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Lin CH, Hsieh FC, Lai CC, Wang WC, Kuo CY, Yang CC, Hsu HW, Tam HMH, Yang CY, Wu HY. Identification of the protein coding capability of coronavirus defective viral genomes by mass spectrometry. Virol J 2023; 20:290. [PMID: 38062493 PMCID: PMC10704767 DOI: 10.1186/s12985-023-02252-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
During coronavirus infection, in addition to the well-known coronavirus genomes and subgenomic mRNAs, an abundance of defective viral genomes (DVGs) can also be synthesized. In this study, we aimed to examine whether DVGs can encode proteins in infected cells. Nanopore direct RNA sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis were employed. With the protein databases generated by nanopore direct RNA sequencing and the cell lysates derived from the RNA-protein pull-down assay, six DVG-encoded proteins were identified by LC-MS/MS based on the featured fusion peptides caused by recombination during DVG synthesis. The results suggest that the coronavirus DVGs have the capability to encode proteins. Consequently, future studies determining the biological function of DVG-encoded proteins may contribute to the understanding of their roles in coronavirus pathogenesis and the development of antiviral strategies.
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Grants
- 109-2313-B-005 -013 -MY3, 110-2327-B-005 -003 and 111-2327-B-005 -003 National Science and Technology Council
- 109-2313-B-005 -013 -MY3, 110-2327-B-005 -003 and 111-2327-B-005 -003 National Science and Technology Council
- 109-2313-B-005 -013 -MY3, 110-2327-B-005 -003 and 111-2327-B-005 -003 National Science and Technology Council
- 109-2313-B-005 -013 -MY3, 110-2327-B-005 -003 and 111-2327-B-005 -003 National Science and Technology Council
- 109-2313-B-005 -013 -MY3, 110-2327-B-005 -003 and 111-2327-B-005 -003 National Science and Technology Council
- 109-2313-B-005 -013 -MY3, 110-2327-B-005 -003 and 111-2327-B-005 -003 National Science and Technology Council
- 109-2313-B-005 -013 -MY3, 110-2327-B-005 -003 and 111-2327-B-005 -003 National Science and Technology Council
- 109-2313-B-005 -013 -MY3, 110-2327-B-005 -003 and 111-2327-B-005 -003 National Science and Technology Council
- 109-2313-B-005 -013 -MY3, 110-2327-B-005 -003 and 111-2327-B-005 -003 National Science and Technology Council
- 109-2313-B-005 -013 -MY3, 110-2327-B-005 -003 and 111-2327-B-005 -003 National Science and Technology Council
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Feng-Cheng Hsieh
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Wei-Chen Wang
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Cheng-Yu Kuo
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chun-Chun Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsuan-Wei Hsu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hon-Man-Herman Tam
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Cheng-Yao Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
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Structural Basis for the IgE-Binding Cross-Reacting Epitopic Peptides of Cup s 3, a PR-5 Thaumatin-like Protein Allergen from Common Cypress (Cupressus sempervirens) Pollen. ALLERGIES 2023. [DOI: 10.3390/allergies3010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The present work was aimed at identifying the IgE-binding epitopic regions on the surface of the Cup s 3 allergen from the common cypress Cupressus sempervirens, that are possibly involved in the IgE-binding cross-reactivity reported between Cupressaceae species. Three main IgE-binding epitopic regions were mapped on the molecular surface of Cup s 3, the PR-5 thaumatin-like allergen of common cypress Cupressus sempervirens. They correspond to exposed areas containing either electropositive (R, K) or electronegative (D, E) residues. A coalescence occurs between epitopes #1 and #2, that creates an extended IgE-binding regions on the surface of the allergen. Epitope #3 contains a putative N-glycosylation site which is actually glycosylated and could therefore comprise a glycotope. However, most of the allergenic potency of Cup s 3 depends on non-glycosylated epitopic peptides. The corresponding regions of thaumatin-like allergens from other closely related Cupressaceae (Cryptomeria, Juniperus, Thuja) exhibit a very similar conformation that should account for the IgE-binding cross-reactivity observed among the Cupressaceae allergens.
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Cavazza C, Collin-Faure V, Pérard J, Diemer H, Cianférani S, Rabilloud T, Darrouzet E. Proteomic analysis of Rhodospirillum rubrum after carbon monoxide exposure reveals an important effect on metallic cofactor biosynthesis. J Proteomics 2022; 250:104389. [PMID: 34601154 DOI: 10.1016/j.jprot.2021.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/14/2022]
Abstract
Some carboxydotrophs like Rhodospirillum rubrum are able to grow with CO as their sole source of energy using a Carbone monoxide dehydrogenase (CODH) and an Energy conserving hydrogenase (ECH) to perform anaerobically the so called water-gas shift reaction (WGSR) (CO + H2O → CO2 + H2). Several studies have focused at the biochemical and biophysical level on this enzymatic system and a few OMICS studies on CO metabolism. Knowing that CO is toxic in particular due to its binding to heme iron atoms, and is even considered as a potential antibacterial agent, we decided to use a proteomic approach in order to analyze R. rubrum adaptation in term of metabolism and management of the toxic effect. In particular, this study allowed highlighting a set of proteins likely implicated in ECH maturation, and important perturbations in term of cofactor biosynthesis, especially metallic cofactors. This shows that even this CO tolerant microorganism cannot avoid completely CO toxic effects associated with its interaction with metallic ions. SIGNIFICANCE: This proteomic study highlights the fact that even in a microorganism able to handle carbon monoxide and in some way detoxifying it via the intrinsic action of the carbon monoxide dehydrogenase (CODH), CO has important effects on metal homeostasis, metal cofactors and metalloproteins. These effects are direct or indirect via transcription regulation, and amplified by the high interdependency of cofactors biosynthesis.
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Affiliation(s)
- Christine Cavazza
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
| | | | - Julien Pérard
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 (CNRS-CEA), 67087 Strasbourg, France.
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 (CNRS-CEA), 67087 Strasbourg, France.
| | - Thierry Rabilloud
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
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IgE-Binding Epitopes of Pis v 1, Pis v 2 and Pis v 3, the Pistachio (Pistacia vera) Seed Allergens. ALLERGIES 2021. [DOI: 10.3390/allergies1010006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Sequential IgE-binding epitopes were identified on the molecular surface of the Pis v 1 (2S albumin), Pis v 2 (11S globulin/legumin) and Pis v 3 (7S globulin/vicilin)—major allergens from pistachio (Pistacia vera) seeds—using the Spot technique. They essentially consist of hydrophilic and electropositively charged residues well exposed on the surface of the allergens. Most of the epitopic regions identified on Pis v 1 and Pis v 3 do not coincide with the putative N-glycosylation sites and thus are not considered as glycotopes. Surface analysis of these epitopic regions indicates a high degree of conformational similarity with the previously identified epitopic regions of the corresponding allergens Ana o 1 (vicilin), Ana o 2 (legumin) and Ana o 3 (2S albumin) from the cashew (Anacardium occidentale) nut. These results offer a molecular basis for the IgE-binding cross-reactivity often observed between pistachio and cashew nut. They support the recommendation for prescribing pistachio avoidance in cashew allergic patients. Other conformational similarities were identified with the corresponding allergens Ses i 1 (2S albumin), Ses i 3 (vicilin) and Ses i 6 (legumin) from sesame (Sesamum indicum), and Jug r 1 (2S albumin), Jug r 2 (vicilin) and Jug r 4 (legumin) from walnut (Juglans regia). Conversely, conformation of most of the epitopic regions of the pistachio allergens often differs from that of epitopes occurring on the molecular surface of the corresponding Ara h 1 (vicilin), Ara h 2 (2S albumin) and Ara h 3 (legumin) allergens from peanut (Arachis hypogaea).
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Tan KY, Herr AE. Ferguson analysis of protein electromigration during single-cell electrophoresis in an open microfluidic device. Analyst 2020; 145:3732-3741. [PMID: 32347219 PMCID: PMC7336862 DOI: 10.1039/c9an02553g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In an open microfluidic device, we investigate protein polyacrylamide gel electrophoresis (PAGE) separation performance on single-cell lysate. Single-cell protein electrophoresis is performed in a thin layer of polyacrylamide (PA) gel into which microwells are molded. Individual cells are isolated in these open microwells, then lysed on-chip with a dual lysis and electrophoresis sodium dodecyl sulfate (SDS) buffer. We scrutinize the effect of sieving gel composition on electromigration of protein targets, using a wide range of cellular protein standards (36 kDa to 289 kDa). We find that as PA concentration increases, protein electromigration deviates from the empirical log-linear relationship predicted between migration distance and molecular mass. We perform Ferguson analysis to calculate retardation coefficients and free solution mobilities of nine cellular protein standards and observe that the largest-molecular-mass protein, mTOR (289 kDa), does not behave as predicted by established linear-fit models for SDS-denatured proteins, indicating that mTOR is beyond the linear range of this assay. Lastly, we performed in-gel immunoprobing on the single-cell electrophoretic separations and observed that smaller pore-size gels (higher gel concentration) reduce protein diffusion out of the gel, which does not notably impact the measured immunoprobed protein expression. Compared to larger pore-size gels, the smaller pore-size gels lead to higher local concentrations of the target protein in each protein band, resulting in an increase in the signal-to-noise ratio (SNR) for each protein. Understanding the separation and immunoprobing performance at different gel concentrations improves assay design and optimization for target proteins.
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Affiliation(s)
- Kristine Y Tan
- The UC Berkeley - UCSF Graduate Program in Bioengineering, 94720 Berkeley, USA.
