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Porzio E, Faraone Mennella MR, Manco G. DING Proteins Extend to the Extremophilic World. Int J Mol Sci 2021; 22:2035. [PMID: 33670786 PMCID: PMC7922408 DOI: 10.3390/ijms22042035] [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: 01/08/2021] [Revised: 02/04/2021] [Accepted: 02/16/2021] [Indexed: 11/16/2022] Open
Abstract
The DING proteins are ubiquitous in the three domains of life, from mesophiles to thermo- and hyperthermophiles. They belong to a family of more than sixty members and have a characteristic N-terminus, DINGGG, which is considered a "signature" of these proteins. Structurally, they share a highly conserved phosphate binding site, and a three dimensional organization resembling the "Venus Flytrap", both reminding the ones of PstS proteins. They have unusually high sequence conservation, even between distantly related species. Nevertheless despite that the genomes of most of these species have been sequenced, the DING gene has not been reported for all the relative characterized DING proteins. Identity of known DING proteins has been confirmed immunologically and, in some cases, by N-terminal sequence analysis. Only a few of the DING proteins have been purified and biochemically characterized. DING proteins are heterogeneous for their wide range of biological activities and some show different activities not always correlated with each other. Most of them have been originally identified for different biological properties, or rather for binding to phosphate and also to other ligands. Their involvement in pathologies is described. This review is an update of the most recent findings on old and new DING proteins.
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Affiliation(s)
- Elena Porzio
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy;
| | | | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy;
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2
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Wang XK, Liao XW, Huang R, Huang JL, Chen ZJ, Zhou X, Yang CK, Han CY, Zhu GZ, Peng T. Clinical significance of long non-coding RNA DUXAP8 and its protein coding genes in hepatocellular carcinoma. J Cancer 2020; 11:6140-6156. [PMID: 32922554 PMCID: PMC7477403 DOI: 10.7150/jca.47902] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/16/2020] [Indexed: 12/14/2022] Open
Abstract
Backgrounds: Hepatocellular carcinoma (HCC) is a lethal malignancy worldwide that is difficult to diagnose during the early stages and its tumors are recurrent. Long non-coding RNAs (lncRNAs) have increasingly been associated with tumor biomarkers for diagnosis and prognosis. This study attempts to explore the potential clinical significance of lncRNA DUXAP8 and its co-expression related protein coding genes (PCGs) for HCC. Method: Data from a total of 370 HCC patients from The Cancer Genome Atlas were utilized for the analysis. DUXAP8 and its top 10 PCGs were explored for their diagnostic and prognostic implications for HCC. A risk score model and nomogram were constructed for prognosis prediction using prognosis-related genes and DUXAP8. Molecular mechanisms of DUXAP8 and its PCGs involved in HCC initiation and progression were investigated. Then, potential target drugs were identified using genome-wide DUXAP8-related differentially expressed genes in a Connectivity Map database. Results: The top 10 PCGs were identified as: RNF2, MAGEA1, GABRA3, MKRN3, FAM133A, MAGEA3, CNTNAP4, MAGEA6, MALRD1, and DGKI. Diagnostic analysis indicated that DUXAP8, MEGEA1, MKRN3, and DGKI show diagnostic implications (all area under curves ≥0.7, p≤0.05). Prognostic analysis indicated that DUXAP8 and RNF2 had prognostic implications for HCC (adjusted p=0.014 and 0.008, respectively). The risk score model and nomogram showed an advantage for prognosis prediction. A total of 3 target drugs were determined: cinchonine, bumetanide and amiprilose and they may serve as potential therapeutic targets for HCC. Conclusion: Functioning as an oncogene, DUXAP8 is overexpressed in tumor tissue and may serve as both a diagnostic and prognosis biomarker for HCC. MEGEA1, MKRN3, and DGKI maybe potential diagnostic biomarkers and DGKI may also be potentially prognostic biomarkers for HCC.
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Affiliation(s)
- Xiang-Kun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Xi-Wen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Rui Huang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, People's Republic of China
| | - Jian-Lu Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China.,Department of Hepatobiliary Surgery, The Third Affiliated Hospital of Guangxi Medical University, Nanning 530031, Guangxi Province, China
| | - Zi-Jun Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Xin Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Cheng-Kun Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Chuang-Ye Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Guang-Zhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
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Qu C, Qu Y. Down-regulation of salt-inducible kinase 1 (SIK1) is mediated by RNF2 in hepatocarcinogenesis. Oncotarget 2018; 8:3144-3155. [PMID: 27911266 PMCID: PMC5356871 DOI: 10.18632/oncotarget.13673] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/07/2016] [Indexed: 11/25/2022] Open
Abstract
Our previous study reported that down-regulation of SIK1 accelerates the growth and invasion of hepatocellular carcinoma (HCC). However, the underlying mechanism leading to SIK1 down-regulation in HCC largely remains to be determined. Herein, we demonstrated that RNF2 expression is negatively correlated with SIK1 levels in HCC tissues. Kaplan-Meier analysis of tumor samples revealed that high RNF2 expression with concurrent low SIK1 expression is associated with poor overall survival. The down-regulation of RNF2 expression in HCC cells significantly reduces tumor cell growth and metastasis, while the simultaneous down-regulation of both RNF2 and SIK1 restores tumor cell growth in vitro and in tumor xenograft models. Mechanistically, we identified RNF2 as an E3 ligase that targets SIK1 for degradation. We further demonstrated that direct physical interaction between RNF2 and SIK1 triggers SIK1 down-regulation in HCC cells. These data suggest that RNF2 is an important upstream negative regulator of SIK1 and that restoration of SIK1 levels induced by loss of RNF2 inhibited HCC cell growth and promoted apoptosis, which may represent a promising therapeutic strategy for HCC treatment.
