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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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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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Disulfide-bond-mediated cross-linking of corneous beta-proteins in lepidosaurian epidermis. ZOOLOGY 2017; 126:145-153. [PMID: 29129393 DOI: 10.1016/j.zool.2017.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 10/27/2017] [Accepted: 10/27/2017] [Indexed: 01/29/2023]
Abstract
Corneous beta-proteins (CBPs), formerly referred to as beta-keratins, are major protein components of the epidermis in lepidosaurian reptiles and are largely responsible for their material properties. These proteins have been suggested to form filaments of 3.4nm in thickness and to interact with themselves or with other proteins, including intermediate filament (IF) keratins. Here, we performed immunocytochemical labeling of CBPs in the epidermis of different lizards and snakes and investigated by immunoblotting analysis whether the reduction of disulfide bonds or protein oxidation affects the solubility and mobility of these CBPs. Immunogold labeling suggested that CBPs are partly co-localized with IF-keratins in differentiating and mature beta-cells. The chemical reduction of epidermal proteins from lizard and snake epidermis increased the abundance of CBP-immunoreactive bands in the size range of CBP monomers on Western blots. Conversely, in vitro oxidation of epidermal proteins reduced the abundance of putative CBP monomers. Some modifications in the IF-keratin range were also noted. These results strongly indicate that CBPs associate with IF-keratins and other proteins via disulfide bonds in the epidermis of lizards and snakes, which likely contributes to the resilience of the cornified beta- and alpha-layers of the lepidosaurian epidermis in live animals and after shedding.
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Wu X, Xu C, Wang W. Reduction and Alkylation of Proteins in 2D Gel Electrophoresis: Before or after Isoelectric Focusing? Front Chem 2017; 5:59. [PMID: 28861411 PMCID: PMC5559430 DOI: 10.3389/fchem.2017.00059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/02/2017] [Indexed: 01/11/2023] Open
Affiliation(s)
- Xiaolin Wu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
| | - Chenhui Xu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
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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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Simultaneous Two-Dimensional Difference Gel Electrophoresis (2D-DIGE) Analysis of Two Distinct Proteomes. Methods Mol Biol 2017; 1546:205-212. [PMID: 27896770 DOI: 10.1007/978-1-4939-6730-8_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This chapter describes the basics, applications, and limitations of two-dimensional gel electrophoresis (2DE) and two-dimensional difference gel electrophoresis (2D-DIGE) for multiplex analysis of distinct proteomes. We also propose a basic protocol for 2D-DIGE, technique that allows the analysis of paired protein extracts, which are labeled with fluorescent Cy3 and Cy5 dyes and electrophoresed with a Cy2-labeled standard extract on the same 2DE gels. Scanning the gels at wavelengths specific for each dye allows direct overlay the two different proteomes and the differences in abundance of specific protein spots can be determined.
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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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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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Darja O, Stanislav M, Saša S, Andrej F, Lea B, Branka J. Responses of CHO cell lines to increased pCO2 at normal (37 °C) and reduced (33 °C) culture temperatures. J Biotechnol 2015; 219:98-109. [PMID: 26707809 DOI: 10.1016/j.jbiotec.2015.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 11/07/2015] [Accepted: 12/11/2015] [Indexed: 12/12/2022]
Abstract
The correlation between dissolved carbon dioxide (pCO2) and cell growth, cell metabolism, productivity and product quality has often been reported. However, since pCO2 values in bioprocesses always vary concurrently with other bioprocess variables, it is very difficult to distinguish only the effect of pCO2. The aim of our work was to investigate further the specific effect of pCO2 and cell response on a proteome level. Proteome responses of three different CHO-Der3 cell lines in the exponential growth phase at normal (37 °C) and reduced (33 °C) culture temperatures, with normal (10%) and increased (20%) pCO2, were studied by comparative proteomic analysis (2D-DIGE). Cell viability and cell density, and the concentration of glucose, glutamine and lactate monitored over 72-h cultures showed that elevated pCO2 did not affect cell viability or productivity at either culture temperature, while metabolic activity was reduced. The specific metabolic profile also indicated altered glucose metabolism toward a less efficient anaerobic metabolism. Two-way ANOVA of proteomic data discriminated many more pCO2-specific changes in protein abundance (p<0.01) at 33 °C than at 37 °C and PCA analysis was able to distinguish clusters distinguishing cell lines and culture conditions at low temperature and elevated pCO2, indicating substantial proteome changes under these culture conditions. Cell sensitivity to increased pCO2 at the lower temperature was further confirmed by a significantly increased abundance of twelve proteins involved in anti- oxidative mechanisms and increased abundance of six proteins involved in glycolysis, including L-lactate dehydrogenase. Proteomic results support the metabolic data and the proposed pCO2 invoked metabolic switch toward anaerobic pathways. Anti- oxidative mechanisms, together with the anaerobic metabolism, allow the cells to detoxify while maintaining sufficient energy levels to preserve their vitality and functionality. This study provides further insight into the proteome responses of CHO cell lines to increased pCO2 at the two culture temperatures.
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Affiliation(s)
| | - Mandelc Stanislav
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia.
| | | | | | - Bojić Lea
- Lek Pharmaceuticals d.d., 1000 Ljubljana, Slovenia.
| | - Javornik Branka
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia.
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Arlas T, Wolf C, Petrucci B, Estanislau J, Gregory R, Jobim M, Mattos R. Proteomics of endometrial fluid after dexamethasone treatment in mares susceptible to endometritis. Theriogenology 2015; 84:617-23. [DOI: 10.1016/j.theriogenology.2015.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/07/2015] [Accepted: 04/22/2015] [Indexed: 10/23/2022]
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Suojalehto H, Kinaret P, Kilpeläinen M, Toskala E, Ahonen N, Wolff H, Alenius H, Puustinen A. Level of Fatty Acid Binding Protein 5 (FABP5) Is Increased in Sputum of Allergic Asthmatics and Links to Airway Remodeling and Inflammation. PLoS One 2015; 10:e0127003. [PMID: 26020772 PMCID: PMC4447257 DOI: 10.1371/journal.pone.0127003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 04/09/2015] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The inflammatory processes in the upper and lower airways in allergic rhinitis and asthma are similar. Induced sputum and nasal lavage fluid provide a non-invasive way to examine proteins involved in airway inflammation in these conditions. OBJECTIVES We conducted proteomic analyses of sputum and nasal lavage fluid samples to reveal differences in protein abundances and compositions between the asthma and rhinitis patients and to investigate potential underlying mechanisms. METHODS Induced sputum and nasal lavage fluid samples were collected from 172 subjects with 1) allergic rhinitis, 2) asthma combined with allergic rhinitis, 3) nonallergic rhinitis and 4) healthy controls. Proteome changes in 21 sputum samples were analysed with two-dimensional difference gel electrophoresis (2D-DIGE), and the found differentially regulated proteins identified with mass spectrometry. Immunological validation of identified proteins in the sputum and nasal lavage fluid samples was performed with Western blot and ELISA. RESULTS Altogether 31 different proteins were identified in the sputum proteome analysis, most of these were found also in the nasal lavage fluid. Fatty acid binding protein 5 (FABP5) was up-regulated in the sputum of asthmatics. Immunological validation in the whole study population confirmed the higher abundance levels of FABP5 in asthmatic subjects in both the sputum and nasal lavage fluid samples. In addition, the vascular endothelial growth factor (VEGF) level was increased in the nasal lavage fluid of asthmatics and there were positive correlations between FABP5 and VEGF levels (r=0.660, p<0.001) and concentrations of FABP5 and cysteinyl leukotriene (CysLT) (r=0.535, p<0.001) in the nasal lavage fluid. CONCLUSIONS FABP5 may contribute to the airway remodeling and inflammation in asthma by fine-tuning the levels of CysLTs, which induce VEGF production.