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6
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Dalzon B, Bons J, Diemer H, Collin-Faure V, Marie-Desvergne C, Dubosson M, Cianferani S, Carapito C, Rabilloud T. A Proteomic View of Cellular Responses to Anticancer Quinoline-Copper Complexes. Proteomes 2019; 7:26. [PMID: 31238524 PMCID: PMC6630412 DOI: 10.3390/proteomes7020026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 02/07/2023] Open
Abstract
Metal-containing drugs have long been used in anticancer therapies. The mechansims of action of platinum-based drugs are now well-understood, which cannot be said of drugs containing other metals, such as gold or copper. To gain further insights into such mechanisms, we used a classical proteomic approach based on two-dimensional elelctrophoresis to investigate the mechanisms of action of a hydroxyquinoline-copper complex, which shows promising anticancer activities, using the leukemic cell line RAW264.7 as the biological target. Pathway analysis of the modulated proteins highlighted changes in the ubiquitin/proteasome pathway, the mitochondrion, the cell adhesion-cytoskeleton pathway, and carbon metabolism or oxido-reduction. In line with these prteomic-derived hypotheses, targeted validation experiments showed that the hydroxyquinoline-copper complex induces a massive reduction in free glutathione and a strong alteration in the actin cytoskeleton, suggesting a multi-target action of the hydroxyquinoline-copper complex on cancer cells.
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Affiliation(s)
- Bastien Dalzon
- Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, IRIG,CBM, F-38054 Grenoble, France.
| | - Joanna Bons
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France.
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France.
| | - Véronique Collin-Faure
- Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, IRIG,CBM, F-38054 Grenoble, France.
| | - Caroline Marie-Desvergne
- Nanosafety Platform, Medical Biology Laboratory (LBM), Univ. Grenoble-Alpes, CEA, 17 rue des Martyrs, F-38054 Grenoble, France.
| | - Muriel Dubosson
- Nanosafety Platform, Medical Biology Laboratory (LBM), Univ. Grenoble-Alpes, CEA, 17 rue des Martyrs, F-38054 Grenoble, France.
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France.
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France.
| | - Thierry Rabilloud
- Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, IRIG,CBM, F-38054 Grenoble, France.
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7
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A quantitative proteomic analysis of cofilin phosphorylation in myeloid cells and its modulation using the LIM kinase inhibitor Pyr1. PLoS One 2018; 13:e0208979. [PMID: 30550596 PMCID: PMC6294390 DOI: 10.1371/journal.pone.0208979] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/28/2018] [Indexed: 01/10/2023] Open
Abstract
LIM kinases are located at a strategic crossroad, downstream of several signaling pathways and upstream of effectors such as microtubules and the actin cytoskeleton. Cofilin is the only LIM kinases substrate that is well described to date, and its phosphorylation on serine 3 by LIM kinases controls cofilin actin-severing activity. Consequently, LIM kinases inhibition leads to actin cytoskeleton disorganization and blockade of cell motility, which makes this strategy attractive in anticancer treatments. LIMK has also been reported to be involved in pathways that are deregulated in hematologic malignancies, with little information regarding cofilin phosphorylation status. We have used proteomic approaches to investigate quantitatively and in detail the phosphorylation status of cofilin in myeloid tumor cell lines of murine and human origin. Our results show that under standard conditions, only a small fraction (10 to 30% depending on the cell line) of cofilin is phosphorylated (including serine 3 phosphorylation). In addition, after a pharmacological inhibition of LIM kinases, a residual cofilin phosphorylation is observed on serine 3. Interestingly, this 2D gel based proteomic study identified new phosphorylation sites on cofilin, such as threonine 63, tyrosine 82 and serine 108.
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Optimization of the cydex blue assay: A one-step colorimetric protein assay using cyclodextrins and compatible with detergents and reducers. PLoS One 2018; 13:e0195755. [PMID: 29641569 PMCID: PMC5895047 DOI: 10.1371/journal.pone.0195755] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/28/2018] [Indexed: 01/21/2023] Open
Abstract
Sodium dodecyl sulfate electrophoresis (SDS) is a protein separation technique widely used, for example, prior to immunoblotting. Samples are usually prepared in a buffer containing both high concentrations of reducers and high concentrations of SDS. This conjunction renders the samples incompatible with common protein assays. By chelating the SDS, cyclodextrins make the use of simple, dye-based colorimetric assays possible. In this paper, we describe the optimization of the assay, focussing on the cyclodextrin/SDS ratio and the use of commercial assay reagents. The adaptation of the assay to a microplate format and using other detergent-containing conventional extraction buffers is also described.
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Laputková G, Schwartzová V, Bánovčin J, Alexovič M, Sabo J. Salivary Protein Roles in Oral Health and as Predictors of Caries Risk. Open Life Sci 2018; 13:174-200. [PMID: 33817083 PMCID: PMC7874700 DOI: 10.1515/biol-2018-0023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/13/2018] [Indexed: 12/13/2022] Open
Abstract
This work describes the current state of research on the potential relationship between protein content in human saliva and dental caries, which remains among the most common oral diseases and causes irreversible damage in the oral cavity. An understanding the whole saliva proteome in the oral cavity could serve as a prerequisite to obtaining insight into the etiology of tooth decay at early stages. To date, however, there is no comprehensive evidence showing that salivary proteins could serve as potential indicators for the early diagnosis of the risk factors causing dental caries. Therefore, proteomics indicates the promising direction of future investigations of such factors, including diagnosis and thus prevention in dental therapy.
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Affiliation(s)
- Galina Laputková
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P. J. Šafárik in Košice, Trieda SNP 1, Košice, 040 11, Slovakia
| | - Vladimíra Schwartzová
- 1st Department of Stomatology, Faculty of Medicine, University of P. J. Šafárik in Košice, Trieda SNP 1, Košice, 040 11, Slovakia
| | - Juraj Bánovčin
- Department of Stomatology and Maxillofacial Surgery, Faculty of Medicine, University of P. J. Šafárik in Košice, Rastislavova 43, Košice, 041 90, Slovakia
| | - Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P. J. Šafárik in Košice, Trieda SNP 1, Košice, 040 11, Slovakia
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P. J. Šafárik in Košice, Trieda SNP 1, Košice, 040 11, Slovakia
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10
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Dalzon B, Aude-Garcia C, Collin-Faure V, Diemer H, Béal D, Dussert F, Fenel D, Schoehn G, Cianférani S, Carrière M, Rabilloud T. Differential proteomics highlights macrophage-specific responses to amorphous silica nanoparticles. NANOSCALE 2017; 9:9641-9658. [PMID: 28671223 DOI: 10.1039/c7nr02140b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The technological and economic benefits of engineered nanomaterials may be offset by their adverse effects on living organisms. One of the highly produced nanomaterials under such scrutiny is amorphous silica nanoparticles, which are known to have an appreciable, although reversible, inflammatory potential. This is due to their selective toxicity toward macrophages, and it is thus important to study the cellular responses of this cell type to silica nanoparticles to better understand the direct or indirect adverse effects of nanosilica. We have here studied the responses of the RAW264.7 murine macrophage cells and of the control MPC11 plasma cells to subtoxic concentrations of nanosilica, using a combination of proteomic and targeted approaches. This allowed us to document alterations in the cellular cytoskeleton, in the phagocytic capacity of the cells as well as their ability to respond to bacterial stimuli. More surprisingly, silica nanoparticles also induce a greater sensitivity of macrophages to DNA alkylating agents, such as styrene oxide, even at doses which do not induce any appreciable cell death.
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Affiliation(s)
- Bastien Dalzon
- Laboratory of Chemistry and Biology of Metals, UMR 5249, Univ. Grenoble Alpes, CNRS, CEA, Grenoble, France.
| | - Catherine Aude-Garcia
- Laboratory of Chemistry and Biology of Metals, UMR 5249, Univ. Grenoble Alpes, CNRS, CEA, Grenoble, France.
| | - Véronique Collin-Faure
- Laboratory of Chemistry and Biology of Metals, UMR 5249, Univ. Grenoble Alpes, CNRS, CEA, Grenoble, France.
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - David Béal
- Chimie Interface Biologie pour l'Environnement, la Santé et la Toxicologie (CIBEST), UMR 5819, Univ. Grenoble Alpes, CEA, CNRS, INAC, SyMMES, F-38000 Grenoble, France
| | - Fanny Dussert
- Chimie Interface Biologie pour l'Environnement, la Santé et la Toxicologie (CIBEST), UMR 5819, Univ. Grenoble Alpes, CEA, CNRS, INAC, SyMMES, F-38000 Grenoble, France
| | - Daphna Fenel
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR5075, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Guy Schoehn
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR5075, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Marie Carrière
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals, UMR 5249, Univ. Grenoble Alpes, CNRS, CEA, Grenoble, France.
