1
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Carrasco Del Amor A, Bautista RH, Ussar S, Cristobal S, Urbatzka R. Insights into the mechanism of action of the chlorophyll derivative 13- 2-hydroxypheophytine a on reducing neutral lipid reserves in zebrafish larvae and mice adipocytes. Eur J Pharmacol 2023; 960:176158. [PMID: 37898286 DOI: 10.1016/j.ejphar.2023.176158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023]
Abstract
Obesity is a worldwide epidemic and natural products may hold promise in its treatment. The chlorophyll derivative 13-2-hydroxypheophytine (hpa) was isolated in a screen with zebrafish larvae to identify lipid reducing molecules from cyanobacteria. However, the mechanisms underlying the lipid-reducing effects of hpa in zebrafish larvae remain poorly understood. Thus, investigating the mechanism of action of hpa and validation in other model organisms such as mice represents important initial steps. In this study, we identified 14 protein targets of hpa in zebrafish larvae by thermal proteome profiling, and selected two targets (malate dehydrogenase and pyruvate kinase) involved in cellular metabolism for further validation by enzymatic measurements. Our findings revealed a dose-dependent inhibition of pyruvate kinase by hpa exposure using protein extracts of zebrafish larvae in vitro, and in exposure experiments from 3 to 5 days post fertilization in vivo. Analysis of untargeted metabolomics of zebrafish larvae detected 940 mass peaks (66 increased, 129 decreased) and revealed that hpa induced the formation of various phospholipid species (phosphoinositol, phosphoethanolamine, phosphatidic acid). Inter-species validation showed that brown adipocytes exposed to hpa significantly reduced the size of lipid droplets, increased maximal mitochondrial respiratory capacity, and the expression of PPARy during adipocyte differentiation. In line with our data, previous work described that reduced pyruvate kinase activity lowered hepatic lipid content via reduced pyruvate and citrate, and improved mitochondrial function via phospholipids. Thus, our data provide new insights into the molecular mechanism underlying the lipid reducing activities of hpa in zebrafish larvae, and species overlapping functions in reduction of lipids.
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Affiliation(s)
- Ana Carrasco Del Amor
- Department of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, SE-58185, Linköping, Sweden.
| | - Rene Hernandez Bautista
- RG Adipocyte and Metabolism, Institute for Diabetes and Obesity, Helmholtz Center Munich, 85764, Neuherberg, Germany.
| | - Siegfried Ussar
- RG Adipocyte and Metabolism, Institute for Diabetes and Obesity, Helmholtz Center Munich, 85764, Neuherberg, Germany.
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, SE-58185, Linköping, Sweden; Ikerbasque, Basque Foundation for Sciences, Department of Physiology, Faculty of Medicine, and Nursing, University of the Basque Country UPV/EHU, Spain.
| | - Ralph Urbatzka
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
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2
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Bertile F, Matallana-Surget S, Tholey A, Cristobal S, Armengaud J. Diversifying the concept of model organisms in the age of -omics. Commun Biol 2023; 6:1062. [PMID: 37857885 PMCID: PMC10587087 DOI: 10.1038/s42003-023-05458-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/13/2023] [Indexed: 10/21/2023] Open
Abstract
In today's post-genomic era, it is crucial to rethink the concept of model organisms. While a few historically well-established organisms, e.g. laboratory rodents, have enabled significant scientific breakthroughs, there is now a pressing need for broader inclusion. Indeed, new organisms and models, from complex microbial communities to holobionts, are essential to fully grasp the complexity of biological principles across the breadth of biodiversity. By fostering collaboration between biology, advanced molecular science and omics communities, we can collectively adopt new models, unraveling their molecular functioning, and uncovering fundamental mechanisms. This concerted effort will undoubtedly enhance human health, environmental quality, and biodiversity conservation.
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Affiliation(s)
- Fabrice Bertile
- Université de Strasbourg, CNRS, IPHC UMR 7178, 23 rue du Loess, 67037, Strasbourg Cedex 2, France.
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping, 581 85, Sweden
- Ikerbasque, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena, s/n, Leioa, 48940, Spain
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
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3
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Lizano-Fallas V, Carrasco del Amor A, Cristobal S. Prediction of Molecular Initiating Events for Adverse Outcome Pathways Using High-Throughput Identification of Chemical Targets. Toxics 2023; 11:189. [PMID: 36851063 PMCID: PMC9965981 DOI: 10.3390/toxics11020189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The impact of exposure to multiple chemicals raises concerns for human and environmental health. The adverse outcome pathway method offers a framework to support mechanism-based assessment in environmental health starting by describing which mechanisms are triggered upon interaction with different stressors. The identification of the molecular initiating event and the molecular interaction between a chemical and a protein target is still a challenge for the development of adverse outcome pathways. The cellular response to chemical exposure studied with omics could not directly identify the protein targets. However, recent mass spectrometry-based methods are offering a proteome-wide identification of protein targets interacting with s but unrevealing a molecular initiating event from a set of targets is still dependent on available knowledge. Here, we directly coupled the target identification findings from the proteome integral solubility alteration assay with an analytical hierarchy process for the prediction of a prioritized molecular initiating event. We demonstrate the applicability of this combination of methodologies with a test compound (TCDD), and it could be further studied and integrated into AOPs. From the eight protein targets identified by the proteome integral solubility alteration assay after analyzing 2824 human hepatic proteins, the analytical hierarchy process can select the most suitable protein for an AOP. Our combined method solves the missing links between high-throughput target identification and prediction of the molecular initiating event. We anticipate its utility to decipher new molecular initiating events and support more sustainable methodologies to gain time and resources in chemical assessment.
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Affiliation(s)
- Veronica Lizano-Fallas
- Department of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Ana Carrasco del Amor
- Department of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, 581 85 Linköping, Sweden
- Ikerbasque, Basque Foundation for Sciences, Department of Physiology, Faculty of Medicine, and Nursing, University of the Basque Country (UPV/EHU), 489 40 Leioa, Spain
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4
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Berlin E, Lizano-Fallas V, Carrasco del Amor A, Fresnedo O, Cristobal S. Nonionic Surfactants can Modify the Thermal Stability of Globular and Membrane Proteins Interfering with the Thermal Proteome Profiling Principles to Identify Protein Targets. Anal Chem 2023; 95:4033-4042. [PMID: 36779864 PMCID: PMC9979136 DOI: 10.1021/acs.analchem.2c04500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
The membrane proteins are essential targets for understanding cellular function. The unbiased identification of membrane protein targets is still the bottleneck for a system-level understanding of cellular response to stimuli or perturbations. It has been suggested to enrich the soluble proteome with membrane proteins by introducing nonionic surfactants in the solubilization solution. This strategy aimed to simultaneously identify the globular and membrane protein targets by thermal proteome profiling principles. However, the thermal shift assay would surpass the cloud point temperature from the nonionic surfactants frequently utilized for membrane protein solubilization. It is expected that around the cloud point temperature, the surfactant micelles would suffer structural modifications altering protein solubility. Here, we show that the presence of nonionic surfactants can alter protein thermal stability from a mixed, globular, and membrane proteome. In the presence of surfactant micelles, the changes in protein solubility analyzed after the thermal shift assay was affected by the thermally dependent modification of the micellar size and its interaction with proteins. We demonstrate that the introduction of nonionic surfactants for the solubilization of membrane proteins is not compatible with the principles of target identification by thermal proteome profiling methodologies. Our results lead to exploring thermally independent strategies for membrane protein solubilization to assure confident membrane protein target identification. The proteome-wide thermal shift methods have already shown their capability to elucidate mechanisms of action from pharma, biomedicine, analytical chemistry, or toxicology, and finding strategies, free from surfactants, to identify membrane protein targets would be the next challenge.
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Affiliation(s)
- Emmanuel Berlin
- Department
of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, Linköping 581 85, Sweden
| | - Veronica Lizano-Fallas
- Department
of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, Linköping 581 85, Sweden
| | - Ana Carrasco del Amor
- Department
of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, Linköping 581 85, Sweden
| | - Olatz Fresnedo
- Department
of Physiology, Faculty of Medicine, and Nursing, University of the Basque Country UPV/EHU, Leioa 489 40, Spain
| | - Susana Cristobal
- Department
of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, Linköping 581 85, Sweden,Ikerbasque,
Basque Foundation for Sciences, Department of Physiology, Faculty
of Medicine, and Nursing, University of
the Basque Country UPV/EHU, Leioa 489 40, Spain,. Tel: +46-730385867
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5
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Spriano F, Barnabei L, Carrasco Del Amor AM, Tomasso MR, Tarantelli C, Riveiro E, Pazzi N, Padrick SB, Cristobal S, Cavalli F, Gaudio E, Bertoni F. Abstract 1817: EG-011 is a first-in-class Wiskott-Aldrich syndrome protein (WASp) activator with anti-tumor activity. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background. Novel therapeutic targets are needed to improve the outcome of individuals with cancer. EG-011 is a small molecule with in vitro and in vivo anti-tumor activity in lymphoma and acute leukemias, but, at least so far, no activity in solid tumor models (Gaudio et al AACR 2019). Since no information was available on its target, we have now performed experiments showing that EG-011 targets WASp.
Methods. Target identification: kinase screens with DiscoverX KINOMEscan, ProQinase Wildtype-Profiler; thermal proteomic profiling. Target validation: pyrene actin polymerization assay. In vitro drug treatment of cell lines followed for changes in actin filaments (F-actin) by confocal imaging with Alexa Fluor 488 Phalloidin.