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Affiliation(s)
- Hille Suojalehto
- Occupational Medicine Team, Finnish Institute of Occupational Health, Helsinki, Finland
- * E-mail:
| | - Pia Kinaret
- Unit of Systems Toxicology, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Maritta Kilpeläinen
- Department of Pulmonary Diseases and Allergology, University of Turku, Turku, Finland
| | - Elina Toskala
- Department of Otolaryngology- Head and Neck Surgery, Temple University, Philadelphia, United States of America
| | - Niina Ahonen
- Unit of Systems Toxicology, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Henrik Wolff
- Unit of Systems Toxicology, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Harri Alenius
- Unit of Systems Toxicology, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Anne Puustinen
- Unit of Systems Toxicology, Finnish Institute of Occupational Health, Helsinki, Finland
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van Tilburg MF, Salles MGF, Silva MM, Moreira RA, Moreno FB, Monteiro-Moreira ACO, Martins JAM, Cândido MJD, Araújo AA, Moura AAA. Semen variables and sperm membrane protein profile of Saanen bucks (Capra hircus) in dry and rainy seasons of the northeastern Brazil (3°S). INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2015; 59:561-573. [PMID: 25086569 DOI: 10.1007/s00484-014-0869-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 07/01/2014] [Accepted: 07/02/2014] [Indexed: 06/03/2023]
Abstract
The Saanen is a highly productive breed, and for this reason, it has been raised in Brazil, but mostly under climate conditions completely different from where the breed originated. The objective of this study was to investigate variations in semen parameters and sperm membrane proteins from Saanen bucks (n = 7) raised in Northeastern Brazil, during dry season (September, October, and November) and rainy season (March, April, and May). We showed that during the dry season, sperm motility, concentration, and the percentage of normal sperm decreased as compared to the rainy season. Rectal temperatures of bucks had no significant (p > 0.05) variations during the dry and rainy seasons. However, temperatures of left and right skin testis were higher (p < 0.05) during the dry as compared to the rainy season. Expression of three proteins (lysine-specific demethylase 5D, adenosine triphosphate (ATP) synthase subunit d, and radial spoke head protein 9 homolog) in sperm membrane were more intense in rainy season and only one protein (cytosol aminopeptidase) had greater expression in the dry season of the year. Our results show that mechanisms of testicular thermoregulation of Saanen bucks did not prevent a decrease in seminal parameters during the dry season. This deterioration may be related to reduced expression of proteins associated with important functions in sperm membrane.
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Affiliation(s)
- M F van Tilburg
- Department of Animal Science, Federal University of Ceará, Av. Mister Hull S/N, Campus Pici, Fortaleza, CE, Brazil, 60021-970
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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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Zhang F, Liu H, Jiang G, Wang H, Wang X, Wang H, Fang R, Cai S, Du J. Changes in the proteomic profile during the differential polarization status of the human monocyte-derived macrophage THP-1 cell line. Proteomics 2015; 15:773-86. [PMID: 25411139 DOI: 10.1002/pmic.201300494] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 10/12/2014] [Accepted: 11/17/2014] [Indexed: 12/25/2022]
Abstract
Macrophages are heterogeneous and plastic populations that are an essential component of inflammation and host defense. To understand how macrophages respond to cytokine signals, we used 2DE to identify protein profiles in macrophages stimulated with interleukin 4 (M2) and those stimulated with lipopolysaccharide and interferon γ (M1). In total, 32 differentially expressed proteins in THP-1 cells were identified by MALDI-TOF MS/MS analysis. The different proteins were mainly involved in cellular structure, protein metabolism, stress response, oxidative response, and nitric oxide production during macrophage polarization. In particular, proteins playing important roles in production of nitric oxide (NO) were downregulated in M2 macrophages. Many antioxidant and heat shock proteins, which are related to oxidative response, were upregulated in M2 macrophages. More importantly, a remarkable decrease in intracellular ROS and NO production were detected in M2 macrophages. Our results provide a proteomic profile of differentially polarized macrophages and validate the function of the identified proteins, which may indicate possible mechanism of macrophage polarization process.
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Affiliation(s)
- Fan Zhang
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, P. R. China
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Santucci L, Bruschi M, Ghiggeri GM, Candiano G. The latest advancements in proteomic two-dimensional gel electrophoresis analysis applied to biological samples. Methods Mol Biol 2015; 1243:103-125. [PMID: 25384742 DOI: 10.1007/978-1-4939-1872-0_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two-dimensional gel electrophoresis (2DE) is one of the fundamental approaches in proteomics for the separation and visualization of complex protein mixtures. Proteins can be analyzed by 2DE using isoelectric focusing (IEF) in the first dimension, combined to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension, gel staining (silver and Coomassie), image analysis, and 2DE gel database. High-resolution 2DE can resolve up to 5,000 different proteins simultaneously (∼2,000 proteins routinely), and detect and quantify <1 ng of protein per spot. Here, we describe the latest developments for a more complete analysis of biological fluids.
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Affiliation(s)
- Laura Santucci
- Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Largo G. Gaslini 5, Genoa, Italy
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17
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Spagnolo A, Magnin-Robert M, Alayi TD, Cilindre C, Schaeffer-Reiss C, Van Dorsselaer A, Clément C, Larignon P, Ramirez-Suero M, Chong J, Bertsch C, Abou-Mansour E, Fontaine F. Differential responses of three grapevine cultivars to Botryosphaeria dieback. PHYTOPATHOLOGY 2014; 104:1021-35. [PMID: 24724741 DOI: 10.1094/phyto-01-14-0007-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Botryosphaeria dieback is a fungal grapevine trunk disease that represents a threat for viticulture worldwide due to the decreased production of affected plants and their premature death. This dieback is characterized by a typical wood discoloration called brown stripe. Herein, a proteome comparison of the brown striped wood from Botryosphaeria dieback-affected standing vines cultivars Chardonnay, Gewurztraminer, and Mourvèdre was performed. The transcript analysis for 15 targeted genes and the quantification of both total phenolics and specific stilbenes were also performed. Several pathogenesis-related proteins and members of the antioxidant system were more abundant in the brown striped wood of the three cultivars, whereas other defense-related proteins were less abundant. Additionally, total phenolics and some specific stilbenes were more accumulated in the brown striped wood. Strongest differences among the cultivars concerned proteins of the primary metabolism, which looked to be particularly impaired in the brown striped wood of 'Chardonnay'. Low abundance of some proteins involved in defense response probably contributes to make global response insufficient to avoid the symptom development. The differential susceptibility of the three grapevine cultivars could be linked to the diverse expression of various proteins involved in defense response, stress tolerance, and metabolism.