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Dalzon B, Diemer H, Collin-Faure V, Cianférani S, Rabilloud T, Aude-Garcia C. Culture medium associated changes in the core proteome of macrophages and in their responses to copper oxide nanoparticles. Proteomics 2016; 16:2864-2877. [DOI: 10.1002/pmic.201600052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/15/2016] [Accepted: 10/06/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Bastien Dalzon
- Laboratory of Chemistry and Biology of Metals; BIG/CBM, CEA Grenoble; Grenoble France
- Laboratory of Chemistry and Biology of Metals; University of Grenoble Alpes; Grenoble France
- Laboratory of Chemistry and Biology of Metals; CNRS UMR5249 Grenoble France
| | - Hélène Diemer
- BioOrganic Mass Spectrometry Laboratory (LSMBO); IPHC, Université de Strasbourg; Strasbourg France
- BioOrganic Mass Spectrometry Laboratory (LSMBO); CNRS UMR7178 Strasbourg France
| | - Véronique Collin-Faure
- Laboratory of Chemistry and Biology of Metals; BIG/CBM, CEA Grenoble; Grenoble France
- Laboratory of Chemistry and Biology of Metals; University of Grenoble Alpes; Grenoble France
- Laboratory of Chemistry and Biology of Metals; CNRS UMR5249 Grenoble France
| | - Sarah Cianférani
- BioOrganic Mass Spectrometry Laboratory (LSMBO); IPHC, Université de Strasbourg; Strasbourg France
- BioOrganic Mass Spectrometry Laboratory (LSMBO); CNRS UMR7178 Strasbourg France
| | - Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals; BIG/CBM, CEA Grenoble; Grenoble France
- Laboratory of Chemistry and Biology of Metals; University of Grenoble Alpes; Grenoble France
- Laboratory of Chemistry and Biology of Metals; CNRS UMR5249 Grenoble France
| | - Catherine Aude-Garcia
- Laboratory of Chemistry and Biology of Metals; BIG/CBM, CEA Grenoble; Grenoble France
- Laboratory of Chemistry and Biology of Metals; University of Grenoble Alpes; Grenoble France
- Laboratory of Chemistry and Biology of Metals; CNRS UMR5249 Grenoble France
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12
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Rabilloud T. A single step protein assay that is both detergent and reducer compatible: The cydex blue assay. Electrophoresis 2016; 37:2595-2601. [PMID: 27445231 DOI: 10.1002/elps.201600270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/06/2016] [Accepted: 07/10/2016] [Indexed: 11/06/2022]
Abstract
Determination of protein concentration is often an absolute prerequisite in preparing samples for biochemical and proteomic analyses. However, current protein assay methods are not compatible with both reducers and detergents, which are however present simultaneously in most denaturing extraction buffers used in proteomics and electrophoresis, and in particular in SDS electrophoresis. It was found that inclusion of cyclodextrins in a Coomassie blue-based assay made it compatible with detergents, as cyclodextrins complex detergents in a 1:1 molecular ratio. As this type of assay is intrinsically resistant to reducers, a single-step assay that is both detergent and reducer compatible was developed. Depending on the type and concentration of detergents present in the sample buffer, either beta-cyclodextrin or alpha-cyclodextrin can be used, the former being able to complex a wider range of detergents and the latter being able to complex higher amounts of detergents due to its greater solubility in water. Cyclodextrins are used at final concentrations of 2-10 mg/mL in the assay mix. This typically allows to measure samples containing as little as 0.1 mg/mL protein, in the presence of up to 2% detergent and reducers such as 5% mercaptoethanol or 50 mM DTT in a single step with a simple spectrophotometric assay.
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Affiliation(s)
- Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals, CNRS UMR 5249 Grenoble, France. .,Laboratory of Chemistry and Biology of Metals, Univ. Grenoble Alpes, Grenoble, France. .,CEA Grenoble, BIG/CBM, Laboratory of Chemistry and Biology of Metals, CEA Grenoble, Grenoble, France.
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Aude-Garcia C, Dalzon B, Ravanat JL, Collin-Faure V, Diemer H, Strub JM, Cianferani S, Van Dorsselaer A, Carrière M, Rabilloud T. A combined proteomic and targeted analysis unravels new toxic mechanisms for zinc oxide nanoparticles in macrophages. J Proteomics 2016; 134:174-185. [DOI: 10.1016/j.jprot.2015.12.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 11/16/2015] [Accepted: 12/09/2015] [Indexed: 12/21/2022]
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Armand L, Biola-Clier M, Bobyk L, Collin-Faure V, Diemer H, Strub JM, Cianferani S, Van Dorsselaer A, Herlin-Boime N, Rabilloud T, Carriere M. Molecular responses of alveolar epithelial A549 cells to chronic exposure to titanium dioxide nanoparticles: A proteomic view. J Proteomics 2015; 134:163-173. [PMID: 26276045 DOI: 10.1016/j.jprot.2015.08.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 12/22/2022]
Abstract
UNLABELLED Although the biological effects of titanium dioxide nanoparticles (TiO2-NPs) have been studied for more than two decades, the mechanisms governing their toxicity are still unclear. We applied 2D-gel proteomics analysis on A549 epithelial alveolar cells chronically exposed for 2months to 2.5 or 50μg/mL of deeply characterized TiO2-NPs, in order to obtain comprehensive molecular responses that may reflect functional outcomes. We show that exposure to TiO2-NPs impacts the abundance of 30 protein species, corresponding to 22 gene products. These proteins are involved in glucose metabolism, trafficking, gene expression, mitochondrial function, proteasome activity and DNA damage response. Besides, our results suggest that p53 pathway is activated, slowing down cell cycle progression and reducing cell proliferation rate. Moreover, we report increased content of chaperones-related proteins, which suggests homeostasis re-establishment. Finally, our results highlight that chronic exposure to TiO2-NPs affects the same cellular functions as acute exposure to TiO2-NPs, although lower exposure concentrations and longer exposure times induce more intense cellular response. BIOLOGICAL SIGNIFICANCE Our results make possible the identification of new mechanisms that explain TiO2-NP toxicity upon long-term, in vitro exposure of A549 cells. It is the first article describing -omics results obtained with this experimental strategy. We show that this long-term exposure modifies the cellular content of proteins involved in functions including mitochondrial activity, intra- and extracellular trafficking, proteasome activity, glucose metabolism, and gene expression. Moreover we observe modification of content of proteins that activate the p53 pathway, which suggest the induction of a DNA damage response. Technically, our results show that exposure of A549 cells to a high concentration of TiO2-NPs leads to the identification of modulations of the same functional categories than exposure to low, more realistic concentrations. Still the intensity differs between these two exposure scenarios. We also show that chronic exposure to TiO2-NPs induces the modulation of cellular functions that have already been reported in the literature as being impacted in acute exposure scenarios. This proves that the exposure protocol in in vitro experiments related to nanoparticle toxicology might be cautiously chosen since inappropriate scenario may lead to inappropriate and/or incomplete conclusions.
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Affiliation(s)
- Lucie Armand
- Université Grenoble-Alpes, INAC-LCIB, Laboratoire Lésions des Acides Nucléiques, 17 rue des Martyrs, F-38000 Grenoble, France; CEA, INAC-SCIB, Laboratoire Lésions des Acides Nucléiques, 17 rue des Martyrs, F-38054 Grenoble, France
| | - Mathilde Biola-Clier
- Université Grenoble-Alpes, INAC-LCIB, Laboratoire Lésions des Acides Nucléiques, 17 rue des Martyrs, F-38000 Grenoble, France; CEA, INAC-SCIB, Laboratoire Lésions des Acides Nucléiques, 17 rue des Martyrs, F-38054 Grenoble, France
| | - Laure Bobyk
- Université Grenoble-Alpes, INAC-LCIB, Laboratoire Lésions des Acides Nucléiques, 17 rue des Martyrs, F-38000 Grenoble, France; CEA, INAC-SCIB, Laboratoire Lésions des Acides Nucléiques, 17 rue des Martyrs, F-38054 Grenoble, France
| | - Véronique Collin-Faure
- CEA Grenoble, iRTSV/CBM, Laboratory of Chemistry and Biology of Metals, Grenoble, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087 Strasbourg, France; CNRS, UMR7178, 67037 Strasbourg, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087 Strasbourg, France; CNRS, UMR7178, 67037 Strasbourg, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087 Strasbourg, France; CNRS, UMR7178, 67037 Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087 Strasbourg, France; CNRS, UMR7178, 67037 Strasbourg, France
| | | | - Thierry Rabilloud
- CNRS UMR 5249, Laboratory of Chemistry and Biology of Metals, Grenoble, France.
| | - Marie Carriere
- Université Grenoble-Alpes, INAC-LCIB, Laboratoire Lésions des Acides Nucléiques, 17 rue des Martyrs, F-38000 Grenoble, France; CEA, INAC-SCIB, Laboratoire Lésions des Acides Nucléiques, 17 rue des Martyrs, F-38054 Grenoble, France.
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15
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Luche S, Eymard-Vernain E, Diemer H, Van Dorsselaer A, Rabilloud T, Lelong C. Zinc oxide induces the stringent response and major reorientations in the central metabolism of Bacillus subtilis. J Proteomics 2015. [PMID: 26211718 DOI: 10.1016/j.jprot.2015.07.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Microorganisms, such as bacteria, are one of the first targets of nanoparticles in the environment. In this study, we tested the effect of two nanoparticles, ZnO and TiO2, with the salt ZnSO4 as the control, on the Gram-positive bacterium Bacillus subtilis by 2D gel electrophoresis-based proteomics. Despite a significant effect on viability (LD50), TiO2 NPs had no detectable effect on the proteomic pattern, while ZnO NPs and ZnSO4 significantly modified B. subtilis metabolism. These results allowed us to conclude that the effects of ZnO observed in this work were mainly attributable to Zn dissolution in the culture media. Proteomic analysis highlighted twelve modulated proteins related to central metabolism: MetE and MccB (cysteine metabolism), OdhA, AspB, IolD, AnsB, PdhB and YtsJ (Krebs cycle) and XylA, YqjI, Drm and Tal (pentose phosphate pathway). Biochemical assays, such as free sulfhydryl, CoA-SH and malate dehydrogenase assays corroborated the observed central metabolism reorientation and showed that Zn stress induced oxidative stress, probably as a consequence of thiol chelation stress by Zn ions. The other patterns affected by ZnO and ZnSO4 were the stringent response and the general stress response. Nine proteins involved in or controlled by the stringent response showed a modified expression profile in the presence of ZnO NPs or ZnSO4: YwaC, SigH, YtxH, YtzB, TufA, RplJ, RpsB, PdhB and Mbl. An increase in the ppGpp concentration confirmed the involvement of the stringent response during a Zn stress. All these metabolic reorientations in response to Zn stress were probably the result of complex regulatory mechanisms including at least the stringent response via YwaC.