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Affiliation(s)
- Chao Qu
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China
| | - Yaqin Qu
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China
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4
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Porzio E, De Maio A, Ricciardi T, Mistretta C, Manco G, Faraone-Mennella MR. Comparison of the DING protein from the archaeon Sulfolobus solfataricus with human phosphate-binding protein and Pseudomonas fluorescence DING counterparts. Extremophiles 2018; 22:177-188. [PMID: 29327280 DOI: 10.1007/s00792-017-0985-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
Abstract
DING proteins represent a new group of 40 kDa-related members, ubiquitous in living organisms. The family also include the DING protein from Sulfolobus solfataricus, functionally related to poly(ADP-ribose) polymerases. Here, the archaeal protein has been compared with the human Phosphate-Binding Protein and the Pseudomonas fluorescence DING enzyme, by enzyme assays and immune cross-reactivity. Surprisingly, as the Sulfolobus enzyme, the Human and Pseudomonas proteins display poly(ADP-ribose) polymerase activity, whereas a phosphatase activity was only present in Sulfolobus and human protein, despite the conserved phosphate-binding site residues in Pseudomonas DING. All proteins were positive to anti-DING antibodies and gave a comparable pattern of anti-poly(ADP-ribose) polymerase immunoreactivity with two bands, at around 40 kDa and roughly at the double of this molecular mass. The latter signal was present in all Sulfolobus enzyme preparations and proved not due to either a contaminant or a precursor protein, but likely being a dimeric form of the 40 kDa polypeptide. The common immunological and partly enzymatic behavior linking human, Pseudomonas and Sulfolobus DING proteins, makes the archaeal protein an important model system to investigate DING protein function and evolution within the cell.
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Affiliation(s)
- Elena Porzio
- Department of Biology, Polytechnic School of Basic Sciences, University of Naples "Federico II", 80126, Naples, Italy. .,Institute of Protein Biochemistry, National Research Council (CNR), 80131, Naples, Italy.
| | - Anna De Maio
- Department of Biology, Polytechnic School of Basic Sciences, University of Naples "Federico II", 80126, Naples, Italy.,National Institute of Biostructures and Biosystems (INBB), via delle medaglie d'oro, 00136, Rome, Italy
| | - Teresa Ricciardi
- Department of Biology, Polytechnic School of Basic Sciences, University of Naples "Federico II", 80126, Naples, Italy
| | - Carmela Mistretta
- Department of Biology, Polytechnic School of Basic Sciences, University of Naples "Federico II", 80126, Naples, Italy.,Institute for Agricultural and Forest Systems in the Mediterranean, CNR, Ercolano, Italy
| | - Giuseppe Manco
- Institute of Protein Biochemistry, National Research Council (CNR), 80131, Naples, Italy.
| | - Maria Rosaria Faraone-Mennella
- Department of Biology, Polytechnic School of Basic Sciences, University of Naples "Federico II", 80126, Naples, Italy.,National Institute of Biostructures and Biosystems (INBB), via delle medaglie d'oro, 00136, Rome, Italy
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Brito-Argáez L, Tamayo-Sansores JA, Madera-Piña D, García-Villalobos FJ, Moo-Puc RE, Kú-González Á, Villanueva MA, Islas-Flores I. Biochemical characterization and immunolocalization studies of a Capsicum chinense Jacq. protein fraction containing DING proteins and anti-microbial activity. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 109:502-514. [PMID: 27835848 DOI: 10.1016/j.plaphy.2016.10.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 06/06/2023]
Abstract
The DING protein family consists of proteins of great biological importance due to their ability to inhibit carcinogenic cell growth. A DING peptide with Mr ∼7.57 kDa and pI ∼5.06 was detected in G10P1.7.57, a protein fraction from Capsicum chinense Jacq. seeds. Amino acid sequencing of the peptide produced three smaller peptides showing identity to the DING protein family. G10P1.7.57 displayed a phosphatase activity capable of dephosphorylating different phosphorylated substrates and inhibited the growth of Saccharomyces cerevisiae cells. Western immunoblotting with a custom-made polyclonal antibody raised against a sequence (ITYMSPDYAAPTLAGLDDATK), derived from the ∼7.57 kDa polypeptide, immunodetected an ∼ 39 kDa polypeptide in G10P1.7.57. Purification by electroelution followed by amino acid sequencing of the ∼39 kDa polypeptide yielded seven new peptide sequences and an additional one identical to that of the initially identified peptide. Western immunoblotting of soluble proteins from C. chinense seeds and leaves revealed the presence of the ∼39 kDa polypeptide at all developmental stages, with increased accumulation when the organs reached maturity. Immunolocalization using Dabsyl chloride- or Alexa fluor 488-conjugated antibodies revealed a specific fluorescent signal in the cell cytoplasm at all developmental stages, giving support to the idea that the ∼39 kDa polypeptide is a soluble DING protein. Thus, we have identified and characterized a protein fraction with a DING protein from C. chinense.
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Affiliation(s)
- Ligia Brito-Argáez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico
| | - José A Tamayo-Sansores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico
| | - Dianeli Madera-Piña
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico
| | - Francisco J García-Villalobos
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico
| | - Rosa E Moo-Puc
- Unidad de Investigación, Instituto Mexicano del Seguro Social, IMSS, T1, C.P. 97150, Mérida, Yucatán, Mexico
| | - Ángela Kú-González
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico
| | - Marco A Villanueva
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo, C.P. 77580, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico.
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Gonzalez D, Elias M, Chabrière E. The DING Family of Phosphate Binding Proteins in Inflammatory Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 824:27-32. [DOI: 10.1007/978-3-319-07320-0_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Sachdeva R, Darbinian N, Khalili K, Amini S, Gonzalez D, Djeghader A, Chabriére E, Suh A, Scott K, Simm M. DING proteins from phylogenetically different species share high degrees of sequence and structure homology and block transcription of HIV-1 LTR promoter. PLoS One 2013; 8:e69623. [PMID: 23936341 PMCID: PMC3735540 DOI: 10.1371/journal.pone.0069623] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/12/2013] [Indexed: 11/19/2022] Open
Abstract
Independent research groups reported that DING protein homologues isolated from bacterial, plant and human cells demonstrate the anti-HIV-1 activity. This might indicate that diverse organisms utilize a DING-mediated broad-range protective innate immunity response to pathogen invasion, and that this mechanism is effective also against HIV-1. We performed structural analyses and evaluated the anti-HIV-1 activity for four DING protein homologues isolated from different species. Our data show that bacterial PfluDING, plant p38SJ (pDING), human phosphate binding protein (HPBP) and human extracellular DING from CD4 T cells (X-DING-CD4) share high degrees of structure and sequence homology. According to earlier reports on the anti-HIV-1 activity of pDING and X-DING-CD4, other members of this protein family from bacteria and humans were able to block transcription of HIV-1 and replication of virus in cell based assays. The efficacy studies for DING-mediated HIV-1 LTR and HIV-1 replication blocking activity showed that the LTR transcription inhibitory concentration 50 (IC50) values ranged from 0.052–0.449 ng/ml; and the HIV-1 replication IC50 values ranged from 0.075–0.311 ng/ml. Treatment of cells with DING protein alters the interaction between p65-NF-κB and HIV-1 LTR. Our data suggest that DING proteins may be part of an innate immunity defense against pathogen invasion; the conserved structure and activity makes them appealing candidates for development of a novel therapeutics targeting HIV-1 transcription.