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Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts. J Biosci 2014; 39:631-42. [DOI: 10.1007/s12038-014-9453-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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19
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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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20
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In vitro biomarker discovery in the parasitic flatworm Fasciola hepatica for monitoring chemotherapeutic treatment. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.02.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Lee DY, Lee SS, Joo WA, Lee EJ, Kim CW. Analysis of Differentially Regulated Proteins in TM4 Cells Treated with Bisphenol A. Biosci Biotechnol Biochem 2014; 68:1201-8. [PMID: 15215581 DOI: 10.1271/bbb.68.1201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BPA, bisphenol A, a monomer of epoxy resins and polycarbonate plastic, is used in many consumer products including the plastic linings of cans for food and babies' bottles. BPA has been reported to cause reproductive toxicity and affects cells in rats and mice at high doses. In this study, the effect of BPA on protein expression in TM4 cells (a mouse Sertoli cell line) known to play an essential role in Spermatogenesis was investigated by two-dimensional electrophoresis (2-DE). After 16 h exposure to 50, 100, 150, 200, and 250 microM of BPA, the viability of TM4 cells decreased to about 90, 85, 78, 55, and 30% of control respectively. Approximately 800 protein spots in TM4 cells were analyzed by 2-DE with pH 4-7 linear immobilized pH gradient (IPG) Dry Strip, and 11 proteins which showed significantly different expression levels were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Among these, HSP 27 and placental calcium binding protein may be proteins differentially expressed by BPA exposure.
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Affiliation(s)
- Do-Youn Lee
- Graduate School of Life Sciences and Biotechnology, Korea University, Seoul, Korea
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22
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Paleoproteomics explained to youngsters: how did the wedding of two-dimensional electrophoresis and protein sequencing spark proteomics on: let there be light. J Proteomics 2014; 107:5-12. [PMID: 24657497 DOI: 10.1016/j.jprot.2014.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 11/22/2022]
Abstract
UNLABELLED Taking the opportunity of the 20th anniversary of the word "proteomics", this young adult age is a good time to remember how proteomics came from enormous progress in protein separation and protein microanalysis techniques, and from the conjugation of these advances into a high performance and streamlined working setup. However, in the history of the almost three decades that encompass the first attempts to perform large scale analysis of proteins to the current high throughput proteomics that we can enjoy now, it is also interesting to underline and to recall how difficult the first decade was. Indeed when the word was cast, the battle was already won. This recollection is mostly devoted to the almost forgotten period where proteomics was being conceived and put to birth, as this collective scientific work will never appear when searched through the keyword "proteomics". BIOLOGICAL SIGNIFICANCE The significance of this manuscript is to recall and review the two decades that separated the first attempts of performing large scale analysis of proteins from the solid technical corpus that existed when the word "proteomics" was coined twenty years ago. This recollection is made within the scientific historical context of this decade, which also saw the blossoming of DNA cloning and sequencing. This article is part of a Special Issue entitled: 20 years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini , Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
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Arlas T, Wolf C, Petrucci B, Estanislau J, Gregory R, Jobim M, Mattos R. Effect of dexamethasone on proteomics of endometrial fluid from mares susceptible to endometritis. J Equine Vet Sci 2014. [DOI: 10.1016/j.jevs.2013.10.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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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25
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Moche M, Albrecht D, Maaß S, Hecker M, Westermeier R, Büttner K. The new horizon in 2D electrophoresis: New technology to increase resolution and sensitivity. Electrophoresis 2013; 34:1510-8. [DOI: 10.1002/elps.201200618] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/18/2013] [Accepted: 02/14/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Martin Moche
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | - Dirk Albrecht
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | - Sandra Maaß
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | - Michael Hecker
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | | | - Knut Büttner
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
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26
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van Tilburg M, Rodrigues M, Moreira R, Moreno F, Monteiro-Moreira A, Cândido M, Moura A. Membrane-associated proteins of ejaculated sperm from Morada Nova rams. Theriogenology 2013; 79:1247-61. [DOI: 10.1016/j.theriogenology.2013.03.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 02/20/2013] [Accepted: 03/16/2013] [Indexed: 12/22/2022]
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27
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Hanreich A, Schimpf U, Zakrzewski M, Schlüter A, Benndorf D, Heyer R, Rapp E, Pühler A, Reichl U, Klocke M. Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst Appl Microbiol 2013; 36:330-8. [PMID: 23694815 DOI: 10.1016/j.syapm.2013.03.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 03/01/2013] [Accepted: 03/07/2013] [Indexed: 11/27/2022]
Abstract
Microbial communities in biogas batch fermentations, using straw and hay as co-substrates, were analyzed at the gene and protein level by metagenomic and metaproteomic approaches. The analysis of metagenomic data revealed that the Clostridiales and Bacteroidales orders were prevalent in the community. However, the number of sequences assigned to the Clostridiales order decreased during fermentation, whereas the number of sequences assigned to the Bacteroidales order increased. In addition, changes at the functional level were monitored and the metaproteomic analyses detected transporter proteins and flagellins, which were expressed mainly by members of the Bacteroidetes and Firmicutes phyla. A high number of sugar transporters, expressed by members of the Bacteroidetes, proved their potential to take up various glycans efficiently. Metagenome data also showed that methanogenic organisms represented less than 4% of the community, while 20-30% of the identified proteins were of archeal origin. These data suggested that methanogens were disproportionally active. In conclusion, the community studied was capable of digesting the recalcitrant co-substrate. Members of the Firmicutes phylum seemed to be the main degraders of cellulose, even though expression of only a few glycoside hydrolases was detected. The Bacteroidetes phylum expressed a high number of sugar transporters and seemed to specialize in the digestion of other polysaccharides. Finally, it was found that key enzymes of methanogenesis were expressed in high quantities, indicating the high metabolic activity of methanogens, although they only represented a minor group within the microbial community.
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Affiliation(s)
- Angelika Hanreich
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, 14469 Potsdam, Germany
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28
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Chalfoun NR, Grellet-Bournonville CF, Martínez-Zamora MG, Díaz-Perales A, Castagnaro AP, Díaz-Ricci JC. Purification and characterization of AsES protein: a subtilisin secreted by Acremonium strictum is a novel plant defense elicitor. J Biol Chem 2013; 288:14098-14113. [PMID: 23530047 DOI: 10.1074/jbc.m112.429423] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this work, the purification and characterization of an extracellular elicitor protein, designated AsES, produced by an avirulent isolate of the strawberry pathogen Acremonium strictum, are reported. The defense eliciting activity present in culture filtrates was recovered and purified by ultrafiltration (cutoff, 30 kDa), anionic exchange (Q-Sepharose, pH 7.5), and hydrophobic interaction (phenyl-Sepharose) chromatographies. Two-dimensional SDS-PAGE of the purified active fraction revealed a single spot of 34 kDa and pI 8.8. HPLC (C2/C18) and MS/MS analysis confirmed purification to homogeneity. Foliar spray with AsES provided a total systemic protection against anthracnose disease in strawberry, accompanied by the expression of defense-related genes (i.e. PR1 and Chi2-1). Accumulation of reactive oxygen species (e.g. H2O2 and O2(˙)) and callose was also observed in Arabidopsis. By using degenerate primers designed from the partial amino acid sequences and rapid amplification reactions of cDNA ends, the complete AsES-coding cDNA of 1167 nucleotides was obtained. The deduced amino acid sequence showed significant identity with fungal serine proteinases of the subtilisin family, indicating that AsES is synthesized as a larger precursor containing a 15-residue secretory signal peptide and a 90-residue peptidase inhibitor I9 domain in addition to the 283-residue mature protein. AsES exhibited proteolytic activity in vitro, and its resistance eliciting activity was eliminated when inhibited with PMSF, suggesting that its proteolytic activity is required to induce the defense response. This is, to our knowledge, the first report of a fungal subtilisin that shows eliciting activity in plants. This finding could contribute to develop disease biocontrol strategies in plants by activating its innate immunity.