Results. Extensive kinome screens excluded kinases as targets of EG-011. We then applied thermal proteomic profiling to identify new protein targets interacting with EG-011. Over 3,300 proteins from the soluble proteome from the EG-011 sensitive mantle cell lymphoma cell line REC1 were analyzed and 48 possible protein targets were initially identified. Among the proteins undergoing a thermal shift, WASp was among the most highly destabilized by EG-011. Due to the pattern of expression of WASp, compatible with the anti-tumor activity observed only in hematological cancers (Gaudio et al AACR 2019), we performed further experiments to confirm the possibility that EG-011 targets WASp. One of the main functions of WASp is the regulation of actin filaments formation. Pyrene actin polymerization assays demonstrated that EG-011 activated the auto-inhibited form of WASP with strong actin polymerization. Further confirmation was obtained using confocal imaging of cell lines exposed to DMSO or EG-011 (500 nM, 5 μM) and stained for F-actin. An increase in actine polymerization was seen in EG-011 sensitive (VL51) and not in resistant (Z138) cell lines at 4, 8 and 24h with both concentrations.
Conclusions. These data demonstrate that EG-011 is the “first-in-class” activator of the auto-inhibited form of WASp with selective anti-tumor activity in lymphomas.
Citation Format: Filippo Spriano, Laura Barnabei, Ana Maria Carrasco Del Amor, Meagan R. Tomasso, Chiara Tarantelli, Eugenia Riveiro, Natalina Pazzi, Shae B. Padrick, Susana Cristobal, Franco Cavalli, Eugenio Gaudio, Francesco Bertoni. EG-011 is a first-in-class Wiskott-Aldrich syndrome protein (WASp) activator with anti-tumor activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1817.
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Affiliation(s)
- Filippo Spriano
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Laura Barnabei
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Ana Maria Carrasco Del Amor
- 2Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Lnköping University, Linköping, Sweden
| | | | - Chiara Tarantelli
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | | | | | - Susana Cristobal
- 2Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Lnköping University, Linköping, Sweden
| | - Franco Cavalli
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Eugenio Gaudio
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Francesco Bertoni
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
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6
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Lizano-Fallas V, Carrasco Del Amor A, Cristobal S. Systematic analysis of chemical-protein interactions from zebrafish embryo by proteome-wide thermal shift assay, bridging the gap between molecular interactions and toxicity pathways. J Proteomics 2021; 249:104382. [PMID: 34555547 DOI: 10.1016/j.jprot.2021.104382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/15/2021] [Indexed: 02/06/2023]
Abstract
The molecular interaction between chemicals and proteins often promotes alteration of cellular function. One of the challenges of the toxicology is to predict the impact of exposure to chemicals. Assessing the impact of exposure implies to understand their mechanism of actions starting from identification of specific protein targets of the interaction. Current methods can mainly predict effects of characterized chemicals with knowledge of its targets, and mechanism of actions. Here, we show that proteome-wide thermal shift methods can identify chemical-protein interactions and the protein targets from bioactive chemicals. We analyzed the identified targets from a soluble proteome extracted from zebrafish embryo, that is a model system for toxicology. To evaluate the utility to predict mechanism of actions, we discussed the applicability in four cases: single chemicals, chemical mixtures, novel chemicals, and novel drugs. Our results showed that this methodology could identify the protein targets, discriminate between protein increasing and decreasing in solubility, and offering additional data to complement the map of intertwined mechanism of actions. We anticipate that the proteome integral solubility alteration (PISA) assay, as it is defined here for the unbiased identification of protein targets of chemicals could bridge the gap between molecular interactions and toxicity pathways. SIGNIFICANCE: One of the challenges of the environmental toxicology is to predict the impact of exposure to chemicals on environment and human health. Our phenotype should be explained by our genotype and the environmental exposure. Genomic methodologies can offer a deep analysis of human genome that alone cannot explain our risks of disease. We are starting to understand the key role of exposure to chemicals on our health and risks of disease. Here, we present a proteomic-based method for the identification of soluble proteins interacting with chemicals in zebrafish embryo and discuss the opportunities to complement the map of toxicity pathway perturbations. We anticipate that this PISA assay could bridge the gap between molecular interactions and toxicity pathways.
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Affiliation(s)
- Veronica Lizano-Fallas
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping 581 85, Sweden
| | - Ana Carrasco Del Amor
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping 581 85, Sweden
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping 581 85, Sweden.; Ikerbasque, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena, s/n, Leioa 48940, Spain..
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7
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Benedé S, Lozano-Ojalvo D, Cristobal S, Costa J, D'Auria E, Velickovic TC, Garrido-Arandia M, Karakaya S, Mafra I, Mazzucchelli G, Picariello G, Romero-Sahagun A, Villa C, Roncada P, Molina E. New applications of advanced instrumental techniques for the characterization of food allergenic proteins. Crit Rev Food Sci Nutr 2021; 62:8686-8702. [PMID: 34060381 DOI: 10.1080/10408398.2021.1931806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Current approaches based on electrophoretic, chromatographic or immunochemical principles have allowed characterizing multiple allergens, mapping their epitopes, studying their mechanisms of action, developing detection and diagnostic methods and therapeutic strategies for the food and pharmaceutical industry. However, some of the common structural features related to the allergenic potential of food proteins remain unknown, or the pathological mechanism of food allergy is not yet fully understood. In addition, it is also necessary to evaluate new allergens from novel protein sources that may pose a new risk for consumers. Technological development has allowed the expansion of advanced technologies for which their whole potential has not been entirely exploited and could provide novel contributions to still unexplored molecular traits underlying both the structure of food allergens and the mechanisms through which they sensitize or elicit adverse responses in human subjects, as well as improving analytical techniques for their detection. This review presents cutting-edge instrumental techniques recently applied when studying structural and functional aspects of proteins, mechanism of action and interaction between biomolecules. We also exemplify their role in the food allergy research and discuss their new possible applications in several areas of the food allergy field.
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Affiliation(s)
- Sara Benedé
- Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM), Madrid, Spain
| | - Daniel Lozano-Ojalvo
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, Jaffe Food Allergy Institute, New York, NY, USA
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden.,IKERBASQUE, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Joana Costa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Enza D'Auria
- Clinica Pediatrica, Ospedale dei Bambini Vittore Buzzi, Università degli Studi, Milano, Italy
| | - Tanja Cirkovic Velickovic
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia.,Ghent University Global Campus, Incheon, South Korea.,Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - María Garrido-Arandia
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Sibel Karakaya
- Department of Food Engineering, Ege University, Izmir, Turkey
| | - Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege, Belgium
| | - Gianluca Picariello
- Institute of Food Sciences, National Research Council (CNR), Avellino, Italy
| | - Alejandro Romero-Sahagun
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Caterina Villa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Paola Roncada
- Department of Health Sciences, University Magna Graecia, Catanzaro, Italy
| | - Elena Molina
- Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM), Madrid, Spain
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8
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Strid T, Okuyama K, Tingvall-Gustafsson J, Kuruvilla J, Jensen CT, Lang S, Prasad M, Somasundaram R, Åhsberg J, Cristobal S, Soneji S, Ungerbäck J, Sigvardsson M. B Lymphocyte Specification Is Preceded by Extensive Epigenetic Priming in Multipotent Progenitors. J Immunol 2021; 206:2700-2713. [PMID: 34021049 DOI: 10.4049/jimmunol.2100048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/27/2021] [Indexed: 11/19/2022]
Abstract
B lymphocyte development is dependent on the interplay between the chromatin landscape and lineage-specific transcription factors. It has been suggested that B lineage commitment is associated with major changes in the nuclear chromatin environment, proposing a critical role for lineage-specific transcription factors in the formation of the epigenetic landscape. In this report, we have used chromosome conformation capture in combination with assay for transposase-accessible chromatin sequencing analysis to enable highly efficient annotation of both proximal and distal transcriptional control elements to genes activated in B lineage specification in mice. A large majority of these genes were annotated to at least one regulatory element with an accessible chromatin configuration in multipotent progenitors. Furthermore, the majority of binding sites for the key regulators of B lineage specification, EBF1 and PAX5, occurred in already accessible regions. EBF1 did, however, cause a dynamic change in assay for transposase-accessible chromatin accessibility and was critical for an increase in distal promoter-enhancer interactions. Our data unravel an extensive epigenetic priming at regulatory elements annotated to lineage-restricted genes and provide insight into the interplay between the epigenetic landscape and transcription factors in cell specification.
