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Guesmi S, Ghedira K, Pujic P, Najjari A, Miotello G, Cherif A, Narumi I, Armengaud J, Normand P, Sghaier H. Effect of gamma irradiation on the proteogenome of cold-acclimated Kocuria rhizophila PT10. Res Microbiol 2024:104230. [PMID: 39089347 DOI: 10.1016/j.resmic.2024.104230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 07/03/2024] [Accepted: 07/25/2024] [Indexed: 08/03/2024]
Abstract
In this paper, we investigated the effects of ionizing radiation (IR) on the protein dynamics of cold-stressed cells of a radioresistant actinobacterium, Kocuria rhizophila PT10, isolated from the rhizosphere of the desert plant Panicum turgidum using a shotgun methodology based on nanoflow liquid chromatography coupled to tandem mass spectrometry (nano LC-MS/MS). Overall, 1,487 proteins were certified, and their abundances were compared between the irradiated condition and control. IR of cold-acclimated PT10 triggered the over-abundance of proteins involved in (1) a strong transcriptional regulation, (2) amidation of peptidoglycan and preservation of cell envelope integrity, (3) detoxification of reactive electrophiles and regulation of the redox status of proteins, (4) base excision repair and prevention of mutagenesis and (5) the tricarboxylic acid (TCA) cycle and production of fatty acids. Also, one of the more significant findings to emerge from this study is the SOS response of stressed PT10. Moreover, a comparison of top hits radio-modulated proteins of cold-acclimated PT10 with proteomics data from gamma-irradiated Deinococcus deserti showed that stressed PT10 has a specific response characterised by a high over-abundance of two transcriptional regulators, NemA, GatD, and UdgB.
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Affiliation(s)
- Sihem Guesmi
- National Agronomy Institute (INAT), Avenue Charles Nicolle, Mahrajène, 1082, Tunis, Tunisia; Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia.
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, 13, Place Pasteur, Tunis, 1002, Tunisia.
| | - Petar Pujic
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622, Villeurbanne, France; CNRS, UMR 5557, Ecologie Microbienne, 69622 Villeurbanne, Cedex, INRA, UMR1418, Villeurbanne, France.
| | - Afef Najjari
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR03ES03 Microorganismes et Biomolécules Actives, 2092, Tunis, Tunisia.
| | - Guylaine Miotello
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols sur Cèze, France.
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia.
| | - Issay Narumi
- Radiation Microbiology Laboratory, Department of Life Sciences, Faculty of Life Sciences, Toyo University, 48-1 Oka, Asaka, Saitama 351-8510, Japan.
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols sur Cèze, France.
| | - Philippe Normand
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622, Villeurbanne, France; CNRS, UMR 5557, Ecologie Microbienne, 69622 Villeurbanne, Cedex, INRA, UMR1418, Villeurbanne, France.
| | - Haïtham Sghaier
- Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia; Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia.
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Laurent J, Diop M, Amara R, Fisson C, Armengaud J, Labadie P, Budzinski H, Couteau J, Maillet G, Le Floch S, Laroche J, Pichereau V. Relevance of flounder caging and proteomics to explore the impact of a major industrial accident caused by fire on the Seine estuarine water quality. MARINE POLLUTION BULLETIN 2024; 201:116178. [PMID: 38401391 DOI: 10.1016/j.marpolbul.2024.116178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 02/11/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024]
Abstract
On September 26th 2019, a major fire occurred in the Lubrizol factory located near the Seine estuary, in Rouen-France. Juvenile flounders were captured in the Canche estuary (a reference system) and caged one month in the Canche and in the Seine downstream the accident site. No significant increases of PAHs, PCBs and PFAS was detected in Seine vs Canche sediments after the accident, but a significant increase of dioxins and furans was observed in water and sewage sludge in the Rouen wastewater treatment plant. The proteomics approach highlighted a dysregulation of proteins associated with cholesterol synthesis and lipid metabolism, in fish caged in the Seine. The overall results suggested that the fire produced air borne dioxins and furans that got deposited on soil and subsequently entered in the Seine estuarine waters via runoff; thus contaminating fish preys and caged flounders in the Seine estuary.
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Affiliation(s)
- Jennifer Laurent
- Univ Brest - CNRS - IRD - Ifremer, UMR 6539 LEMAR, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France; CEDRE, 715 rue Alain Colas, 29200 Brest, France.
| | - Mamadou Diop
- Univ. Littoral Côte d'Opale, Univ. Lille, CNRS, IRD, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France
| | - Rachid Amara
- Univ. Littoral Côte d'Opale, Univ. Lille, CNRS, IRD, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France
| | - Cédric Fisson
- GIP Seine-Aval, Hangar C - Espace des Marégraphes, CS 41174, 76176 Rouen Cedex 1, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRAe, F-30207 Bagnols-sur-Cèze, France
| | - Pierre Labadie
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Hélène Budzinski
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Jérôme Couteau
- TOXEM, 12 rue des 4 saisons, 76290 Montivilliers, France
| | | | | | - Jean Laroche
- Univ Brest - CNRS - IRD - Ifremer, UMR 6539 LEMAR, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France
| | - Vianney Pichereau
- Univ Brest - CNRS - IRD - Ifremer, UMR 6539 LEMAR, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France.
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Dumas T, Gomez E, Boccard J, Ramirez G, Armengaud J, Escande A, Mathieu O, Fenet H, Courant F. Mixture effects of pharmaceuticals carbamazepine, diclofenac and venlafaxine on Mytilus galloprovincialis mussel probed by metabolomics and proteogenomics combined approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:168015. [PMID: 37879482 DOI: 10.1016/j.scitotenv.2023.168015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023]
Abstract
Exposure to single molecules under laboratory conditions has led to a better understanding of the mechanisms of action (MeOAs) and effects of pharmaceutical active compounds (PhACs) on non-target organisms. However, not taking the co-occurrence of contaminants in the environment and their possible interactions into account may lead to underestimation of their impacts. In this study, we combined untargeted metabolomics and proteogenomics approaches to assess the mixture effects of diclofenac, carbamazepine and venlafaxine on marine mussels (Mytilus galloprovincialis). Our multi-omics approach and data fusion strategy highlighted how such xenobiotic cocktails induce important cellular changes that can be harmful to marine bivalves. This response is mainly characterized by energy metabolism disruption, fatty acid degradation, protein synthesis and degradation, and the induction of endoplasmic reticulum stress and oxidative stress. The known MeOAs and molecular signatures of PhACs were taken into consideration to gain insight into the mixture effects, thereby revealing a potential additive effect. Multi-omics approaches on mussels as sentinels offer a comprehensive overview of molecular and cellular responses triggered by exposure to contaminant mixtures, even at environmental concentrations.
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Affiliation(s)
- Thibaut Dumas
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Elena Gomez
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Julien Boccard
- School of Pharmaceutical Sciences, University of Geneva, Geneva 1211, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva 1211, Switzerland
| | - Gaëlle Ramirez
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Aurélie Escande
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Olivier Mathieu
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France; Laboratoire de Pharmacologie-Toxicologie, CHU de Montpellier, Montpellier, France
| | - Hélène Fenet
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Frédérique Courant
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France.
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Ramos-Nascimento A, Grenga L, Haange SB, Himmelmann A, Arndt FS, Ly YT, Miotello G, Pible O, Jehmlich N, Engelmann B, von Bergen M, Mulder E, Frings-Meuthen P, Hellweg CE, Jordan J, Rolle-Kampczyk U, Armengaud J, Moeller R. Human gut microbiome and metabolite dynamics under simulated microgravity. Gut Microbes 2023; 15:2259033. [PMID: 37749878 PMCID: PMC10524775 DOI: 10.1080/19490976.2023.2259033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023] Open
Abstract
The Artificial Gravity Bed Rest - European Space Agency (AGBRESA) study was the first joint bed rest study by ESA, DLR, and NASA that examined the effect of simulated weightlessness on the human body and assessed the potential benefits of artificial gravity as a countermeasure in an analog of long-duration spaceflight. In this study, we investigated the impact of simulated microgravity on the gut microbiome of 12 participants during a 60-day head-down tilt bed rest at the :envihab facilities. Over 60 days of simulated microgravity resulted in a mild change in the gut microbiome, with distinct microbial patterns and pathway expression in the feces of the countermeasure group compared to the microgravity simulation-only group. Additionally, we found that the countermeasure protocols selectively increased the abundance of beneficial short-chain fatty acids in the gut, such as acetate, butyrate, and propionate. Some physiological signatures also included the modulation of taxa reported to be either beneficial or opportunistic, indicating a mild adaptation in the microbiome network balance. Our results suggest that monitoring the gut microbial catalog along with pathway clustering and metabolite profiling is an informative synergistic strategy to determine health disturbances and the outcome of countermeasure protocols for future space missions.