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Affiliation(s)
- Rakhee Sachdeva
- Molecular Virology Division, St. Luke's-Roosevelt Institute for Health Sciences/Columbia University, New York, New York, United States of America
| | - Nune Darbinian
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Kamel Khalili
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Shohreh Amini
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Daniel Gonzalez
- Enzymologie Structurale, Université de la Méditerranée, Faculté de Médecine, Marseille, France
| | - Ahmed Djeghader
- Enzymologie Structurale, Université de la Méditerranée, Faculté de Médecine, Marseille, France
| | - Eric Chabriére
- Enzymologie Structurale, Université de la Méditerranée, Faculté de Médecine, Marseille, France
| | - Andrew Suh
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Ken Scott
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Malgorzata Simm
- Molecular Virology Division, St. Luke's-Roosevelt Institute for Health Sciences/Columbia University, New York, New York, United States of America
- * E-mail:
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Bookland MJ, Darbinian N, Weaver M, Amini S, Khalili K. Growth inhibition of malignant glioblastoma by DING protein. J Neurooncol 2011; 107:247-56. [PMID: 22052333 DOI: 10.1007/s11060-011-0743-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 10/20/2011] [Indexed: 11/25/2022]
Abstract
Malignant gliomas are a highly aggressive type of brain tumor with extremely poor prognosis. These tumors are highly invasive and are often surgically incurable and resistant to chemotherapeutics and radiotherapy. Thus, novel therapies that target pathways involved in growth and survival of the tumor cells are required for the treatment of this class of brain tumors. Previous studies revealed that epidermal growth factor receptor and extracellular-signal-regulated kinases (ERKs), which are involved in the induction of cell proliferation, are activated in the most aggressive type of glioma, i.e. glioblastoma multiforme (GBM). In fact, GBMs with increased levels of ERK activity exhibit a more aggressive phenotype than the others with moderate ERK activity, pointing to the importance of ERK and its kinase activity in the development and progression of these tumors. In this study, we have evaluated the effect of p38SJ, a novel member of the DING family of proteins, derived from Hypericum perforatum calluses, on the growth of malignant glioma cell lines, T98G and U-87MG by focusing on cell cycle and signaling pathways controlled by phosphorylation of various regulatory proteins including ERK. p38SJ, which exhibits profound phosphatase activity, shows the capacity to affect the phosphorylation status of several important kinases modulating signaling pathways, and cell growth and proliferation. Our results demonstrate that p38SJ reduces glioma cell viability and arrests cell cycle progression at G0/G1. The observed growth inhibitory effect of p38SJ is likely mediated by the downregulation of several cell cycle gatekeeper proteins, including cyclin E, Cdc2, and E2F-1. These results suggest that p38SJ may serve as a potential candidate for development of a therapeutic agent for the direct treatment of malignant gliomas and/or as a potential radiosensitizer.
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Affiliation(s)
- Markus J Bookland
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Room 741 MERB, 3500 North Broad St., Philadelphia, PA 19140, USA
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Hendriks M, Lambalk C, Helder M, de Koning J. Purification of a candidate gonadotrophin surge-inhibiting/attenuating factor (GnSIF/AF) showing MAPK as a possible target. Mol Reprod Dev 2011; 78:292-304. [DOI: 10.1002/mrd.21305] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 02/22/2011] [Indexed: 11/05/2022]
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Collombet JM, Elias M, Gotthard G, Four E, Renault F, Joffre A, Baubichon D, Rochu D, Chabrière E. Eukaryotic DING proteins are endogenous: an immunohistological study in mouse tissues. PLoS One 2010; 5:e9099. [PMID: 20161715 PMCID: PMC2817009 DOI: 10.1371/journal.pone.0009099] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 01/20/2010] [Indexed: 11/19/2022] Open
Abstract
Background DING proteins encompass an intriguing protein family first characterized by their conserved N-terminal sequences. Some of these proteins seem to have key roles in various human diseases, e.g., rheumatoid arthritis, atherosclerosis, HIV suppression. Although this protein family seems to be ubiquitous in eukaryotes, their genes are consistently lacking from genomic databases. Such a lack has considerably hampered functional studies and has fostered therefore the hypothesis that DING proteins isolated from eukaryotes were in fact prokaryotic contaminants. Principal Findings In the framework of our study, we have performed a comprehensive immunological detection of DING proteins in mice. We demonstrate that DING proteins are present in all tissues tested as isoforms of various molecular weights (MWs). Their intracellular localization is tissue-dependant, being exclusively nuclear in neurons, but cytoplasmic and nuclear in other tissues. We also provide evidence that germ-free mouse plasma contains as much DING protein as wild-type. Significance Hence, data herein provide a valuable basis for future investigations aimed at eukaryotic DING proteins, revealing that these proteins seem ubiquitous in mouse tissue. Our results strongly suggest that mouse DING proteins are endogenous. Moreover, the determination in this study of the precise cellular localization of DING proteins constitute a precious evidence to understand their molecular involvements in their related human diseases.