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Affiliation(s)
- Tobias Strid
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden.,Division of Molecular Hematology, Lund University, Lund, Sweden; and.,Department of Clinical Pathology, Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Kazuki Okuyama
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | | | - Jacob Kuruvilla
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | | | - Stefan Lang
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | - Mahadesh Prasad
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Rajesh Somasundaram
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Josefine Åhsberg
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Susana Cristobal
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Shamit Soneji
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | - Jonas Ungerbäck
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | - Mikael Sigvardsson
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden; .,Division of Molecular Hematology, Lund University, Lund, Sweden; and
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9
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Legler J, Zalko D, Jourdan F, Jacobs M, Fromenty B, Balaguer P, Bourguet W, Munic Kos V, Nadal A, Beausoleil C, Cristobal S, Remy S, Ermler S, Margiotta-Casaluci L, Griffin JL, Blumberg B, Chesné C, Hoffmann S, Andersson PL, Kamstra JH. The GOLIATH Project: Towards an Internationally Harmonised Approach for Testing Metabolism Disrupting Compounds. Int J Mol Sci 2020; 21:E3480. [PMID: 32423144 PMCID: PMC7279023 DOI: 10.3390/ijms21103480] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/29/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
The purpose of this project report is to introduce the European "GOLIATH" project, a new research project which addresses one of the most urgent regulatory needs in the testing of endocrine-disrupting chemicals (EDCs), namely the lack of methods for testing EDCs that disrupt metabolism and metabolic functions. These chemicals collectively referred to as "metabolism disrupting compounds" (MDCs) are natural and anthropogenic chemicals that can promote metabolic changes that can ultimately result in obesity, diabetes, and/or fatty liver in humans. This project report introduces the main approaches of the project and provides a focused review of the evidence of metabolic disruption for selected EDCs. GOLIATH will generate the world's first integrated approach to testing and assessment (IATA) specifically tailored to MDCs. GOLIATH will focus on the main cellular targets of metabolic disruption-hepatocytes, pancreatic endocrine cells, myocytes and adipocytes-and using an adverse outcome pathway (AOP) framework will provide key information on MDC-related mode of action by incorporating multi-omic analyses and translating results from in silico, in vitro, and in vivo models and assays to adverse metabolic health outcomes in humans at real-life exposures. Given the importance of international acceptance of the developed test methods for regulatory use, GOLIATH will link with ongoing initiatives of the Organisation for Economic Development (OECD) for test method (pre-)validation, IATA, and AOP development.
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Affiliation(s)
- Juliette Legler
- Institute for Risk Assessment Sciences, Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3508 TD Utrecht, The Netherlands;
| | - Daniel Zalko
- INRAE Toxalim (Research Centre in Food Toxicology), Metabolism and Xenobiotics (MeX) Team, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (D.Z.); (F.J.)
| | - Fabien Jourdan
- INRAE Toxalim (Research Centre in Food Toxicology), Metabolism and Xenobiotics (MeX) Team, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (D.Z.); (F.J.)
| | - Miriam Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OXON. OX11 0RQ, UK;
| | - Bernard Fromenty
- Institut NUMECAN (Nutrition Metabolisms and Cancer) INSERM UMR_A 1341, UMR_S 1241, Université de Rennes, F-35000 Rennes, France;
| | - Patrick Balaguer
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, ICM, Université de Montpellier, 34298 Montpellier, France;
| | - William Bourguet
- Center for Structural Biochemistry (CBS), INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France;
| | - Vesna Munic Kos
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden;
| | - Angel Nadal
- IDiBE and CIBERDEM, Universitas Miguel Hernandez, 03202 Elche (Alicante), Spain;
| | - Claire Beausoleil
- ANSES, Direction de l’Evaluation des Risques, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort CEDEX, France;
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences (BKV), Cell Biology, Medical Faculty, Linköping University, SE-581 85 Linköping, Sweden;
| | - Sylvie Remy
- Sustainable Health, Flemish Institute for Technological Research, VITO, 2400 Mol, Belgium;
| | - Sibylle Ermler
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (S.E.); (L.M.-C.)
| | - Luigi Margiotta-Casaluci
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (S.E.); (L.M.-C.)
| | - Julian L. Griffin
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington, London SW7 2AZ, UK;
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, University of California Irvine, 2011 BioSci 3, University of California, Irvine, CA 92697-2300, USA;
| | - Christophe Chesné
- Biopredic International, Parc d’Activité de la Bretèche Bâtiment A4, 35760 Saint Grégoire, France;
| | | | | | - Jorke H. Kamstra
- Institute for Risk Assessment Sciences, Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3508 TD Utrecht, The Netherlands;
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10
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Okuyama K, Strid T, Kuruvilla J, Somasundaram R, Cristobal S, Smith E, Prasad M, Fioretos T, Lilljebjörn H, Soneji S, Lang S, Ungerbäck J, Sigvardsson M. PAX5 is part of a functional transcription factor network targeted in lymphoid leukemia. PLoS Genet 2019; 15:e1008280. [PMID: 31381561 PMCID: PMC6695195 DOI: 10.1371/journal.pgen.1008280] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 08/15/2019] [Accepted: 07/02/2019] [Indexed: 12/02/2022] Open
Abstract
One of the most frequently mutated proteins in human B-lineage leukemia is the transcription factor PAX5. These mutations often result in partial rather than complete loss of function of the transcription factor. While the functional dose of PAX5 has a clear connection to human malignancy, there is limited evidence for that heterozygote loss of PAX5 have a dramatic effect on the development and function of B-cell progenitors. One possible explanation comes from the finding that PAX5 mutated B-ALL often display complex karyotypes and additional mutations. Thus, PAX5 might be one component of a larger transcription factor network targeted in B-ALL. To investigate the functional network associated with PAX5 we used BioID technology to isolate proteins associated with this transcription factor in the living cell. This identified 239 proteins out of which several could be found mutated in human B-ALL. Most prominently we identified the commonly mutated IKZF1 and RUNX1, involved in the formation of ETV6-AML1 fusion protein, among the interaction partners. ChIP- as well as PLAC-seq analysis supported the idea that these factors share a multitude of target genes in human B-ALL cells. Gene expression analysis of mouse models and primary human leukemia suggested that reduced function of PAX5 increased the ability of an oncogenic form of IKZF1 or ETV6-AML to modulate gene expression. Our data reveals that PAX5 belong to a regulatory network frequently targeted by multiple mutations in B-ALL shedding light on the molecular interplay in leukemia cells. The use of modern high throughput DNA-sequencing has dramatically increased our ability to identify genetic alterations associated with cancer. However, while the mutations per se are rather easily identified, our understanding of how these mutations impact cellular functions and drive malignant transformation is more limited. We have explored the function of the transcription factor PAX5, commonly mutated in human B-lymphocyte leukemia, to identify a regulatory network of transcription factors often targeted in human disease. Hence, we propose that malignant conversion of B-lymphocyte progenitors involves multiple targeting of a central transcription factor network aggravating the impact of the individual mutations. These data increase our understanding for how individual mutations collaborate to drive the formation of B—lineage leukemia.
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Affiliation(s)
- Kazuki Okuyama
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Tobias Strid
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Division of Molecular Hematology, Lund University, Lund, Sweden
| | - Jacob Kuruvilla
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Division of Molecular Hematology, Lund University, Lund, Sweden
| | - Rajesh Somasundaram
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Emma Smith
- Division of Molecular Hematology, Lund University, Lund, Sweden
| | - Mahadesh Prasad
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics Lund University, Lund, Sweden
| | | | - Shamit Soneji
- Division of Molecular Hematology, Lund University, Lund, Sweden
- Division of Clinical Genetics Lund University, Lund, Sweden
| | - Stefan Lang
- Division of Molecular Hematology, Lund University, Lund, Sweden
| | - Jonas Ungerbäck
- Division of Molecular Hematology, Lund University, Lund, Sweden
- Lund Stemcell Center, Lund University, Lund, Sweden
| | - Mikael Sigvardsson
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Division of Molecular Hematology, Lund University, Lund, Sweden
- Lund Stemcell Center, Lund University, Lund, Sweden
- * E-mail:
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11
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Gouveia D, Almunia C, Cogne Y, Pible O, Degli-Esposti D, Salvador A, Cristobal S, Sheehan D, Chaumot A, Geffard O, Armengaud J. Ecotoxicoproteomics: A decade of progress in our understanding of anthropogenic impact on the environment. J Proteomics 2019; 198:66-77. [DOI: 10.1016/j.jprot.2018.12.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/19/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022]
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12
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Kuruvilla J, Bayat N, Cristobal S. Proteomic Analysis of Endothelial Cells Exposed to Ultrasmall Nanoparticles Reveals Disruption in Paracellular and Transcellular Transport. Proteomics 2019; 19:e1800228. [PMID: 30632670 DOI: 10.1002/pmic.201800228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/12/2018] [Indexed: 11/10/2022]
Abstract
The large interactive surfaces of nanoparticles (NPs) increase the opportunities to develop NPs for vascular targeting. Proteomic analysis of endothelial cells exposed to NPs reveals the cellular response and turns the focus into the impairment of the endothelial permeability. Here, quantitative proteomics and transcriptome sequencing are combined to evaluate the effects of exposure to sub-lethal concentrations of TiO2 -USNPs and TiO2 -NPs on human dermal microvascular endothelial cells. Endothelial cells react to preserve the semi-permeable properties that are essential for vascular tissue fluid homeostasis, vascular development, and angiogenesis. The main impact of the exposure was alteration of functional complexes involved in cell adhesion, vesicular transport, and cytoskeletal structure. Those are the core cellular structures that are linked to the permeability and the integrity of the endothelial tissue. Moreover, the extracellular proteins uptake along wih the NPs into the endothelial cells escape the lysosomal degradation pathway. These findings improve the understanding of the interaction of NPs with endothelial cell. The effects of the studied NPs modulating cell-cell adhesion and vesicular transport can help to evaluate the distribution of NPs via intravenous administration.