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Affiliation(s)
- Ana Ramos-Nascimento
- Institute of Aerospace Medicine, German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Lucia Grenga
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols sur Cèze, France
| | - Sven-Bastiaan Haange
- Department of Metabolomics, UFZ-Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany
| | - Alexandra Himmelmann
- Institute of Aerospace Medicine, German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Franca Sabine Arndt
- Institute of Aerospace Medicine, German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Yen-Tran Ly
- Institute of Aerospace Medicine, German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Guylaine Miotello
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols sur Cèze, France
| | - Olivier Pible
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols sur Cèze, France
| | - Nico Jehmlich
- Department of Metabolomics, UFZ-Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany
| | - Beatrice Engelmann
- Department of Metabolomics, UFZ-Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany
| | - Martin von Bergen
- Department of Metabolomics, UFZ-Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany
| | - Edwin Mulder
- Institute of Aerospace Medicine, German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Petra Frings-Meuthen
- Institute of Aerospace Medicine, German Aerospace Center (DLR e.V.), Cologne, Germany
| | | | - Jens Jordan
- Institute of Aerospace Medicine, German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Metabolomics, UFZ-Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols sur Cèze, France
| | - Ralf Moeller
- Institute of Aerospace Medicine, German Aerospace Center (DLR e.V.), Cologne, Germany
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Baratange C, Baali H, Gaillet V, Bonnard I, Delahaut L, Gaillard JC, Grandjean D, Sayen S, Gallorini A, Le Bris N, Renault D, Breider F, Loizeau JL, Armengaud J, Cosio C. Bioaccumulation and molecular effects of carbamazepine and methylmercury co-exposure in males of Dreissena polymorpha. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165379. [PMID: 37423277 DOI: 10.1016/j.scitotenv.2023.165379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023]
Abstract
Dreissena polymorpha is a bivalve promising for biomonitoring in freshwater ecosystems thanks to its abundance and high filtration activity allowing rapid uptake of toxicants and identification of their negative effects. Nonetheless, we still lack knowledge on its molecular responses to stress under realistic scenario, e.g. multi-contamination. Carbamazepine (CBZ) and Hg are ubiquitous pollutants sharing molecular toxicity pathways, e.g. oxidative stress. A previous study in zebra mussels showed their co-exposure to cause more alterations than single exposures, but molecular toxicity pathways remained unidentified. D. polymorpha was exposed 24 h (T24) and 72 h (T72) to CBZ (6.1 ± 0.1 μg L-1), MeHg (430 ± 10 ng L-1) and the co-exposure (6.1 ± 0.1 μg L-1CBZ and 500 ± 10 ng L-1 MeHg) at concentrations representative of polluted areas (~10× EQS). RedOx system at the gene and enzyme level, the proteome and the metabolome were compared. The co-exposure resulted in 108 differential abundant proteins (DAPs), as well as 9 and 10 modulated metabolites at T24 and T72, respectively. The co-exposure specifically modulated DAPs and metabolites involved in neurotransmission, e.g. dopaminergic synapse and GABA. CBZ specifically modulated 46 DAPs involved in calcium signaling pathways and 7 amino acids at T24. MeHg specifically modulated 55 DAPs involved in the cytoskeleton remodeling and hypoxia-induced factor 1 pathway, without altering the metabolome. Single and co-exposures commonly modulated proteins and metabolites involved in energy and amino acid metabolisms, response to stress and development. Concomitantly, lipid peroxidation and antioxidant activities were unchanged, supporting that D. polymorpha tolerated experimental conditions. The co-exposure was confirmed to cause more alterations than single exposures. This was attributed to the combined toxicity of CBZ and MeHg. Altogether, this study underlined the necessity to better characterize molecular toxicity pathways of multi-contamination that are not predictable on responses to single exposures, to better anticipate adverse effects in biota and improve risk assessment.
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Affiliation(s)
- Clément Baratange
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France
| | - Hugo Baali
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France
| | - Véronique Gaillet
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France
| | - Isabelle Bonnard
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France
| | - Laurence Delahaut
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze Cedex, France
| | - Dominique Grandjean
- Ecole Polytechnique Fédérale de Lausanne (EPFL), ENAC, IIE, Central Environmental Laboratory, Station 2, 1015 Lausanne, Switzerland
| | - Stéphanie Sayen
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), UMR CNRS 7312, BP 1039, F-51687 Reims Cedex, 2, France
| | - Andrea Gallorini
- Department F.-A. Forel for Environmental and Aquatic Sciences, Institute for Environmental Sciences, University of Geneva, Boulevard Carl-Vogt 66, 1211, Geneva 4, Switzerland
| | - Nathalie Le Bris
- Université de Rennes, CNRS, EcoBio (Ecosystèmes, biodiversité, évolution) - UMR 6553, F-35000 Rennes, France
| | - David Renault
- Université de Rennes, CNRS, EcoBio (Ecosystèmes, biodiversité, évolution) - UMR 6553, F-35000 Rennes, France; Institut Universitaire de France, 1 rue Descartes, 75231 Paris Cedex 05, France
| | - Florian Breider
- Ecole Polytechnique Fédérale de Lausanne (EPFL), ENAC, IIE, Central Environmental Laboratory, Station 2, 1015 Lausanne, Switzerland
| | - Jean-Luc Loizeau
- Department F.-A. Forel for Environmental and Aquatic Sciences, Institute for Environmental Sciences, University of Geneva, Boulevard Carl-Vogt 66, 1211, Geneva 4, Switzerland
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze Cedex, France
| | - Claudia Cosio
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France.
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Broca-Brisson L, Harati R, Disdier C, Mozner O, Gaston-Breton R, Maïza A, Costa N, Guyot AC, Sarkadi B, Apati A, Skelton MR, Madrange L, Yates F, Armengaud J, Hamoudi R, Mabondzo A. Deciphering neuronal deficit and protein profile changes in human brain organoids from patients with creatine transporter deficiency. eLife 2023; 12:RP88459. [PMID: 37830910 PMCID: PMC10575631 DOI: 10.7554/elife.88459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
Creatine transporter deficiency (CTD) is an X-linked disease caused by mutations in the SLC6A8 gene. The impaired creatine uptake in the brain results in intellectual disability, behavioral disorders, language delay, and seizures. In this work, we generated human brain organoids from induced pluripotent stem cells of healthy subjects and CTD patients. Brain organoids from CTD donors had reduced creatine uptake compared with those from healthy donors. The expression of neural progenitor cell markers SOX2 and PAX6 was reduced in CTD-derived organoids, while GSK3β, a key regulator of neurogenesis, was up-regulated. Shotgun proteomics combined with integrative bioinformatic and statistical analysis identified changes in the abundance of proteins associated with intellectual disability, epilepsy, and autism. Re-establishment of the expression of a functional SLC6A8 in CTD-derived organoids restored creatine uptake and normalized the expression of SOX2, GSK3β, and other key proteins associated with clinical features of CTD patients. Our brain organoid model opens new avenues for further characterizing the CTD pathophysiology and supports the concept that reinstating creatine levels in patients with CTD could result in therapeutic efficacy.
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Affiliation(s)
- Léa Broca-Brisson
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la SantéGif sur YvetteFrance
| | - Rania Harati
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of SharjahSharjahUnited Arab Emirates
- Sharjah Institute for Medical Research, University of SharjahSharjahUnited Arab Emirates
| | | | - Orsolya Mozner
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, and Doctoral School of Molecular Medicine, Semmelweis UniversityBudapestHungary
| | - Romane Gaston-Breton
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la SantéGif sur YvetteFrance
| | - Auriane Maïza
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la SantéGif sur YvetteFrance
| | - Narciso Costa
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la SantéGif sur YvetteFrance
| | - Anne-Cécile Guyot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la SantéGif sur YvetteFrance
| | - Balazs Sarkadi
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, and Doctoral School of Molecular Medicine, Semmelweis UniversityBudapestHungary
| | - Agota Apati
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, and Doctoral School of Molecular Medicine, Semmelweis UniversityBudapestHungary
| | - Matthew R Skelton
- Department of Pediatrics, University of Cincinnati College of Medicine and Division of Neurology, Cincinnati Children’s Research FoundationCincinnatiUnited States
| | - Lucie Madrange
- SupBiotech/Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, CEA, Université Paris SaclayParisFrance
| | - Frank Yates
- SupBiotech/Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, CEA, Université Paris SaclayParisFrance
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPIBagnols-sur-CèzeFrance
| | - Rifat Hamoudi
- Clinical Sciences Department, College of Medicine, University of SharjahSharjahUnited Arab Emirates
- Division of Surgery and Interventional Science, University College LondonLondonUnited Kingdom
- ASPIRE Precision Medicine Research Institute Abu Dhabi, University of SharjahSharjahUnited Arab Emirates
| | - Aloïse Mabondzo
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la SantéGif sur YvetteFrance
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7
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Steunou AS, Babot M, Durand A, Bourbon ML, Liotenberg S, Miotello G, Armengaud J, Ouchane S. Discriminating Susceptibility of Xanthine Oxidoreductase Family to Metals. Microbiol Spectr 2023; 11:e0481422. [PMID: 37458582 PMCID: PMC10434068 DOI: 10.1128/spectrum.04814-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/16/2023] [Indexed: 08/19/2023] Open
Abstract
The xanthine oxidoreductase (XOR) family are metal-containing enzymes that use the molybdenum cofactor (Moco), 2Fe-2S clusters, and flavin adenine dinucleotide (FAD) for their catalytic activity. This large molybdoenzyme family includes xanthine, aldehyde, and CO dehydrogenases. XORs are widely distributed from bacteria to humans due to their key roles in the catabolism of purines, aldehydes, drugs, and xenobiotics, as well as interconversions between CO and CO2. Assessing the effect of excess metals on the Rubrivivax gelatinosus bacterium, we found that exposure to copper (Cu) or cadmium (Cd) caused a dramatic decrease in the activity of a high-molecular-weight soluble complex exhibiting nitroblue tetrazolium reductase activity. Mass spectrometry and genetic analyses showed that the complex corresponds to a putative CO dehydrogenase (pCOD). Using mutants that accumulate either Cu+ or Cd2+ in the cytoplasm, we show that Cu+ or Cd2+ is a potent inhibitor of XORs (pCOD and the xanthine dehydrogenase [XDH]) in vivo. This is the first in vivo demonstration that Cu+ affects Moco-containing enzymes. The specific inhibitory effect of these compounds on the XOR activity is further supported in vitro by direct addition of competing metals to protein extracts. Moreover, emphasis is given on the inhibitory effect of Cu on bovine XOR, showing that the XOR family could be a common target of Cu. Given the conservation of XOR structure and function across the tree of life, we anticipate that our findings could be transferable to other XORs and organisms. IMPORTANCE The high toxicity of Cu, Cd, Pb, As, and other metals arises from their ability to cross membranes and target metalloenzymes in the cytoplasm. Identifying these targets provides insights into the toxicity mechanisms. The vulnerability of metalloenzymes arises from the accessibility of their cofactors to ions. Accordingly, many enzymes whose cofactors are solvent exposed are likely to be targets of competing metals. Here, we describe for the first time, with in vivo and in vitro experiments, a direct effect of excess Cu on the xanthine oxidoreductase family (XOR/XDH/pCOD). We show that toxic metal affects these Moco enzymes, and we suggest that access to the Moco center by Cu ions could explain the Cu inhibition of XORs in living organisms. Human XOR activity is associated with hyperuricemia, xanthinuria, gout arthritis, and other diseases. Our findings in vivo highlight XOR as a Cu target and thus support the potential use of Cu in metal-based therapeutics against these diseases.
