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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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Darbinian N, Darbinyan A, Merabova N, Gomberg R, Chabriere E, Simm M, Selzer ME, Amini S. DING Protein Inhibits Transcription of HIV-1 Gene through Suppression of Phosphorylation of NF-κB p65. ACTA ACUST UNITED AC 2020; 6. [PMID: 34307877 PMCID: PMC8296972 DOI: 10.16966/2380-5536.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Introduction: Novel plant DING proteins (full-length 38 kDa p38SJ, and 27 kDa p27SJ) exhibit phosphatase activity and modulate HIV-1 gene transcription. Previously, we demonstrated that DING regulates HIV-1 gene transcription by dephosphorylation and inactivation of CTD RNA polymerase II, the major elongating factor of HIV-1 Long Terminal Repeats (LTR). Because the transcription of HIV-1 is controlled by several viral and cellular factors, including p65/p50 subunits of NF-κB, we hypothesized that DING phosphatase can also affect the phosphorylation and activity of p65 NF-κB, in addition to C-terminal Domain (CTD) of RNA Polymerase II (RNAPII), to suppress HIV-1 gene transcription and inhibit HIV-1 infection. Methods: Here, we describe the inhibition of HIV-1 infection and the p65/p50 NF-κB phosphorylation by DING protein, analyzed by ELISA and northern-blot assays, western-blot assays, cell fractionation, and promoter-reporter assays in DING-expressing cells, using a pTet-on inducible system. Results: Results from HIV-1 infection assays demonstrate a strong inhibition of HIV-1 and HIV-LTR RNA expression by DING protein, determined by p24 ELISA and by northern blot assay. Results from the western blot assays and cell fractionation assays show that there is an increase in the level of hypo-phosphorylated form of p65 NF-κB in DING-expressing cells. Both fractions of p65/p50, nuclear or cytoplasmic, are affected by DING phosphatase, but more cytoplasmic accumulation of p65 NF-κB was found in the presence of DING, suggesting that subsequent activation and nuclear import of active NF-κB is affected by DING. The major portion of nuclear p65 was dephosphorylated in DING-expressing cells. The promoter-reporter assay demonstrated that DING-mediated dephosphorylation and dysregulation of NF-κB p65 lead to the suppression of its binding to HIV-1 LTR, and resulted in the inhibition of p65-mediated activation of LTR transcription. Mapping of the region within LTR that was affected by DING revealed that both, NF-κB and CTD RNA Polymerase II binding sites were important, and cooperativity of these cellular factors was diminished by DING. In addition, mapping of the region within DING-p38SJ that affected LTR transcription, revealed that phosphate-binding domain is essential for this inhibitory activity. Conclusion: We have demonstrated the effect of DING phosphatases on HIV-1 infection, phosphorylation of p65 NF-κB, and transcription of HIV-1 LTR. Our studies suggest that one possible mechanism by which DING can regulate the expression of HIV-1 LTR can be through dysregulation of the transcription factor NF-κB p65 by preventing its phosphorylation and translocation to the nucleus and binding to the HIV-1 LTR, an action that could contribute to the utility of DING p38SJ as an antiviral agent. Importantly, DING not only inhibits HIV-1 LTR gene transcription in the presence of increased p65 NF-κB, but also suppresses HIV-1 infection. DING protein improved inhibitory effects of the known anti-retroviral drugs, Tenofovir (TFV) and Emtricitabine (FTS) on HIV-1, since in the combination with these drugs; the suppression of HIV-1 by DNG was significantly higher when it was in combination with these drugs, compared to controls or cases without DING. Thus, our data support the use of neuroprotective DING proteins as novel therapeutic antiviral drugs that suppress HIV-1 LTR transcription by interfering with the function of NF-κB.
