7-dichlorofluorescein oxidation. Therefore, members of the cyclophilin gene family, such as cyclophilin D (a component of the mitochondrial permeability transition pore previously linked with oxidative stress and apoptosis), may play a role in the ROS-mediated apoptotic effects of 4-HPR.
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Affiliation(s)
- Stephen D Hursting
- Laboratory of Biosystems and Cancer, National Cancer Institute at Frederick, Frederick, Maryland, USA
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Kung L, Batiuk TD, Palomo-Pinon S, Noujaim J, Helms LM, Halloran PF. Tissue distribution of calcineurin and its sensitivity to inhibition by cyclosporine. Am J Transplant 2001; 1:325-33. [PMID: 12099376 DOI: 10.1034/j.1600-6143.2001.10407.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The immunosuppressive activity of cyclosporine is mediated by inhibiting calcineurin phosphatase. However, calcineurin is widely distributed in other tissues. We examined the degree of calcineurin inhibition by cyclosporine in various tissues. In vitro, the cyclosporine concentration inhibiting 50% (IC50) of calcineurin was to approximately 10 ng/mL in human and mouse leukocytes suspensions. In vitro and in vivo IC50s of cyclosporine in homogenates of mouse kidney, heart, liver, testis, and spleen were also comparable (9-48 ng/mL). The maximum calcineurin inhibition by cyclosporine varied, from 83 to 95% of calcineurin activity in spleen, kidney, liver, and testis to 60% in heart and only 10% in brain. Maximum calcineurin inhibition was increased by the addition of cyclophilin A, indicating that cyclophilin concentrations were limiting in some tissues, at least in this assay. Western analysis of mouse tissues showed significantly less cyclophilin in heart than other tissues. cyclosporine concentrations per weight of tissue protein were highest in kidney and liver and lowest in brain and testis after oral dosing, with intermediate levels in spleen, heart, and whole blood. Thus each cyclosporine dose produces rapid and wide-spread inhibition of calcineurin in tissues, with differences in total susceptibility of each tissue.
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Affiliation(s)
- L Kung
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada
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Isolation and Characterisation of cDNAs Encoding Protein Disulphide Isomerases and Cyclophilins in Wheat. J Cereal Sci 2001. [DOI: 10.1006/jcrs.2001.0382] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Tamura M, Nishizaka S, Maeda Y, Ito M, Harashima N, Harada M, Shichijo S, Itoh K. Identification of cyclophilin B-derived peptides capable of inducing histocompatibility leukocyte antigen-A2-restricted and tumor-specific cytotoxic T lymphocytes. Jpn J Cancer Res 2001; 92:762-7. [PMID: 11473727 PMCID: PMC5926786 DOI: 10.1111/j.1349-7006.2001.tb01159.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We recently suggested that cyclophilin B (Cyp-B) is a tumor antigen recognized by histocompatibility leukocyte antigen (HLA)-A24-restricted and tumor-specific cytotoxic T lymphocytes (CTLs). In this study, we tried to identify Cyp-B-derived epitopes, which can induce HLA-A2-restricted and tumor-specific CTLs in cancer patients. The tumor-infiltrating lymphocytes (TILs) from an HLA-A0207 patient with colon cancer were found to respond to COS-7 cells when co-transfected with the Cyp-B gene and either HLA-A0201, -A0206, or -A0207 cDNA. These TILs contained CTLs capable of recognizing either the Cyp-B(129 - 138) or the Cyp-B(172 - 179) peptide among 28 different peptides, all of which were prepared based on the HLA-A2 binding motif. Both Cyp-B peptides possessed the ability to induce tumor-specific CTLs in HLA-A2(+) cancer patients. Cyp-B(172 - 180 (V)), which is a 9-mer peptide with valine added at the C terminus, showed no clear superiority over the parental Cyp-B(172 - 179) peptide in an in vitro sensitization experiment. In vitro-sensitized T cells with these peptides responded to cancer cells in an HLA-A2-restricted manner. These two Cyp-B peptides could be useful for specific immunotherapy of HLA-A2(+) cancer patients.
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Affiliation(s)
- M Tamura
- Department of Immunology, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan.
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