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Affiliation(s)
- Anne-Soisig Steunou
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Marion Babot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Anne Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Marie-Line Bourbon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sylviane Liotenberg
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Guylaine Miotello
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Soufian Ouchane
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Laurent J, Le Berre I, Armengaud J, Kailasam S, Couteau J, Waeles M, Le Floch S, Laroche J, Pichereau V. Integration of environmental signatures and omics-based approaches on the European flounder to assist with health assessment of estuarine ecosystems in Brittany, France. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163195. [PMID: 37003335 DOI: 10.1016/j.scitotenv.2023.163195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 05/13/2023]
Abstract
This study aimed to develop a multidisciplinary approach to assess the ecological status of six moderate-sized French estuaries. For each estuary, we gathered geographical information, hydrobiological data, chemistry of pollutants and fish biology, including integration of proteomics and transcriptomics data. This integrative study covered the entire hydrological system studied, from the watershed to the estuary, and considered all the anthropogenic factors that can impact this environment. To reach this goal, European flounder (Platichthys flesus) were collected from six estuaries in September, which ensures a minimum residence time of five months within an estuary. Geographical metrics are used to characterize land use in each watershed. The concentrations of nitrite, nitrate, organic pollutants, and trace elements were measured in water, sediments and biota. All of these environmental parameters allowed to set up a typology of estuaries. Classical fish biomarkers, coupled with molecular data from transcriptomics and shotgun proteomics, highlighted the flounder's responses to stressors in its environment. We analysed the protein abundances and gene expression levels in the liver of fish from the different estuaries. We showed clear positive deregulation of proteins associated with xenobiotic detoxification in a system characterized by a large population density and industrial activity, as well as in a predominantly agricultural catchment area (mostly cultures of vegetables and pig breeding) mainly impacted by pesticides. Fish from the latter estuary also displayed strong deregulation of the urea cycle, most probably related to high nitrogen load. Proteomic and transcriptomic data also revealed a deregulation of proteins and genes related to the response to hypoxia, and a probable endocrine disruption in some estuaries. Coupling these data allowed the precise identification of the main stressors interacting within each hydrosystem.
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Affiliation(s)
- Jennifer Laurent
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France; CEDRE, 715 rue Alain Colas, 29200 Brest, France.
| | - Iwan Le Berre
- LETG-Brest GEOMER, UMR 6554 CNRS, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRAe, F-30207 Bagnols-sur-Cèze, France
| | - Senthilkumar Kailasam
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec H3A 0G1, Canada; Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Jérôme Couteau
- TOXEM, 12 rue des 4 saisons, 76290 Montivilliers, France
| | - Matthieu Waeles
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France
| | | | - Jean Laroche
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France
| | - Vianney Pichereau
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France.
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Gonzales M, Plener L, Armengaud J, Armstrong N, Chabrière É, Daudé D. Lactonase-mediated inhibition of quorum sensing largely alters phenotypes, proteome, and antimicrobial activities in Burkholderia thailandensis E264. Front Cell Infect Microbiol 2023; 13:1190859. [PMID: 37333853 PMCID: PMC10272358 DOI: 10.3389/fcimb.2023.1190859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction Burkholderia thailandensis is a study model for Burkholderia pseudomallei, a highly virulent pathogen, known to be the causative agent of melioidosis and a potential bioterrorism agent. These two bacteria use an (acyl-homoserine lactone) AHL-mediated quorum sensing (QS) system to regulate different behaviors including biofilm formation, secondary metabolite productions, and motility. Methods Using an enzyme-based quorum quenching (QQ) strategy, with the lactonase SsoPox having the best activity on B. thailandensis AHLs, we evaluated the importance of QS in B. thailandensis by combining proteomic and phenotypic analyses. Results We demonstrated that QS disruption largely affects overall bacterial behavior including motility, proteolytic activity, and antimicrobial molecule production. We further showed that QQ treatment drastically decreases B. thailandensis bactericidal activity against two bacteria (Chromobacterium violaceum and Staphylococcus aureus), while a spectacular increase in antifungal activity was observed against fungi and yeast (Aspergillus niger, Fusarium graminearum and Saccharomyces cerevisiae). Discussion This study provides evidence that QS is of prime interest when it comes to understanding the virulence of Burkholderia species and developing alternative treatments.
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Affiliation(s)
- Mélanie Gonzales
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
- Gene&GreenTK, Marseille, France
| | | | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | | | - Éric Chabrière
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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10
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Schvartz M, Saudrais F, Devineau S, Chédin S, Jamme F, Leroy J, Rakotozandriny K, Taché O, Brotons G, Pin S, Boulard Y, Renault JP. Role of the Protein Corona in the Colloidal Behavior of Microplastics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4291-4303. [PMID: 36930733 DOI: 10.1021/acs.langmuir.2c03237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microparticles of polyethylene and polypropylene are largely found in aquatic environments because they are the most produced and persistent plastic materials. Once in biological media, they are covered by a layer of molecules, the so-called corona, mostly composed of proteins. A yeast protein extract from Saccharomyces cerevisiae was used as a protein system to observe interactions in complex biological media. Proteins, acting as surfactants and providing hydrophilic surfaces, allow the dispersion of highly hydrophobic particles in water and stabilize them. After 24 h, the microplastic quantity was up to 1 × 1011 particles per liter, whereas without protein, no particles remained in solution. Label-free imaging of the protein corona by synchrotron radiation deep UV fluorescence microscopy (SR-DUV) was performed. In situ images of the protein corona were obtained, and the adsorbed protein quantity, the coverage rate, and the corona heterogeneity were determined. The stability kinetics of the microplastic suspensions were measured by light transmission using a Turbiscan analyzer. Together, the microscopic and kinetics results demonstrate that the protein corona can very efficiently stabilize microplastics in solution provided that the protein corona quality is sufficient. Microplastic stability depends on different parameters such as the particle's intrinsic properties (size, density, hydrophobicity) and the protein corona formation that changes the particle wettability, electrostatic charge, and steric hindrance. By controlling these parameters with proteins, it becomes possible to keep microplastics in and out of solution, paving the way for applications in the field of microplastic pollution control and remediation.
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Affiliation(s)
- Marion Schvartz
- Université Paris-Saclay, CEA, CNRS, NIMBE, F-91191 Gif Sur Yvette, France
- Institut des Molécules et Matériaux du Mans (IMMM), UMR 6283 CNRS, Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans Cedex, France
| | - Florent Saudrais
- Université Paris-Saclay, CEA, CNRS, NIMBE, F-91191 Gif Sur Yvette, France
| | - Stéphanie Devineau
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Stéphane Chédin
- Université Paris-Saclay, CEA, CNRS, NIMBE, F-91191 Gif Sur Yvette, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Frédéric Jamme
- Synchrotron SOLEIL, Saint-Aubin, 91190 Gif sur Yvette Cedex, France
| | - Jocelyne Leroy
- Université Paris-Saclay, CEA, CNRS, NIMBE, F-91191 Gif Sur Yvette, France
| | - Karol Rakotozandriny
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Olivier Taché
- Université Paris-Saclay, CEA, CNRS, NIMBE, F-91191 Gif Sur Yvette, France
| | - Guillaume Brotons
- Institut des Molécules et Matériaux du Mans (IMMM), UMR 6283 CNRS, Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans Cedex, France
| | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, F-91191 Gif Sur Yvette, France
| | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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11
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Schvartz M, Saudrais F, Devineau S, Aude JC, Chédin S, Henry C, Millán-Oropeza A, Perrault T, Pieri L, Pin S, Boulard Y, Brotons G, Renault JP. A proteome scale study reveals how plastic surfaces and agitation promote protein aggregation. Sci Rep 2023; 13:1227. [PMID: 36681766 PMCID: PMC9867740 DOI: 10.1038/s41598-023-28412-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Protein aggregation in biotherapeutics can reduce their activity and effectiveness. It may also promote immune reactions responsible for severe adverse effects. The impact of plastic materials on protein destabilization is not totally understood. Here, we propose to deconvolve the effects of material surface, air/liquid interface, and agitation to decipher their respective role in protein destabilization and aggregation. We analyzed the effect of polypropylene, TEFLON, glass and LOBIND surfaces on the stability of purified proteins (bovine serum albumin, hemoglobin and α-synuclein) and on a cell extract composed of 6000 soluble proteins during agitation (P = 0.1-1.2 W/kg). Proteomic analysis revealed that chaperonins, intrinsically disordered proteins and ribosomes were more sensitive to the combined effects of material surfaces and agitation while small metabolic oligomers could be protected in the same conditions. Protein loss observations coupled to Raman microscopy, dynamic light scattering and proteomic allowed us to propose a mechanistic model of protein destabilization by plastics. Our results suggest that protein loss is not primarily due to the nucleation of small aggregates in solution, but to the destabilization of proteins exposed to material surfaces and their subsequent aggregation at the sheared air/liquid interface, an effect that cannot be prevented by using LOBIND tubes. A guidance can be established on how to minimize these adverse effects. Remove one of the components of this combined stress - material, air (even partially), or agitation - and proteins will be preserved.
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Affiliation(s)
- Marion Schvartz
- Université Paris-Saclay, CEA, CNRS, NIMBE, LIONS, 91191, Gif-Sur-Yvette, France.
- Institut des Molécules et Matériaux du Mans (IMMM), UMR 6283 CNRS, Le Mans Université, Avenue Olivier Messiaen, 72085, Le Mans Cedex, France.
| | - Florent Saudrais
- Université Paris-Saclay, CEA, CNRS, NIMBE, LIONS, 91191, Gif-Sur-Yvette, France
| | - Stéphanie Devineau
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, 75013, Paris, France
| | - Jean-Christophe Aude
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-Sur-Yvette, France
| | - Stéphane Chédin
- Université Paris-Saclay, CEA, CNRS, NIMBE, LIONS, 91191, Gif-Sur-Yvette, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-Sur-Yvette, France
| | - Céline Henry
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, PAPPSO, 78350, Jouy-en-Josas, France
| | - Aarón Millán-Oropeza
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, PAPPSO, 78350, Jouy-en-Josas, France
| | - Thomas Perrault
- Institut des Molécules et Matériaux du Mans (IMMM), UMR 6283 CNRS, Le Mans Université, Avenue Olivier Messiaen, 72085, Le Mans Cedex, France
| | - Laura Pieri
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-Sur-Yvette, France
| | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, LIONS, 91191, Gif-Sur-Yvette, France
| | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-Sur-Yvette, France
| | - Guillaume Brotons
- Institut des Molécules et Matériaux du Mans (IMMM), UMR 6283 CNRS, Le Mans Université, Avenue Olivier Messiaen, 72085, Le Mans Cedex, France
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12
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Park Y, Eyal Z, Pekker P, Chevrier DM, Lefèvre CT, Arnoux P, Armengaud J, Monteil CL, Gal A, Pósfai M, Faivre D. Periplasmic Bacterial Biomineralization of Copper Sulfide Nanoparticles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203444. [PMID: 35975419 PMCID: PMC9534983 DOI: 10.1002/advs.202203444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Metal sulfides are a common group of extracellular bacterial biominerals. However, only a few cases of intracellular biomineralization are reported in this group, mostly limited to greigite (Fe3 S4 ) in magnetotactic bacteria. Here, a previously unknown periplasmic biomineralization of copper sulfide produced by the magnetotactic bacterium Desulfamplus magnetovallimortis strain BW-1, a species known to mineralize greigite (Fe3 S4 ) and magnetite (Fe3 O4 ) in the cytoplasm is reported. BW-1 produces hundreds of spherical nanoparticles, composed of 1-2 nm substructures of a poorly crystalline hexagonal copper sulfide structure that remains in a thermodynamically unstable state. The particles appear to be surrounded by an organic matrix as found from staining and electron microscopy inspection. Differential proteomics suggests that periplasmic proteins, such as a DegP-like protein and a heavy metal-binding protein, could be involved in this biomineralization process. The unexpected periplasmic formation of copper sulfide nanoparticles in BW-1 reveals previously unknown possibilities for intracellular biomineralization that involves intriguing biological control and holds promise for biological metal recovery in times of copper shortage.