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Affiliation(s)
- Sylvie Luche
- Pro-MD team, Université Joseph Fourier, CEA Grenoble, iRTSV, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France
| | - Elise Eymard-Vernain
- Pro-MD team, Université Joseph Fourier, CEA Grenoble, iRTSV, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, Université de Strasbourg, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, Université de Strasbourg, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France
| | - Thierry Rabilloud
- Pro-MD team, UMR CNRS 5249, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France
| | - Cécile Lelong
- Pro-MD team, Université Joseph Fourier, CEA Grenoble, iRTSV, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France.
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16
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Triboulet S, Aude-Garcia C, Armand L, Collin-Faure V, Chevallet M, Diemer H, Gerdil A, Proamer F, Strub JM, Habert A, Herlin N, Van Dorsselaer A, Carrière M, Rabilloud T. Comparative proteomic analysis of the molecular responses of mouse macrophages to titanium dioxide and copper oxide nanoparticles unravels some toxic mechanisms for copper oxide nanoparticles in macrophages. PLoS One 2015; 10:e0124496. [PMID: 25902355 PMCID: PMC4406518 DOI: 10.1371/journal.pone.0124496] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/03/2015] [Indexed: 12/12/2022] Open
Abstract
Titanium dioxide and copper oxide nanoparticles are more and more widely used because of their catalytic properties, of their light absorbing properties (titanium dioxide) or of their biocidal properties (copper oxide), increasing the risk of adverse health effects. In this frame, the responses of mouse macrophages were studied. Both proteomic and targeted analyses were performed to investigate several parameters, such as phagocytic capacity, cytokine release, copper release, and response at sub toxic doses. Besides titanium dioxide and copper oxide nanoparticles, copper ions were used as controls. We also showed that the overall copper release in the cell does not explain per se the toxicity observed with copper oxide nanoparticles. In addition, both copper ion and copper oxide nanoparticles, but not titanium oxide, induced DNA strands breaks in macrophages. As to functional responses, the phagocytic capacity was not hampered by any of the treatments at non-toxic doses, while copper ion decreased the lipopolysaccharide-induced cytokine and nitric oxide productions. The proteomic analyses highlighted very few changes induced by titanium dioxide nanoparticles, but an induction of heme oxygenase, an increase of glutathione synthesis and a decrease of tetrahydrobiopterin in response to copper oxide nanoparticles. Subsequent targeted analyses demonstrated that the increase in glutathione biosynthesis and the induction of heme oxygenase (e.g. by lovastatin/monacolin K) are critical for macrophages to survive a copper challenge, and that the intermediates of the catecholamine pathway induce a strong cross toxicity with copper oxide nanoparticles and copper ions.
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Affiliation(s)
- Sarah Triboulet
- Laboratory of Chemistry and Biology of Metals, Univ. Grenoble Alpes, Grenoble, France
| | - Catherine Aude-Garcia
- Laboratory of Chemistry and Biology of Metals, CEA/ iRTSV, Grenoble, France
- Laboratory of Chemistry and Biology of Metals, CNRS UMR5249, Grenoble, France
| | - Lucie Armand
- Service de Chimie Inorganique et Biologique, Univ. Grenoble Alpes & CEA, Grenoble, France
| | | | - Mireille Chevallet
- Laboratory of Chemistry and Biology of Metals, CEA/ iRTSV, Grenoble, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg & CNRS UMR 7178, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France
| | - Adèle Gerdil
- Laboratoire Francis Perrin (Unité de recherche Associée 2453), Commissariat à l’Energie Atomique, CEA-Saclay 91191 Gif/Yvette, France
| | - Fabienne Proamer
- Etablissement Français du Sang-Alsace, Unité MIxte de recherche S949 Institut National de la Santé Et de la Recherche Médicale (INSERM)-Université de Strasbourg, Strasbourg, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg & CNRS UMR 7178, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France
| | - Aurélie Habert
- Laboratoire Francis Perrin (Unité de recherche Associée 2453), Commissariat à l’Energie Atomique, CEA-Saclay 91191 Gif/Yvette, France
| | - Nathalie Herlin
- Laboratoire Francis Perrin (Unité de recherche Associée 2453), Commissariat à l’Energie Atomique, CEA-Saclay 91191 Gif/Yvette, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg & CNRS UMR 7178, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France
| | - Marie Carrière
- Service de Chimie Inorganique et Biologique, Univ. Grenoble Alpes & CEA, Grenoble, France
| | - Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals, CNRS UMR5249, Grenoble, France
- * E-mail:
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17
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Triboulet S, Aude-Garcia C, Armand L, Gerdil A, Diemer H, Proamer F, Collin-Faure V, Habert A, Strub JM, Hanau D, Herlin N, Carrière M, Van Dorsselaer A, Rabilloud T. Analysis of cellular responses of macrophages to zinc ions and zinc oxide nanoparticles: a combined targeted and proteomic approach. NANOSCALE 2014; 6:6102-6114. [PMID: 24788578 DOI: 10.1039/c4nr00319e] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Two different zinc oxide nanoparticles, as well as zinc ions, are used to study the cellular responses of the RAW 264 macrophage cell line. A proteomic screen is used to provide a wide view of the molecular effects of zinc, and the most prominent results are cross-validated by targeted studies. Furthermore, the alteration of important macrophage functions (e.g. phagocytosis) by zinc is also investigated. The intracellular dissolution/uptake of zinc is also studied to further characterize zinc toxicity. Zinc oxide nanoparticles dissolve readily in the cells, leading to high intracellular zinc concentrations, mostly as protein-bound zinc. The proteomic screen reveals a rather weak response in the oxidative stress response pathway, but a strong response both in the central metabolism and in the proteasomal protein degradation pathway. Targeted experiments confirm that carbohydrate catabolism and proteasome are critical determinants of sensitivity to zinc, which also induces DNA damage. Conversely, glutathione levels and phagocytosis appear unaffected at moderately toxic zinc concentrations.
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Affiliation(s)
- Sarah Triboulet
- Univ. Grenoble Alpes, Laboratory of Chemistry and Biology of Metals, UMR CNRS-CEA-UJF 5249, iRTSV/LCBM, CEA Grenoble, 17 rue des martyrs, F-38054 Grenoble Cedex 9, France.
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18
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Drago F, Sautière PE, Le Marrec-Croq F, Accorsi A, Van Camp C, Salzet M, Lefebvre C, Vizioli J. Microglia of medicinal leech (Hirudo medicinalis) express a specific activation marker homologous to vertebrate ionized calcium-binding adapter molecule 1 (Iba1/alias aif-1). Dev Neurobiol 2014; 74:987-1001. [PMID: 24723370 DOI: 10.1002/dneu.22179] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 04/07/2014] [Indexed: 01/13/2023]
Abstract
The Ionized calcium-Binding Adapter molecule 1 (Iba1), also known as Allograft Inflammatory Factor 1 (AIF-1), is a 17 kDa cytokine-inducible protein, produced by activated macrophages during chronic transplant rejection and inflammatory reactions in Vertebrates. In mammalian central nervous system (CNS), Iba1 is a sensitive marker associated with activated macrophages/microglia and is upregulated following neuronal death or brain lesions. The medicinal leech Hirudo medicinalis is able to regenerate its CNS after injury, leading to a complete functional repair. Similar to Vertebrates, leech neuroinflammatory processes are linked to microglia activation and recruitment at the lesion site. We identified a gene, named Hmiba1, coding a 17.8 kDa protein showing high similarity with Vertebrate AIF-1. The present work constitutes the first report on an Iba1 protein in the nervous system of an invertebrate. Immunochemistry and gene expression analyses showed that HmIba1, like its mammalian counterpart, is modulated in leech CNS by mechanical injury or chemical stimuli (ATP). We presently demonstrate that most of leech microglial cells migrating and accumulating at the lesion site specifically expressed the activation marker HmIba1. While the functional role of Iba1, whatever species, is still unclear in reactive microglia, this molecule appeared as a good selective marker of activated cells in leech and presents an interesting tool to investigate the functions of these cells during nerve repair events.
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Affiliation(s)
- Francesco Drago
- Université Lille 1, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée, EA4550, Villeneuve d'Ascq, 59655, France
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19
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Abstract
AbstractLung cancer is one of the most common cancers in terms of both incidence and mortality.The major reasons for the increasing number of deaths from lung cancer are late detection and lack of effective therapies. To improve our understanding of lung cancer biology, there is urgent need for blood-based, non-invasive molecular tests to assist in its detection in a cost-effective manner at an early stage when curative interventions are still possible. Recent advances in proteomic technology have provided extensive, high throughput analytical tools for identification, characterization and functional studies of proteomes. Changes in protein expression patterns in response to stimuli can serve as indicators or biomarkers of biological and pathological processes as well as physiological and pharmacological responses to drug treatment, thus aiding in early diagnosis and prognosis of disease. However, only a few biomarkers have been approved by the FDA to date for screening and diagnostic purposes. This review provides a brief overview of currently available proteomic techniques, their applications and limitations and the current state of knowledge about important serum biomarkers in lung cancer and their potential value as prognostic and diagnostic tools.