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Affiliation(s)
- Jean-Marc Collombet
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Mikael Elias
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique-Aix Marseille Université, Marseille, France
| | - Guillaume Gotthard
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique-Aix Marseille Université, Marseille, France
| | - Elise Four
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Frédérique Renault
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Aurélie Joffre
- Service de Microscopie et d'Imagerie Médicale, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Dominique Baubichon
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Daniel Rochu
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, Centre de Recherche du Service de Santé des Armées, La Tronche, France
| | - Eric Chabrière
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique-Aix Marseille Université, Marseille, France
- * E-mail:
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Amini S, Merabova N, Khalili K, Darbinian N. p38SJ, a novel DINGG protein protects neuronal cells from alcohol induced injury and death. J Cell Physiol 2009; 221:499-504. [PMID: 19739100 DOI: 10.1002/jcp.21903] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ethanol induces neuronal cell injury and death by dysregulating several signaling events that are controlled, in part, by activation of MAPK/ERK1/2 and/or inactivation of its corresponding phosphatase, PP1. Recently, we have purified a novel protein of 38 kDa in size, p38SJ, from a callus culture of Hypericum perforatum, which belongs to an emerging DINGG family of proteins with phosphate binding activity. Here, we show that treatment of neuronal cells with p38SJ protects cells against injury induced by exposure to ethanol. Furthermore, pre-treatment of neuronal cells with p38SJ diminishes the level of the pro-apoptotic protein Bax and some events associated with apoptosis such as caspase 3 cleavage. In addition, by inducing stress, alcohol can elevate production of reactive oxygen species (ROS) that leads to a decrease in the activity of superoxide dismutase (SOD). Our results showed that p38SJ restores the activity of SOD in the ethanol treated neuronal cells. These observations provide a novel biological tool for developing new approaches for preventing neuronal cell death induced by ethanol and possibly treatment of neurological disorders associated with alcohol abuse.
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Affiliation(s)
- Shohreh Amini
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania 19122, USA.
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12
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Darbinian N, Czernik M, Darbinyan A, Elias M, Chabriere E, Bonasu S, Khalili K, Amini S. Evidence for phosphatase activity of p27SJ and its impact on the cell cycle. J Cell Biochem 2009; 107:400-7. [PMID: 19343785 DOI: 10.1002/jcb.22135] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
p27SJ, a novel protein isolated from St John's wort (Hypericum perforatum), belongs to an emerging family of DING proteins that are related to a prokaryotic phosphate-binding protein superfamily. Here we demonstrate that p27SJ exhibits phosphatase activity and that its expression in cells decreases the level of phosphorylated Erk1/2, a key protein of several signaling pathways. Treatment of p27SJ-expressing cells with phosphatase inhibitors including okadaic acid, maintained Erk1/2 in its phosphorylated form, suggesting that dephosphorylation of Erk1/2 is mediated by p27SJ. Further, expression of p27SJ affects Erk1/2 downstream regulatory targets such as STAT3 and CREB. Moreover, the level of expression of cyclin A that associates with active ERK1/2 and is regulated by CREB, was modestly reduced in p27SJ-expressing cells. Accordingly, results from in vitro kinase assays revealed a noticeable decrease in the activity of cyclin A in cells expressing p27SJ. Cell cycle analysis demonstrated dysregulation at S and G2/M phases in cells expressing p27SJ, supporting the notion that a decline in cyclin A activity by p27SJ has a biological impact on cell growth. These observations provide evidence that p27SJ alters the state of Erk1/2 phosphorylation, and impacts several biological events associated with cell growth and function.
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Affiliation(s)
- Nune Darbinian
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania 19122, USA
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13
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Lesner A, Shilpi R, Ivanova A, Gawinowicz MA, Lesniak J, Nikolov D, Simm M. Identification of X-DING-CD4, a new member of human DING protein family that is secreted by HIV-1 resistant CD4(+) T cells and has anti-viral activity. Biochem Biophys Res Commun 2009; 389:284-9. [PMID: 19720052 DOI: 10.1016/j.bbrc.2009.08.140] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 08/25/2009] [Indexed: 10/20/2022]
Abstract
We reported previously the anti-viral activity named HRF (HIV-1 Resistance Factor) secreted by HIV-1 resistant cells. This work describes the identification of HRF from cell culture supernatant of HRF-producing cells (HRF(+) cells). Employing the proteomics and cell based activity assay we recovered ten peptides sharing 80-93% sequence homology with other eukaryotic DING proteins; discrete amino acid characteristics found in our material suggested that HRF is a new member of DING proteins family and consequently we designated it as X-DING-CD4 (extracellular DING from CD4(+) T cells). The presence of X-DING-CD4 in the extracellular compartment of HRF(+) but not control HRF(-) cells was confirmed by specific anti-X-DING-CD4 antibody. Similar as the un-fractionated HRF(+) cell culture supernatant, the purified X-DING-CD4 blocked transcription of HIV-1 LTR-promoted expression of luciferase gene and replication of HIV-1 in MAGI cells. The X-DING-CD4 -mediated anti-viral activity in MAGI cells could be blocked by specific antibody.
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Affiliation(s)
- Adam Lesner
- Protein Chemistry Laboratory, St. Luke's/Roosevelt Institute for Health Sciences, Columbia University, New York, NY 10019, USA
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14
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Liebschner D, Elias M, Moniot S, Fournier B, Scott K, Jelsch C, Guillot B, Lecomte C, Chabrière E. Elucidation of the phosphate binding mode of DING proteins revealed by subangstrom X-ray crystallography. J Am Chem Soc 2009; 131:7879-86. [PMID: 19445459 DOI: 10.1021/ja901900y] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PfluDING is a bacterial protein isolated from Pseudomonas fluorescens that belongs to the DING protein family, which is ubiquitous in eukaryotes and extends to prokaryotes. DING proteins and PfluDING have very similar topologies to phosphate Solute Binding Proteins (SBPs). The three-dimensional structure of PfluDING was obtained at subangstrom resolution (0.88 and 0.98 A) at two different pH's (4.5 and 8.5), allowing us to discuss the hydrogen bond network that sequesters the phosphate ion in the binding site. From this high resolution data, we experimentally elucidated the molecular basis of phosphate binding in phosphate SBPs. The phosphate ion is tightly bound to the protein via 12 hydrogen bonds between phosphate oxygen atoms and OH and NH groups of the protein. The proton on one oxygen atom of the phosphate dianion forms a 2.5 A low barrier hydrogen bond with an aspartate, with the energy released by forming this strong bond ensuring the specificity for the dianion even at pH 4.5. In particular, contrary to previous theories on phosphate SBPs, accurate electrostatic potential calculations show that the binding cleft is positively charged. PfluDING structures reveal that only dibasic phosphate binds to the protein at both acidic and basic phosphate, suggesting that the protein binding site environment stabilizes the HPO(4)(2-) form of phosphate.