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Affiliation(s)
- Yeseul Park
- Aix‐Marseille UniversityFrench Alternative Energies and Atomic Energy Commission (CEA)French National Center for Scientific Research (CNRS)UMR7265 Institute of Biosciences and Biotechnologies of Aix‐Marseille (BIAM)Saint‐Paul‐lez‐Durance13108France
| | - Zohar Eyal
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovot7610001Israel
| | - Péter Pekker
- Nanolab, Research Institute of Biomolecular and Chemical EngineeringUniversity of PannoniaEgyetem st. 10Veszprém8200Hungary
| | - Daniel M. Chevrier
- Aix‐Marseille UniversityFrench Alternative Energies and Atomic Energy Commission (CEA)French National Center for Scientific Research (CNRS)UMR7265 Institute of Biosciences and Biotechnologies of Aix‐Marseille (BIAM)Saint‐Paul‐lez‐Durance13108France
| | - Christopher T. Lefèvre
- Aix‐Marseille UniversityFrench Alternative Energies and Atomic Energy Commission (CEA)French National Center for Scientific Research (CNRS)UMR7265 Institute of Biosciences and Biotechnologies of Aix‐Marseille (BIAM)Saint‐Paul‐lez‐Durance13108France
| | - Pascal Arnoux
- Aix‐Marseille UniversityFrench Alternative Energies and Atomic Energy Commission (CEA)French National Center for Scientific Research (CNRS)UMR7265 Institute of Biosciences and Biotechnologies of Aix‐Marseille (BIAM)Saint‐Paul‐lez‐Durance13108France
| | - Jean Armengaud
- Medicines and Healthcare Technologies Department (DMTS) University of Paris‐SaclayFrench Alternative Energies and Atomic Energy Commission (CEA)National Research Institute for Agriculture, Food and the Environment (INRAE)Pharmacology and Immunoanalysis unit (SPI)Bagnols‐sur‐Cèze30200France
| | - Caroline L. Monteil
- Aix‐Marseille UniversityFrench Alternative Energies and Atomic Energy Commission (CEA)French National Center for Scientific Research (CNRS)UMR7265 Institute of Biosciences and Biotechnologies of Aix‐Marseille (BIAM)Saint‐Paul‐lez‐Durance13108France
| | - Assaf Gal
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovot7610001Israel
| | - Mihály Pósfai
- Nanolab, Research Institute of Biomolecular and Chemical EngineeringUniversity of PannoniaEgyetem st. 10Veszprém8200Hungary
- ELKH‐PE Environmental Mineralogy Research GroupEgyetem st. 10Veszprém8200Hungary
| | - Damien Faivre
- Aix‐Marseille UniversityFrench Alternative Energies and Atomic Energy Commission (CEA)French National Center for Scientific Research (CNRS)UMR7265 Institute of Biosciences and Biotechnologies of Aix‐Marseille (BIAM)Saint‐Paul‐lez‐Durance13108France
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Gonçalves LG, Santos S, Gomes LP, Armengaud J, Miragaia M, Coelho AV. Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis. Front Microbiol 2022; 13:1000737. [PMID: 36246270 PMCID: PMC9554481 DOI: 10.3389/fmicb.2022.1000737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus epidermidis is one of the most common bacteria of the human skin microbiota. Despite its role as a commensal, S. epidermidis has emerged as an opportunistic pathogen, associated with 80% of medical devices related infections. Moreover, these bacteria are extremely difficult to treat due to their ability to form biofilms and accumulate resistance to almost all classes of antimicrobials. Thus new preventive and therapeutic strategies are urgently needed. However, the molecular mechanisms associated with S. epidermidis colonisation and disease are still poorly understood. A deeper understanding of the metabolic and cellular processes associated with response to environmental factors characteristic of SE ecological niches in health and disease might provide new clues on colonisation and disease processes. Here we studied the impact of pH conditions, mimicking the skin pH (5.5) and blood pH (7.4), in a S. epidermidis commensal strain by means of next-generation proteomics and 1H NMR-based metabolomics. Moreover, we evaluated the metabolic changes occurring during a sudden pH change, simulating the skin barrier break produced by a catheter. We found that exposure of S. epidermidis to skin pH induced oxidative phosphorylation and biosynthesis of peptidoglycan, lipoteichoic acids and betaine. In contrast, at blood pH, the bacterial assimilation of monosaccharides and its oxidation by glycolysis and fermentation was promoted. Additionally, several proteins related to virulence and immune evasion, namely extracellular proteases and membrane iron transporters were more abundant at blood pH. In the situation of an abrupt skin-to-blood pH shift we observed the decrease in the osmolyte betaine and changes in the levels of several metabolites and proteins involved in cellular redoxl homeostasis. Our results suggest that at the skin pH S. epidermidis cells are metabolically more active and adhesion is promoted, while at blood pH, metabolism is tuned down and cells have a more virulent profile. pH increase during commensal-to-pathogen conversion appears to be a critical environmental signal to the remodelling of the S. epidermidis metabolism toward a more pathogenic state. Targeting S. epidermidis proteins induced by pH 7.4 and promoting the acidification of the medical device surface or surrounding environment might be new strategies to treat and prevent S. epidermidis infections.
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Affiliation(s)
- Luis Gafeira Gonçalves
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susana Santos
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Laidson Paes Gomes
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé, SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Maria Miragaia
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- *Correspondence: Maria Miragaia,
| | - Ana Varela Coelho
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Kashikar R, Kotha AK, Shah S, Famta P, Singh SB, Srivastava S, Chougule MB. Advances in nanoparticle mediated targeting of RNA binding protein for cancer. Adv Drug Deliv Rev 2022; 185:114257. [PMID: 35381306 DOI: 10.1016/j.addr.2022.114257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/28/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022]
Abstract
RNA binding proteins (RBPs) enact a very crucial part in the RNA directive processes. Atypical expression of these RBPs affects many steps of RNA metabolism, majorly altering its expression. Altered expression and dysfunction of RNA binding proteins lead to cancer progression and other diseases. We enumerate various available interventions, and recent findings focused on targeting RBPs for cancer therapy and diagnosis. The treatment, sensitization, chemoprevention, gene-mediated, and virus mediated interventions were studied to treat and diagnose cancer. The application of passively and actively targeted lipidic nanoparticles, polymeric nanoparticles, virus-based particles, and vaccine-based immunotherapy for the delivery of therapeutic agent/s against cancer are discussed. We also discuss the formulation aspect of nanoparticles for achieving delivery at the site of action and ongoing clinical trials targeting RBPs.
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15
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Grenga L, Pible O, Miotello G, Culotta K, Ruat S, Roncato MA, Gas F, Bellanger L, Claret PG, Dunyach-Remy C, Laureillard D, Sotto A, Lavigne JP, Armengaud J. Taxonomical and functional changes in COVID-19 faecal microbiome could be related to SARS-CoV-2 faecal load. Environ Microbiol 2022; 24:4299-4316. [PMID: 35506300 PMCID: PMC9347659 DOI: 10.1111/1462-2920.16028] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 01/08/2023]
Abstract
Since the beginning of the pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the gastro-intestinal (GI) tract has emerged as an important organ influencing the propensity to and potentially the severity of the related COVID-19 disease. However, the contribution of the SARS-CoV-2 intestinal infection on COVID-19 pathogenesis remains to be clarified. In this exploratory study, we highlighted a possible link between alterations in the composition of the gut microbiota and the levels of SARS-CoV-2 RNA in the gastrointestinal tract, which could be more important than the presence of SARS-CoV-2 in the respiratory tract, COVID-19 severity and GI symptoms. As established by metaproteomics, altered molecular functions in the microbiota profiles of high SARS-CoV-2 RNA level faeces highlight mechanisms such as inflammation-induced enterocyte damage, increased intestinal permeability and activation of immune response that may contribute to vicious cycles. Uncovering the role of this gut microbiota dysbiosis could drive the investigation of alternative therapeutic strategies to favour the clearance of the virus and potentially mitigate the effect of the SARS-CoV-2 infection. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Lucia Grenga
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Olivier Pible
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Guylaine Miotello
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Karen Culotta
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Sylvie Ruat
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Marie-Anne Roncato
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Fabienne Gas
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Laurent Bellanger
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | | | - Catherine Dunyach-Remy
- Virulence Bactérienne et Infections Chroniques, INSERM U1047, Université Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908, Nîmes, France
| | - Didier Laureillard
- Service des Maladies Infectieuses et Tropicales, CHU Nîmes, 30029, Nîmes, France
| | - Albert Sotto
- Virulence Bactérienne et Infections Chroniques, INSERM U1047, Université de Montpellier, Service des Maladies Infectieuses et Tropicales, CHU Nîmes, 30908, Nîmes, France
| | - Jean-Philippe Lavigne
- Virulence Bactérienne et Infections Chroniques, INSERM U1047, Université Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908, Nîmes, France
| | - 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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16
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Pujic P, Alloisio N, Miotello G, Armengaud J, Abrouk D, Fournier P, Normand P. The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules. Microorganisms 2022; 10:microorganisms10030651. [PMID: 35336227 PMCID: PMC8951365 DOI: 10.3390/microorganisms10030651] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023] Open
Abstract
Omics are the most promising approaches to investigate microbes for which no genetic tools exist such as the nitrogen-fixing symbiotic Frankia. A proteogenomic analysis of symbiotic Frankia alni was done by comparing those proteins more and less abundant in Alnus glutinosa nodules relative to N2-fixing pure cultures with propionate as the carbon source. There were 250 proteins that were significantly overabundant in nodules at a fold change (FC) ≥ 2 threshold, and 1429 with the same characteristics in in vitro nitrogen-fixing pure culture. Nitrogenase, SuF (Fe–Su biogenesis) and hopanoid lipids synthesis determinants were the most overabundant proteins in symbiosis. Nitrogenase was found to constitute 3% of all Frankia proteins in nodules. Sod (superoxide dismutase) was overabundant, indicating a continued oxidative stress, while Kats (catalase) were not. Several transporters were overabundant including one for dicarboxylates and one for branched amino acids. The present results confirm the centrality of nitrogenase in the actinorhizal symbiosis.