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Affiliation(s)
- Nadia R Chalfoun
- Instituto Superior de Investigaciones Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, and Instituto de Química Biológica "Dr. Bernabé Bloj," Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, T4000ILJ San Miguel de Tucumán, Argentina
| | - Carlos F Grellet-Bournonville
- Instituto Superior de Investigaciones Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, and Instituto de Química Biológica "Dr. Bernabé Bloj," Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, T4000ILJ San Miguel de Tucumán, Argentina
| | - Martín G Martínez-Zamora
- Instituto Superior de Investigaciones Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, and Instituto de Química Biológica "Dr. Bernabé Bloj," Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, T4000ILJ San Miguel de Tucumán, Argentina
| | - Araceli Díaz-Perales
- Unidad de Química y Bioquímica, Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Atilio P Castagnaro
- Sección Biotecnología, Estación Experimental Agroindustrial Obispo Colombres, T4101XAC Las Talitas, Tucumán, Argentina
| | - Juan C Díaz-Ricci
- Instituto Superior de Investigaciones Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, and Instituto de Química Biológica "Dr. Bernabé Bloj," Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, T4000ILJ San Miguel de Tucumán, Argentina.
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Identification of fitness determinants in Enterococcus faecalis by differential proteomics. Arch Microbiol 2012; 195:121-30. [PMID: 23239053 DOI: 10.1007/s00203-012-0857-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/14/2012] [Accepted: 11/26/2012] [Indexed: 01/25/2023]
Abstract
Enterococcus (E.) faecalis is found as commensal in healthy humans, in a variety of fermented foods. It can serve as probiotic but also as pathogen causing endocarditis, bacteremia and urinary tract infections. We have employed a proteomic study with E. faecalis strain OG1RF under different growth conditions and in contact to mouse intestinal cells to identify novel latent and adaptive fitness determinants. These relate to changes in catabolic pathways (BudA), protein biosynthesis (AsnS), cellular surface biosynthesis (RmlA) and regulatory mechanisms (OmpR). This knowledge can be used to derive novel evidence-based targets, which can be used to further elucidate gene expression changes enhancing pathogenicity or fitness in a commensal strain and possibly delineate this species into groups of higher and lower risk for applications in a food or a medical context versus improved treatment strategies of the so far hard to cure diseases.
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Jha S, Agarwal S, Sanyal I, Jain GK, Amla DV. Differential subcellular targeting of recombinant human α₁-proteinase inhibitor influences yield, biological activity and in planta stability of the protein in transgenic tomato plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 196:53-66. [PMID: 23017899 DOI: 10.1016/j.plantsci.2012.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 07/06/2012] [Accepted: 07/09/2012] [Indexed: 06/01/2023]
Abstract
The response of protein accumulation site on yield, biological activity and in planta stability of therapeutic recombinant human proteinase inhibitor (α₁-PI) was analyzed via targeting to different subcellular locations, like endoplasmic reticulum (ER), apoplast, vacuole and cytosol in leaves of transgenic tomato plants. In situ localization of the recombinant α₁-PI protein in transgenic plant cells was monitored by immunohistochemical staining. Maximum accumulation of recombinant α₁-PI in T₀ and T₁ transgenic tomato plants was achieved from 1.5 to 3.2% of total soluble protein (TSP) by retention in ER lumen, followed by vacuole and apoplast, whereas cytosolic targeting resulted into degradation of the protein. The plant-derived recombinant α₁-PI showed biological activity for elastase inhibition, as monitored by residual porcine pancreatic elastase (PPE) activity assay and band-shift assay. Recombinant α₁-PI was purified from transgenic tomato plants with high yield, homogeneity and biological activity. Purified protein appeared as a single band of ∼48-50 kDa on SDS-PAGE with pI value ranging between 5.1 and 5.3. Results of mass spectrometry and optical spectroscopy of purified recombinant α₁-PI revealed the structural integrity of the recombinant protein comparable to native serum α₁-PI. Enzymatic deglycosylation and lectin-binding assays with the purified recombinant α₁-PI showed compartment-specific N-glycosylation of the protein targeted to ER, apoplast and vacuole. Conformational studies based on urea-induced denaturation and circular dichroism (CD) spectroscopy revealed relatively lower stability of the recombinant α₁-PI protein, compared to its serum counterpart. Pharmacokinetic evaluation of plant derived recombinant and human plasma-purified α₁-PI in rat, by intravenous route, revealed significantly faster plasma clearance and lower area under curve (AUC) of recombinant protein. Our data suggested significance of protein sorting sequences and feasibility to use transgenic plants for the production of stable, glycosylated and biologically active recombinant α₁-PI for further therapeutic applications.
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Affiliation(s)
- Shweta Jha
- Plant Transgenic Lab, CSIR-National Botanical Research Institute, Rana Pratap Marg, P.O. Box 436, Lucknow 226001, India
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31
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Föcking M, Chen WQ, Dicker P, Dunn MJ, Lubec G, Cotter DR. Proteomic analysis of human hippocampus shows differential protein expression in the different hippocampal subfields. Proteomics 2012; 12:2477-81. [DOI: 10.1002/pmic.201200031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Melanie Föcking
- Department of Psychiatry; Royal College of Surgeons in Ireland; Dublin; Ireland
| | - Wei-Qiang Chen
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - Patrick Dicker
- Department of Epidemiology; Royal College of Surgeons in Ireland; Dublin; Ireland
| | - Michael J. Dunn
- Proteome Research Centre; UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences; Dublin; Ireland
| | - Gert Lubec
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - David R. Cotter
- Department of Psychiatry; Royal College of Surgeons in Ireland; Dublin; Ireland
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32
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Hanreich A, Heyer R, Benndorf D, Rapp E, Pioch M, Reichl U, Klocke M. Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass. Can J Microbiol 2012; 58:917-22. [DOI: 10.1139/w2012-058] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Complex consortia of microorganisms are responsible for biogas production. A lot of information about the taxonomic structure and enzymatic potential of such communities has been collected by a variety of gene-based approaches, yet little is known about which of all the assumable metabolic pathways are active throughout the process of biogas formation. To tackle this problem, we established a protocol for the metaproteomic analysis of samples taken from biogas reactors fed with agricultural biomass. In contrast to previous studies where an anaerobic digester was fed with synthetic wastewater, the complex matrix in this study required the extraction of proteins with liquid phenol and the application of paper bridge loading for 2-dimensional gel electrophoresis. Proteins were subjected to nanoHPLC (high-performance liquid chromatography) coupled to tandem mass spectrometry for characterization. Several housekeeping proteins as well as methanogenesis-related enzymes were identified by a MASCOT search and de novo sequencing, which proved the feasibility of our approach. The establishment of such an approach is the basis for further metaproteomic studies of biogas-producing communities. In particular, the apparent status of metabolic activities within the communities can be monitored. The knowledge collected from such experiments could lead to further improvements of biogas production.