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Affiliation(s)
- Dorothee Liebschner
- Cristallographie Resonnance Magnetique et Modelisations, CNRS UMR 7036 Nancy-Universite, 54506 Vandoeuvre-les-Nancy, France
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15
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Berna A, Bernier F, Chabrière E, Elias M, Scott K, Suh A. For whom the bell tolls? DING proteins in health and disease. Cell Mol Life Sci 2009; 66:2205-18. [PMID: 19290474 PMCID: PMC11115607 DOI: 10.1007/s00018-009-0006-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 02/09/2009] [Accepted: 02/13/2009] [Indexed: 11/29/2022]
Abstract
DING proteins, identified mainly by their eponymous N-terminal sequences, are ubiquitous in living organisms. Amongst bacteria, they are common in pseudomonads, and have been characterised with respect to genetics and structure. They form part of a wider family of phosphate-binding proteins, with emerging roles in phosphate acquisition and pathogenicity. Many DING proteins have been isolated in eukaryotes, in which they have been associated with very diverse biological activities, often in the context of possible signalling roles. Disease states in which DING proteins have been implicated include rheumatoid arthritis, lithiasis, atherosclerosis, some tumours and tumour-associated cachexia, and bacterial and viral adherence. Complete genetic and structural characterisation of eukaryotic DING genes and proteins is still lacking, though the phosphate-binding site seems to be conserved. Whether as bacterial proteins related to bacterial pathogenicity, or as eukaryotic components of biochemical signalling systems, DING proteins require further study.
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Affiliation(s)
- Anne Berna
- Institut de Biologie Moléculaire des Plantes du CNRS, Institut de Botanique, Université de Strasbourg, 28 rue Goethe, Strasbourg Cedex, France.
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16
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Berna A, Scott K, Chabrière E, Bernier F. The DING family of proteins: ubiquitous in eukaryotes, but where are the genes? Bioessays 2009; 31:570-80. [PMID: 19360767 DOI: 10.1002/bies.200800174] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PstS and DING proteins are members of a superfamily of secreted, high-affinity phosphate-binding proteins. Whereas microbial PstS have a well-defined role in phosphate ABC transporters, the physiological function of DING proteins, named after their DINGGG N termini, still needs to be determined. PstS and DING proteins co-exist in some Pseudomonas strains, to which they confer a highly adhesive and virulent phenotype. More than 30 DING proteins have now been purified, mostly from eukaryotes. They are often associated with infections or with dysregulation of cell proliferation. Consequently, eukaryotic DING proteins could also be involved in cell-cell communication or adherence. The ubiquitous presence in eukaryotes of proteins structurally and functionally related to bacterial virulence factors is intriguing, as is the absence of eukaryotic genes encoding DING proteins in databases. DING proteins in eukaryotes could originate from unidentified commensal or symbiotic bacteria and could contribute to essential functions. Alternatively, DING proteins could be encoded by eukaryotic genes sharing special features that prevent their cloning. Both hypotheses are discussed.
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Affiliation(s)
- Anne Berna
- Institut de Biologie Moléculaire des Plantes du CNRS, Université Louis Pasteur, Institut de Botanique, Strasbourg Cedex, France
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17
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Perera T, Berna A, Scott K, Lemaitre-Guillier C, Bernier F. Proteins related to St. John's Wort p27SJ, a suppressor of HIV-1 expression, are ubiquitous in plants. PHYTOCHEMISTRY 2008; 69:865-72. [PMID: 18006028 DOI: 10.1016/j.phytochem.2007.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Revised: 09/28/2007] [Accepted: 10/01/2007] [Indexed: 05/25/2023]
Abstract
Proteins belonging to the family of DING proteins are ubiquitous in animals and several of them are associated with various diseases. Their presence in a few plant species has previously been reported and the St John's Wort DING protein was recently described as an inhibitor of HIV replication and transcription. However, data about DING protein occurrence in plants and their biochemical properties remain almost nonexistent. We describe methods for the purification of DING proteins from plants that may have general applicability since they are not dependent upon specific affinity ligands, contrary to previously described protocols. Cibacron Blue chromatography, sometimes preceded by an ion-exchange chromatographic step, is suitable for most plant extracts. DING proteins were purified from various species and cell types and their identity was confirmed immunologically and, in some cases, by N-terminal sequence analysis, indicating that they are ubiquitous in the plant kingdom. They are associated with the cell wall and sometimes secreted in the medium for in vitro grown cells. High-molecular-weight DING precursors were often observed. Internal peptides were also sequenced, as a prelude to gene cloning experiments.
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Affiliation(s)
- Tekla Perera
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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18
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Creation of a bi-directional protein transduction system for suppression of HIV-1 expression by p27SJ. Antiviral Res 2007; 79:136-41. [PMID: 18378326 DOI: 10.1016/j.antiviral.2007.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Revised: 11/16/2007] [Accepted: 11/19/2007] [Indexed: 11/24/2022]
Abstract
p27SJ is a novel protein from a callus culture of St. John's wort that modulates transcription of the HIV-1 promoter in several mammalian cells [Darbinian-Sarkissian, N., Darbinyan, A., Otte, J., Radhakrishnan, S., Sawaya, B.E., Arzumanyan, A., Chipitsyna, G., Popov, Y., Rappaport, J., Amini, S., Khalili, K., 2006. p27(SJ), a novel protein from St. John's wort, that suppresses expression of HIV-1 genome. Gene Ther. 13, 288-295]. Here, we armed p27SJ with signals from Ig-kappa light chain that allow its efficient excretion from the cells, and from HIV-1 Tat that facilitates its uptake by other cells for its utilization by a protein transduction method. We demonstrate that treatment of cells containing the HIV-1 LTR with conditioned media from cells expressing the armed p27SJ ((exc)p27SJ(upt)) results in suppression of the viral activation by the C/EBPbeta transcription factor. Once imported into the cells, (exc)p27SJ(upt) impacts the nuclear localization of C/EBPbeta and by retaining the protein in the cytoplasm affects its DNA binding and hence transcriptional activity. The armed p27SJ also inhibits Tat-induced activation of the LTR and decreases the level of viral replication in promonocytic cells including U-937 and T-lymphocytic cells. Our observations introduce a new bi-directional protein transduction system with a broad spectrum of applications for manufacturing therapeutic peptides by a specific group of cells called donor, and delivery to the target cells named recipient. Furthermore, our results support the utility of soluble p27SJ in suppressing transcription and replication of HIV-1 by interfering with the function of cellular proteins such as C/EBPbeta and viral activators including Tat.