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Affiliation(s)
- Petar Pujic
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
- Correspondence: (P.P.); (P.N.)
| | - Nicole Alloisio
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, Université Paris-Saclay, SPI, 30200 Bagnols sur Cèze, France; (G.M.); (J.A.)
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, Université Paris-Saclay, SPI, 30200 Bagnols sur Cèze, France; (G.M.); (J.A.)
| | - Danis Abrouk
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
| | - Pascale Fournier
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
| | - Philippe Normand
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
- Correspondence: (P.P.); (P.N.)
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17
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Grosjean N, Le Jean M, Armengaud J, Schikora A, Chalot M, Gross EM, Blaudez D. Combined omics approaches reveal distinct responses between light and heavy rare earth elements in Saccharomyces cerevisiae. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127830. [PMID: 34896703 DOI: 10.1016/j.jhazmat.2021.127830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The rapid development of green energy sources and new medical technologies contributes to the increased exploitation of rare earth elements (REEs). They can be subdivided into light (LREEs) and heavy (HREEs) REEs. Mining, industrial processing, and end-use practices of REEs has led to elevated environmental concentrations and raises concerns about their toxicity to organisms and their impact on ecosystems. REE toxicity has been reported, but its precise underlying molecular effects have not been well described. Here, transcriptomic and proteomic approaches were combined to decipher the molecular responses of the model organism Saccharomyces cerevisiae to La (LREE) and Yb (HREE). Differences were observed between the early and late responses to La and Yb. Several crucial pathways were modulated in response to both REEs, such as oxidative-reduction processes, DNA replication, and carbohydrate metabolism. REE-specific responses involving the cell wall and pheromone signalling pathways were identified, and these responses have not been reported for other metals. REE exposure also modified the expression and abundance of several ion transport systems, with strong discrepancies between La and Yb. These findings are valuable for prioritizing key genes and proteins involved in La and Yb detoxification mechanisms that deserve further characterization to better understand REE environmental and human health toxicity.
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Affiliation(s)
- Nicolas Grosjean
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France; Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
| | - Marie Le Jean
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze, France
| | - Adam Schikora
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, D-38104 Braunschweig, Germany
| | - Michel Chalot
- Université de Bourgogne Franche-Comté, CNRS, Laboratoire Chrono-Environnement, F-25000 Besançon, France; Université de Lorraine, F-54000 Nancy, France
| | | | - Damien Blaudez
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France.
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18
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Gallois N, Alpha-Bazin B, Bremond N, Ortet P, Barakat M, Piette L, Mohamad Ali A, Lemaire D, Legrand P, Theodorakopoulos N, Floriani M, Février L, Den Auwer C, Arnoux P, Berthomieu C, Armengaud J, Chapon V. Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria. THE ISME JOURNAL 2022; 16:705-716. [PMID: 34556817 PMCID: PMC8857325 DOI: 10.1038/s41396-021-01113-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39-47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO22+ and Fe3+. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.
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Affiliation(s)
- Nicolas Gallois
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Béatrice Alpha-Bazin
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Nicolas Bremond
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Philippe Ortet
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Laurie Piette
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Abbas Mohamad Ali
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - David Lemaire
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Pierre Legrand
- grid.426328.9Synchrotron SOLEIL. L’Orme des Merisiers Saint-Aubin. BP 48, 91192 Gif-sur-Yvette, France
| | - Nicolas Theodorakopoulos
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France ,grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Magali Floriani
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LECO, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Laureline Février
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Christophe Den Auwer
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, CNRS, ICN, 06108 Nice, France
| | - Pascal Arnoux
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Catherine Berthomieu
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Jean Armengaud
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Virginie Chapon
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France.
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19
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Dumas T, Courant F, Almunia C, Boccard J, Rosain D, Duporté G, Armengaud J, Fenet H, Gomez E. An integrated metabolomics and proteogenomics approach reveals molecular alterations following carbamazepine exposure in the male mussel Mytilus galloprovincialis. CHEMOSPHERE 2022; 286:131793. [PMID: 34364230 DOI: 10.1016/j.chemosphere.2021.131793] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/05/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Carbamazepine is one of the most abundant pharmaceutical active compounds detected in aquatic systems. Based on laboratory exposures, carbamazepine has been proven to adversely affect aquatic organisms. However, the underlying molecular events remain poorly understood. This study aims to investigate the molecular mechanisms potentially associated with toxicological effects of carbamazepine on the mussel Mytilus galloprovincialis exposed for 3 days at realistic concentrations encountered in coastal environments (80 ng/L and 8 μg/L). An integrated metabolomics and proteogenomics approach, including data fusion strategy, was applied to gain more insight in molecular events and cellular processes triggered by carbamazepine exposure. Consistent metabolic and protein signatures revealed a metabolic rewiring and cellular stress at both concentrations (e.g. intensification of protein synthesis, transport and catabolism processes, disruption of lipid and amino acid metabolisms). These highlighted molecular signatures point to the induction of autophagy, closely related with carbamazepine mechanism of action, as well as a destabilization of the lysosomal membranes and an enzymatic overactivity of the peroxisomes. Induction of programmed cell death was highlighted by the modulation of apoptotic cognate proteins. The proposed integrative omics data analysis was shown to be highly relevant to identify the modulations of the two molecular levels, i.e. metabolites and proteins. Multi-omics approach is able to explain the resulting complex biological system, and document stronger toxicological pieces of evidence on pharmaceutical active compounds at environmental concentrations in sentinel organisms.
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Affiliation(s)
- Thibaut Dumas
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Frédérique Courant
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France.
| | - Christine Almunia
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Julien Boccard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, 1211, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, 1211, Switzerland
| | - David Rosain
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Geoffroy Duporté
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Hélène Fenet
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Elena Gomez
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France
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20
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Fadeel B. Understanding the immunological interactions of engineered nanomaterials: Role of the bio-corona. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1798. [PMID: 36416023 PMCID: PMC9787869 DOI: 10.1002/wnan.1798] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/09/2022] [Accepted: 03/15/2022] [Indexed: 11/24/2022]
Abstract
Engineered nanomaterials are a broad class of materials with the potential for breakthrough applications in many sectors of society not least in medicine. Consequently, safety assessment of nanomaterials and nano-enabled products with respect to human health and the environment is of key importance. To this end, the biological interactions of nanoscale materials must be understood. Here, the dual "identities" of nanomaterials, namely, the material-intrinsic properties or synthetic identity and the acquired, context-dependent properties or biological identity, are discussed in relation to nanomaterial interactions with the immune system, our main defense against foreign intrusion. Specifically, we address whether macrophages and other innate immune cells respond to the synthetic identity or the biological identity of nanomaterials, that is, the surface adsorbed proteins and/or other biomolecules known as the bio-corona, or both? This article is categorized under: Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials.
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Affiliation(s)
- Bengt Fadeel
- Nanosafety & Nanomedicine Laboratory (NNL), Division of Molecular ToxicologyInstitute of Environmental Medicine, Karolinska InstitutetStockholmSweden
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21
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Boulghobra D, Dubois M, Alpha-Bazin B, Coste F, Olmos M, Gayrard S, Bornard I, Meyer G, Gaillard JC, Armengaud J, Reboul C. Increased protein S-nitrosylation in mitochondria: a key mechanism of exercise-induced cardioprotection. Basic Res Cardiol 2021; 116:66. [PMID: 34940922 DOI: 10.1007/s00395-021-00906-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022]
Abstract
Endothelial nitric oxide synthase (eNOS) activation in the heart plays a key role in exercise-induced cardioprotection during ischemia-reperfusion, but the underlying mechanisms remain unknown. We hypothesized that the cardioprotective effect of exercise training could be explained by the re-localization of eNOS-dependent nitric oxide (NO)/S-nitrosylation signaling to mitochondria. By comparing exercised (5 days/week for 5 weeks) and sedentary Wistar rats, we found that exercise training increased eNOS level and activation by phosphorylation (at serine 1177) in mitochondria, but not in the cytosolic subfraction of cardiomyocytes. Using confocal microscopy, we confirmed that NO production in mitochondria was increased in response to H2O2 exposure in cardiomyocytes from exercised but not sedentary rats. Moreover, by S-nitrosoproteomic analysis, we identified several key S-nitrosylated proteins involved in mitochondrial function and cardioprotection. In agreement, we also observed that the increase in Ca2+ retention capacity by mitochondria isolated from the heart of exercised rats was abolished by exposure to the NOS inhibitor L-NAME or to the reducing agent ascorbate, known to denitrosylate proteins. Pre-incubation with ascorbate or L-NAME also increased mitochondrial reactive oxygen species production in cardiomyocytes from exercised but not from sedentary animals. We confirmed these results using isolated hearts perfused with L-NAME before ischemia-reperfusion. Altogether, these results strongly support the hypothesis that exercise training increases eNOS/NO/S-nitrosylation signaling in mitochondria, which might represent a key mechanism of exercise-induced cardioprotection.
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Affiliation(s)
| | | | - Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Florence Coste
- LAPEC EA-4278, Avignon Université, 84000, Avignon, France
| | - Maxime Olmos
- LAPEC EA-4278, Avignon Université, 84000, Avignon, France
| | | | | | - Gregory Meyer
- LAPEC EA-4278, Avignon Université, 84000, Avignon, France
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Cyril Reboul
- LAPEC EA-4278, Avignon Université, 84000, Avignon, France. .,Cardiovascular Physiology Laboratory, UPR4278, UFR Sciences Technologies Santé, Centre INRAE-Site Agroparc, 228 route de l'Aérodrome, 84914, Avignon Cedex 9, France.