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Affiliation(s)
- Angelika Hanreich
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Robert Heyer
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Dirk Benndorf
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtor Straße 1, 39106 Magdeburg, Germany
| | - Markus Pioch
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Udo Reichl
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtor Straße 1, 39106 Magdeburg, Germany
| | - Michael Klocke
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, 14469 Potsdam, Germany
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Junrong T, Huancheng Z, Feng H, Yi G, Xiaoqin Y, Zhengmao L, Hong Z, Jianying Z, Yin W, Yuanhang H, Jianlin Z, Longhua S, Guolin H. Proteomic identification of CIB1 as a potential diagnostic factor in hepatocellular carcinoma. J Biosci 2012; 36:659-68. [PMID: 21857112 DOI: 10.1007/s12038-011-9101-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC), among the most common malignancies worldwide, remains a major threat to public health, and there is an urgent need to identify novel biomarkers for diagnosis, prognosis and targets for anti-cancer treatment. In this study, two-dimensional polyacrylamide gel electrophoresis coupled with ESI-Q-TOF MS/MS analysis was used to identify differentially expressed proteins among the HCC tumour centre, tumour margin and nontumourous liver tissues. In total, 52 spots with significant alteration were positively identified byMS/MSanalysis. Altered expression of representative proteins, including CIB1, was validated by Western blotting. Immunostaining suggested an increase tendency of CIB1 expression from nontumourous liver tissue to tumour centre. Knockdown of CIB1 expression by RNA interference led to the significant suppression of the cell growth in hepatoma HepG2 cells. These data suggest that CIB1 may be used as a novel prognostic factor and possibly an attractive therapeutic target for HCC.
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Affiliation(s)
- Tong Junrong
- Department of Nephrology, Guangzhou Army General Hospital Guangzhou 510010, China.
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Giuliano S, Iadarola P, Leva V, Montecucco A, Camerini S, Crescenzi M, Salvini R, Bardoni A. An insight into the abundant proteome of 46BR.1G1 fibroblasts deficient of DNA ligase I. Electrophoresis 2012; 33:307-15. [DOI: 10.1002/elps.201100332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Serena Giuliano
- Department of Biochemistry “A. Castellani”, University of Pavia, Pavia, Italy
| | - Paolo Iadarola
- Department of Biochemistry “A. Castellani”, University of Pavia, Pavia, Italy
| | - Valentina Leva
- Institute of Molecular Genetics, National Council of Research, Pavia, Italy
| | | | - Serena Camerini
- Department of Cell Biology and Neurosciences, National Institute of Health, Rome, Italy
| | - Marco Crescenzi
- Department of Cell Biology and Neurosciences, National Institute of Health, Rome, Italy
| | - Roberta Salvini
- Department of Biochemistry “A. Castellani”, University of Pavia, Pavia, Italy
| | - Anna Bardoni
- Department of Biochemistry “A. Castellani”, University of Pavia, Pavia, Italy
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Abstract
Two-dimensional electrophoresis (2-DE) is a high-resolution technique for analysis and comparison of complex protein mixtures. With the advent of recent technical developments, its application has become significant in a wide range of fields. This chapter describes a proteomic approach for the analysis of metastasis-associated proteins using pre-fractionation of glycosylated proteins via lectin (HPA) affinity chromatography prior to separation by 2-DE. Guidelines for the preparation and storage of buffers, experimental conditions and protocols of affinity chromatography, isoelectric focussing, and SDS-PAGE conditions are provided. Critical parameters associated with the different steps of 2-DE are discussed.
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Affiliation(s)
- Miriam Dwek
- Department of Molecular and Applied Biosciences, School of Life Sciences, University of Westminster, London, UK.
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Rajjou L, Belghazi M, Catusse J, Ogé L, Arc E, Godin B, Chibani K, Ali-Rachidi S, Collet B, Grappin P, Jullien M, Gallardo K, Job C, Job D. Proteomics and posttranslational proteomics of seed dormancy and germination. Methods Mol Biol 2011; 773:215-36. [PMID: 21898259 DOI: 10.1007/978-1-61779-231-1_14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The seed is the dispersal unit of plants and must survive the vagaries of the environment. It is the object of intense genetic and genomic studies because processes related to seed quality affect crop yield and the seed itself provides food for humans and animals. Presently, the general aim of postgenomics analyses is to understand the complex biochemical and molecular processes underlying seed quality, longevity, dormancy, and vigor. Due to advances in functional genomics, the recent past years have seen a tremendous progress in our understanding of several aspects of seed development and germination. Here, we describe the proteomics protocols (from protein extraction to mass spectrometry) that can be used to investigate several aspects of seed physiology, including germination and its hormonal regulation, dormancy release, and seed longevity. These techniques can be applied to the study of both model plants (such as Arabidopsis) and crops.
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Affiliation(s)
- Loïc Rajjou
- AgroParisTech, Unité de Formation et de Recherche de Physiologie Végétale, Paris, France.
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Spagnolo A, Magnin-Robert M, Alayi TD, Cilindre C, Mercier L, Schaeffer-Reiss C, Van Dorsselaer A, Clément C, Fontaine F. Physiological changes in green stems of Vitis vinifera L. cv. Chardonnay in response to esca proper and apoplexy revealed by proteomic and transcriptomic analyses. J Proteome Res 2011; 11:461-75. [PMID: 22050466 DOI: 10.1021/pr200892g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Among grapevine trunk diseases, esca proper and apoplexy commonly represent a threat for viticulture worldwide. To retrieve further information about the mechanisms activated in apoplectic and esca proper-affected plants, a two-dimensional gel electrophoresis (2-DE) based analysis was conducted on green stems from 26-year-old standing vines. Symptomatic and asymptomatic stems from both apoplectic (A) and esca proper-affected (E) plants compared to control (without visual symptom since 10 years) stems were studied. Thirty-three differentially expressed proteins were identified by nanoLC-MS/MS and included into three groups conceptually defined as proteins involved in (i) metabolism and energy, (ii) stress tolerance, and (iii) defense response. For nine of them, expression of the relative mRNA's was also monitored by qRT-PCR. Proteome variations were specifically related to apoplexy and esca proper but were more similar in asymptomatic stems than in the symptomatic ones. Remarkable quantitative differences were noted for several proteins in symptomatic stems according to the expressed form, A and E. Results further indicate that similar responses are likely activated in asymptomatic stems but a various quantitative expression is triggered upon onset of apoplexy or esca proper symptoms while both kind of plants are infected by the same pathogenic fungi.