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Affiliation(s)
- Jacob Kuruvilla
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, SE-58185, Sweden
| | - Narges Bayat
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-10691, Sweden
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, SE-58185, Sweden.,IKERBASQUE, Basque Foundation for Science, Departments of Physiology, Faculty of Medicine and Dentistry, University of the Basque Country, Leioa, ES-48490, Spain
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13
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Kuruvilla J, Farinha AP, Bayat N, Cristobal S. Surface proteomics on nanoparticles: a step to simplify the rapid prototyping of nanoparticles. Nanoscale Horiz 2017; 2:55-64. [PMID: 32260678 DOI: 10.1039/c6nh00162a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Engineered nanoparticles for biomedical applications require increasing effectiveness in targeting specific cells while preserving non-target cells' safety. We developed a surface proteomics method for a rapid and systematic analysis of the interphase between the nanoparticle protein corona and the targeted cells that could implement the rapid prototyping of nanomedicines. Native nanoparticles entering in a protein-rich liquid medium quickly form a macromolecular structure called protein corona. This protein structure defines the physical interaction between nanoparticles and target cells. The surface proteins compose the first line of interaction between this macromolecular structure and the cell surface of a target cell. We demonstrated that SUSTU (SUrface proteomics, Safety, Targeting, Uptake) provides a qualitative and quantitative analysis from the protein corona surface. With SUSTU, the spatial dynamics of the protein corona surface can be studied. Data from SUSTU would ascertain the nanoparticle functionalized groups exposed at a destiny that could circumvent preliminary in vitro experiments. Therefore, this method could implement in the analysis of nanoparticle targeting and uptake capability and could be integrated into a rapid prototyping strategy which is a major challenge in nanomaterials science. Data are available via ProteomeXchange with the identifier PXD004636.
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Affiliation(s)
- J Kuruvilla
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden.
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14
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Lopes VR, Loitto V, Audinot JN, Bayat N, Gutleb AC, Cristobal S. Dose-dependent autophagic effect of titanium dioxide nanoparticles in human HaCaT cells at non-cytotoxic levels. J Nanobiotechnology 2016; 14:22. [PMID: 27001369 PMCID: PMC4802894 DOI: 10.1186/s12951-016-0174-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/07/2016] [Indexed: 02/14/2023] Open
Abstract
BACKGROUND Interactions between nanoparticles and cells are now the focus of a fast-growing area of research. Though many nanoparticles interact with cells without any acute toxic responses, metal oxide nanoparticles including those composed of titanium dioxide (TiO2-NPs) may disrupt the intracellular process of macroautophagy. Autophagy plays a key role in human health and disease, particularly in cancer and neurodegenerative diseases. We herein investigated the in vitro biological effects of TiO2-NPs (18 nm) on autophagy in human keratinocytes (HaCaT) cells at non-cytotoxic levels. RESULTS TiO2-NPs were characterized by transmission electron microscopy (TEM) and dynamic light scattering techniques. Cellular uptake, as evaluated by TEM and NanoSIMS revealed that NPs internalization led to the formation of autophagosomes. TiO2-NPs treatment did not reduce cell viability of HaCaT cells nor increased oxidative stress. Cellular autophagy was additionally evaluated by confocal microscopy using eGFP-LC3 keratinocytes, western blotting of autophagy marker LC3I/II, immunodetection of p62 and NBR1 proteins, and gene expression of LC3II, p62, NBR1, beclin1 and ATG5 by RT-qPCR. We also confirmed the formation and accumulation of autophagosomes in NPs treated cells with LC3-II upregulation. Based on the lack of degradation of p62 and NBR1 proteins, autophagosomes accumulation at a high dose (25.0 μg/ml) is due to blockage while a low dose (0.16 μg/ml) promoted autophagy. Cellular viability was not affected in either case. CONCLUSIONS The uptake of TiO2-NPs led to a dose-dependent increase in autophagic effect under non-cytotoxic conditions. Our results suggest dose-dependent autophagic effect over time as a cellular response to TiO2-NPs. Most importantly, these findings suggest that simple toxicity data are not enough to understand the full impact of TiO2-NPs and their effects on cellular pathways or function.
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Affiliation(s)
- Viviana R Lopes
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, 581 83, Linköping, Sweden
| | - Vesa Loitto
- Department of Clinical and Experimental Medicine, Medical Microbiology, Faculty of Medicine, Linköping University, 581 83, Linköping, Sweden
| | - Jean-Nicolas Audinot
- Material Research & Technology Department (MRT), Luxembourg Institute of Science and Technology (LIST), 4422, Belvaux, Luxembourg
| | - Narges Bayat
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Arno C Gutleb
- Environmental Research and Innovation (ERIN) Department 41, Luxembourg Institute of Science and Technology (LIST), 4422, Belvaux, Luxembourg
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, 581 83, Linköping, Sweden. .,IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Bizkaia, Spain. .,Department of Physiology, Faculty of Medicine and Dentistry of University of Basque Country UPV/EHU, 48940, Leioa, Bizkaia, Spain.
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15
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Campos A, Danielsson G, Farinha AP, Kuruvilla J, Warholm P, Cristobal S. Shotgun proteomics to unravel marine mussel (Mytilus edulis) response to long-term exposure to low salinity and propranolol in a Baltic Sea microcosm. J Proteomics 2016; 137:97-106. [PMID: 26820222 DOI: 10.1016/j.jprot.2016.01.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/23/2015] [Accepted: 01/19/2016] [Indexed: 02/06/2023]
Abstract
UNLABELLED Pharmaceuticals, among them the β-adrenoceptor blocker propranolol, are an important group of environmental contaminants reported in European waters. Laboratory exposure to pharmaceuticals on marine species has been performed without considering the input of the ecosystem flow. To unravel the ecosystem response to long-term exposure to propranolol we have performed long-term exposure to propranolol and low salinity in microcosms. We applied shotgun proteomic analysis to gills of Mytilus edulis from those Baltic Sea microcosms and identified 2071 proteins with a proteogenomic strategy. The proteome profiling patterns from the 587 highly reproductive proteins among groups define salinity as a key factor in the mussel's response to propranolol. Exposure at low salinity drives molecular mechanisms of adaptation based on a decrease in the abundance of several cytoskeletal proteins, signalling and intracellular membrane trafficking pathway combined with a response towards the maintenance of transcription and translation. The exposure to propranolol combined with low salinity modulates the expression of structural proteins including cilia functions and decreases the expression of membrane protein transporters. This study reinforces the environment concerns of the impact of low salinity in combination with anthropogenic pollutants and anticipates critical physiological conditions for the survival of the blue mussel in the northern areas. BIOLOGICAL SIGNIFICANCE Applying shotgun proteomic analysis to M. edulis gills samples from a long-term microcosm exposure to propranolol and following a proteogenomic identification strategy, we have identified 2071 proteins. The proteomic analysis unrevealed which molecular mechanisms drive the adaptation to low salinity stress and how salinity modulates the effects of exposure to propranolol. These results reinforce the idea of the impact of low salinity in combination with anthropogenic pollutants and anticipate critical physiological condition.
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Affiliation(s)
- Alexandre Campos
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden
| | - Gabriela Danielsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ana Paula Farinha
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden
| | - Jacob Kuruvilla
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden
| | - Per Warholm
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of Basque Country UPV/EHU, Bizkaia, Spain.
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16
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Marco-Ramell A, de Almeida AM, Cristobal S, Rodrigues P, Roncada P, Bassols A. Proteomics and the search for welfare and stress biomarkers in animal production in the one-health context. Mol BioSyst 2016; 12:2024-35. [DOI: 10.1039/c5mb00788g] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stress and welfare are important factors in animal production in the context of growing production optimization and scrutiny by the general public.
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Affiliation(s)
- A. Marco-Ramell
- Departament de Bioquímica i Biologia Molecular
- Facultat de Veterinària
- Universitat Autònoma de Barcelona
- 08193 Cerdanyola del Vallès
- Spain
| | - A. M. de Almeida
- Instituto de Biologia Experimental e Tecnologica
- Oeiras
- Portugal
- CIISA/FMV – Centro Interdisciplinar de Investigação em Sanidade Animal
- Faculdade de Medicina Veterinária
| | - S. Cristobal
- Department of Clinical and Experimental Medicine
- Cell Biology
- Faculty of Medicine
- Linköping University
- Linköping
| | - P. Rodrigues
- CCMAR
- Center of Marine Science
- University of Algarve
- 8005-139 Faro
- Portugal
| | - P. Roncada
- Istituto Sperimentale Italiano L. Spallanzani
- Milano
- Italy
| | - A. Bassols
- Departament de Bioquímica i Biologia Molecular
- Facultat de Veterinària
- Universitat Autònoma de Barcelona
- 08193 Cerdanyola del Vallès
- Spain
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17
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Rajapakse K, Drobne D, Kastelec D, Kogej K, Makovec D, Gallampois C, Amelina H, Danielsson G, Fanedl L, Marinsek-Logar R, Cristobal S. Proteomic analyses of early response of unicellular eukaryotic microorganism Tetrahymena thermophila exposed to TiO₂ particles. Nanotoxicology 2015; 10:542-56. [PMID: 26524663 DOI: 10.3109/17435390.2015.1091107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Key biological functions involved in cell survival have been studied to understand the difference between the impact of exposure to TiO2 nanoparticles (TiO2-NPs) and their bulk counterparts (bulk-TiO2). By selecting a unicellular eukaryotic model organism and applying proteomic analysis an overview of the possible impact of exposure could be obtained. In this study, we investigated the early response of unicellular eukaryotic protozoan Tetrahymena thermophila exposed to TiO2-NPs or bulk-TiO2 particles at subtoxic concentrations for this organism. The proteomic analysis based on 2DE + nLC-ESI-MS/MS revealed 930 distinct protein spots, among which 77 were differentially expressed and 18 were unambiguously identified. We identified alterations in metabolic pathways, including lipid and fatty acid metabolism, purine metabolism and energetic metabolism, as well as salt stress and protein degradation. This proteomic study is consistent with our previous findings, where the early response of T. thermophila to subtoxic concentrations of TiO2 particles included alterations in lipid and fatty acid metabolism and ion regulation. The response to the lowest TiO2-NPs concentration differed significantly from the response to higher TiO2-NPs concentration and both bulk-TiO2 concentrations. Alterations on the physiological landscape were significant after exposure to both nano- and bulk-TiO2; however, no toxic effects were evidenced even at very high exposure concentrations. This study confirms the relevance of the alteration of the lipid profile and lipid metabolism in understanding the early impact of TiO2-NPs in eukaryotic cells, for example, phagocytosing cells like macrophages and ciliated cells in the respiratory epithelium.