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22
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Gueddou A, Sarker I, Sen A, Ghodhbane-Gtari F, Benson DR, Armengaud J, Gtari M. Effect of actinorhizal root exudates on the proteomes of Frankia soli NRRL B-16219, a strain colonizing the root tissues of its actinorhizal host via intercellular pathway. Res Microbiol 2021; 173:103900. [PMID: 34800660 DOI: 10.1016/j.resmic.2021.103900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/27/2022]
Abstract
Frankia and actinorhizal plants exchange signals in the rhizosphere leading to specific mutual recognition of partners and nitrogen-fixing nodule organogenesis. Frankia soli strain NRRL B-16219, from the Elaeagnus specificity group, colonizes the root tissues of its actinorhizal host through direct intercellular penetration of root epidermis cells and cortex. Here, we studied the early proteogenomic response of strain NRRL B-16219 to treatment with root exudates from compatible Elaeagnus angustifolia, and incompatible Ceanothus thyrsiflorus and Coriaria myrtifolia, host plants grown in nitrogen depleted hydroponic medium. Next-generation proteomics was used to identify the main Frankia proteins differentially expressed in response to the root exudates. No products of the nod genes present in B-16219 were detected. Proteins specifically upregulated in presence of E. angustifolia root exudates include those connected to nitrogen fixation and assimilation (glutamate synthetase, hydrogenase and squalene synthesis), respiration (oxidative phosphorylation and citric acid cycle pathways), oxidative stress (catalase, superoxide dismutase, and peroxidase), proteolysis (proteasome, protease, and peptidase) and plant cell wall degrading proteins involved in the depolymerization of celluloses (endoglucanase, glycosyltransferase, beta-mannanases, glycoside hydrolase and glycosyl hydrolase). Proteomic data obtained in this study will help link signaling molecules/factors to their biosynthetic pathways once those factors have been fully characterized.
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Affiliation(s)
- Abdellatif Gueddou
- USCR Bactériologie Moléculaire & Génomique, Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080, Tunis Cedex, Tunisia; LR Microorganismes & Biomolécules Actives, Faculté des Sciences de Tunis, Université Tunis El Manar, 2092 - El Manar Tunisia
| | - Indrani Sarker
- Bioinformatics Facility, University of North Bengal, Siliguri, India
| | - Arnab Sen
- Bioinformatics Facility, University of North Bengal, Siliguri, India
| | - Faten Ghodhbane-Gtari
- USCR Bactériologie Moléculaire & Génomique, Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080, Tunis Cedex, Tunisia; LR Microorganismes & Biomolécules Actives, Faculté des Sciences de Tunis, Université Tunis El Manar, 2092 - El Manar Tunisia
| | - David R Benson
- Department of Molecular and Cell Biology, U-3125, University of Connecticut, Storrs, CT, USA
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour La Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France
| | - Maher Gtari
- USCR Bactériologie Moléculaire & Génomique, Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080, Tunis Cedex, Tunisia; LR Microorganismes & Biomolécules Actives, Faculté des Sciences de Tunis, Université Tunis El Manar, 2092 - El Manar Tunisia.
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Stimmer L, Confais J, Jong A, Veth J, Fovet CM, Horellou P, Massonneau J, Perrin A, Miotello G, Avazeri E, Hart B, Deiva K, Le Grand R, Armengaud J, Bajramovic JJ, Contamin H, Serguera C. Recombinant myelin oligodendrocyte glycoprotein quality modifies evolution of experimental autoimmune encephalitis in macaques. J Transl Med 2021; 101:1513-1522. [PMID: 34376778 DOI: 10.1038/s41374-021-00646-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/11/2021] [Accepted: 07/16/2021] [Indexed: 11/09/2022] Open
Abstract
Experimental autoimmune encephalitis (EAE) is a well-recognized model for the study of human acquired demyelinating diseases (ADD), a group of inflammatory disorders of the central nervous system (CNS) characterized by inflammation, myelin loss, and neurological impairment of variable severity. In rodents, EAE is typically induced by active immunization with a combination of myelin-derived antigen and a strong adjuvant as complete Freund's adjuvant (CFA), containing components of the mycobacterial wall, while myelin antigen alone or associated with other bacterial components, as lipopolysaccharides (LPS), often fails to induce EAE. In contrast to this, EAE can be efficiently induced in non-human primates by immunization with the recombinant human myelin oligodendrocyte glycoprotein (rhMOG), produced in Escherichia coli (E. coli), purified and formulated with incomplete Freund's adjuvant (IFA), which lacks bacterial elements. Here, we provide evidence indicating how trace amounts of bacterial contaminants within rhMOG may influence the course and severity of EAE in the cynomolgus macaque immunized with rhMOG/IFA. The residual amount of E. coli contaminants, as detected with mass spectrometry within rhMOG protein stocks, were found to significantly modulate the severity of clinical, radiological, and histologic hallmarks of EAE in macaques. Indeed, animals receiving the purest rhMOG showed milder disease severity, increased numbers of remissions, and reduced brain damage. Histologically, these animals presented a wider diversity of lesion types, including changes in normal-appearing white matter and prephagocytic lesions. Non-human primates EAE model with milder histologic lesions reflect more accurately ADD and permits to study of the pathogenesis of disease initiation and progression.
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Affiliation(s)
- Lev Stimmer
- Commissariat à l'Énergie Atomique (CEA), Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Fontenay-aux-Roses, France. .,INSERM, UMR 1127, Paris Brain & Spine Institute (ICM), Paris, France.
| | | | - Anke't Jong
- Alternatives Unit, Biomedical Primate Research Centre (BPRC), Rijswijk, the Netherlands
| | - Jennifer Veth
- Alternatives Unit, Biomedical Primate Research Centre (BPRC), Rijswijk, the Netherlands
| | - Claire-Maëlle Fovet
- Commissariat à l'Énergie Atomique (CEA), Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Fontenay-aux-Roses, France.,Université Paris-Sud, CEA, Inserm UMR 1184 and Institut de biologie François Jacob, Infectious Diseases Models for Innovative Therapies (IDMIT), Fontenay-aux-Roses, France
| | - Philippe Horellou
- Université Paris-Sud, CEA, Inserm UMR 1184 and Institut de biologie François Jacob, Infectious Diseases Models for Innovative Therapies (IDMIT), Fontenay-aux-Roses, France
| | - Julie Massonneau
- Commissariat à l'Énergie Atomique (CEA), Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Fontenay-aux-Roses, France
| | - Audrey Perrin
- Commissariat à l'Énergie Atomique (CEA), Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Fontenay-aux-Roses, France
| | - Guylaine Miotello
- Département Médicaments et Technologie pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, Bagnols-sur-Cèze, France
| | - Emilie Avazeri
- Département Médicaments et Technologie pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, Bagnols-sur-Cèze, France
| | - Bert't Hart
- Department Anatomy and Neuroscience, Amsterdam University Medical Center (VUMC), Amsterdam, Netherlands and University of Groningen, Department Biomedical Sciences of Cells and Systems, University Medical Center Groningen, Groningen, the Netherlands
| | - Kumaran Deiva
- Université Paris-Sud, CEA, Inserm UMR 1184 and Institut de biologie François Jacob, Infectious Diseases Models for Innovative Therapies (IDMIT), Fontenay-aux-Roses, France.,AP-HP, Hôpitaux Universitaires Paris Saclay, Department of Pediatric Neurology, National Reference Center for Rare Inflammatory and Auto-immune Brain and Spinal Diseases, Paris, France
| | - Roger Le Grand
- Université Paris-Sud, CEA, Inserm UMR 1184 and Institut de biologie François Jacob, Infectious Diseases Models for Innovative Therapies (IDMIT), Fontenay-aux-Roses, France
| | - Jean Armengaud
- Département Médicaments et Technologie pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, Bagnols-sur-Cèze, France
| | - Jeffrey J Bajramovic
- Alternatives Unit, Biomedical Primate Research Centre (BPRC), Rijswijk, the Netherlands
| | | | - Ché Serguera
- Commissariat à l'Énergie Atomique (CEA), Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Fontenay-aux-Roses, France.,INSERM, UMR 1127, Paris Brain & Spine Institute (ICM), Paris, France.,Asfalia Biologics, Paris Brain & Spine Institute (ICM), Paris, France
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Rauwolf S, Steegmüller T, Schwaminger SP, Berensmeier S. Purification of a peptide tagged protein via an affinity chromatographic process with underivatized silica. Eng Life Sci 2021; 21:549-557. [PMID: 34690628 PMCID: PMC8518568 DOI: 10.1002/elsc.202100019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/06/2021] [Accepted: 05/25/2021] [Indexed: 11/11/2022] Open
Abstract
Silica is widely used for chromatography resins due to its high mechanical strength, column efficiency, easy manufacturing (i.e. controlled size and porosity), and low-cost. Despite these positive attributes to silica, it is currently used as a backbone for chromatographic resins in biotechnological downstream processing. The aim of this study is to show how the octapeptide (RH)4 can be used as peptide tag for high-purity protein purification on bare silica. The tag possesses a high affinity to deprotonated silanol groups because the tag's arginine groups interact with the surface via an ion pairing mechanism. A chromatographic workflow to purify GFP fused with (RH)4 could be implemented. Purities were determined by SDS-PAGE and RP-HPLC. The equilibrium binding capacity of the fusion protein GFP-(RH)4 on silica is 450 mg/g and the dynamic binding capacity around 3 mg/mL. One-step purification from clarified lysate achieved a purity of 93% and a recovery of 94%. Overloading the column enhances the purity to >95%. Static experiments with different buffers showed variability of the method making the system independent from buffer choice. Our designed peptide tag allows bare silica to be utilized in preparative chromatography for downstream bioprocessing; thus, providing a cost saving factor regarding expensive surface functionalization. Underivatized silica in combination with our (RH)4 peptide tag allows the purification of proteins, in all scales, without relying on complex resins.