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Affiliation(s)
- Alessandro Spagnolo
- Université de Reims Champagne-Ardenne, URVVC EA 2069, Laboratoire Stress, Défenses et Reproduction des Plantes, BP 1039, 51687 Reims Cedex 2, France
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Virlouvet L, Jacquemot MP, Gerentes D, Corti H, Bouton S, Gilard F, Valot B, Trouverie J, Tcherkez G, Falque M, Damerval C, Rogowsky P, Perez P, Noctor G, Zivy M, Coursol S. The ZmASR1 protein influences branched-chain amino acid biosynthesis and maintains kernel yield in maize under water-limited conditions. PLANT PHYSIOLOGY 2011; 157:917-36. [PMID: 21852416 PMCID: PMC3192578 DOI: 10.1104/pp.111.176818] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 08/04/2011] [Indexed: 05/02/2023]
Abstract
Abscisic acid-, stress-, and ripening-induced (ASR) proteins were first described about 15 years ago as accumulating to high levels during plant developmental processes and in response to diverse stresses. Currently, the effects of ASRs on water deficit tolerance and the ways in which their physiological and biochemical functions lead to this stress tolerance remain poorly understood. Here, we characterized the ASR gene family from maize (Zea mays), which contains nine paralogous genes, and showed that maize ASR1 (ZmASR1) was encoded by one of the most highly expressed paralogs. Ectopic expression of ZmASR1 had a large overall impact on maize yield that was maintained under water-limited stress conditions in the field. Comparative transcriptomic and proteomic analyses of wild-type and ZmASR1-overexpressing leaves led to the identification of three transcripts and 16 proteins up- or down-regulated by ZmASR1. The majority of them were involved in primary and/or cellular metabolic processes, including branched-chain amino acid (BCAA) biosynthesis. Metabolomic and transcript analyses further indicated that ZmASR1-overexpressing plants showed a decrease in BCAA compounds and changes in BCAA-related gene expression in comparison with wild-type plants. Interestingly, within-group correlation matrix analysis revealed a close link between 13 decreased metabolites in ZmASR1-overexpressing leaves, including two BCAAs. Among these 13 metabolites, six were previously shown to be negatively correlated to biomass, suggesting that ZmASR1-dependent regulation of these 13 metabolites might contribute to regulate leaf growth, resulting in improvement in kernel yield.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sylvie Coursol
- Université Paris-Sud, UMR 320/UMR 8120 Génétique Végétale, F–91190 Gif-sur-Yvette, France (L.V.); INRA, UMR 320/UMR 8120 Génétique Végétale, F–91190 Gif-sur-Yvette, France (M.-P.J., H.C., S.B., B.V., J.T., M.F., S.C.); Biogemma Auvergne, F–63028 Clermont-Ferrand cedex, France (D.G., P.P.); CNRS, UMR 8618 Institut de Biotechnologie des Plantes, F–91405 Orsay, France (F.G.); Université Paris-Sud, UMR 8618 Institut de Biotechnologie des Plantes, F–91405 Orsay, France (G.T., G.N.); CNRS, UMR 320/UMR 8120 Génétique Végétale, F–91190 Gif-sur-Yvette, France (C.D., M.Z.); INRA, UMR 879 Reproduction et Développement des Plantes, F–69364 Lyon, France (P.R.)
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Lorenz K, Bader M, Klaus A, Weiss W, Görg A, Hofmann T. Orosensory stimulation effects on human saliva proteome. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:10219-10231. [PMID: 21846099 DOI: 10.1021/jf2024352] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Saliva flow induced by 6-gingerol (pungent), hydroxy-α/β-sanshools (tingling), and citric acid (sour) was measured, and the time-dependent changes in the whole saliva proteome were analyzed by means of 2D-PAGE, followed by tryptic in-gel digestion and MALDI-TOF-MS peptide mass fingerprint analysis. The proteins showing significantly decreased abundance after oral 6-gingerol stimulation were identified as glutathione S-transferase P, the heat shock protein β-1, the heat shock 70 kDa protein 1, annexin A1, and cytoplasmic β-actin, whereas prolactin inducible proteins (PIP), short palate, lung and nasal epithelium carcinoma-associated protein 2 (SPLUNC2), zinc-α-2-glycoproteins (Zn-α-GP), and carbonic anhydrase VI (CAVI) were found with increased abundance. As the effects of this study were observed instantaneously upon stimulation, any proteome modulation is very likely to result from the release of proteins from preformed vesicles and not from de novo synthesis. The elevated levels of SPLUNC2, Zn-α-GP, and CAVI might be interpreted to trigger innate protective mechanisms in mucosal immunity and in nonimmune mucosal defense and might play an important role during the initial stage of inflammation.
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Affiliation(s)
- Katharina Lorenz
- Food Chemistry and Molecular Sensory Science, Technische Universität München, Lise-Meitner Strasse 34, D-85354 Freising, Germany
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Comparative proteomic analysis of irinotecan-sensitive colorectal carcinoma cell line and its chemoresistant counterpart. Anticancer Drugs 2011; 22:500-6. [PMID: 21637159 DOI: 10.1097/cad.0b013e3283408596] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In this study, we used two-dimensional gel electrophoresis and MALDI-Q-TOF-MS/MS analysis to examine the global protein expression of a pair of colorectal carcinoma cell lines, SW620 and irinotecan-resistant SW620. Of the 30 spots identified as differentially expressed proteins (±over twofold, P<0.05) between the two cell lines, 26 spots (corresponding to 26 unique proteins) were positively identified by MALDI-Q-TOF-MS/MS analysis. These proteins could be grouped into main classes including metabolism (15.38%), cell SSproliferation/differentiation (11.53%), molecular chaperone (11.53%), mRNA splicing (11.53%), and so on. The proteins, which might be involved in the development of tumor drug resistance, such as α-enolase, cofilin, and thioredoxin-dependent peroxide 1, have been validated by western blot analysis and have been discussed. The proteins identified in this study may be useful in showing the mechanisms underlying irinotecan resistance.
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Cangahuala-Inocente GC, Da Silva MF, Johnson JM, Manga A, van Tuinen D, Henry C, Lovato PE, Dumas-Gaudot E. Arbuscular mycorrhizal symbiosis elicits proteome responses opposite of P-starvation in SO4 grapevine rootstock upon root colonisation with two Glomus species. MYCORRHIZA 2011; 21:473-493. [PMID: 21210159 DOI: 10.1007/s00572-010-0352-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 12/09/2010] [Indexed: 05/08/2023]
Abstract
Although plant biotisation with arbuscular mycorrhizal fungi (AMF) is a promising strategy for improving plant health, a better knowledge regarding the molecular mechanisms involved is required. In this context, we sought to analyse the root proteome of grapevine rootstock Selection Oppenheim 4 (SO4) upon colonisation with two AMF. As expected, AMF colonisation stimulates plant biomass. At the proteome level, changes in protein amounts due to AMF colonisation resulted in 39 differentially accumulated two-dimensional electrophoresis spots in AMF roots relative to control. Out of them, 25 were co-identified in SO4 roots upon colonisation by Glomus irregulare and Glomus mosseae supporting the existence of conserved plant responses to AM symbiosis in a woody perennial species. Among the 18 proteins whose amount was reduced in AMF-colonised roots were proteins involved in glycolysis, protein synthesis and fate, defence and cell rescue, ethylene biosynthesis and purine and pyrimidine salvage degradation. The six co-identified proteins whose amount was increased had functions in energy production, signalling, protein synthesis and fate including proteases. Altogether these data confirmed that a part of the accommodation program of AMF previously characterized in annual plants is maintained within roots of the SO4 rootstock cuttings. Nonetheless, particular responses also occurred involving proteins of carbon metabolism, development and root architecture, defence and cell rescue, anthocyanin biosynthesis and P remobilization, previously reported as induced upon P-starvation. This suggests the occurrence of P reprioritization upon AMF colonization in a woody perennial plant species with agronomical interest.
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Affiliation(s)
- Gabriela Claudia Cangahuala-Inocente
- Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga 1346, Itacorubi, Caixa Postal 476, CEP 88034-001, Florianópolis, Santa Catarina, Brazil
| | - Maguida Fabiana Da Silva
- Embrapa-Centro de Pesquisa Agroflorestal do Amapá, Code Postal 10, CEP 68902-280, Macapá, Amapá, Brazil
| | - Jean-Martial Johnson
- UMR INRA 1088, CNRS 5184, U. Bourgogne, PME, INRA, BP 86510, 21065, Dijon Cedex, France
| | - Anicet Manga
- Laboratoire de Biotechnologies des Champignons, Département de Biologie Végétale, Université Cheikh Anta Diop de Dakar, BP 5005, Dakar, Sénégal
| | - Diederik van Tuinen
- UMR INRA 1088, CNRS 5184, U. Bourgogne, PME, INRA, BP 86510, 21065, Dijon Cedex, France
| | | | - Paulo Emílio Lovato
- Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga 1346, Itacorubi, Caixa Postal 476, CEP 88034-001, Florianópolis, Santa Catarina, Brazil.