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Affiliation(s)
| | | | | | - K Kogej
- d Faculty of Chemistry and Chemical Technology , University of Ljubljana , Ljubljana , Slovenia
| | - D Makovec
- e Jožef Stefan Institute , Ljubljana , Slovenia
| | - C Gallampois
- f Department of Clinical and Experimental Medicine , Cell Biology, Medical Faculty, Linköping University , Linköping , Sweden
| | - H Amelina
- g Department of Biochemistry and Biophysics , Stockholm University , Stockholm , Sweden
| | - G Danielsson
- g Department of Biochemistry and Biophysics , Stockholm University , Stockholm , Sweden
| | - L Fanedl
- h Biotechnical Faculty, Department of Animal Science , University of Ljubjana , Slovenia , and
| | - R Marinsek-Logar
- h Biotechnical Faculty, Department of Animal Science , University of Ljubjana , Slovenia , and
| | - S Cristobal
- f Department of Clinical and Experimental Medicine , Cell Biology, Medical Faculty, Linköping University , Linköping , Sweden .,i Department of Physiology , Faculty of Medicine and Dentistry, IKERBASQUE, Basque Foundation for Science, University of the Basque Country , Leioa , Spain
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18
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Campos A, Apraiz I, da Fonseca RR, Cristobal S. Shotgun analysis of the marine musselMytilus edulishemolymph proteome and mapping the innate immunity elements. Proteomics 2015; 15:4021-9. [DOI: 10.1002/pmic.201500118] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/17/2015] [Accepted: 09/02/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Alexandre Campos
- Department of Clinical and Experimental Medicine; Cell Biology; Faculty of Medicine and Health Sciences; Linköping University; Linköping Sweden
| | - Itxaso Apraiz
- Department of Biochemistry and Biophysics; Stockholm University; Stockholm Sweden
| | - Rute R. da Fonseca
- The Bioinformatics Centre; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine; Cell Biology; Faculty of Medicine and Health Sciences; Linköping University; Linköping Sweden
- IKERBASQUE; Basque Foundation for Science, Department of Physiology; Faculty of Medicine and Dentistry; University of the Basque Country; Leioa Spain
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19
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Bayat N, Lopes VR, Schölermann J, Jensen LD, Cristobal S. Vascular toxicity of ultra-small TiO2 nanoparticles and single walled carbon nanotubes in vitro and in vivo. Biomaterials 2015; 63:1-13. [PMID: 26066004 DOI: 10.1016/j.biomaterials.2015.05.044] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/26/2015] [Accepted: 05/28/2015] [Indexed: 01/13/2023]
Abstract
Ultra-small nanoparticles (USNPs) at 1-3 nm are a subset of nanoparticles (NPs) that exhibit intermediate physicochemical properties between molecular dispersions and larger NPs. Despite interest in their utilization in applications such as theranostics, limited data about their toxicity exist. Here the effect of TiO2-USNPs on endothelial cells in vitro, and zebrafish embryos in vivo, was studied and compared to larger TiO2-NPs (30 nm) and to single walled carbon nanotubes (SWCNTs). In vitro exposure showed that TiO2-USNPs were neither cytotoxic, nor had oxidative ability, nevertheless were genotoxic. In vivo experiment in early developing zebrafish embryos in water at high concentrations of TiO2-USNPs caused mortality possibly by acidifying the water and caused malformations in the form of pericardial edema when injected. Myo1C involved in glomerular development of zebrafish embryos was upregulated in embryos exposed to TiO2-USNPs. They also exhibited anti-angiogenic effects both in vitro and in vivo plus decreased nitric oxide concentration. The larger TiO2-NPs were genotoxic but not cytotoxic. SWCNTs were cytotoxic in vitro and had the highest oxidative ability. Neither of these NPs had significant effects in vivo. To our knowledge this is the first study evaluating the effects of TiO2-USNPs on vascular toxicity in vitro and in vivo and this strategy could unravel USNPs potential applications.
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Affiliation(s)
- Narges Bayat
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Viviana R Lopes
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine and Health Sciences Linköping University, Linköping, Sweden
| | - Julia Schölermann
- Department of Clinical Dentistry, Biomaterials, University of Bergen, Bergen, Norway
| | - Lasse Dahl Jensen
- Division of Cardiovascular Medicine, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden
| | - Susana Cristobal
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine and Health Sciences Linköping University, Linköping, Sweden; IKERBASQUE, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Dentistry, University of the Basque Country, Leioa, Spain.
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20
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García-Sánchez S, Bernales I, Cristobal S. Early response to nanoparticles in the Arabidopsis transcriptome compromises plant defence and root-hair development through salicylic acid signalling. BMC Genomics 2015; 16:341. [PMID: 25903678 PMCID: PMC4417227 DOI: 10.1186/s12864-015-1530-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 04/13/2015] [Indexed: 12/01/2022] Open
Abstract
Background The impact of nano-scaled materials on photosynthetic organisms needs to be evaluated. Plants represent the largest interface between the environment and biosphere, so understanding how nanoparticles affect them is especially relevant for environmental assessments. Nanotoxicology studies in plants allude to quantum size effects and other properties specific of the nano-stage to explain increased toxicity respect to bulk compounds. However, gene expression profiles after exposure to nanoparticles and other sources of environmental stress have not been compared and the impact on plant defence has not been analysed. Results Arabidopsis plants were exposed to TiO2-nanoparticles, Ag-nanoparticles, and multi-walled carbon nanotubes as well as different sources of biotic (microbial pathogens) or abiotic (saline, drought, or wounding) stresses. Changes in gene expression profiles and plant phenotypic responses were evaluated. Transcriptome analysis shows similarity of expression patterns for all plants exposed to nanoparticles and a low impact on gene expression compared to other stress inducers. Nanoparticle exposure repressed transcriptional responses to microbial pathogens, resulting in increased bacterial colonization during an experimental infection. Inhibition of root hair development and transcriptional patterns characteristic of phosphate starvation response were also observed. The exogenous addition of salicylic acid prevented some nano-specific transcriptional and phenotypic effects, including the reduction in root hair formation and the colonization of distal leaves by bacteria. Conclusions This study integrates the effect of nanoparticles on gene expression with plant responses to major sources of environmental stress and paves the way to remediate the impact of these potentially damaging compounds through hormonal priming. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1530-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susana García-Sánchez
- Department of Physiology, Faculty of Medicine and Dentistry, University of the Basque Country UPV/EHU, Leioa, Spain.
| | - Irantzu Bernales
- Gene Expression Unit, Genomics Facility of General Research Services (SGIker), Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain.
| | - Susana Cristobal
- IKERBASQUE, Basque Country Foundation for Science. Department of Physiology, Faculty of Medicine and Dentistry, University of the Basque Country UPV/EHU, Leioa, Spain. .,Department of Clinical and Experimental Medicine, Health Science Faculty, Linköping University, Linköping, Sweden.
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21
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Almeida AM, Bassols A, Bendixen E, Bhide M, Ceciliani F, Cristobal S, Eckersall PD, Hollung K, Lisacek F, Mazzucchelli G, McLaughlin M, Miller I, Nally JE, Plowman J, Renaut J, Rodrigues P, Roncada P, Staric J, Turk R. Animal board invited review: advances in proteomics for animal and food sciences. Animal 2015; 9:1-17. [PMID: 25359324 PMCID: PMC4301196 DOI: 10.1017/s1751731114002602] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 09/27/2014] [Indexed: 01/15/2023] Open
Abstract
Animal production and health (APH) is an important sector in the world economy, representing a large proportion of the budget of all member states in the European Union and in other continents. APH is a highly competitive sector with a strong emphasis on innovation and, albeit with country to country variations, on scientific research. Proteomics (the study of all proteins present in a given tissue or fluid - i.e. the proteome) has an enormous potential when applied to APH. Nevertheless, for a variety of reasons and in contrast to disciplines such as plant sciences or human biomedicine, such potential is only now being tapped. To counter such limited usage, 6 years ago we created a consortium dedicated to the applications of Proteomics to APH, specifically in the form of a Cooperation in Science and Technology (COST) Action, termed FA1002--Proteomics in Farm Animals: www.cost-faproteomics.org. In 4 years, the consortium quickly enlarged to a total of 31 countries in Europe, as well as Israel, Argentina, Australia and New Zealand. This article has a triple purpose. First, we aim to provide clear examples on the applications and benefits of the use of proteomics in all aspects related to APH. Second, we provide insights and possibilities on the new trends and objectives for APH proteomics applications and technologies for the years to come. Finally, we provide an overview and balance of the major activities and accomplishments of the COST Action on Farm Animal Proteomics. These include activities such as the organization of seminars, workshops and major scientific conferences, organization of summer schools, financing Short-Term Scientific Missions (STSMs) and the generation of scientific literature. Overall, the Action has attained all of the proposed objectives and has made considerable difference by putting proteomics on the global map for animal and veterinary researchers in general and by contributing significantly to reduce the East-West and North-South gaps existing in the European farm animal research. Future activities of significance in the field of scientific research, involving members of the action, as well as others, will likely be established in the future.