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20
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Leonardi A, Sajevic T, Kovačič L, Pungerčar J, Lang Balija M, Halassy B, Trampuš Bakija A, Križaj I. Hemorrhagin VaH4, a covalent heterodimeric P-III metalloproteinase from Vipera ammodytes ammodytes with a potential antitumour activity. Toxicon 2013; 77:141-55. [PMID: 24269369 DOI: 10.1016/j.toxicon.2013.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 10/30/2013] [Accepted: 11/14/2013] [Indexed: 01/23/2023]
Abstract
In the envenomation caused by a bite of Vipera ammodytes ammodytes, the most venomous snake in Europe, hemorrhage is usually the most severe consequence in man. Identifying and understanding the hemorrhagic components of its venom is therefore particularly important in optimizing medical treatment of patients. We describe a novel high molecular mass hemorrhagin, VaH4. The isolated molecule is a covalent dimer of two homologous subunits, VaH4-A and VaH4-B. Complete structural characterization of A and partial characterization of B revealed that both belong to the P-III class of snake venom metalloproteinases (SVMPs), comprising a metalloproteinase, a disintegrin-like domain and a cysteine-rich domain. However, neither VaH4-A nor VaH4-B possess the Cys174 involved in the inter-subunit disulphide bond of P-III SVMPs. A three-dimensional model of the VaH4 dimer suggests that Cys132 serves this function. This implies that dimers in the P-III class of SVMPs can be formed either between their Cys132 or Cys174 residues. The proteolytic activity and stability of VaH4 depend on Zn²⁺ and Ca²⁺ ions and the presence of glycosaminoglycans, which indicates physiological interaction of VaH4 with the latter element of the extracellular matrix (ECM). The molecular mass of VaH4, determined by MALDI/TOF mass spectrometry, is 110.2 kDa. N-deglycosylation reduced the mass of each monomer by 8.7 kDa. The two possible N-glycosylation sites in VaH4-A are located at completely different positions from those in homodimeric P-IIIc VaH3 from the same venom, however, without any evident functional implications. The hemorrhagic activity of this slightly acidic SVMP is ascribed to its hydrolysis of components of the ECM, particularly fibronectin and nidogen, and of some blood coagulation proteins, in particular the α-chain of fibrinogen. VaH4 is also significant medically as we found it cytotoxic against cancer cells and due to its substantial sequence similarity to ADAM/ADAMTS family of physiologically very important human proteins of therapeutic potential.
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Affiliation(s)
- Adrijana Leonardi
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Tamara Sajevic
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Lidija Kovačič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Jože Pungerčar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Maja Lang Balija
- Research and Development Department, Institute of Immunology, Inc., Rockefellerova 10, HR-10 000 Zagreb, Croatia
| | - Beata Halassy
- University of Zagreb, Centre for Research and Knowledge Trasfer in Biotechnology, Rockefellerova 10, HR-10000 Zagreb, Croatia
| | | | - Igor Križaj
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva cesta 5, SI-1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia.
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21
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Triboulet S, Aude-Garcia C, Carrière M, Diemer H, Proamer F, Habert A, Chevallet M, Collin-Faure V, Strub JM, Hanau D, Van Dorsselaer A, Herlin-Boime N, Rabilloud T. Molecular responses of mouse macrophages to copper and copper oxide nanoparticles inferred from proteomic analyses. Mol Cell Proteomics 2013; 12:3108-22. [PMID: 23882024 DOI: 10.1074/mcp.m113.030742] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The molecular responses of macrophages to copper-based nanoparticles have been investigated via a combination of proteomic and biochemical approaches, using the RAW264.7 cell line as a model. Both metallic copper and copper oxide nanoparticles have been tested, with copper ion and zirconium oxide nanoparticles used as controls. Proteomic analysis highlighted changes in proteins implicated in oxidative stress responses (superoxide dismutases and peroxiredoxins), glutathione biosynthesis, the actomyosin cytoskeleton, and mitochondrial proteins (especially oxidative phosphorylation complex subunits). Validation studies employing functional analyses showed that the increases in glutathione biosynthesis and in mitochondrial complexes observed in the proteomic screen were critical to cell survival upon stress with copper-based nanoparticles; pharmacological inhibition of these two pathways enhanced cell vulnerability to copper-based nanoparticles, but not to copper ions. Furthermore, functional analyses using primary macrophages derived from bone marrow showed a decrease in reduced glutathione levels, a decrease in the mitochondrial transmembrane potential, and inhibition of phagocytosis and of lipopolysaccharide-induced nitric oxide production. However, only a fraction of these effects could be obtained with copper ions. In conclusion, this study showed that macrophage functions are significantly altered by copper-based nanoparticles. Also highlighted are the cellular pathways modulated by cells for survival and the exemplified cross-toxicities that can occur between copper-based nanoparticles and pharmacological agents.
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Affiliation(s)
- Sarah Triboulet
- Pro-MD team, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Université Joseph Fourier, Grenoble 38054, France
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22
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Rabilloud T, Triboulet S. Two-dimensional SDS-PAGE fractionation of biological samples for biomarker discovery. Methods Mol Biol 2013; 1002:151-165. [PMID: 23625402 DOI: 10.1007/978-1-62703-360-2_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Two-dimensional electrophoresis is still a very valuable tool in proteomics, due to its reproducibility and its ability to analyze complete proteins. However, due to its sensitivity to dynamic range issues, its most suitable use in the frame of biomarker discovery is not on very complex fluids such as plasma, but rather on more proximal, simpler fluids such as CSF, urine, or secretome samples. Here, we describe the complete workflow for the analysis of such dilute samples by two-dimensional electrophoresis, starting from sample concentration, then the two-dimensional electrophoresis step per se, ending with the protein detection by fluorescence.
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Affiliation(s)
- Thierry Rabilloud
- Chemistry and Biology of Metals Grenoble, CEA Grenoble, Grenoble, France
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23
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Lelong C, Chevallet M, Diemer H, Luche S, Van Dorsselaer A, Rabilloud T. Improved proteomic analysis of nuclear proteins, as exemplified by the comparison of two myeloid cell lines nuclear proteomes. J Proteomics 2012; 77:577-602. [DOI: 10.1016/j.jprot.2012.09.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 09/18/2012] [Accepted: 09/22/2012] [Indexed: 02/04/2023]
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24
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Jesse S, Lehnert S, Jahn O, Parnetti L, Soininen H, Herukka SK, Steinacker P, Tawfik S, Tumani H, von Arnim CAF, Neumann M, Kretzschmar HA, Kulaksiz H, Lenter M, Wiltfang J, Ferger B, Hengerer B, Otto M. Differential sialylation of serpin A1 in the early diagnosis of Parkinson's disease dementia. PLoS One 2012; 7:e48783. [PMID: 23144969 PMCID: PMC3493604 DOI: 10.1371/journal.pone.0048783] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 10/01/2012] [Indexed: 12/27/2022] Open
Abstract
The prevalence of Parkinson’s disease (PD) increases with age. Up to 50% of PD show cognitive decline in terms of a mild cognitive impairment already in early stages that predict the development of dementia, which can occur in up to 80% of PD patients over the long term, called Parkinson’s disease dementia (PDD). So far, diagnosis of PD/PDD is made according to clinical and neuropsychological examinations while laboratory data is only used for exclusion of other diseases. The aim of this study was the identification of possible biomarkers in cerebrospinal fluid (CSF) of PD, PDD and controls (CON) which predict the development of dementia in PD. For this, a proteomic approach optimized for CSF was performed using 18 clinically well characterized patients in a first step with subsequent validation using 84 patients. Here, we detected differentially sialylated isoforms of Serpin A1 as marker for differentiation of PD versus PDD in CSF. Performing 2D-immunoblots, all PDD patients could be identified correctly (sensitivity 100%). Ten out of 24 PD patients showed Serpin A1 isoforms in a similar pattern like PDD, indicating a specificity of 58% for the test-procedure. In control samples, no additional isoform was detected. On the basis of these results, we conclude that differentially sialylated products of Serpin A1 are an interesting biomarker to indicate the development of a dementia during the course of PD.
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Affiliation(s)
- Sarah Jesse
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Stefan Lehnert
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute for Experimental Medicine, Goettingen, Germany
- DFG Research Center for Molecular Physiology of the Brain, Goettingen, Germany
| | | | - Hilkka Soininen
- Department of Neurology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Sanna-Kaisa Herukka
- Department of Neurology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Saskia Tawfik
- Department of Neurology, University of Ulm, Ulm, Germany
| | | | | | - Manuela Neumann
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | | | - Hasan Kulaksiz
- Department of Internal Medicine, University of Ulm, Ulm, Germany
| | - Martin Lenter
- CNS Diseases Research, Boehringer Ingelheim GmbH & Co. KG, Biberach an der Riss, Germany
| | - Jens Wiltfang
- Department of Psychiatry, University of Essen-Duisburg, Essen-Duisburg, Germany
| | - Boris Ferger
- CNS Diseases Research, Boehringer Ingelheim GmbH & Co. KG, Biberach an der Riss, Germany
| | - Bastian Hengerer
- CNS Diseases Research, Boehringer Ingelheim GmbH & Co. KG, Biberach an der Riss, Germany
| | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany
- * E-mail:
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Amado FML, Ferreira RP, Vitorino R. One decade of salivary proteomics: current approaches and outstanding challenges. Clin Biochem 2012; 46:506-17. [PMID: 23103441 DOI: 10.1016/j.clinbiochem.2012.10.024] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/13/2012] [Accepted: 10/16/2012] [Indexed: 12/12/2022]
Abstract
Efforts have been made in the last decade towards the complete characterization of saliva proteome using gel-based and gel-free approaches. The combination of these strategies resulted in the increment of the dynamic range of saliva proteome, which yield in the identification of more than 3,000 different protein species. Comparative protein profiling using isotope labeling and label free approaches has been used for the identification of novel biomarkers for oral and related diseases. Although progresses have been made in saliva proteome characterization, the comparative profiling in different pathophysiological conditions is still at the beginning if compared to other bodily fluids. The potential biomarkers identified so far lack specificity once common differentially expressed proteins were detected in the saliva of patients with distinct diseases. In addition, recent research works focused on saliva peptidome profiling already allowed a better understanding of peptides' physiological role in oral cavity. This review provides an overview of the major achievements in saliva proteomics giving emphasis to methodological concerns related with saliva collection, treatment and analysis, as well as the main advantages and pitfalls underlying salivary proteomic strategies and potential clinical outcomes.