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19
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Zhang XX, Scott K, Meffin R, Rainey PB. Genetic characterization of psp encoding the DING protein in Pseudomonas fluorescens SBW25. BMC Microbiol 2007; 7:114. [PMID: 18088430 PMCID: PMC2225411 DOI: 10.1186/1471-2180-7-114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 12/18/2007] [Indexed: 11/13/2022] Open
Abstract
Background DING proteins constitute a conserved and broadly distributed set of proteins found in bacteria, fungi, plants and animals (including humans). Characterization of DING proteins from animal and plant tissues indicated ligand-binding ability suggesting a role for DING proteins in cell signaling and biomineralization. Surprisingly, the genes encoding DING proteins in eukaryotes have not been identified in the eukaryotic genome or EST databases. Recent discovery of a DING homologue (named Psp here) in the genome of Pseudomonas fluorescens SBW25 provided a unique opportunity to investigate the physiological roles of DING proteins. P. fluorescens SBW25 is a model bacterium that can efficiently colonize plant surfaces and enhance plant health. In this report we genetically characterize Psp with a focus on conditions under which psp is expressed and the protein exported. Results Psp is closely related to the periplasmic Pi binding component of the ABC-type phosphate transporter system (Pst). psp is flanked by a gene cluster predicted to function as a type II protein secretion system (Hxc). Deletion analysis combined with chromosomally integrated 'lacZ fusions showed that both psp and pstC are induced by Pi limitation and that pstC is required for competitive growth of the bacterium in Pi limited medium. hxcR is not regulated by Pi limitation. Psp was detected (using anti-DING serum) in the supernatant of wild-type culture but was greatly reduced in the supernatant of an isogenic strain carrying an hxcR mutation (ΔhxcR). A promoter fusion between hxcR and a promoterless copy of a gene ('dapB) essential for growth in the plant environment showed that expression of hxcR is elevated during colonization of sugar beet seedlings. A similar analysis of psp showed that it is not induced in the plant environment. Conclusion Psp gene is expressed under conditions of Pi limitation. It is an exoprotein secreted mainly via the Hxc type II secretion system, whose expression is elevated on plant surfaces. We propose that Psp is involved in extracellular scavenging of phosphates, which are subsequently taken up by the cell-bound Pst transport system.
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Affiliation(s)
- Xue-Xian Zhang
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
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20
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Diemer H, Elias M, Renault F, Rochu D, Contreras-Martel C, Schaeffer C, Van Dorsselaer A, Chabriere E. Tandem use of X-ray crystallography and mass spectrometry to obtain ab initio the complete and exact amino acids sequence of HPBP, a human 38-kDa apolipoprotein. Proteins 2007; 71:1708-20. [DOI: 10.1002/prot.21866] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Moniot S, Elias M, Kim D, Scott K, Chabriere E. Crystallization, diffraction data collection and preliminary crystallographic analysis of DING protein from Pseudomonas fluorescens. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:590-2. [PMID: 17620718 PMCID: PMC2335140 DOI: 10.1107/s1744309107028102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 06/07/2007] [Indexed: 11/11/2022]
Abstract
PfluDING is a phosphate-binding protein expressed in Pseudomonas fluorescens. This protein is clearly distinct from the bacterial ABC transporter soluble phosphate-binding protein PstS and is more homologous to eukaryotic DING proteins. Interestingly, bacterial DING proteins have only been detected in certain Pseudomonas species. Although DING proteins seem to be ubiquitous in eukaryotes, they are systematically absent from eukaryotic genomic databases and thus are still quite mysterious and poorly characterized. PfluDING displays mitogenic activity towards human cells and binds various ligands such as inorganic phosphate, pyrophosphate, nucleotide triphosphates and cotinine. Here, the crystallization of PfluDING is reported in a monoclinic space group (P2(1)), with typical unit-cell parameters a = 36.7, b = 123.7, c = 40.8 A, alpha = 90, beta = 116.7, gamma = 90 degrees. Preliminary crystallographic analysis reveals good diffraction quality for these crystals and a 1.43 A resolution data set has been collected.
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Affiliation(s)
- Sebastien Moniot
- Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS–Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy, France
| | - Mikael Elias
- Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS–Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy, France
| | - Donghyo Kim
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Ken Scott
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Eric Chabriere
- Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS–Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy, France
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22
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Ahn S, Moniot S, Elias M, Chabriere E, Kim D, Scott K. Structure-function relationships in a bacterial DING protein. FEBS Lett 2007; 581:3455-60. [PMID: 17612529 DOI: 10.1016/j.febslet.2007.06.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 06/20/2007] [Accepted: 06/20/2007] [Indexed: 10/23/2022]
Abstract
A recombinant DING protein from Pseudomonas fluorescens has been previously shown to have a phosphate-binding site, and to be mitogenic for human cells. Here we report the three-dimensional structure of the protein, confirming a close similarity to the "Venus flytrap" structure seen in other human and bacterial phosphate-binding proteins. Site-directed mutagenesis confirms the role of a key residue involved in phosphate binding, and that the mitogenic activity is not dependent on this property. Deletion of one of the two hinged domains that constitute the Venus flytrap also eliminates phosphate binding whilst enhancing mitogenic activity.
