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Selmansberger M, Michna A, Braselmann H, Höfig I, Schorpp K, Weber P, Anastasov N, Zitzelsberger H, Hess J, Unger K. Transcriptome network of the papillary thyroid carcinoma radiation marker CLIP2. Radiat Oncol 2020; 15:182. [PMID: 32727620 PMCID: PMC7392692 DOI: 10.1186/s13014-020-01620-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 07/15/2020] [Indexed: 11/29/2022] Open
Abstract
Background We present a functional gene association network of the CLIP2 gene, generated by de-novo reconstruction from transcriptomic microarray data. CLIP2 was previously identified as a potential marker for radiation induced papillary thyroid carcinoma (PTC) of young patients in the aftermath of the Chernobyl reactor accident. Considering the rising thyroid cancer incidence rates in western societies, potentially related to medical radiation exposure, the functional characterization of CLIP2 is of relevance and contributes to the knowledge about radiation-induced thyroid malignancies. Methods We generated a transcriptomic mRNA expression data set from a CLIP2-perturbed thyroid cancer cell line (TPC-1) with induced CLIP2 mRNA overexpression and siRNA knockdown, respectively, followed by gene-association network reconstruction using the partial correlation-based approach GeneNet. Furthermore, we investigated different approaches for prioritizing differentially expressed genes for network reconstruction and compared the resulting networks with existing functional interaction networks from the Reactome, Biogrid and STRING databases. The derived CLIP2 interaction partners were validated on transcript and protein level. Results The best reconstructed network with regard to selection parameters contained a set of 20 genes in the 1st neighborhood of CLIP2 and suggests involvement of CLIP2 in the biological processes DNA repair/maintenance, chromosomal instability, promotion of proliferation and metastasis. Peptidylprolyl Isomerase Like 3 (PPIL3), previously identified as a potential direct interaction partner of CLIP2, was confirmed in this study by co-expression at the transcript and protein level. Conclusion In our study we present an optimized preselection approach for genes subjected to gene-association network reconstruction, which was applied to CLIP2 perturbation transcriptome data of a thyroid cancer cell culture model. Our data support the potential carcinogenic role of CLIP2 overexpression in radiation-induced PTC and further suggest potential interaction partners of the gene.
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Affiliation(s)
- Martin Selmansberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Agata Michna
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Herbert Braselmann
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Ines Höfig
- Institute of Radiation Biology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Kenji Schorpp
- Institute for Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Peter Weber
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Natasa Anastasov
- Institute of Radiation Biology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany. .,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany. .,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany.
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Zhao X, Xia C, Wang X, Wang H, Xin M, Yu L, Liang Y. Cyclophilin J PPIase Inhibitors Derived from 2,3-Quinoxaline-6 Amine Exhibit Antitumor Activity. Front Pharmacol 2018. [PMID: 29520233 PMCID: PMC5826973 DOI: 10.3389/fphar.2018.00126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cyclophilin J (CyPJ), also called peptidylprolyl isomerase like 3, has been identified as a novel member of the cyclophilin family. Our previous research has resolved the three-dimensional structure of CyPJ and demonstrated the peptidylprolyl cis–trans isomerase (PPIase) activity of CyPJ, which can be inhibited by the common immunosuppressive drug cyclosporine A (CsA). Importantly, CyPJ is upregulated in hepatocellular carcinoma (HCC) and promotes tumor growth; CyPJ inhibition by CsA- or siRNA-based knockdown results in a remarkable suppression of HCC. These findings suggest that CyPJ may be a potential therapeutic target for HCC, and discovery of relevant inhibitors may facilitate development of a novel CyPJ-based targeting therapy. However, apart from the common inhibitor CsA, CyPJ has yet to be investigated as a target for cancer therapy. Here, we report structure-based identification of novel small molecule non-peptidic CyPJ inhibitors and their potential as antitumor lead compounds. Based on computer-aided virtual screening, in silico, and subsequently surface plasmon resonance analysis, 19 potential inhibitors of CyPJ were identified and selected for further evaluation of PPIase CyPJ inhibition in vitro. Thirteen out of 19 compounds exhibited notable inhibition against PPIase activity. Among them, the compound ZX-J-19, with a quinoxaline nucleus, showed potential for tumor inhibition; thus, we selected it for further structure–activity optimization. A total of 22 chemical derivatives with 2,3-substituted quinoxaline-6-amine modifications were designed and successfully synthesized. At least 2 out of the 22 derivatives, such as ZX-J-19j and ZX-J-19l, demonstrated remarkable inhibition of tumor cell growth, comparable to CsA but much stronger than 5-fluorouracil. These results indicate that these two small molecules represent novel potential lead compounds for CyPJ-based antitumor drug development.