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Affiliation(s)
- Francisco M L Amado
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal.
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Leonardi A, Biass D, Kordiš D, Stöcklin R, Favreau P, Križaj I. Conus consors Snail Venom Proteomics Proposes Functions, Pathways, and Novel Families Involved in Its Venomic System. J Proteome Res 2012; 11:5046-58. [DOI: 10.1021/pr3006155] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Adrijana Leonardi
- Department of Molecular and
Biomedical Sciences, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Daniel Biass
- Atheris Laboratories,
Case postale 314, CH-1233 Bernex-Geneva, Switzerland
| | - Dušan Kordiš
- Department of Molecular and
Biomedical Sciences, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Reto Stöcklin
- Atheris Laboratories,
Case postale 314, CH-1233 Bernex-Geneva, Switzerland
| | - Philippe Favreau
- Atheris Laboratories,
Case postale 314, CH-1233 Bernex-Geneva, Switzerland
| | - Igor Križaj
- Department of Molecular and
Biomedical Sciences, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
- Department of Chemistry and Biochemistry,
Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana,
Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, SI-1000 Ljubljana, Slovenia
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Peptide fractionation by SDS-free polyacrylamide gel electrophoresis for proteomic analysis via DF-PAGE. Methods Mol Biol 2012; 869:197-204. [PMID: 22585487 DOI: 10.1007/978-1-61779-821-4_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Here we present a procedure for peptide fractionation by SDS-free polyacrylamide gel electrophoresis, based on discontinuous buffer systems. In the absence of SDS, peptide migration depends both on their molecular mass and on their net charge at the electrophoresis pH. By selecting the separation pH, peptide mobility is modulated. In the original discontinuous buffer system (Tris/glycine), peptides that migrate to the anode have pI values below 6.8 and distribute along the lane in a pI decreasing order, while at acidic pH, as that afforded by histidine/MOPS buffer system, peptides with pI below 5.5 are fractionated. Separation at acid pH is particularly useful for recovering phosphopeptides as well as other highly negatively charged peptides, as those containing sialic or sulfate substituents. Both separation conditions in Tris/glycine and in histidine/MOPS are applicable to proteomic studies, by dual-fractionation polyacrylamide gel electrophoresis (DF-PAGE). First, complex protein samples are separated via SDS-PAGE, and after in-gel proteolysis, peptides are loaded on a second SDS-free gel, where they are separated as described here.
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Vitorino R, Guedes S, Manadas B, Ferreira R, Amado F. Toward a standardized saliva proteome analysis methodology. J Proteomics 2012; 75:5140-65. [PMID: 22809520 DOI: 10.1016/j.jprot.2012.05.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 05/26/2012] [Accepted: 05/30/2012] [Indexed: 01/01/2023]
Abstract
The present study aimed the evaluation of saliva sample pre-treatment, in particular the sample clearance usually performed by centrifugation, to the contribution of salivary proteome and peptidome. Using in-gel and off-gel approaches, a large content of salivary proteins was detected in the pellet fraction that is usually discarded. In addition, chaotropic/detergent treatment in combination with sonication, before the centrifugation step, resulted in salivary complex disruption and consequently in the extraction of high amounts of proteins. Based on this data, we suggest the use of urea/detergent with sonication as a standard saliva sample pre-treatment procedure. We also described a procedure to extract salivary peptides which can be performed even after saliva sample treatment with chaotropic/detergents. In overall, we reported for the first time the contribution of the pellet fraction to the whole saliva proteome. iTRAQ analysis highlighted a higher number of different peptides as well as distinct quantities of each protein class when after sample treatment with urea and sonication, acetone precipitation followed by solubilization with acetonitrile/HCl was performed.
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Affiliation(s)
- Rui Vitorino
- QOPNA, Mass spectrometry center, Department of Chemistry, University of Aveiro, Portugal.
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Tahtouh M, Garçon-Bocquet A, Croq F, Vizioli J, Sautière PE, Van Camp C, Salzet M, Nagnan-le Meillour P, Pestel J, Lefebvre C. Interaction of HmC1q with leech microglial cells: involvement of C1qBP-related molecule in the induction of cell chemotaxis. J Neuroinflammation 2012; 9:37. [PMID: 22356764 PMCID: PMC3298539 DOI: 10.1186/1742-2094-9-37] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 02/22/2012] [Indexed: 01/24/2023] Open
Abstract
Background In invertebrates, the medicinal leech is considered to be an interesting and appropriate model to study neuroimmune mechanisms. Indeed, this non-vertebrate animal can restore normal function of its central nervous system (CNS) after injury. Microglia accumulation at the damage site has been shown to be required for axon sprouting and for efficient regeneration. We characterized HmC1q as a novel chemotactic factor for leech microglial cell recruitment. In mammals, a C1q-binding protein (C1qBP alias gC1qR), which interacts with the globular head of C1q, has been reported to participate in C1q-mediated chemotaxis of blood immune cells. In this study, we evaluated the chemotactic activities of a recombinant form of HmC1q and its interaction with a newly characterized leech C1qBP that acts as its potential ligand. Methods Recombinant HmC1q (rHmC1q) was produced in the yeast Pichia pastoris. Chemotaxis assays were performed to investigate rHmC1q-dependent microglia migration. The involvement of a C1qBP-related molecule in this chemotaxis mechanism was assessed by flow cytometry and with affinity purification experiments. The cellular localization of C1qBP mRNA and protein in leech was investigated using immunohistochemistry and in situ hybridization techniques. Results rHmC1q-stimulated microglia migrate in a dose-dependent manner. This rHmC1q-induced chemotaxis was reduced when cells were preincubated with either anti-HmC1q or anti-human C1qBP antibodies. A C1qBP-related molecule was characterized in leech microglia. Conclusions A previous study showed that recruitment of microglia is observed after HmC1q release at the cut end of axons. Here, we demonstrate that rHmC1q-dependent chemotaxis might be driven via a HmC1q-binding protein located on the microglial cell surface. Taken together, these results highlight the importance of the interaction between C1q and C1qBP in microglial activation leading to nerve repair in the medicinal leech.
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Affiliation(s)
- Muriel Tahtouh
- Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée - EA4550, Microglial activation group, Université Lille Nord de France, Université Lille 1, IFR 147, bâtiment SN3, 59655 Villeneuve d'Ascq, France
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Recruitment of glycosyl hydrolase proteins in a cone snail venomous arsenal: further insights into biomolecular features of Conus venoms. Mar Drugs 2012; 10:258-280. [PMID: 22412800 PMCID: PMC3296996 DOI: 10.3390/md10020258] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/13/2012] [Accepted: 01/14/2012] [Indexed: 01/06/2023] Open
Abstract
Cone snail venoms are considered an untapped reservoir of extremely diverse peptides, named conopeptides, displaying a wide array of pharmacological activities. We report here for the first time, the presence of high molecular weight compounds that participate in the envenomation cocktail used by these marine snails. Using a combination of proteomic and transcriptomic approaches, we identified glycosyl hydrolase proteins, of the hyaluronidase type (Hyal), from the dissected and injectable venoms (“injectable venom” stands for the venom variety obtained by milking of the snails. This is in contrast to the “dissected venom”, which was obtained from dissected snails by extraction of the venom glands) of a fish-hunting cone snail, Conus consors (Pionoconus clade). The major Hyal isoform, Conohyal-Cn1, is expressed as a mixture of numerous glycosylated proteins in the 50 kDa molecular mass range, as observed in 2D gel and mass spectrometry analyses. Further proteomic analysis and venom duct mRNA sequencing allowed full sequence determination. Additionally, unambiguous segment location of at least three glycosylation sites could be determined, with glycans corresponding to multiple hexose (Hex) and N-acetylhexosamine (HexNAc) moieties. With respect to other known Hyals, Conohyal-Cn1 clearly belongs to the hydrolase-type of Hyals, with strictly conserved consensus catalytic donor and positioning residues. Potent biological activity of the native Conohyals could be confirmed in degrading hyaluronic acid. A similar Hyal sequence was also found in the venom duct transcriptome of C. adamsonii (Textilia clade), implying a possible widespread recruitment of this enzyme family in fish-hunting cone snail venoms. These results provide the first detailed Hyal sequence characterized from a cone snail venom, and to a larger extent in the Mollusca phylum, thus extending our knowledge on this protein family and its evolutionary selection in marine snail venoms.
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Abstract
Two-dimensional electrophoresis (2 DE) is one of the most important proteomic tools and allows studying the complexity of proteomes of different origin. This chapter describes a setup for 2D DIGE with minimal labeling for qualitative and quantitative applications. It relies on homemade gels of medium size and in our hands has been found useful for a wide variety of separation problems involving complex protein mixtures of animal or human origin. The basic method is given for serum proteins of different species, but with minor modifications the method may be easily adapted to other sample materials (other body fluids, cells, tissues), conditions, or size. Examples are given for simple pattern comparisons (e.g., quality control, fast comparison of just two samples) as well as for quantitative applications to larger sample sets.
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Affiliation(s)
- Ingrid Miller
- Department for Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria.