| | - Eliane Dumas-Gaudot
- UMR INRA 1088, CNRS 5184, U. Bourgogne, PME, INRA, BP 86510, 21065, Dijon Cedex, France
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Two-dimensional gel electrophoresis in proteomics: a tutorial. J Proteomics 2011; 74:1829-41. [PMID: 21669304 DOI: 10.1016/j.jprot.2011.05.040] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 05/23/2011] [Accepted: 05/26/2011] [Indexed: 12/12/2022]
Abstract
Two-dimensional electrophoresis of proteins has preceded, and accompanied, the birth of proteomics. Although it is no longer the only experimental scheme used in modern proteomics, it still has distinct features and advantages. The purpose of this tutorial paper is to guide the reader through the history of the field, then through the main steps of the process, from sample preparation to in-gel detection of proteins, commenting the constraints and caveats of the technique. Then the limitations and positive features of two-dimensional electrophoresis are discussed (e.g. its unique ability to separate complete proteins and its easy interfacing with immunoblotting techniques), so that the optimal type of applications of this technique in current and future proteomics can be perceived. This is illustrated by a detailed example taken from the literature and commented in detail. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 2).
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Morphew RM, Wright HA, Lacourse EJ, Porter J, Barrett J, Woods DJ, Brophy PM. Towards delineating functions within the fasciola secreted cathepsin l protease family by integrating in vivo based sub-proteomics and phylogenetics. PLoS Negl Trop Dis 2011; 5:e937. [PMID: 21245911 PMCID: PMC3014944 DOI: 10.1371/journal.pntd.0000937] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 12/04/2010] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND fasciola hepatica, along with Fasciola gigantica, is the causative agent of fasciolosis, a foodborne zoonotic disease affecting grazing animals and humans worldwide. Pathology is directly related to the release of parasite proteins that facilitate establishment within the host. The dominant components of these excretory-secretory (ES) products are also the most promising vaccine candidates, the cathepsin L (Cat L) protease family. METHODOLOGY/PRINCIPAL FINDINGS the sub-proteome of Cat L proteases from adult F. hepatica ES products derived from in vitro culture and in vivo from ovine host bile were compared by 2-DE. The individual Cat L proteases were identified by tandem mass spectrometry with the support of an in-house translated liver fluke EST database. The study reveals plasticity within the CL1 clade of Cat L proteases; highlighted by the identification of a novel isoform and CL1 sub-clade, resulting in a new Cat L phylogenetic analysis including representatives from other adult Cat L phylogenetic clades. Additionally, for the first time, mass spectrometry was shown to be sufficiently sensitive to reveal single amino acid polymorphisms in a resolved 2-DE protein spot derived from pooled population samples. CONCLUSIONS/SIGNIFICANCE we have investigated the sub-proteome at the population level of a vaccine target family using the Cat L proteases from F. hepatica as a case study. We have confirmed that F. hepatica exhibits more plasticity in the expression of the secreted CL1 clade of Cat L proteases at the protein level than previously realised. We recommend that superfamily based vaccine discovery programmes should screen parasite populations from different host populations and, if required, different host species via sub-proteomic assay in order to confirm the relative expression at the protein level prior to the vaccine development phase.
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Affiliation(s)
- Russell M Morphew
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom.
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Martins-de-Souza D, Guest PC, Vanattou-Saifoudine N, Harris LW, Bahn S. Proteomic technologies for biomarker studies in psychiatry: advances and needs. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2011; 101:65-94. [PMID: 22050849 DOI: 10.1016/b978-0-12-387718-5.00004-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In the postgenome era, proteomics has arisen as a promising tool for more complete comprehension of diseases and for biomarker discovery. Some of these objectives have already been partly achieved for illnesses such as cancer. In the case of psychiatric conditions, however, proteomic advances have had a less profound impact. Here, we outline the necessity of improving and applying proteomic methods for biomarker discovery and validation in the field of psychiatric disorders. While proteomic-based applications in neurosciences have increased in accuracy and sensitivity over the past 10 years, the development of orthogonal validation technologies has fallen behind. These issues are discussed along with the importance of integrating systems biology approaches and combining proteomics with other research approaches. The future development of such technologies may put proteomics closer to clinical applications in psychiatry.
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Affiliation(s)
- Daniel Martins-de-Souza
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
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Gong F, Peng X, Zeng Z, Yu M, Zhao Y, Tong A. Proteomic analysis of cisplatin resistance in human ovarian cancer using 2-DE method. Mol Cell Biochem 2010; 348:141-7. [PMID: 21080034 DOI: 10.1007/s11010-010-0648-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 10/28/2010] [Indexed: 02/05/2023]
Abstract
Platinum-based chemotherapy, such as cisplatin, is the primary treatment for human ovarian cancer. However, overcoming drug resistance has become an important issue in cancer chemotherapy. In this study, we performed 2-DE and ESI-Q-TOF MS/MS analysis to identify differential proteins expression between cisplatin-sensitive (A2780S) and cisplatin-resistant (A2780-CP) ovarian cancer cell lines. Of the 14 spots identified as differentially expressed (±over twofold, P < 0.05) between the two cell lines, ten spots (corresponding to ten unique proteins) were positively identified by ESI-Q-TOF MS/MS analysis. These proteins include capsid glycoprotein, fructose-bisphosphate aldolase C, heterogeneous nuclear ribonucleoproteins A2/B1, putative RNA-binding protein 3, Ran-specific GTPase-activating protein, ubiquitin carboxyl-terminal hydrolase isozyme L1, stathmin, ATPSH protein, chromobox protein homolog3 and phosphoglycerate kinase 1. The proteins identified in this study would be useful in revealing the mechanisms underlying cisplatin resistance and also provide some clues for further research.
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Affiliation(s)
- Fengming Gong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, People's Republic of China
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Proteomic Signatures of the Zebrafish (Danio rerio) Embryo: Sensitivity and Specificity in Toxicity Assessment of Chemicals. INTERNATIONAL JOURNAL OF PROTEOMICS 2010; 2010:630134. [PMID: 22084678 PMCID: PMC3200224 DOI: 10.1155/2010/630134] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 05/26/2010] [Accepted: 07/19/2010] [Indexed: 12/25/2022]
Abstract
Studies using embryos of the zebrafish Danio rerio (DarT) instead of adult fish for characterising the (eco-) toxic potential of chemicals have been proposed as animal replacing methods. Effect analysis at the molecular level might enhance sensitivity, specificity, and predictive value of the embryonal studies. The present paper aimed to test the potential of toxicoproteomics with zebrafish eleutheroembryos for sensitive and specific toxicity assessment. 2-DE-based toxicoproteomics was performed applying low-dose (EC10) exposure for 48 h with three-model substances Rotenone, 4,6-dinitro-o-cresol (DNOC) and Diclofenac. By multivariate “pattern-only” PCA and univariate statistical analyses, alterations in the embryonal proteome were detectable in nonetheless visibly intact organisms and treatment with the three substances was distinguishable at the molecular level. Toxicoproteomics enabled the enhancement of sensitivity and specificity of the embryonal toxicity assay and bear the potency to identify protein markers serving as general stress markers and early diagnosis of toxic stress.