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Affiliation(s)
- Soyeon Ahn
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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23
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Pantazaki AA, Tsolkas GP, Kyriakidis DA. A DING phosphatase in Thermus thermophilus. Amino Acids 2007; 34:437-48. [PMID: 17497305 DOI: 10.1007/s00726-007-0549-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2007] [Accepted: 03/21/2007] [Indexed: 10/23/2022]
Abstract
Phosphate transport in bacteria occurs via a phosphate specific transporter system (PSTS) that belongs to the ABC family of transporters, a multisubunit system, containing an alkaline phosphatase. DING proteins were characterized due to the N-terminal amino acid sequence DINGG GATL, which is highly conserved in animal and plant isolates, but more variable in microbes. Most prokaryotic homologues of the DING proteins often have some structural homology to phosphatases or periplasmic phosphate-binding proteins. In E. coli, the product of the inducible gene DinG, possesses ATP hydrolyzing helicase enzymic activity. An alkaline phosphorolytic enzyme of the PSTS system was purified to homogeneity from the thermophilic bacterium Thermus thermophilus. N-terminal sequence analysis of this protein revealed the same high degree of similarity to DING proteins especially to the human synovial stimulatory protein P205, the steroidogenesis-inducing protein and to the phosphate ABC transporter, periplasmic phosphate-binding protein, putative (P. fluorescens Pf-5). The enzyme had a molecular mass of 40 kDa on SDS/PAGE, exhibiting optimal phosphatase activity at pH 12.3 and 70 degrees C. The enzyme possessed characteristics of a DING protein, such as ATPase, ds endonuclease and 3' phosphodiesterase (3'-exonuclease) activities and binding to linear dsDNA, displaying helicase activity on supercoiled DNA. Purification and biochemical characterization of a T. thermophilus DING protein was achieved. The biochemical properties, N-terminal sequence similarities of this protein implied that the enzyme belongs to the PSTS family and might be involved in the DNA repair mechanism of this microorganism.
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Affiliation(s)
- A A Pantazaki
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, Greece.
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24
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Morales R, Berna A, Carpentier P, Contreras-Martel C, Renault F, Nicodeme M, Chesne-Seck ML, Bernier F, Dupuy J, Schaeffer C, Diemer H, Van-Dorsselaer A, Fontecilla-Camps JC, Masson P, Rochu D, Chabrière E. Découverte et structure cristallographique d’une apolipoprotéine humaine. ANNALES PHARMACEUTIQUES FRANÇAISES 2007; 65:98-107. [PMID: 17404543 DOI: 10.1016/s0003-4509(07)90023-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report the serendipitous discovery of a human plasma phosphate binding protein (HPBP). This 38 kDa protein is co-purified with paraoxonase (PON1). The association between HPON1 and HPBP is modulated by phosphate and calcium concentrations. The HPBP X-ray structure solved at 1.9 A resolution is similar to the prokaryotic phosphate solute-binding proteins (SBPs) associated with ATP binding cassette transmembrane transporters, though phosphate-SBPs have never been characterized or predicted from nucleic acid databases in eukaryotes. However, HPBP belongs to the family of ubiquitous eukaryotic proteins named DING, meaning that phosphate-SBPs are also widespread in eukaryotes. The absence of complete genes for eukaryotic phosphate-SBP from databases is intriguing, but the astonishing 90% sequence conservation of genes between evolutionary distant species suggests that the corresponding proteins play an important function. HPBP is the first identified transporter capable of binding phosphate ions in human plasma. Thus it is thought to become a new predictor and a potential therapeutic agent for phosphate-related diseases such as atherosclerosis.
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Affiliation(s)
- R Morales
- Laboratoire de cristallogenèse et cristallographie des Protéines, Institut de Biologie Structurale J.-P. Ebel, F 38027 Grenoble
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25
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Berna A, Bernier F, Chabrière E, Perera T, Scott K. DING proteins; novel members of a prokaryotic phosphate-binding protein superfamily which extends into the eukaryotic kingdom. Int J Biochem Cell Biol 2007; 40:170-5. [PMID: 17368078 DOI: 10.1016/j.biocel.2007.02.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2006] [Revised: 02/04/2007] [Accepted: 02/05/2007] [Indexed: 10/23/2022]
Abstract
PstS proteins are the cell-bound phosphate-binding elements of the ubiquitous bacterial ABC phosphate uptake mechanisms. Primary and tertiary structures, characteristic of pstS proteins, are conserved in proteins, which are expressed in secretory operons and induced by phosphate deprivation, in Pseudomonas species. There are two subsets of these proteins; AP proteins, which are alkaline phosphatases, and DING proteins, named for their N-terminal sequence, which are phosphate-binding proteins. Both form elements of a proposed phosphate-scavenging system in pseudomonads. DING proteins have also been isolated from many eukaryotic sources, and are associated with both normal and pathological functions in mammals. Their phosphate-binding function suggests a role in biomineralization, but the ability to bind other ligands may be related to signal transduction in eukaryotes. Though it has been claimed that all such proteins may originate from pseudomonads, many eukaryotic DING proteins have unique features which are incompatible with a bacterial origin.
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Affiliation(s)
- Anne Berna
- Institut de Biologie Moléculaire des Plantes du C.N.R.S., Université Louis Pasteur, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France.
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26
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Morales R, Berna A, Carpentier P, Contreras-Martel C, Renault F, Nicodeme M, Chesne-Seck ML, Bernier F, Dupuy J, Schaeffer C, Diemer H, Van-Dorsselaer A, Fontecilla-Camps JC, Masson P, Rochu D, Chabriere E. Serendipitous discovery and X-ray structure of a human phosphate binding apolipoprotein. Structure 2006; 14:601-9. [PMID: 16531243 DOI: 10.1016/j.str.2005.12.012] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Revised: 11/09/2005] [Accepted: 12/20/2005] [Indexed: 11/23/2022]
Abstract
We report the serendipitous discovery of a human plasma phosphate binding protein (HPBP). This 38 kDa protein is copurified with the enzyme paraoxonase. Its X-ray structure is similar to the prokaryotic phosphate solute binding proteins (SBPs) associated with ATP binding cassette transmembrane transporters, though phosphate-SBPs have never been characterized or predicted from nucleic acid databases in eukaryotes. However, HPBP belongs to the family of ubiquitous eukaryotic proteins named DING, meaning that phosphate-SBPs are also widespread in eukaryotes. The systematic absence of complete genes for eukaryotic phosphate-SBP from databases is intriguing, but the astonishing 90% sequence conservation between genes belonging to evolutionary distant species suggests that the corresponding proteins play an important function. HPBP is the only known transporter capable of binding phosphate ions in human plasma and may become a new predictor of or a potential therapeutic agent for phosphate-related diseases such as atherosclerosis.