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Croq F, Vizioli J, Tuzova M, Tahtouh M, Sautiere PE, Van Camp C, Salzet M, Cruikshank WW, Pestel J, Lefebvre C. A homologous form of human interleukin 16 is implicated in microglia recruitment following nervous system injury in leech Hirudo medicinalis. Glia 2011; 58:1649-62. [PMID: 20578037 DOI: 10.1002/glia.21036] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In contrast to mammals, the medicinal leech Hirudo medicinalis can completely repair its central nervous system (CNS) after injury. This invertebrate model offers unique opportunities to study the molecular and cellular basis of the CNS repair processes. When the leech CNS is injured, microglial cells migrate and accumulate at the site of lesion, a phenomenon known to be essential for the usual sprouting of injured axons. In the present study, we demonstrate that a new molecule, designated HmIL-16, having functional homologies with human interleukin-16 (IL-16), has chemotactic activity on leech microglial cells as observed using a gradient of human IL-16. Preincubation of microglial cells either with an anti-human IL-16 antibody or with anti-HmIL-16 antibody significantly reduced microglia migration induced by leech-conditioned medium. Functional homology was demonstrated further by the ability of HmIL-16 to promote human CD4+ T cell migration which was inhibited by antibody against human IL-16, an IL-16 antagonist peptide or soluble CD4. Immunohistochemistry of leech CNS indicates that HmIL-16 protein present in the neurons is rapidly transported and stored along the axonal processes to promote the recruitment of microglial cells to the injured axons. To our knowledge, this is the first identification of a functional interleukin-16 homologue in invertebrate CNS. The ability of HmIL-16 to recruit microglial cells to sites of CNS injury suggests a role for HmIL-16 in the crosstalk between neurons and microglia in the leech CNS repair.
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Affiliation(s)
- Françoise Croq
- Université Lille Nord de France, Université Lille 1, Laboratoire de Neuroimmunologie des Annélides, Centre National de la Recherche Scientifique, FRE 3249, IFR 147, F59655 Villeneuve d'Ascq, France
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Ramos Y, Garcia Y, Pérez-Riverol Y, Leyva A, Padrón G, Sánchez A, Castellanos-Serra L, González LJ, Besada V. Peptide fractionation by acid pH SDS-free electrophoresis. Electrophoresis 2011; 32:1323-6. [DOI: 10.1002/elps.201000677] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 01/25/2011] [Accepted: 01/26/2011] [Indexed: 11/11/2022]
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Pluder F, Barjaktarovic Z, Azimzadeh O, Mörtl S, Krämer A, Steininger S, Sarioglu H, Leszczynski D, Nylund R, Hakanen A, Sriharshan A, Atkinson MJ, Tapio S. Low-dose irradiation causes rapid alterations to the proteome of the human endothelial cell line EA.hy926. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2011; 50:155-166. [PMID: 21104263 DOI: 10.1007/s00411-010-0342-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 11/01/2010] [Indexed: 05/30/2023]
Abstract
High doses of ionising radiation damage the heart by an as yet unknown mechanism. A concern for radiological protection is the recent epidemiological data indicating that doses as low as 100-500 mGy may induce cardiac damage. The aim of this study was to identify potential molecular targets and/or mechanisms involved in the pathogenesis of low-dose radiation-induced cardiovascular disease. The vascular endothelium plays a pivotal role in the regulation of cardiac function and is therefore a potential target tissue. We report here that low-dose radiation induced rapid and time-dependent changes in the cytoplasmic proteome of the human endothelial cell line EA.hy926. The proteomes were investigated at 4 and 24 h after irradiation at two different dose rates (Co-60 gamma ray total dose 200 mGy; 20 mGy/min and 190 mGy/min) using 2D-DIGE technology. Differentially expressed proteins were identified, after in-gel trypsin digestion, by MALDI-TOF/TOF tandem mass spectrometry, and peptide mass fingerprint analyses. We identified 15 significantly differentially expressed proteins, of which 10 were up-regulated and 5 down-regulated, with more than ±1.5-fold difference compared with unexposed cells. Pathways influenced by the low-dose exposures included the Ran and RhoA pathways, fatty acid metabolism and stress response.
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Affiliation(s)
- Franka Pluder
- Institute of Radiation Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
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Abril N, Ruiz-Laguna J, Osuna-Jiménez I, Vioque-Fernández A, Fernández-Cisnal R, Chicano-Gálvez E, Alhama J, López-Barea J, Pueyo C. Omic approaches in environmental issues. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2011; 74:1001-1019. [PMID: 21707425 DOI: 10.1080/15287394.2011.582259] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Biomonitoring requires the application of batteries of different biomarkers, as environmental contaminants induce multiple responses in organisms that are not necessarily correlated. Omic technologies were proposed as an alternative to conventional biomarkers since these techniques quantitatively monitor many biological molecules in a high-throughput manner and thus provide a general appraisal of biological responses altered by exposure to contaminants. As the studies using omic technologies increase, it is becoming clear that any single omic approach may not be sufficient to characterize the complexity of ecosystems. This work aims to provide a preliminary working scheme for the use of combined transcriptomic and proteomic methodologies in environmental biomonitoring. There are difficulties in working with nonmodel organisms as bioindicators when combining several omic approaches. As a whole, our results with heterologous microarrays in M. spretus and suppressive subtractive hybridization (SSH) in P. clarkii indicated that animals sustaining a heavy pollution burden exhibited an enhanced immune response and/or cell apoptosis. The proteomic studies, although preliminary, provide a holistic insight regarding the manner by which pollution shifts protein intensity in two-dimensional gel electrophoresis (2-DE), completing the transcriptomic approach. In our study, the sediment element concentration was in agreement with the intensity of protein expression changes in C. maenas crabs. In conclusion, omics are useful technologies in addressing environmental issues and the determination of contamination threats.
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Affiliation(s)
- Nieves Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain.
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Aude-Garcia C, Collin-Faure V, Luche S, Rabilloud T. Improvements and simplifications in in-gel fluorescent detection of proteins using ruthenium II tris-(bathophenanthroline disulfonate): the poor man's fluorescent detection method. Proteomics 2010; 11:324-8. [PMID: 21204259 DOI: 10.1002/pmic.201000370] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 09/10/2010] [Accepted: 10/14/2010] [Indexed: 11/09/2022]
Abstract
Fluorescent detection of proteins is a popular method of detection allying sensitivity, linearity and compatibility with mass spectrometry. Among the numerous methods described in the literature, staining with ruthenium II tris(bathophenanthroline disulfonate) is particularly cost-effective, but slightly cumbersome owing to difficulties in the preparation of the complex and complexity of staining protocols. We describe here the modifications on both aspects that allow to perform a higher contrast staining and offer a more robust method of complex preparation, thereby maximizing the advantages of the method.
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Affiliation(s)
- Catherine Aude-Garcia
- CEA-DSV/iRTSV/LBBSI, Biophysique et Biochimie des Systèmes Intégrés, CEA-Grenoble, Grenoble, France
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Min Q, Wu R, Zhao L, Qin H, Ye M, Zhu JJ, Zou H. Size-selective proteolysis on mesoporous silica-based trypsin nanoreactor for low-MW proteome analysis. Chem Commun (Camb) 2010; 46:6144-6. [PMID: 20664869 DOI: 10.1039/c0cc00619j] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, the concept of size-selective proteolysis was first described by using the mesoporous silica-based trypsin nanoreactor. For analysis of a complex protein sample, low-MW proteins were preferentially digested for identification while high-MW proteins were excluded from digestion.
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Affiliation(s)
- Qianhao Min
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China
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Variations on a theme: Changes to electrophoretic separations that can make a difference. J Proteomics 2010; 73:1562-72. [DOI: 10.1016/j.jprot.2010.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 04/01/2010] [Accepted: 04/03/2010] [Indexed: 11/19/2022]
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A proteomic approach for the diagnosis of bacterial meningitis. PLoS One 2010; 5:e10079. [PMID: 20386697 PMCID: PMC2851643 DOI: 10.1371/journal.pone.0010079] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 03/16/2010] [Indexed: 11/19/2022] Open
Abstract
Background The discrimination of bacterial meningitis (BM) versus viral meningitis (VM) shapes up as a problem, when laboratory data are not equivocal, in particular, when Gram stain is negative. Methodology/Principal Findings With the aim to determine reliable marker for bacterial or viral meningitis, we subjected cerebrospinal fluid (CSF) to a quantitative proteomic screening. By using a recently established 2D-DIGE protocol which was adapted to the individual CSF flow, we compared a small set of patients with proven BM and VM. Thereby, we identified six potential biomarkers out of which Prostaglandin-H2 D-isomerase was already described in BM, showing proof of concept. In the subsequent validation phase on a more comprehensive collective of 80 patients, we could validate that in BM high levels of glial fibrillary acidic protein (GFAP) and low levels of soluble amyloid precursor protein alpha/beta (sAPPα/β) are present as possible binding partner of Fibulin-1. Conclusions/Significance We conclude that our CSF flow-adapted 2D-DIGE protocol is valid especially in comparing samples with high differences in total protein and suppose that GFAP and sAPPα/β have a high potential as additional diagnostic markers for differentiation of BM from VM. In the clinical setting, this might lead to an improved early diagnosis and to an individual therapy.