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Affiliation(s)
- Stefan Rauwolf
- Department of Mechanical EngineeringTechnical University of MunichMunichGermany
| | - Tobias Steegmüller
- Department of Mechanical EngineeringTechnical University of MunichMunichGermany
| | | | - Sonja Berensmeier
- Department of Mechanical EngineeringTechnical University of MunichMunichGermany
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25
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Jouffret V, Miotello G, Culotta K, Ayrault S, Pible O, Armengaud J. Increasing the power of interpretation for soil metaproteomics data. MICROBIOME 2021; 9:195. [PMID: 34587999 PMCID: PMC8482631 DOI: 10.1186/s40168-021-01139-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/29/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Soil and sediment microorganisms are highly phylogenetically diverse but are currently largely under-represented in public molecular databases. Their functional characterization by means of metaproteomics is usually performed using metagenomic sequences acquired for the same sample. However, such hugely diverse metagenomic datasets are difficult to assemble; in parallel, theoretical proteomes from isolates available in generic databases are of high quality. Both these factors advocate for the use of theoretical proteomes in metaproteomics interpretation pipelines. Here, we examined a number of database construction strategies with a view to increasing the outputs of metaproteomics studies performed on soil samples. RESULTS The number of peptide-spectrum matches was found to be of comparable magnitude when using public or sample-specific metagenomics-derived databases. However, numbers were significantly increased when a combination of both types of information was used in a two-step cascaded search. Our data also indicate that the functional annotation of the metaproteomics dataset can be maximized by using a combination of both types of databases. CONCLUSIONS A two-step strategy combining sample-specific metagenome database and public databases such as the non-redundant NCBI database and a massive soil gene catalog allows maximizing the metaproteomic interpretation both in terms of ratio of assigned spectra and retrieval of function-derived information. Video abstract.
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Affiliation(s)
- Virginie Jouffret
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France
- Laboratoire des Sciences et de l'Environnement (LSCE-IPSL), UMR 8212 (CEA/CNRS/UVSQ), CEA Saclay, Université Paris-Saclay, Orme des Merisiers, F-91191, Gif-sur-Yvette, France
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, F-30207, Bagnols-sur-Cèze, France
| | - Guylaine Miotello
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France
| | - Karen Culotta
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France
| | - Sophie Ayrault
- Laboratoire des Sciences et de l'Environnement (LSCE-IPSL), UMR 8212 (CEA/CNRS/UVSQ), CEA Saclay, Université Paris-Saclay, Orme des Merisiers, F-91191, Gif-sur-Yvette, France
| | - Olivier Pible
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France.
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Hamitouche F, Gaillard JC, Schmitt P, Armengaud J, Duport C, Dedieu L. Redox proteomic study of Bacillus cereus thiol proteome during fermentative anaerobic growth. BMC Genomics 2021; 22:648. [PMID: 34493209 PMCID: PMC8425097 DOI: 10.1186/s12864-021-07962-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/05/2021] [Indexed: 11/15/2022] Open
Abstract
Background Bacillus cereus is a notorious foodborne pathogen, which can grow under anoxic conditions. Anoxic growth is supported by endogenous redox metabolism, for which the thiol redox proteome serves as an interface. Here, we studied the cysteine (Cys) proteome dynamics of B. cereus ATCC 14579 cells grown under fermentative anoxic conditions. We used a quantitative thiol trapping method combined with proteomics profiling. Results In total, we identified 153 reactive Cys residues in 117 proteins participating in various cellular processes and metabolic pathways, including translation, carbohydrate metabolism, and stress response. Of these reactive Cys, 72 were detected as reduced Cys. The B. cereus Cys proteome evolved during growth both in terms of the number of reduced Cys and the Cys-containing proteins identified, reflecting its growth-phase-dependence. Interestingly, the reduced status of the B. cereus thiol proteome increased during growth, concomitantly to the decrease of extracellular oxidoreduction potential. Conclusions Taken together, our data show that the B. cereus Cys proteome during unstressed fermentative anaerobic growth is a dynamic entity and provide an important foundation for future redox proteomic studies in B. cereus and other organisms. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07962-y.
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Affiliation(s)
- Fella Hamitouche
- Avignon Université, INRAE, UMR SQPOV, Site Agroparc, F-84914, Avignon Cedex 9, France
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Philippe Schmitt
- Avignon Université, INRAE, UMR SQPOV, Site Agroparc, F-84914, Avignon Cedex 9, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Catherine Duport
- Avignon Université, INRAE, UMR SQPOV, Site Agroparc, F-84914, Avignon Cedex 9, France
| | - Luc Dedieu
- Avignon Université, INRAE, UMR SQPOV, Site Agroparc, F-84914, Avignon Cedex 9, France.
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27
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Tudor M, Gilbert A, Lepleux C, Temelie M, Hem S, Armengaud J, Brotin E, Haghdoost S, Savu D, Chevalier F. A Proteomic Study Suggests Stress Granules as New Potential Actors in Radiation-Induced Bystander Effects. Int J Mol Sci 2021; 22:ijms22157957. [PMID: 34360718 PMCID: PMC8347418 DOI: 10.3390/ijms22157957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 01/07/2023] Open
Abstract
Besides the direct effects of radiations, indirect effects are observed within the surrounding non-irradiated area; irradiated cells relay stress signals in this close proximity, inducing the so-called radiation-induced bystander effect. These signals received by neighboring unirradiated cells induce specific responses similar with those of direct irradiated cells. To understand the cellular response of bystander cells, we performed a 2D gel-based proteomic study of the chondrocytes receiving the conditioned medium of low-dose irradiated chondrosarcoma cells. The conditioned medium was directly analyzed by mass spectrometry in order to identify candidate bystander factors involved in the signal transmission. The proteomic analysis of the bystander chondrocytes highlighted 20 proteins spots that were significantly modified at low dose, implicating several cellular mechanisms, such as oxidative stress responses, cellular motility, and exosomes pathways. In addition, the secretomic analysis revealed that the abundance of 40 proteins in the conditioned medium of 0.1 Gy irradiated chondrosarcoma cells was significantly modified, as compared with the conditioned medium of non-irradiated cells. A large cluster of proteins involved in stress granules and several proteins involved in the cellular response to DNA damage stimuli were increased in the 0.1 Gy condition. Several of these candidates and cellular mechanisms were confirmed by functional analysis, such as 8-oxodG quantification, western blot, and wound-healing migration tests. Taken together, these results shed new lights on the complexity of the radiation-induced bystander effects and the large variety of the cellular and molecular mechanisms involved, including the identification of a new potential actor, namely the stress granules.
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Affiliation(s)
- Mihaela Tudor
- Department of Life and Environmental Physics, HoriaHulubei National Institute of Physics and Nuclear Engineering, 077125 Magurele, Romania; (M.T.); (M.T.); (D.S.)
- Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
| | - Antoine Gilbert
- UMR6252 CIMAP, Team Applications in Radiobiology with Accelerated Ions, CEA-CNRS-ENSICAEN-Université de Caen Normandie, 14000 Caen, France; (A.G.); (C.L.); (S.H.)
| | - Charlotte Lepleux
- UMR6252 CIMAP, Team Applications in Radiobiology with Accelerated Ions, CEA-CNRS-ENSICAEN-Université de Caen Normandie, 14000 Caen, France; (A.G.); (C.L.); (S.H.)
| | - Mihaela Temelie
- Department of Life and Environmental Physics, HoriaHulubei National Institute of Physics and Nuclear Engineering, 077125 Magurele, Romania; (M.T.); (M.T.); (D.S.)
| | - Sonia Hem
- BPMP, Montpellier University, CNRS, INRAE, Institut Agro, 34000 Montpellier, France;
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France;
| | - Emilie Brotin
- ImpedanCELL Platform, Federative Structure 4206 ICORE, NormandieUniv, UNICAEN, Inserm U1086 ANTICIPE, Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Comprehensive Cancer Center F. Baclesse, 14000 Caen, France;
| | - Siamak Haghdoost
- UMR6252 CIMAP, Team Applications in Radiobiology with Accelerated Ions, CEA-CNRS-ENSICAEN-Université de Caen Normandie, 14000 Caen, France; (A.G.); (C.L.); (S.H.)
| | - Diana Savu
- Department of Life and Environmental Physics, HoriaHulubei National Institute of Physics and Nuclear Engineering, 077125 Magurele, Romania; (M.T.); (M.T.); (D.S.)
| | - François Chevalier
- UMR6252 CIMAP, Team Applications in Radiobiology with Accelerated Ions, CEA-CNRS-ENSICAEN-Université de Caen Normandie, 14000 Caen, France; (A.G.); (C.L.); (S.H.)
- Correspondence: ; Tel.: +33-(0)231-454-564
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Guesmi S, Pujic P, Nouioui I, Dubost A, Najjari A, Ghedira K, Igual JM, Miotello G, Cherif A, Armengaud J, Klenk HP, Normand P, Sghaier H. Ionizing-radiation-resistant Kocuria rhizophila PT10 isolated from the Tunisian Sahara xerophyte Panicum turgidum: Polyphasic characterization and proteogenomic arsenal. Genomics 2020; 113:317-330. [PMID: 33279651 DOI: 10.1016/j.ygeno.2020.11.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/17/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
A new strain belonging to the genus Kocuria, designed PT10, was isolated from irradiated roots of the xerophyte Panicum turgidum. Isolate PT10 is a Gram-positive, coccoid, aerobic and ionizing-radiation (IR)-resistant actinobacterium. PT10 has shown an ability to survive under extreme conditions, such as gamma irradiation, desiccation and high concentration of hydrogen peroxide. Phenotypic, chemotaxonomic and comparative genome analyses support the assignment of strain PT10 (LMG 31102 = DSM 108617) as Kocuria rhizophila. The complete genome sequence of PT10 consists of one chromosome (2,656,287 bps), with a 70.7% G + C content and comprises 2481 protein-coding sequences. A total of 1487 proteins were identified by LC-MS/MS profiling. In silico analyses revealed that the proteome of the oxidation-tolerant PT10 possesses several features explaining its IR-resistant phenotype and many adaptive pathways implicated in response to environmental pressures - desiccation, cold, reactive oxygen species and other stressors.
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Affiliation(s)
- Sihem Guesmi
- National Agronomy Institute of Tunisia, 43, Avenue Charles Nicolle, 1082 Tunis, Mahrajène, Tunisia; Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Tunisia.
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon, France; CNRS, UMR 5557, Ecologie Microbienne, 69622 Villeurbanne, Cedex, INRA, UMR1418, Villeurbanne, France
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne NE1 7RU, UK; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Afef Najjari
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR03ES03 Microorganismes et Biomolécules Actives, 2092 Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, 13, Place Pasteur, Tunis 1002, Tunisia
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Guylaine Miotello
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne NE1 7RU, UK
| | | | - Haïtham Sghaier
- Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Tunisia; Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia.