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Affiliation(s)
- Nune Darbinian
- Center for Neural Repair and Rehabilitation, Lewis Katz School of Medicine, Temple University, USA
| | - Armine Darbinyan
- Department of Pathology, Yale University School of Medicine, USA
| | - Nana Merabova
- Center for Neural Repair and Rehabilitation, Lewis Katz School of Medicine, Temple University, USA
| | - Rebeccah Gomberg
- Center for Neural Repair and Rehabilitation, Lewis Katz School of Medicine, Temple University, USA
| | - Erik Chabriere
- Aix-Marseille Université, Institut Universitaire de France, IHU Mediterranée Infection, France
| | - Malgorzata Simm
- University of Pikeville, Kentucky College of Osteopathic Medicine, USA
| | - Michael E Selzer
- Center for Neural Repair and Rehabilitation, Lewis Katz School of Medicine, Temple University, USA
| | - Shohreh Amini
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, USA
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Afroz M, Akter S, Ahmed A, Rouf R, Shilpi JA, Tiralongo E, Sarker SD, Göransson U, Uddin SJ. Ethnobotany and Antimicrobial Peptides From Plants of the Solanaceae Family: An Update and Future Prospects. Front Pharmacol 2020; 11:565. [PMID: 32477108 PMCID: PMC7232569 DOI: 10.3389/fphar.2020.00565] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/14/2020] [Indexed: 12/03/2022] Open
Abstract
The Solanaceae is an important plant family that has been playing an essential role in traditional medicine and human nutrition. Members of the Solanaceae are rich in bioactive metabolites and have been used by different tribes around the world for ages. Antimicrobial peptides (AMPs) from plants have drawn great interest in recent years and raised new hope for developing new antimicrobial agents for meeting the challenges of antibiotic resistance. This review aims to summarize the reported AMPs from plants of the Solanaceae with possible molecular mechanisms of action as well as to correlate their traditional uses with reported antimicrobial actions of the peptides. A systematic literature study was conducted using different databases until August 2019 based on the inclusion and exclusion criteria. According to literature, a variety of AMPs including defensins, protease inhibitor, lectins, thionin-like peptides, vicilin-like peptides, and snaking were isolated from plants of the Solanaceae and were involved in their defense mechanism. These peptides exhibited significant antibacterial, antifungal and antiviral activity against organisms for both plant and human host. Brugmansia, Capsicum, Datura, Nicotiana, Salpichora, Solanum, Petunia, and Withania are the most commonly studied genera for AMPs. Among these genera, Capsicum and the Solanum ranked top according to the total number of studies (35%–38% studies) for different AMPs. The mechanisms of action of the reported AMPs from Solanaceae was not any new rather similar to other reported AMPs including alteration of membrane potential and permeability, membrane pore formation, and cell aggregation. Whereas, induction of cell membrane permiabilization, inhibition of germination and alteration of hyphal growth were reported as mechanisms of antifungal activity. Plants of the Solanaceae have been used traditionally as antimicrobial, insecticidal, and antiinfectious agents, and as poisons. The reported AMPs from the Solanaceae are the products of chemical shields to protect plants from microorganisms and pests which unfold an obvious link with their traditional medicinal use. In summary, it is evident that AMPs from this family possess considerable antimicrobial activity against a wide range of bacterial and fungal pathogens and can be regarded as a potential source for lead molecules to develop new antimicrobial agents.
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Affiliation(s)
- Mohasana Afroz
- Pharmacy Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Sanzida Akter
- Pharmacy Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Asif Ahmed
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Razina Rouf
- Department of Pharmacy, Faculty of Life Science, Bangabandhu Sheikh Mujibur Rahman Science & Technology University, Gopalganj, Bangladesh
| | - Jamil A Shilpi
- Pharmacy Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Evelin Tiralongo
- School of Pharmacy and Pharmacology, Griffith University, Southport, QLD, Australia
| | - Satyajit D Sarker
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Ulf Göransson
- Biomedical Center, Division of Pharmacognosy, Uppsala University, Uppsala, Sweden.,Biomedical Center, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Shaikh Jamal Uddin
- Pharmacy Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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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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Madunić J, Matulić M, Friščić M, Pilepić KH. Evaluation of the cytotoxic activity of Hypericum spp. on human glioblastoma A1235 and breast cancer MDA MB-231 cells. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2016; 51:1157-1163. [PMID: 27458758 DOI: 10.1080/10934529.2016.1206385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cytotoxic activity of 16 Hypericum ethanolic extracts was evaluated by MTT assay on two human cancer cell lines: glioblastoma A1235 and breast cancer MDA MB-231. Morphology and the type of induced cell death were determined using light and fluorescence microscopy. The majority of Hypericum extracts had no significant cytotoxic effect on MDA MB-231 cells. Eight extracts exhibited mild cytotoxic effect on A1235 cells after 24 h incubation, ranging from 8.0% (H. patulum) to 21.7% (H. oblongifolium). After 72 h of treatment, the strongest inhibition of A1235 viability was observed for extracts of H. androsaemum (26.4-43.9%), H. balearicum (25.8-36.3%), H. delphicum (14.8-27.4%) and H. densiflorum (11.2-24.1%). Micro-scopic examination of cells showed apoptosis as the dominant type of cell death. Due to observed high viability of treated cells, we propose that cytotoxic effects of Hypericum extracts could be related to alternations/interruptions in the cell cycle.