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Borges JP, Culerrier R, Aldon D, Barre A, Benoist H, Saurel O, Milon A, Didier A, Rougé P. GATEWAY™ technology and E. coli recombinant system produce a properly folded and functional recombinant allergen of the lipid transfer protein of apple (Mal d 3). Protein Expr Purif 2010; 70:277-82. [DOI: 10.1016/j.pep.2009.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 09/17/2009] [Indexed: 10/20/2022]
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Lagadec C, Romon R, Tastet C, Meignan S, Com E, Page A, Bidaux G, Hondermarck H, Le Bourhis X. Ku86 is important for TrkA overexpression-induced breast cancer cell invasion. Proteomics Clin Appl 2010; 4:580-90. [PMID: 21137076 DOI: 10.1002/prca.200900148] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 11/07/2009] [Accepted: 11/08/2009] [Indexed: 11/08/2022]
Abstract
PURPOSE We have recently shown that breast tumors express high levels of TrkA compared with normal breast tissues, with TrkA overexpression enhancing breast cancer cell invasion in vitro and metastasis in animal models. In this study, we tried to identify molecules involved in TrkA overexpression-mediated biological effects in breast cancer cells. EXPERIMENTAL DESIGN We used a proteomic-based approach to identify proteins involved in TrkA overexpression-stimulated invasion of MDA-MB-231 breast cancer cells. Proteins from control and TrkA overexpressing cells were separated using a cup-loading two-dimensional electrophoresis system before MALDI and LC-MS/MS mass spectrometry analysis. RESULTS Among several putative regulated proteins, Ku86 was found increased in TrkA overexpressing cells. Moreover, Ku86 was co-immunoprecipitated with TrkA, suggesting the interaction of these two proteins in TrkA overexpressing cells. Interestingly, inhibition with small-interfering RNA and neutralizing antibodies showed that Ku86 was required for TrkA-stimulated cell invasion. CONCLUSIONS AND CLINICAL RELEVANCE These data allowed the identification of Ku86 as a new player involved in metastasis in breast cancer cells. Our findings suggest that TrkA and its down stream signaling pathways should be regarded as potential new targets for the development of future breast cancer therapy.
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Affiliation(s)
- Chann Lagadec
- Signalisation des facteurs de croissance dans le cancer du sein. Proteomique fonctionnelle, Université Lille 1, Villeneuve d'Ascq, France
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Schikorski D, Cuvillier-Hot V, Boidin-Wichlacz C, Slomianny C, Salzet M, Tasiemski A. Deciphering the Immune Function and Regulation by a TLR of the Cytokine EMAPII in the Lesioned Central Nervous System Using a Leech Model. THE JOURNAL OF IMMUNOLOGY 2009; 183:7119-28. [DOI: 10.4049/jimmunol.0900538] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Linker RA, Brechlin P, Jesse S, Steinacker P, Lee DH, Asif AR, Jahn O, Tumani H, Gold R, Otto M. Proteome profiling in murine models of multiple sclerosis: identification of stage specific markers and culprits for tissue damage. PLoS One 2009; 4:e7624. [PMID: 19865482 PMCID: PMC2765069 DOI: 10.1371/journal.pone.0007624] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Accepted: 09/10/2009] [Indexed: 12/20/2022] Open
Abstract
The identification of new biomarkers is of high interest for the prediction of the disease course and also for the identification of pathomechanisms in multiple sclerosis (MS). To specify markers of the chronic disease phase, we performed proteome profiling during the later phase of myelin oligodendrocyte glycoprotein induced experimental autoimmune encephalomyelitis (MOG-EAE, day 35 after immunization) as a model disease mimicking many aspects of secondary progressive MS. In comparison to healthy controls, high resolution 2 dimensional gel electrophoresis revealed a number of regulated proteins, among them glial fibrilary acidic protein (GFAP). Phase specific up-regulation of GFAP in chronic EAE was confirmed by western blotting and immunohistochemistry. Protein levels of GFAP were also increased in the cerebrospinal fluid of MS patients with specificity for the secondary progressive disease phase. In a next step, proteome profiling of an EAE model with enhanced degenerative mechanisms revealed regulation of alpha-internexin, syntaxin binding protein 1, annexin V and glutamate decarboxylase in the ciliary neurotrophic factor (CNTF) knockout mouse. The identification of these proteins implicate an increased apoptosis and enhanced axonal disintegration and correlate well the described pattern of tissue injury in CNTF −/− mice which involve oligodendrocyte (OL) apoptosis and axonal injury. In summary, our findings underscore the value of proteome analyses as screening method for stage specific biomarkers and for the identification of new culprits for tissue damage in chronic autoimmune demyelination.
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Affiliation(s)
- Ralf A. Linker
- Department of Neurology, St. Josef-Hospital, Ruhr-University, Bochum, Germany
| | - Peter Brechlin
- Department of Neurodegeneration and Restorative Research, Center of Neurological Medicine, University of Goettingen, Goettingen, Germany
- DFG Research Center for Molecular Physiology of the Brain, Goettingen, Germany
| | - Sarah Jesse
- Department of Neurology, University of Ulm, Ulm, Germany
| | | | - D. H. Lee
- Department of Neurology, St. Josef-Hospital, Ruhr-University, Bochum, Germany
| | - Abdul R. Asif
- Department of Clinical Chemistry, University of Goettingen, Goettingen, Germany
| | - Olaf Jahn
- DFG Research Center for Molecular Physiology of the Brain, Goettingen, Germany
- Max-Planck-Institute for Experimental Medicine, Goettingen, Germany
| | | | - Ralf Gold
- Department of Neurology, St. Josef-Hospital, Ruhr-University, Bochum, Germany
| | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany
- * E-mail:
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Rabilloud T, Vaezzadeh AR, Potier N, Lelong C, Leize-Wagner E, Chevallet M. Power and limitations of electrophoretic separations in proteomics strategies. MASS SPECTROMETRY REVIEWS 2009; 28:816-843. [PMID: 19072760 DOI: 10.1002/mas.20204] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed.
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Sordet C, Culerrier R, Granier C, Rancé F, Didier A, Barre A, Rougé P. Expression of Jug r 1, the 2S albumin allergen from walnut (Juglans regia), as a correctly folded and functional recombinant protein. Peptides 2009; 30:1213-21. [PMID: 19540419 DOI: 10.1016/j.peptides.2009.03.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 03/13/2009] [Accepted: 03/13/2009] [Indexed: 11/23/2022]
Abstract
Jug r 1, the 2S albumin allergen from walnut, was isolated from ripe nuts as a native allergen and expressed in Escherichia coli using the Gateway technology as a recombinant allergen. The recombinant Jug r 1 (15 kDa) differs from the native allergen by the absence of cleavage of the polypeptide chain in two covalently associated light (3.5 kDa) and heavy (8 kDa) chains. Recombinant rJug r 1 adopts the canonical alpha-helical fold of plant 2S albumins as checked on CD spectra. Four IgE-binding epitopic stretches were identified along the amino acid sequence of Jug r 1 and localized on the molecular surface of the modeled allergen. Both native and recombinant allergens exhibit similar IgE-binding activity and similarly trigger the degranulation of a FcepsilonRI-expressing rat basophilic leukaemia cell line previously treated by IgE-containing sera. Native Jug r 1 resists to heat denaturation and to the proteolytic attack of trypsin and chymotrypsin but is readily hydrolyzed in the presence of pepsin at acidic pH after 1 h of incubation at 37 degrees C in vitro. Recombinant Jug r 1 could be used for a component-resolved diagnosis of food-allergy.
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Affiliation(s)
- Camille Sordet
- UMR Université Paul Sabatier-CNRS 5546, Pôle de Biotechnologie végétale, 24 Chemin de Borde Rouge, 31326 Castanet Tolosan, France
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Sordet C, Culerrier R, Granier C, Didier A, Rougé P. IgE-binding epitopic peptide mapping on a three-dimensional model built for the 13S globulin allergen of buckwheat (Fagopyrum esculentum). Peptides 2009; 30:1021-7. [PMID: 19463732 DOI: 10.1016/j.peptides.2009.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 03/05/2009] [Accepted: 03/05/2009] [Indexed: 11/25/2022]
Abstract
The three-dimensional model built for the 13S globulin allergen of buckwheat (Fagopyrum esculentum) consists of three protomers exhibiting the cupin motif, arranged in a homotrimer around a three-fold symmetry axis. Using the SPOT technique, 11 continuous IgE-binding epitopic peptides were characterized on the molecular surface of the 13S globulin allergen of buckwheat. Except for one of them, they all correspond to well exposed regions containing electropositiveley and/or electronegatively charged residues, which cover up to 40% of the molecular surface of the allergen. Some of these epitopes come in close contact to probably create more extended discontinuous epitopes, especially those located on the edge of the 13S globulin homotrimer. Half of the identified epitope peptides remain unaltered in a core structure protected against hydrolysis by digestive proteases and are thus assumed to promote the allergenicity of the 13S globulin. In addition, a few of these epitopes coincide with sequential IgE-binding epitopes previously characterized in soybean 11S globulins, that could account for the IgE-binding cross-reactions observed between soybean and buckwheat in Western blot experiments.
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Affiliation(s)
- Camille Sordet
- UMR-CNRS 5546, Université de Toulouse, Castanet Tolosan, France
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Tahtouh M, Croq F, Vizioli J, Sautiere PE, Van Camp C, Salzet M, Daha MR, Pestel J, Lefebvre C. Evidence for a novel chemotactic C1q domain-containing factor in the leech nerve cord. Mol Immunol 2009; 46:523-31. [DOI: 10.1016/j.molimm.2008.07.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 07/15/2008] [Accepted: 07/15/2008] [Indexed: 10/21/2022]
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Chevallet M, Luche S, Diemer H, Strub JM, Van Dorsselaer A, Rabilloud T. Sweet silver: A formaldehyde-free silver staining using aldoses as developing agents, with enhanced compatibility with mass spectrometry. Proteomics 2008; 8:4853-61. [DOI: 10.1002/pmic.200800321] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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50
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Brechlin P, Jahn O, Steinacker P, Cepek L, Kratzin H, Lehnert S, Jesse S, Mollenhauer B, Kretzschmar HA, Wiltfang J, Otto M. Cerebrospinal fluid-optimized two-dimensional difference gel electrophoresis (2-D DIGE) facilitates the differential diagnosis of Creutzfeldt-Jakob disease. Proteomics 2008; 8:4357-66. [DOI: 10.1002/pmic.200800375] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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