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Affiliation(s)
- Xuemei Zhao
- College of Pharmacy, Taishan Medical University, Tai'an, China
| | - Chengcai Xia
- College of Pharmacy, Taishan Medical University, Tai'an, China
| | - Xiaodan Wang
- College of Pharmacy, Taishan Medical University, Tai'an, China
| | - Hao Wang
- College of Pharmacy, Taishan Medical University, Tai'an, China
| | - Ming Xin
- College of Pharmacy, Taishan Medical University, Tai'an, China
| | - Long Yu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yulong Liang
- College of Pharmacy, Taishan Medical University, Tai'an, China.,Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, United States
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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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4
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Chen J, Chen S, Wang J, Zhang M, Gong Z, Wei Y, Li L, Zhang Y, Zhao X, Jiang S, Yu L. Cyclophilin J is a novel peptidyl-prolyl isomerase and target for repressing the growth of hepatocellular carcinoma. PLoS One 2015; 10:e0127668. [PMID: 26020957 PMCID: PMC4447340 DOI: 10.1371/journal.pone.0127668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 04/17/2015] [Indexed: 11/18/2022] Open
Abstract
Cyclophilin J (CYPJ) is a new member of the peptidyl-prolyl cis/trans-isomerase (PPIase) identified with upregulated expression in human glioma. However, the biological function of CYPJ remained unclear. We aimed to study the role of CYPJ in hepatocellular carcinoma (HCC) carcinogenesis and its therapeutic potential. We determined the expression of CYPJ in HCC/adjacent normal tissues using Western blot, Northern blot and semi-quantitative RT-PCR, analyzed the biochemical characteristics of CYPJ, and resolved the 3D-structure of CYPJ/Cyclosporin A (CsA) complex. We also studied the roles of CYPJ in cell cycle, cyclin D1 regulation, in vitro and in vivo tumor growth. We found that CYPJ expression was upregulated in over 60% HCC tissues. The PPIase activity of CYPJ could be inhibited by the widely used immunosuppressive drug CsA. CYPJ was found expressed in the whole cell of HCC with preferential location at the cell nucleus. CYPJ promoted the transition of cells from G1 phase to S phase in a PPIase-dependent manner by activating cyclin D1 promoter. CYPJ overexpression accelerated liver cell growth in vitro (cell growth assay, colony formation) and in vivo (xenograft tumor formation). Inhibition of CYPJ by its inhibitor CsA or CYPJ-specific RNAi diminished the growth of liver cancer cells in vitro and in vivo. In conclusion, CYPJ could facilitate HCC growth by promoting cell cycle transition from G1 to S phase through the upregulation of cyclin D1. Suppression of CYPJ could repress the growth of HCC, which makes CYPJ a potential target for the development of new strategies to treat this malignancy.
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Affiliation(s)
- Jian Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
- Shandong Research Center of Stem Cell Engineering, Yantai Yuhuangding Hospital, Affiliated Hospital of Qingdao University, Yantai, Shandong, P.R. China
- * E-mail: (SJ); (JC)
| | - Shuai Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Jiahui Wang
- Shandong Research Center of Stem Cell Engineering, Yantai Yuhuangding Hospital, Affiliated Hospital of Qingdao University, Yantai, Shandong, P.R. China
| | - Mingjun Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Zhaohua Gong
- Department of Oncology, Yantai Yuhuangding Hospital, Affiliated Hospital of Qingdao University, Yantai, Shandong, P.R. China
| | - Youheng Wei
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Li Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Yuanyuan Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Xuemei Zhao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Songmin Jiang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
- * E-mail: (SJ); (JC)
| | - Long Yu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
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Roles of Prolyl Isomerases in RNA-Mediated Gene Expression. Biomolecules 2015; 5:974-99. [PMID: 25992900 PMCID: PMC4496705 DOI: 10.3390/biom5020974] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/01/2015] [Accepted: 05/07/2015] [Indexed: 12/16/2022] Open
Abstract
The peptidyl-prolyl cis-trans isomerases (PPIases) that include immunophilins (cyclophilins and FKBPs) and parvulins (Pin1, Par14, Par17) participate in cell signaling, transcription, pre-mRNA processing and mRNA decay. The human genome encodes 19 cyclophilins, 18 FKBPs and three parvulins. Immunophilins are receptors for the immunosuppressive drugs cyclosporin A, FK506, and rapamycin that are used in organ transplantation. Pin1 has also been targeted in the treatment of Alzheimer’s disease, asthma, and a number of cancers. While these PPIases are characterized as molecular chaperones, they also act in a nonchaperone manner to promote protein-protein interactions using surfaces outside their active sites. The immunosuppressive drugs act by a gain-of-function mechanism by promoting protein-protein interactions in vivo. Several immunophilins have been identified as components of the spliceosome and are essential for alternative splicing. Pin1 plays roles in transcription and RNA processing by catalyzing conformational changes in the RNA Pol II C-terminal domain. Pin1 also binds several RNA binding proteins such as AUF1, KSRP, HuR, and SLBP that regulate mRNA decay by remodeling mRNP complexes. The functions of ribonucleoprotein associated PPIases are largely unknown. This review highlights PPIases that play roles in RNA-mediated gene expression, providing insight into their structures, functions and mechanisms of action in mRNP remodeling in vivo.