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Fanous A, Hecker M, Görg A, Parlar H, Jacob F. Corynebacterium glutamicum as an indicator for environmental cobalt and silver stress--a proteome analysis. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2010; 45:666-675. [PMID: 20818520 DOI: 10.1080/03601234.2010.502442] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Cobalt and silver are toxic for cells, but mechanisms of this toxicity are largely unknown. Analysis of Corynebacterium glutamicum proteome from cells grown in control and cobalt or silver enriched media was performed by two dimensional gel electrophoresis (2DE) followed by mass spectrometry. Our results indicate that the cell adapted to cobalt stress by inducing five defense mechanisms: Scavenging of free radicals, promotion of the generation of energy, reparation of DNA, reparation and biogenesis of Fe-S cluster proteins and supporting and reparation of cell wall. In response to the detoxification of Ag+ many proteins were up-regulated, which involved reparation of damaged DNA, minimizing the toxic effect of reactive oxygen species (ROS) and energy generation. Overexpression of proteins involved in cell wall biosynthesis (1,4-alpha-glucan branching enzyme and nucleoside-diphosphate-sugar epimerase) upon cobalt stress and induction of proteins involved in energy metabolism (2-methylcitrate dehydratase and 1, 2-methylcitrate synthase) upon silver demonstrate the potential of these enzymes as biomarkers of sub-lethal Ag+ and Co toxicity.
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Affiliation(s)
- Ali Fanous
- Department for Chemical-Technical Analysis and Chemical Food Technology, Research Center Weihenstephan for Brewing and Food Quality, Technische Universität München, Freising-Weihenstephan, Germany
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Levert M, Zamfir O, Clermont O, Bouvet O, Lespinats S, Hipeaux MC, Branger C, Picard B, Saint-Ruf C, Norel F, Balliau T, Zivy M, Le Nagard H, Cruvellier S, Chane-Woon-Ming B, Nilsson S, Gudelj I, Phan K, Ferenci T, Tenaillon O, Denamur E. Molecular and evolutionary bases of within-patient genotypic and phenotypic diversity in Escherichia coli extraintestinal infections. PLoS Pathog 2010; 6:e1001125. [PMID: 20941353 PMCID: PMC2947995 DOI: 10.1371/journal.ppat.1001125] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 08/31/2010] [Indexed: 12/22/2022] Open
Abstract
Although polymicrobial infections, caused by combinations of viruses, bacteria, fungi and parasites, are being recognised with increasing frequency, little is known about the occurrence of within-species diversity in bacterial infections and the molecular and evolutionary bases of this diversity. We used multiple approaches to study the genomic and phenotypic diversity among 226 Escherichia coli isolates from deep and closed visceral infections occurring in 19 patients. We observed genomic variability among isolates from the same site within 11 patients. This diversity was of two types, as patients were infected either by several distinct E. coli clones (4 patients) or by members of a single clone that exhibit micro-heterogeneity (11 patients); both types of diversity were present in 4 patients. A surprisingly wide continuum of antibiotic resistance, outer membrane permeability, growth rate, stress resistance, red dry and rough morphotype characteristics and virulence properties were present within the isolates of single clones in 8 of the 11 patients showing genomic micro-heterogeneity. Many of the observed phenotypic differences within clones affected the trade-off between self-preservation and nutritional competence (SPANC). We showed in 3 patients that this phenotypic variability was associated with distinct levels of RpoS in co-existing isolates. Genome mutational analysis and global proteomic comparisons in isolates from a patient revealed a star-like relationship of changes amongst clonally diverging isolates. A mathematical model demonstrated that multiple genotypes with distinct RpoS levels can co-exist as a result of the SPANC trade-off. In the cases involving infection by a single clone, we present several lines of evidence to suggest diversification during the infectious process rather than an infection by multiple isolates exhibiting a micro-heterogeneity. Our results suggest that bacteria are subject to trade-offs during an infectious process and that the observed diversity resembled results obtained in experimental evolution studies. Whatever the mechanisms leading to diversity, our results have strong medical implications in terms of the need for more extensive isolate testing before deciding on antibiotic therapies. We investigated whether an infection is a site of pathogen within-species diversity. Our results indicate that there is indeed extensive diversity during human extraintestinal infections by Escherichia coli. This diversity was of two types, not mutually exclusive, as we found that patients were infected either by several distinct E. coli clones or by members of a single clone that exhibit micro-heterogeneity. The high degree of phenotypic diversity, including antibiotic resistance, suggests that there is no uniform selection pressure leading to a single fitter clone during an infection. We discuss a possible mechanism and a mathematical model that explains these unexpected results. Our data suggest that the evolution of diversity in the course of an infection and in in vitro experimental evolution in the absence of host immune selective pressure may have many parallels. Whatever the mechanisms leading to diversity, our results have strong medical implications in terms of the need for more extensive isolate testing before deciding on antibiotic therapies.
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Affiliation(s)
- Maxime Levert
- INSERM U722 and Université Paris 7 Denis Diderot, Faculté de Médecine, Site Xavier Bichat, Paris, France
| | - Oana Zamfir
- INSERM U722 and Université Paris 7 Denis Diderot, Faculté de Médecine, Site Xavier Bichat, Paris, France
| | - Olivier Clermont
- INSERM U722 and Université Paris 7 Denis Diderot, Faculté de Médecine, Site Xavier Bichat, Paris, France
| | - Odile Bouvet
- INSERM U722 and Université Paris 7 Denis Diderot, Faculté de Médecine, Site Xavier Bichat, Paris, France
| | - Sylvain Lespinats
- INSERM U722 and Université Paris 7 Denis Diderot, Faculté de Médecine, Site Xavier Bichat, Paris, France
| | - Marie Claire Hipeaux
- Assistance Publique - Hôpitaux de Paris, Hôpital Louis Mourier, Laboratoire de Microbiologie, Colombes, France
| | - Catherine Branger
- INSERM U722 and Université Paris 7 Denis Diderot, Faculté de Médecine, Site Xavier Bichat, Paris, France
- Assistance Publique - Hôpitaux de Paris, Hôpital Louis Mourier, Laboratoire de Microbiologie, Colombes, France
| | - Bertrand Picard
- INSERM U722 and Université Paris 7 Denis Diderot, Faculté de Médecine, Site Xavier Bichat, Paris, France
| | - Claude Saint-Ruf
- INSERM U1001 and Université Paris 5 René Descartes, Faculté de Médecine, Paris, France
| | - Françoise Norel
- Unité de Génétique Moléculaire and CNRS URA2172, Institut Pasteur, Paris, France
| | - Thierry Balliau
- CNRS UMR 0320/UMR8120 Génétique Végétale, Plate-Forme de Protéomique PAPPSO, Gif-sur-Yvette, France
| | - Michel Zivy
- CNRS UMR 0320/UMR8120 Génétique Végétale, Plate-Forme de Protéomique PAPPSO, Gif-sur-Yvette, France
| | - Hervé Le Nagard
- INSERM U738 and Université Paris 7 Denis Diderot, Faculté de Médecine, Site Xavier Bichat, Paris, France
| | - Stéphane Cruvellier
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Genoscope, Evry, France
| | - Béatrice Chane-Woon-Ming
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Genoscope, Evry, France
| | - Susanna Nilsson
- Department of Mathematics, Imperial College, London, United Kingdom
| | - Ivana Gudelj
- Department of Mathematics, Imperial College, London, United Kingdom
| | - Katherine Phan
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Thomas Ferenci
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Olivier Tenaillon
- INSERM U722 and Université Paris 7 Denis Diderot, Faculté de Médecine, Site Xavier Bichat, Paris, France
| | - Erick Denamur
- INSERM U722 and Université Paris 7 Denis Diderot, Faculté de Médecine, Site Xavier Bichat, Paris, France
- * E-mail:
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