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Affiliation(s)
- A. M. Almeida
- Instituto de Investigação Científica Tropical, CVZ – Centro de Veterinária e Zootecnia, Av. Univ. Técnica, 1300-477 Lisboa, Portugal
- CIISA – Centro Interdisciplinar de Investigação em Sanidade Animal, 1300-477 Lisboa, Portugal
- ITQB – Instituto de Tecnologia Química e Biológica da UNL, 2780-157 Oeiras, Portugal
- IBET – Instituto de Biologia Experimental e Tecnológica, 2780-157 Oeiras, Portugal
| | - A. Bassols
- Departament de Bioquímica i Biologia Molecular, Facultat de Veterinària, Universitat Autònoma de Barcelona,08193 Cerdanyola del Vallès, Spain
| | - E. Bendixen
- Institute of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - M. Bhide
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenskeho-73 Kosice, Slovakia
| | - F. Ceciliani
- Department of Veterinary Science and Public Health, Università di Milano, Via Celoria 10, 20133 Milano, Italy
| | - S. Cristobal
- Department of Clinical and Experimental Medicine, Division of Cell Biology, Faculty of Health Science, Linköping University, SE-581 85 Linköping, Sweden
- IKERBASQUE, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Dentistry, University of Basque Country,48940 Leioa, Bizkaia, Spain
| | - P. D. Eckersall
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK
| | - K. Hollung
- Nofima AS, PO Box 210, NO-1431 Aas, Norway
| | - F. Lisacek
- Swiss Institute of Bioinformatics, CMU – Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - G. Mazzucchelli
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, 4000 Liège, Belgium
| | - M. McLaughlin
- Division of Veterinary Bioscience, School of Veterinary Medicine, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK
| | - I. Miller
- Institute of Medical Biochemistry, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - J. E. Nally
- National Animal Disease Center, Bacterial Diseases of Livestock Research Unit, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - J. Plowman
- Food & Bio-Based Products, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - J. Renaut
- Department of Environment and Agrobiotechnologies, Centre de Recherche Public – Gabriel Lippmann, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - P. Rodrigues
- CCMAR – Centre of Marine Sciences of Algarve, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - P. Roncada
- Department of Veterinary Science and Public Health, Istituto Sperimentale Italiano L. Spallanzani Milano, University of Milano, 20133 Milano, Italy
| | - J. Staric
- Clinic for Ruminants with Ambulatory Clinic, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - R. Turk
- Department of Pathophysiology, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
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Virkki MT, Agrawal N, Edsbäcker E, Cristobal S, Elofsson A, Kauko A. Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core. Protein Sci 2014; 23:981-92. [PMID: 24777974 PMCID: PMC4088982 DOI: 10.1002/pro.2483] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/23/2014] [Accepted: 04/24/2014] [Indexed: 12/29/2022]
Abstract
The folding of most integral membrane proteins follows a two-step process: initially, individual transmembrane helices are inserted into the membrane by the Sec translocon. Thereafter, these helices fold to shape the final conformation of the protein. However, for some proteins, including Aquaporin 1 (AQP1), the folding appears to follow a more complicated path. AQP1 has been reported to first insert as a four-helical intermediate, where helix 2 and 4 are not inserted into the membrane. In a second step, this intermediate is folded into a six-helical topology. During this process, the orientation of the third helix is inverted. Here, we propose a mechanism for how this reorientation could be initiated: first, helix 3 slides out from the membrane core resulting in that the preceding loop enters the membrane. The final conformation could then be formed as helix 2, 3, and 4 are inserted into the membrane and the reentrant regions come together. We find support for the first step in this process by showing that the loop preceding helix 3 can insert into the membrane. Further, hydrophobicity curves, experimentally measured insertion efficiencies and MD-simulations suggest that the barrier between these two hydrophobic regions is relatively low, supporting the idea that helix 3 can slide out of the membrane core, initiating the rearrangement process.
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Affiliation(s)
- Minttu T Virkki
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm UniversitySolna, SE-171 21, Sweden
| | - Nitin Agrawal
- Department of Biosciences, Biochemistry, Åbo AkademiTurku, FI-20520, Finland
| | - Elin Edsbäcker
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm UniversitySolna, SE-171 21, Sweden
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Health Science, Linköping UniversityLinköping, Sweden
- Department of Physiology, IKERBASQUE, Basque Foundation for Science, Faculty of Medicine and Dentistry, University of the Basque CountryLeioa, Spain
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm UniversitySolna, SE-171 21, Sweden
| | - Anni Kauko
- Department of Biosciences, Biochemistry, Åbo AkademiTurku, FI-20520, Finland
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Virkki MT, Peters C, Nilsson D, Sörensen T, Cristobal S, Wallner B, Elofsson A. The positive inside rule is stronger when followed by a transmembrane helix. J Mol Biol 2014; 426:2982-91. [PMID: 24927974 DOI: 10.1016/j.jmb.2014.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 11/30/2022]
Abstract
The translocon recognizes transmembrane helices with sufficient level of hydrophobicity and inserts them into the membrane. However, sometimes less hydrophobic helices are also recognized. Positive inside rule, orientational preferences of and specific interactions with neighboring helices have been shown to aid in the recognition of these helices, at least in artificial systems. To better understand how the translocon inserts marginally hydrophobic helices, we studied three naturally occurring marginally hydrophobic helices, which were previously shown to require the subsequent helix for efficient translocon recognition. We find no evidence for specific interactions when we scan all residues in the subsequent helices. Instead, we identify arginines located at the N-terminal part of the subsequent helices that are crucial for the recognition of the marginally hydrophobic transmembrane helices, indicating that the positive inside rule is important. However, in two of the constructs, these arginines do not aid in the recognition without the rest of the subsequent helix; that is, the positive inside rule alone is not sufficient. Instead, the improved recognition of marginally hydrophobic helices can here be explained as follows: the positive inside rule provides an orientational preference of the subsequent helix, which in turn allows the marginally hydrophobic helix to be inserted; that is, the effect of the positive inside rule is stronger if positively charged residues are followed by a transmembrane helix. Such a mechanism obviously cannot aid C-terminal helices, and consequently, we find that the terminal helices in multi-spanning membrane proteins are more hydrophobic than internal helices.
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Affiliation(s)
- Minttu T Virkki
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Christoph Peters
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm, Sweden.
| | - Daniel Nilsson
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Therese Sörensen
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Health Science, Linköping University, 581 83 Linköping, Sweden; Department of Physiology, IKERBASQUE, Basque Foundation for Science, Faculty of Medicine and Dentistry, University of the Basque Country, 48949 Leioa, Spain.
| | - Björn Wallner
- Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm, Sweden; Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden.
| | - Arne Elofsson
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm, Sweden.
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Tedesco S, Mullen W, Cristobal S. High-Throughput Proteomics: A New Tool for Quality and Safety in Fishery Products. Curr Protein Pept Sci 2014; 15:118-33. [DOI: 10.2174/1389203715666140221120219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 10/13/2013] [Accepted: 11/19/2013] [Indexed: 11/22/2022]
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Ge Y, Wang DZ, Chiu JF, Cristobal S, Sheehan D, Silvestre F, Peng X, Li H, Gong Z, Lam SH, Wentao H, Iwahashi H, Liu J, Mei N, Shi L, Bruno M, Foth H, Teichman K. Environmental OMICS: Current Status and Future Directions. ACTA ACUST UNITED AC 2013. [DOI: 10.5584/jiomics.v3i2.141] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Bayat N, Rajapakse K, Marinsek-Logar R, Drobne D, Cristobal S. The effects of engineered nanoparticles on the cellular structure and growth of Saccharomyces cerevisiae. Nanotoxicology 2013; 8:363-73. [PMID: 23521755 DOI: 10.3109/17435390.2013.788748] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In order to study the effects of nanoparticles (NPs) with different physicochemical properties on cellular viability and structure, Saccharomyces cerevisiae were exposed to different concentrations of TiO2-NPs (1-3 nm), ZnO-NPs (<100 nm), CuO-NPs (<50 nm), their bulk forms, Ag-NPs (10 nm) and single-walled carbon nanotubes (SWCNTs). The GreenScreen assay was used to measure cyto- and genotoxicity, and transmission electron microscopy (TEM) used to assess ultrastructure. CuO-NPs were highly cytotoxic, reducing the cell density by 80% at 9 cm(2)/ml, and inducing lipid droplet formation. Cells exposed to Ag-NPs (19 cm(2)/ml) and TiO2-NPs (147 cm(2)/ml) contained dark deposits in intracellular vacuoles, the cell wall and vesicles, and reduced cell density (40 and 30%, respectively). ZnO-NPs (8 cm(2)/ml) caused an increase in the size of intracellular vacuoles, despite not being cytotoxic. SWCNTs did not cause cytotoxicity or significant alterations in ultrastructure, despite high oxidative potential. Two genotoxicity assays, GreenScreen and the comet assay, produced different results and the authors discuss the reasons for this discrepancy. Classical assays of toxicity may not be the most suitable for studying the effects of NPs in cellular systems, and the simultaneous assessment of other measures of the state of cells, such as TEM are highly recommended.