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6
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Cyclophilins as modulators of viral replication. Viruses 2013; 5:1684-701. [PMID: 23852270 PMCID: PMC3738956 DOI: 10.3390/v5071684] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/26/2013] [Accepted: 07/03/2013] [Indexed: 01/11/2023] Open
Abstract
Cyclophilins are peptidyl‐prolyl cis/trans isomerases important in the proper folding of certain proteins. Mounting evidence supports varied roles of cyclophilins, either positive or negative, in the life cycles of diverse viruses, but the nature and mechanisms of these roles are yet to be defined. The potential for cyclophilins to serve as a drug target for antiviral therapy is evidenced by the success of non-immunosuppressive cyclophilin inhibitors (CPIs), including Alisporivir, in clinical trials targeting hepatitis C virus infection. In addition, as cyclophilins are implicated in the predisposition to, or severity of, various diseases, the ability to specifically and effectively modulate their function will prove increasingly useful for disease intervention. In this review, we will summarize the evidence of cyclophilins as key mediators of viral infection and prospective drug targets.
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7
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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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8
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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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9
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Pasquariello N, Catanzaro G, Marzano V, Amadio D, Barcaroli D, Oddi S, Federici G, Urbani A, Finazzi Agrò A, Maccarrone M. Characterization of the endocannabinoid system in human neuronal cells and proteomic analysis of anandamide-induced apoptosis. J Biol Chem 2009; 284:29413-26. [PMID: 19690173 DOI: 10.1074/jbc.m109.044412] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Anandamide (AEA) is an endogenous agonist of type 1 cannabinoid receptors (CB1R) that, along with metabolic enzymes of AEA and congeners, compose the "endocannabinoid system." Here we report the biochemical, morphological, and functional characterization of the endocannabinoid system in human neuroblastoma SH-SY5Y cells that are an experimental model for neuronal cell damage and death, as well as for major human neurodegenerative disorders. We also show that AEA dose-dependently induced apoptosis of SH-SY5Y cells. Through proteomic analysis, we further demonstrate that AEA-induced apoptosis was paralleled by an approximately 3 to approximately 5-fold up-regulation or down-regulation of five genes; IgG heavy chain-binding protein, stress-induced phosphoprotein-1, and triose-phosphate isomerase-1, which were up-regulated, are known to act as anti-apoptotic agents; actin-related protein 2/3 complex subunit 5 and peptidylprolyl isomerase-like protein 3 isoform PPIL3b were down-regulated, and the first is required for actin network formation whereas the second is still function-orphan. Interestingly, only the effect of AEA on BiP was reversed by the CB1R antagonist SR141716, in SH-SY5Y cells as well as in human neuroblastoma LAN-5 cells (that express a functional CB1R) but not in SK-NBE cells (which do not express CB1R). Silencing or overexpression of BiP increased or reduced, respectively, AEA-induced apoptosis of SH-SY5Y cells. In addition, the expression of BiP and of the BiP-related apoptotic markers p53 and PUMA was increased by AEA through a CB1R-dependent pathway that engages p38 and p42/44 mitogen-activated protein kinases. Consistently, this effect of AEA was minimized by SR141716. In conclusion, we identified BiP as a key protein in neuronal apoptosis induced by AEA.