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Affiliation(s)
- Renaud Morales
- Laboratoire de Cristallogenèse et Cristallographie des Protéines, Institut de Biologie Structurale JP EBEL, 38027 Grenoble, France
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27
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Scott K, Wu L. Functional properties of a recombinant bacterial DING protein: comparison with a homologous human protein. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1744:234-44. [PMID: 15950753 DOI: 10.1016/j.bbamcr.2005.02.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2004] [Revised: 01/28/2005] [Accepted: 02/15/2005] [Indexed: 11/20/2022]
Abstract
DING proteins are highly-conserved proteins with poorly-defined cell-signalling roles in mammals. Conserved homologues are also commonplace in plants, though not as yet functionally characterized. Poor availability of the proteins, and a lack of genetic structure, hamper progress in elucidating the roles of these eukaryotic DING proteins, but highly-homologous hypothetical DING proteins have recently been identified in Pseudomonas genomes. We have cloned and expressed a DING protein from P. fluorescens SWB25 in Escherichia coli. The recombinant protein, and its natural human homologue, act as phosphate-binding proteins, as predicted by structural homologies with other bacterial proteins. The recombinant protein also displays other functional similarities with mammalian DING proteins, in that, like the human version, it acts as a mitogen for cultured human cells, and can bind cotinine, known to be a binding ligand for a rat neuronal DING protein.
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Affiliation(s)
- Ken Scott
- School of Biological Sciences, University of Auckland, New Zealand.
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28
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Wang Z, Hsieh TC, Zhang Z, Ma Y, Wu JM. Identification and purification of resveratrol targeting proteins using immobilized resveratrol affinity chromatography. Biochem Biophys Res Commun 2004; 323:743-9. [PMID: 15381063 PMCID: PMC3641935 DOI: 10.1016/j.bbrc.2004.08.174] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2004] [Indexed: 11/24/2022]
Abstract
The phytochemical resveratrol (trans-3,4',5-trihydroxystilbene) is a naturally occurring polyphenol with a plethora of health-beneficial properties, including a preventive role in cancer. We surmise that resveratrol may exert its diverse biological effects by interacting with specific target proteins, denoted RTPs. To test this possibility, resveratrol was immobilized on epoxy-activated agarose forming a resveratrol affinity column (RAC), which was used to detect and isolate RTPs. Distinct RTPs can be resolved on RAC by fractionation with increasing NaCl, followed by 1mM ATP, and finally, with 1-2mM resveratrol. A 22-kDa polypeptide, RTP-22, eluted with resveratrol was identified by MALDI-TOF MS and cloning/expression in Escherichia coli, as dihydronicotinamide riboside quinone reductase 2 (NQO2). The utility of RAC was additionally explored with extracts derived from different staging prostate cancer cells. NQO2 was most abundant in CWR22Rv1, a model for prostate cancer transition from androgen-dependent to the hormone-refractory state, but was marginally expressed in JCA-1 cells as representing more advanced stage prostate cancer. These results provide evidence for the existence of distinctive RTPs in mammalian cells and that RAC is a facile approach to identify and purify RTPs.
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Affiliation(s)
- Zhirong Wang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Tze-chen Hsieh
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
- Brander Cancer Research Institute, New York Medical College, Valhalla, NY 10595, USA
| | - Zhongtao Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Yuliang Ma
- Proteomics Facility, The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Joseph M. Wu
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
- Brander Cancer Research Institute, New York Medical College, Valhalla, NY 10595, USA
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29
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Abstract
The weak estrogen-like properties of isoflavonoids were discovered over 50 y ago. In recent years, the overall effects of the isoflavones in soy on human health have been the subject of lively debate largely based on their presumed estrogenic properties. Missing from our knowledge base is the systematic identification of the cellular and biochemical targets of isoflavones and the mechanisms that they influence. Because of the benign effects of isoflavones on cellular integrity, a concentration of the isoflavones can be reached in cell culture models where almost any process can be modulated. Modern systems biology approaches and high dimensional analysis techniques offer new ways to better understand the function of how cells and integrated biological mechanisms respond to compounds such as isoflavones. Data from experiments using DNA microarray analysis for examining the effects of genistein in the developing rat uterus indicate that genistein alters the expression of 6-8 times as many genes as does a physiological estrogen such as 17 beta-estradiol. Although these new approaches are exciting, their incipient high dimensionality places considerable strain on the quality of experimental design and meaningful statistical interpretation of the resulting data. In another approach using affinity chromatography methods, DING, a novel genistein-binding protein of yet unknown function, was isolated from human breast cancer MCF-7 cells. Its function remains to be established.
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Affiliation(s)
- Stephen Barnes
- Department of Pharmacology & Toxicology, Center for Nutrient-Gene Interaction, University of Alabama at Birmingham, and Purdue University-University of Alabama at Birmingham Botanicals Center for Age-Related Disease, 35294, USA.
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Kumar V, Yu S, Farell G, Toback FG, Lieske JC. Renal epithelial cells constitutively produce a protein that blocks adhesion of crystals to their surface. Am J Physiol Renal Physiol 2004; 287:F373-83. [PMID: 15100100 DOI: 10.1152/ajprenal.00418.2003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Attachment of newly formed crystals to renal tubular epithelial cells appears to be a critical step in the development of kidney stones. The present study was undertaken to identify autocrine factors released from renal epithelial cells into the culture medium that inhibit adhesion of calcium oxalate crystals to the cell surface. A 39-kDa glycoprotein that is constitutively secreted by renal cells was purified by gel filtration chromatography. Amino acid microsequencing revealed that it is novel and not structurally related to known inhibitors of calcium oxalate crystallization. Hence, it was named crystal adhesion inhibitor, or CAI. Immunoreactive CAI was detected in diverse rat tissues, including kidney, heart, pancreas, liver, and testis. Immunohistochemistry revealed that CAI is present in the renal cell cytosol and is also on the plasma membrane. Importantly, CAI is present in normal human urine, from which it can be purified using calcium oxalate monohydrate crystal affinity chromatography. CAI could be an important defense against crystal attachment to tubular cells and the subsequent development of renal stones in vivo.
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Affiliation(s)
- Vivek Kumar
- Division of Nephrology, Department of Internal Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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