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Affiliation(s)
- Narges Bayat
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm , Sweden
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Bendz M, Skwark M, Nilsson D, Granholm V, Cristobal S, Käll L, Elofsson A. Membrane protein shaving with thermolysin can be used to evaluate topology predictors. Proteomics 2013; 13:1467-80. [DOI: 10.1002/pmic.201200517] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/23/2013] [Accepted: 02/25/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Maria Bendz
- Department of Biochemistry and Biophysics; Science for Life Laboratory, Center for Biomembrane Research, Stockholm University; Stockholm Sweden
| | - Marcin Skwark
- Department of Biochemistry and Biophysics; Science for Life Laboratory, Center for Biomembrane Research, Stockholm University; Stockholm Sweden
| | - Daniel Nilsson
- Department of Biochemistry and Biophysics; Science for Life Laboratory, Center for Biomembrane Research, Stockholm University; Stockholm Sweden
| | - Viktor Granholm
- Department of Biochemistry and Biophysics; Science for Life Laboratory, Center for Biomembrane Research, Stockholm University; Stockholm Sweden
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology; Faculty of Health Science, Linköping University; Linköping Sweden
- IKERBASQUE, Basque Foundation for Science; Department of Physiology, Basque Country Medical School; Bilbao Spain
| | - Lukas Käll
- Science for Life Laboratory, School of Biotechnology; Royal Institute of Technology (KTH); Solna Sweden
| | - Arne Elofsson
- Department of Biochemistry and Biophysics; Science for Life Laboratory, Center for Biomembrane Research, Stockholm University; Stockholm Sweden
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Amelina H, Sjödin MOD, Bergquist J, Cristobal S. Quantitative subproteomic analysis of age-related changes in mouse liver peroxisomes by iTRAQ LC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3393-400. [PMID: 21963482 DOI: 10.1016/j.jchromb.2011.08.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 08/07/2011] [Accepted: 08/26/2011] [Indexed: 10/17/2022]
Abstract
Aging is a complex multifactorial phenomenon, which is believed to result from the accumulation of cellular damage to biological macromolecules. Peroxisomes recently emerged as another important source of reactive oxygen species (ROS) production in addition to mitochondria. However, the role of these organelles in the process of aging is still not clear. The aim of this study was to characterize the changes in protein expression profiles of young (10 weeks old) versus old (18 months old) mouse liver peroxisome-enriched fractions. We have applied shotgun proteomic approach based on liquid chromatography and tandem mass spectrometry (LC-MS/MS) combined with iTRAQ (isobaric tags for relative and absolute quantitation) labeling that allows comparative quantitative multiplex analysis. Our analysis led to identification and quantification of 150 proteins, 8 out of which were differentially expressed between two age groups at a statistically significant level (p<0.05), with folds ranging from 1.2 to 4.1. These proteins involved in peroxisomal β-oxidation, detoxification of xenobiotics and production of ROS. Noteworthy, differences in liver proteome have been observed between as well as within different age groups. In conclusion, our subproteomic quantitative study suggests that mouse liver proteome is sufficiently maintained until certain age.
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Affiliation(s)
- Hanna Amelina
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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Apraiz I, Lind J, Käll L, Bergquist J, Cristobal S. Fish peptidome patterns can distinguish from exposure to antropogenic pollution. Comp Biochem Physiol A Mol Integr Physiol 2010. [DOI: 10.1016/j.cbpa.2010.06.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Apraiz I, Cajaraville MP, Cristobal S. Peroxisomal proteomics: biomonitoring in mussels after the Prestige's oil spill. Mar Pollut Bull 2009; 58:1815-1826. [PMID: 19732914 DOI: 10.1016/j.marpolbul.2009.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 07/28/2009] [Accepted: 08/03/2009] [Indexed: 05/28/2023]
Abstract
Peroxisomal proteomics was applied to assess possible biological effects after the Prestige's oil spill. Mussels were sampled in July 2004 and 2005 in four stations in the NW (closest to the spill) and NE coasts of the Iberian Peninsula. Principal components analysis (PCA) suggested differences in protein expression among stations and sampling years. Several proteins were putatively identified by mass spectrometry and immunolocalization. PC1 separated the NW stations in 2004 from the rest of the stations and sampling years mainly due to up-regulation of peroxisomal beta-oxidation proteins and PMP70. PC3 separated the NE stations, based on up-regulation of the antioxidant enzyme catalase in 2004 compared to 2005. PC4 separated the stations in the NE and the NW. This work shows that environmental proteomics, together with multivariate data analysis, could provide information to interpret the effects of oil spills at cellular level in mussels.
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Affiliation(s)
- Itxaso Apraiz
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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Hedin LE, Ojemalm K, Bernsel A, Hennerdal A, Illergård K, Enquist K, Kauko A, Cristobal S, von Heijne G, Lerch-Bader M, Nilsson I, Elofsson A. Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context. J Mol Biol 2009; 396:221-9. [PMID: 19931281 DOI: 10.1016/j.jmb.2009.11.036] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 11/11/2009] [Accepted: 11/13/2009] [Indexed: 11/25/2022]
Abstract
In mammalian cells, most integral membrane proteins are initially inserted into the endoplasmic reticulum membrane by the so-called Sec61 translocon. However, recent predictions suggest that many transmembrane helices (TMHs) in multispanning membrane proteins are not sufficiently hydrophobic to be recognized as such by the translocon. In this study, we have screened 16 marginally hydrophobic TMHs from membrane proteins of known three-dimensional structure. Indeed, most of these TMHs do not insert efficiently into the endoplasmic reticulum membrane by themselves. To test if loops or TMHs immediately upstream or downstream of a marginally hydrophobic helix might influence the insertion efficiency, insertion of marginally hydrophobic helices was also studied in the presence of their neighboring loops and helices. The results show that flanking loops and nearest-neighbor TMHs are sufficient to ensure the insertion of many marginally hydrophobic helices. However, for at least two of the marginally hydrophobic helices, the local interactions are not enough, indicating that post-insertional rearrangements are involved in the folding of these proteins.
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Affiliation(s)
- Linnea E Hedin
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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Apraiz I, Leoni G, Lindenstrand D, Persson JO, Cristobal S. Proteomic Analysis of Mussels Exposed to Fresh and Weathered Prestige’s Oil. ACTA ACUST UNITED AC 2009. [DOI: 10.4172/jpb.1000084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Background This study aims to analyze sex differences in mice aging kidney. We applied a proteomic technique based on subfractionation, and liquid chromatography coupled with 2-DE. Samples from male and female CD1-Swiss outbred mice from 28 weeks, 52 weeks, and 76 weeks were analysed by 2-DE, and selected proteins were identified by matrix assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Results This proteomic analysis detected age-related changes in protein expression in 55 protein-spots, corresponding to 22 spots in males and 33 spots in females. We found a protein expression signature (PES) of aging composed by 8 spots, common for both genders. The identified proteins indicated increases in oxidative and proteolytic proteins and decreases in glycolytic proteins, and antioxidant enzymes. Conclusion Our results provide insights into the gender differences associated to the decline of kidney function in aging. Thus, we show that proteomics can provide valuable information on age-related changes in expression levels of proteins and related modifications. This pilot study is still far from providing candidates for aging-biomarkers. However, we suggest that the analysis of these proteins could suggest mechanisms of cellular aging in kidney, and improve the kidney selection for transplantation.
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Affiliation(s)
- Hanna Amelina
- Department of Biochemistry and Biophysics, Stockholm University, Sweden.
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Abstract
Peroxisomal proteomic protein profiles of exposure to marine pollution have been recently introduced in biomonitoring experiments. However, laboratory experiments to study the independent effect of common pollutants are needed to define a minimal protein expression signature (PES) of exposure to a specific pollutant. The aim of this study was to obtain PESs in blue mussels (Mytilus edulis) exposed to two different crude oil mixtures for future application in biomonitoring areas affected by oil spills. In the study, peroxisome-enriched fractions from digestive gland of M. edulis (L., 1758) were analysed by two-dimensional fluorescence difference electrophoresis (DIGE) and mass spectrometry (MS) after 3 weeks of exposure to crude oil mixtures: crude oil or crude oil spiked with alkylated phenols (AP) and extra polycyclic aromatic hydrocarbons (PAH) in a laboratory flow-through system. A minimal PES composed by 13 protein spots and unique PESs of exposure to the two different mixtures were identified. A total of 22 spots from the two-dimensional maps that had shown a significant increase or decrease in abundance in each of the exposed groups exposed were analysed. The hierarchical clustering analysis succeeded in discriminating the exposed groups from the control groups based on the unique PES. The PESs obtained were consistent with protein patterns obtained in previous field experiments. The results suggest that the protein profiles obtained by peroxisomal proteomics could be used to assess oil exposure in marine pollution assessments.