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Affiliation(s)
- Josip Madunić
- a Department of Molecular Biology , Faculty of Science, University of Zagreb , Zagreb , Croatia
| | - Maja Matulić
- a Department of Molecular Biology , Faculty of Science, University of Zagreb , Zagreb , Croatia
| | - Maja Friščić
- b Department of Pharmaceutical Botany , Faculty of Pharmacy and Biochemistry, University of Zagreb , Zagreb , Croatia
| | - Kroata Hazler Pilepić
- b Department of Pharmaceutical Botany , Faculty of Pharmacy and Biochemistry, University of Zagreb , Zagreb , Croatia
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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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Darbinian N, Khalili K, Amini S. Neuroprotective activity of pDING in response to HIV-1 Tat. J Cell Physiol 2013; 229:153-61. [PMID: 23955241 DOI: 10.1002/jcp.24392] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 04/17/2013] [Indexed: 12/13/2022]
Abstract
Although neurons are not productively infected with HIV-1, neuronal injury and death are frequently seen in the brains of AIDS patients with neurological and neurocognitive disorders. Evidently, viral proteins including Tat and cellular inflammatory factors released by activated and/or infected microglia, macrophages, and astrocytes contribute to neuronal cell death. Several studies have demonstrated that HIV-1 associated neuronal cell injury is mediated by dysregulation of signaling pathways that are controlled, in part, by a class of serine/threonine kinases. In this study, we demonstrate that pDING, a novel plant-derived phosphate binding protein has the capacity to reduce the severity of injury and death caused by HIV-1 and its neurotoxic Tat protein. We demonstrate that pDING, also called p27SJ/p38SJ, protects cells from the loss of neuronal processes induced by Tat and promotes neuronal outgrowth after Tat-mediated injury. Further, expression of pDING prevents Tat-induced oxidative stress and mitochondrial permeability. With its profound phosphatase activity, pDING controls the activity of several kinases including MAPK, Cdk5, and their downstream target protein, MEF2, which is implicated in neuronal cell protection. Our results show that expression of pDING in neuronal cells diminishes the level of hyperphosphorylated forms of Cdk5 and MEF2 caused by Tat and the other neurotoxic agents that are secreted by the HIV-1 infected cells. These observations suggest that pDING, through its phosphatase activity, has the ability to manipulate the state of phosphorylation and activity of several factors involved in neuronal cell health in response to HIV-1.
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Affiliation(s)
- Nune Darbinian
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania
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Gai Z, Nakamura A, Tanaka Y, Hirano N, Tanaka I, Yao M. Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:854-858. [PMID: 24121327 PMCID: PMC3795543 DOI: 10.1107/s0909049513020694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/25/2013] [Indexed: 06/02/2023]
Abstract
After crystallization of a certain protein-RNA complex, well diffracting crystals were obtained. However, the asymmetric unit of the crystal was too small to locate any components. Mass spectrometry and X-ray crystal structure analysis showed that it was a member of the DING protein family (HPBP). Surprisingly, the structure of HPBP reported previously was also determined accidentally as a contaminant, suggesting that HPBP has a strong tendency to crystallize. Furthermore, DING proteins were reported to relate in disease. These observations suggest that DING has potential for application in a wide range of research fields. To enable further analyses, a system for preparation of HPBP was constructed. As HPBP was expressed in insoluble form in Escherichia coli, it was unfolded chemically and refolded. Finally, a very high yield preparation method was constructed, in which 43 mg of HPBP was obtained from 1 L of culture. Furthermore, to evaluate the validity of refolding, its crystal structure was determined at 1.03 Å resolution. The determined structure was identical to the native structure, in which two disulfide bonds were recovered correctly and a phosphate ion was captured. Based on these results, it was concluded that the refolded HPBP recovers its structure correctly.
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Affiliation(s)
- Zuoqi Gai
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Akiyoshi Nakamura
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Yoshikazu Tanaka
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nagisa Hirano
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Min Yao
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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Bernier F. DING proteins: numerous functions, elusive genes, a potential for health. Cell Mol Life Sci 2013; 70:3045-56. [PMID: 23743708 PMCID: PMC11113660 DOI: 10.1007/s00018-013-1377-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/24/2013] [Accepted: 05/16/2013] [Indexed: 10/26/2022]
Abstract
DING proteins, named after their conserved N-terminus, form an overlooked protein family whose members were generally discovered through serendipity. It is characterized by an unusually high sequence conservation, even between distantly related species, and by an outstanding diversity of activities and ligands. They all share a demonstrated capacity to bind phosphate with high affinity or at least a predicted phosphate-binding site. However, DING protein genes are conspicuously absent from databases. The many novel family members identified in recent years have confirmed that DING proteins are ubiquitous not only in animals and plants but probably also in prokaryotes. At the functional level, there is increasing evidence that they participate in many health-related processes such as cancers as well as bacterial (Pseudomonas) and viral (HIV) infections, by mechanisms that are now beginning to be understood. They thus represent potent targets for the development of novel therapeutic approaches, especially against HIV. The few genomic sequences that are now available are starting to give some clues on why DING protein genes and mRNAs are well conserved and difficult to clone. This could open a new era of research, of both fundamental and applied importance.
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Affiliation(s)
- François Bernier
- Institut de Biologie Moléculaire des Plantes du C.N.R.S., Université de Strasbourg, 28 rue Goethe, 67083, Strasbourg Cedex, France.
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