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Affiliation(s)
- Nicoletta Pasquariello
- Dipartimento di Scienze Biomediche, Università degli Studi di Teramo, 64100 Teramo, Italy
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Huo DH, Yi LN, Yang J. Interaction with Ppil3 leads to the cytoplasmic localization of Apoptin in tumor cells. Biochem Biophys Res Commun 2008; 372:14-8. [DOI: 10.1016/j.bbrc.2008.04.178] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 04/08/2008] [Indexed: 10/22/2022]
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Mesa A, Somarelli JA, Herrera RJ. Spliceosomal immunophilins. FEBS Lett 2008; 582:2345-51. [PMID: 18544344 DOI: 10.1016/j.febslet.2008.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 05/16/2008] [Accepted: 06/02/2008] [Indexed: 11/17/2022]
Abstract
The spliceosome is a dynamic, macromolecular complex, which removes non-protein-coding introns from pre-mRNA to form mature mRNA in a process known as splicing. This ribonucleoprotein assembly is comprised of five uridine-rich small nuclear RNAs (snRNAs) as well as over 300 proteins. In humans, several of the known proteinaceous splicing factors are members of the immunophilin superfamily. Immunophilins are peptidyl-prolyl cis-trans isomerases that catalyze the conversion of proteins from cis to trans at Xaa-Pro bonds. Our review of the data indicates that some members of this protein family are activators of spliceosomal proteins by way of folding and transport.
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Affiliation(s)
- Annia Mesa
- Florida International University, Department of Biological Sciences, University Park, 11200 SW 8th Street, OE 304, Miami, FL 33199, United States
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12
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Potenza M, Galat A, Minning TA, Ruiz AM, Duran R, Tarleton RL, Marín M, Fichera LE, Búa J. Analysis of the Trypanosoma cruzi cyclophilin gene family and identification of Cyclosporin A binding proteins. Parasitology 2006; 132:867-82. [PMID: 16700961 DOI: 10.1017/s0031182005009558] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Revised: 10/08/2005] [Accepted: 10/14/2005] [Indexed: 01/22/2023]
Abstract
The Trypanosoma cruzi cyclophilin gene family comprises 15 paralogues whose nominal masses vary from 19 to 110 kDa, namely TcCyP19, TcCyP20, TcCyP21, TcCyP22, TcCyP24, TcCyP25, TcCyP26, TcCyP28, TcCyP29, TcCyP30, TcCyP34, TcCyP35, TcCyP40, TcCyP42 and TcCyP110. Under the conditions used, only some of the T. cruzi cyclophilin paralogue products could be isolated by affinity chromatography. The 15 paralogues were aligned with 495 cyclophilins from diverse organisms. Analyses of clusters formed by the T. cruzi cyclophilins with others encoded in various genomes revealed that 8 of them (TcCyP19, TcCyP21, TcCyP22, TcCyP24, TcCyP35, TcCyP40, TcCyP42 and TcCyP110) have orthologues in many different genomes whereas the other 7 display less-defined patterns of their sequence attributes and their classification to a specific group of cyclophilin's orthologues remains uncertain. Seven epimastigote cDNA clones encoding cyclophilin isoforms were further studied. These genes were found dispersed throughout the genome of the parasite. Amastigote and trypomastigote mRNAs encoding these 7 genes were also detected. We isolated 4 cyclosporin A-binding proteins in T. cruzi epimastigote extracts, which were identified by mass spectrometry as TcCyP19, TcCyP22, TcCyP28 and TcCyP40. Cyclosporin A-binding to these cyclophilins might be of importance to the mechanism of action of Cyclosporin A and its non-immunosuppressive analogues, whose trypanocidal effects were previously reported, and therefore, of potential interest in the chemotherapy of Chagas' disease.
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Affiliation(s)
- M Potenza
- Instituto Nacional de Parasitología, Dr. M. Fatala Chabén, A.N.L.I.S. Malbrán, Buenos Aires, Argentina
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Hu H, Huang CQ, Liu HL, Han Y, Yu L, Bi RC. Crystallization and preliminary X-ray crystallographic studies of human cyclophilin J. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:216-8. [PMID: 16510998 PMCID: PMC1952245 DOI: 10.1107/s1744309105000643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Accepted: 01/07/2005] [Indexed: 11/10/2022]
Abstract
Human cyclophilin J, a new member of the cyclophilin family, has been expressed and crystallized. Diffraction data have been collected to 2.0 A resolution and preliminary crystallographic studies have been completed. The space group of the crystals is P3(1)21, with unit-cell parameters a = b = 40.597, c = 170.732 A, alpha = beta = 90, gamma = 120 degrees.
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Affiliation(s)
- Hao Hu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Chao-Qun Huang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - He-Li Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yi Han
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Long Yu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Ru-Chang Bi
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Correspondence e-mail:
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14
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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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