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Affiliation(s)
- J Mi
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
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Abstract
Pollution in aquatic environment is of increasing concern for its impact on both human and natural populations. Applying proteomics to monitor marine pollution is a new approach to evaluate the effects of environmental pollutants on the biota. Aquatic organisms living in coastal and estuarine areas are particularly prone to exposures to a variety of pollutants, some of which can act as peroxisome proliferators. However, peroxisomal responses in particular and biomarker responses in general can be influenced by several biotic and abiotic factors. Utilizing proteomics-based techniques that permit the evaluation of hundreds to thousands of proteins in a single experiment can circumvent those drawbacks. Applying this method, the peroxisomal proteome from digestive glands of mussels Mytilus sp. can be analyzed by two-dimensional electrophoresis (2-DE) and the 2-DE maps from control samples and samples obtained in a polluted area can be compared. The up- and down-regulated proteins compose the protein expression signature (PES) associated with exposure to peroxisome proliferating pollutants. This method generates highly reproducible patterns that can be applied to laboratory or field experiments.
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Affiliation(s)
- Susana Cristobal
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
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Mi J, Garcia-Arcos I, Alvarez R, Cristobal S. Age-related subproteomic analysis of mouse liver and kidney peroxisomes. Proteome Sci 2007; 5:19. [PMID: 18042274 PMCID: PMC2231346 DOI: 10.1186/1477-5956-5-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 11/27/2007] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Despite major recent advances in the understanding of peroxisomal functions and how peroxisomes arise, only scant information is available regarding this organelle in cellular aging. The aim of this study was to characterize the changes in the protein expression profile of aged versus young liver and kidney peroxisome-enriched fractions from mouse and to suggest possible mechanisms underlying peroxisomal aging. Peroxisome-enriched fractions from 10 weeks, 18 months and 24 months C57bl/6J mice were analyzed by quantitative proteomics. RESULTS Peroxisomal proteins were enriched by differential and density gradient centrifugation and proteins were separated by two-dimensional electrophoresis (2-DE), quantified and identified by mass spectrometry (MS). In total, sixty-five proteins were identified in both tissues. Among them, 14 proteins were differentially expressed in liver and 21 proteins in kidney. The eight proteins differentially expressed in both tissues were involved in beta-oxidation, alpha-oxidation, isoprenoid biosynthesis, amino acid metabolism, and stress response. Quantitative proteomics, clustering methods, and prediction of transcription factors, all indicated that there is a decline in protein expression at 18 months and a recovery at 24 months. CONCLUSION These results indicate that some peroxisomal proteins show a tissue-specific functional response to aging. This response is probably dependent on their differential regeneration capacity. The differentially expressed proteins could lead several cellular effects: such as alteration of fatty acid metabolism that could alert membrane protein functions, increase of the oxidative stress and contribute to decline in bile salt synthesis. The ability to detect age-related variations in the peroxisomal proteome can help in the search for reliable and valid aging biomarkers.
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Affiliation(s)
- Jia Mi
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Itsaso Garcia-Arcos
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Ruben Alvarez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Susana Cristobal
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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37
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Abstract
The peroxisome plays a central role in the catabolic and anabolic pathways that contribute to the lipid homeostasis. Besides this main function, this organelle has gained functional diversity. Although several approaches have been used for peroxisomal proteome analysis, a quantitative protein expression analysis of peroxisomes from different tissues has not been elucidated yet. Here, we applied a 2-DE-based method on mouse liver and kidney peroxisomal enriched fractions to study the tissue-dependent protein expression. Ninety-one spots were identified from the 2-DE maps from pH 3.0-10.0 and 51 spots from the basic range corresponding to 31 peroxisomal proteins, 10 putative peroxisomal, 6 cytosolic, 17 mitochondrial and 1 protein from endoplasmic reticulum. Based on the identification and on the equivalent quality of both tissue preparations, the differences emerging from the comparison could be quantified. In liver, proteins involved in pathways such as alpha- and beta-oxidation, isoprenoid biosynthesis, amino acid metabolism and purine and pyrimidine metabolism were more abundant whereas in kidney, proteins from the straight-chain fatty acid beta-oxidation were highly expressed. These results indicate that tissue-specific functional classes of peroxisomal proteins could be relevant to study peroxisomal cellular responses or pathologies. Finally, a web-based peroxisomal proteomic database was built.
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Affiliation(s)
- Jia Mi
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
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38
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Amelina H, Apraiz I, Sun W, Cristobal S. Proteomics-Based Method for the Assessment of Marine Pollution Using Liquid Chromatography Coupled with Two-Dimensional Electrophoresis. J Proteome Res 2007; 6:2094-104. [PMID: 17458988 DOI: 10.1021/pr060689s] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Using a proteomic approach, we have developed a new method for the assessment of marine pollution that generates highly reproducible protein expression patterns and it is simple and scalable. The protocol is based on applying liquid chromatography (LC) coupled with two-dimensional electrophoresis (2-DE) to analyze changes in the protein expression pattern after exposure to marine pollution. The digestive gland of the sentinel "blue mussel" (Mytilus edulis) was batch-processed through a simple cell fractionation followed by ion-exchange chromatography and 2-DE. The selection of ligands, elution method, and small volume design was carefully considered to define a protocol that could be mainly robotized. A pilot study with samples collected from different Gothenburg harbor areas indicated that the clean area could be distinguished from the polluted ones based on a protein expression pattern (PES) composed of 13 proteins. Principal component analysis (PCA) and hierarchical clustering confirmed that the PES was sufficient to discriminate polluted and unpolluted areas and to provide a spatial gradient from the polluted source. Several proteins from the PES were identified by electrospray ionization tandem mass spectrometry (ESI-MS/MS), and they are involved in beta-oxidation, amino acid metabolism, detoxification, protein degradation, organelle biogenesis, and protein folding. In the near future, this methodology could show potential advantages to assess marine pollution and could become a stable platform to elucidate ecotoxicological questions.
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Affiliation(s)
- Hanna Amelina
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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39
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Abstract
Bivalves and especially mussels are very good indicators of marine and estuarine pollution, and so they have been widely used in biomonitoring programs all around the world. However, traditional single parameter biomarkers face the problem of high sensitivity to biotic and abiotic factors. In our study, digestive gland peroxisome-enriched fractions of Mytilus edulis (L., 1758) were analyzed by DIGE and MS. We identified several proteomic signatures associated with the exposure to several marine pollutants (diallyl phthalate, PBDE-47, and bisphenol-A). Animals collected from North Atlantic Sea were exposed to the contaminants independently under controlled laboratory conditions. One hundred and eleven spots showed a significant increase or decrease in protein abundance in the two-dimensional electrophoresis maps from the groups exposed to pollutants. We obtained a unique protein expression signature of exposure to each of those chemical compounds. Moreover a set of proteins composed a proteomic signature in common to the three independent exposures. It is remarkable that the principal component analysis of these spots showed a discernible separation between groups, and so did the hierarchical clustering into four classes. The 14 proteins identified by MS participate in alpha- and beta-oxidation pathways, xenobiotic and amino acid metabolism, cell signaling, oxyradical metabolism, peroxisomal assembly, respiration, and the cytoskeleton. Our results suggest that proteomic signatures could become a valuable tool to monitor the presence of pollutants in field experiments where a mixture of pollutants is often present. Further studies on the identified proteins could provide crucial information to understand possible mechanisms of toxicity of single xenobiotics or mixtures of them in marine ecosystems.
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Affiliation(s)
- Itxaso Apraiz
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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40
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Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A. A study of quality measures for protein threading models. BMC Bioinformatics 2001; 2:5. [PMID: 11545673 PMCID: PMC55330 DOI: 10.1186/1471-2105-2-5] [Citation(s) in RCA: 148] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2001] [Accepted: 08/01/2001] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prediction of protein structures is one of the fundamental challenges in biology today. To fully understand how well different prediction methods perform, it is necessary to use measures that evaluate their performance. Every two years, starting in 1994, the CASP (Critical Assessment of protein Structure Prediction) process has been organized to evaluate the ability of different predictors to blindly predict the structure of proteins. To capture different features of the models, several measures have been developed during the CASP processes. However, these measures have not been examined in detail before. In an attempt to develop fully automatic measures that can be used in CASP, as well as in other type of benchmarking experiments, we have compared twenty-one measures. These measures include the measures used in CASP3 and CASP2 as well as have measures introduced later. We have studied their ability to distinguish between the better and worse models submitted to CASP3 and the correlation between them. RESULTS Using a small set of 1340 models for 23 different targets we show that most methods correlate with each other. Most pairs of measures show a correlation coefficient of about 0.5. The correlation is slightly higher for measures of similar types. We found that a significant problem when developing automatic measures is how to deal with proteins of different length. Also the comparisons between different measures is complicated as many measures are dependent on the size of the target. We show that the manual assessment can be reproduced to about 70% using automatic measures. Alignment independent measures, detects slightly more of the models with the correct fold, while alignment dependent measures agree better when selecting the best models for each target. Finally we show that using automatic measures would, to a large extent, reproduce the assessors ranking of the predictors at CASP3. CONCLUSIONS We show that given a sufficient number of targets the manual and automatic measures would have given almost identical results at CASP3. If the intent is to reproduce the type of scoring done by the manual assessor in in CASP3, the best approach might be to use a combination of alignment independent and alignment dependent measures, as used in several recent studies.
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Affiliation(s)
- Susana Cristobal
- Cell and Molecular Biology Department, Box 596. BMC Uppsala University, SE-751 24 Uppsala, Sweden
| | - Adam Zemla
- Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550-9234 USA
| | - Daniel Fischer
- Department Bioinformatics/Computer Science, Ben Gurion University, Beer-Sheva 84015, Israel
| | - Leszek Rychlewski
- International Institute of Molecular and Cell Biology, Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Arne Elofsson
- Stockholm Bioinformatics Center, Stockholm University, SE-106 91 Stockholm, Sweden
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