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Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics. Microorganisms 2020; 8:microorganisms8121876. [PMID: 33260855 PMCID: PMC7760279 DOI: 10.3390/microorganisms8121876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/23/2022] Open
Abstract
Several bacteria are able to degrade the major industrial solvent dichloromethane (DCM) by using the conserved dehalogenase DcmA, the only system for DCM degradation characterised at the sequence level so far. Using differential proteomics, we rapidly identified key determinants of DCM degradation for Hyphomicrobium sp. MC8b, an unsequenced facultative methylotrophic DCM-degrading strain. For this, we designed a pan-proteomics database comprising the annotated genome sequences of 13 distinct Hyphomicrobium strains. Compared to growth with methanol, growth with DCM induces drastic changes in the proteome of strain MC8b. Dichloromethane dehalogenase DcmA was detected by differential pan-proteomics, but only with poor sequence coverage, suggesting atypical characteristics of the DCM dehalogenation system in this strain. More peptides were assigned to DcmA by error-tolerant search, warranting subsequent sequencing of the genome of strain MC8b, which revealed a highly divergent set of dcm genes in this strain. This suggests that the dcm enzymatic system is less strongly conserved than previously believed, and that substantial molecular evolution of dcm genes has occurred beyond their horizontal transfer in the bacterial domain. Our study showed the power of pan-proteomics for quick characterization of new strains belonging to branches of the Tree of Life that are densely genome-sequenced.
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Petit PCM, Pible O, Eesbeeck VV, Alban C, Steinmetz G, Mysara M, Monsieurs P, Armengaud J, Rivasseau C. Direct Meta-Analyses Reveal Unexpected Microbial Life in the Highly Radioactive Water of an Operating Nuclear Reactor Core. Microorganisms 2020; 8:E1857. [PMID: 33255667 PMCID: PMC7760952 DOI: 10.3390/microorganisms8121857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 02/04/2023] Open
Abstract
The pools of nuclear reactor facilities constitute harsh environments for life, bathed with ionizing radiation, filled with demineralized water and containing toxic radioactive elements. The very few studies published to date have explored water pools used to store spent nuclear fuels. Due to access restrictions and strong handling constraints related to the high radioactivity level, nothing is presently known about life in water pools that directly cool nuclear cores. In this work, we investigated the microbial communities in the cooling pool of the French Osiris nuclear reactor using direct meta-omics approaches, namely, DNA metabarcoding and proteotyping based on 16S ribosomal RNA gene sequencing and on peptide analysis, respectively. We identified 25 genera in the highly radioactive core water supply during operation with radionuclide activity higher than 3 × 109 Bq/m3. The prevailing genera Variovorax and Sphingomonas at operation were supplanted by Methylobacterium, Asanoa, and Streptomyces during shutdown. Variovorax might use dihydrogen produced by water radiolysis as an energy source.
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Affiliation(s)
- Pauline C. M. Petit
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), CNRS, INRAE, Université Grenoble Alpes, F-38054 Grenoble, France; (P.C.M.P.); (C.A.)
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, F-30200 Bagnols-sur-Cèze, France; (O.P.); (G.S.); (J.A.)
| | - Valérie Van Eesbeeck
- Microbiology Unit, The Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium; (V.V.E.); (M.M.); (P.M.)
| | - Claude Alban
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), CNRS, INRAE, Université Grenoble Alpes, F-38054 Grenoble, France; (P.C.M.P.); (C.A.)
| | - Gérard Steinmetz
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, F-30200 Bagnols-sur-Cèze, France; (O.P.); (G.S.); (J.A.)
| | - Mohamed Mysara
- Microbiology Unit, The Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium; (V.V.E.); (M.M.); (P.M.)
| | - Pieter Monsieurs
- Microbiology Unit, The Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium; (V.V.E.); (M.M.); (P.M.)
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, F-30200 Bagnols-sur-Cèze, France; (O.P.); (G.S.); (J.A.)
| | - Corinne Rivasseau
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), CNRS, INRAE, Université Grenoble Alpes, F-38054 Grenoble, France; (P.C.M.P.); (C.A.)
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Gouveia D, Miotello G, Gallais F, Gaillard JC, Debroas S, Bellanger L, Lavigne JP, Sotto A, Grenga L, Pible O, Armengaud J. Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window. J Proteome Res 2020; 19:4407-4416. [PMID: 32697082 PMCID: PMC7640971 DOI: 10.1021/acs.jproteome.0c00535] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Indexed: 12/13/2022]
Abstract
Rapid but yet sensitive, specific, and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostics that would not require specific reagents are worthy to investigate not only for fighting the COVID-19 pandemic but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC-MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry.
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Affiliation(s)
- Duarte Gouveia
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Guylaine Miotello
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Fabrice Gallais
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Jean-Charles Gaillard
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Stéphanie Debroas
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Laurent Bellanger
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Jean-Philippe Lavigne
- U1047,
Institut National de la Santé et de la Recherche Médicale, Université Montpellier, Montpellier, France
- VBMI,
INSERM U1047, Université de Montpellier, Service de Microbiologie
et Hygiène Hospitalière, CHU
Nîmes, Nîmes, France
| | - Albert Sotto
- VBMI,
INSERM U1047, Université de Montpellier, Service des Maladies
Infectieuses et Tropicales, CHU Nîmes, Nîmes, France
| | - Lucia Grenga
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Olivier Pible
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
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32
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Alpha-Bazin B, Gorlas A, Lagorce A, Joulié D, Boyer JB, Dutertre M, Gaillard JC, Lopes A, Zivanovic Y, Dedieu A, Confalonieri F, Armengaud J. Lysine-specific acetylated proteome from the archaeon Thermococcus gammatolerans reveals the presence of acetylated histones. J Proteomics 2020; 232:104044. [PMID: 33161166 DOI: 10.1016/j.jprot.2020.104044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 11/20/2022]
Abstract
Thermococcus gammatolerans EJ3 is an extremophile archaeon which was revealed as one of the most radioresistant organisms known on Earth, withstanding up to 30 kGy gamma-ray radiations. While its theoretical proteome is rather small, T. gammatolerans may enhance its toolbox by post-translational modification of its proteins. Here, we explored its extent of Nε-acetylation of lysines. For this, we immunopurified with two acetylated-lysine antibodies the acetylated peptides resulting from a proteolysis of soluble proteins with trypsin. The comparison of acetylated proteomes of two archaea highlights some common acetylation patterns but only 4 out of 26 orthologous proteins found to be acetylated in both species, are acetylated on the same lysine site. We evidenced that histone B is acetylated in T. gammatolerans at least at two different sites (K27 and K36), and a peptide common at the C-terminus of histones A and B is also acetylated. We verified that acetylation of histones is a common trait among Thermococcales after recording data on Thermococcus kodakaraensis histones and identifying three acetylated sites. This discovery reinforces the strong evolutionary link between Archaea and Eukaryotes and should be an incentive for further investigation on the extent and role of acetylation of histones in Archaea. SIGNIFICANCE: Acetylation is an important post-translational modification of proteins that has been extensively described in Eukaryotes, and more recently in Bacteria. Here, we report for the first time ever that histones in Archaea are also modified by acetylation after a systematic survey of acetylated peptides in Thermococcus gammatolerans. Structural models of histones A and B indicates that acetylation of the identified modified residues may play an important role in histone assembly and/or interaction with DNA. The in-depth protein acetylome landscape in T. gammatolerans includes at least 181 unique protein sequences, some of them being modified on numerous residues. Proteins involved in metabolic processes, information storage and processing mechanisms are over-represented categories in this dataset, highlighting the ancient role of this protein post-translational modification in primitive cells.
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Affiliation(s)
- Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Aurore Gorlas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Arnaud Lagorce
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan, Via Domitia, Perpignan, France
| | - Damien Joulié
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Murielle Dutertre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Anne Lopes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Yvan Zivanovic
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Alain Dedieu
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Fabrice Confalonieri
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - 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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33
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Liu S, Wang Z, Jiang X, Gan J, Tian X, Xing Z, Yan Y, Chen J, Zhang J, Wang C, Dong L. Denatured corona proteins mediate the intracellular bioactivities of nanoparticles via the unfolded protein response. Biomaterials 2020; 265:120452. [PMID: 33190736 DOI: 10.1016/j.biomaterials.2020.120452] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/22/2020] [Accepted: 10/11/2020] [Indexed: 12/15/2022]
Abstract
Biomolecular corona formed on nanoparticles (NPs) influences the latter's in vivo biological effects. Nanomaterials with different physicochemical properties exert similar adverse effects, such as cytotoxicity, suggesting the existence of ubiquitous signals during various corona formations that mediate common and fundamental cellular events. Here, we discover the involvement of the unfolded protein response (UPR) and recruited chaperones in the corona. Specially, heat shock protein 90 kDa α class B member 1 (Hsp90ab1) is abundantly enriched in the corona, accompanied by substantial aggregation of misfolded protein on particles intracellularly. Further analysis reveals the particulate matter 2.5 (PM2.5) and metal-containing particles are more capable of denaturing proteins. The recruited Hsp90ab1 activates diverse NPs' pathological behaviour by heat stress response (HSR), which were significantly reversed by geldanamycin (GA), the inhibitor of Hsp90ab1. Murine lung inflammation induced by PM2.5 and iron oxide NPs (Fe3O4NPs) is suppressed by GA, highlighting that Hsp90ab1-mediated UPR is a potential target for the treatment of environmental pollution-related illnesses. Based on our findings, the UPR and Hsp90ab1 presented in the corona of particles initiate fundamental intracellular reactions that lead to common pathological outcomes, which may provide new insights for understanding nanotoxicity and designing therapeutic approaches for diseases associated with environmental pollution.
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Affiliation(s)
- Shang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences and Medical School, Nanjing University, 163 Xianlin Avenue, Nanjing, 210093, China
| | - Zhenzhen Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences and Medical School, Nanjing University, 163 Xianlin Avenue, Nanjing, 210093, China; State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Xinbang Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences and Medical School, Nanjing University, 163 Xianlin Avenue, Nanjing, 210093, China
| | - Jingjing Gan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences and Medical School, Nanjing University, 163 Xianlin Avenue, Nanjing, 210093, China
| | - Xuejiao Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences and Medical School, Nanjing University, 163 Xianlin Avenue, Nanjing, 210093, China
| | - Zhen Xing
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences and Medical School, Nanjing University, 163 Xianlin Avenue, Nanjing, 210093, China
| | - Yiqing Yan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences and Medical School, Nanjing University, 163 Xianlin Avenue, Nanjing, 210093, China
| | - Jiahui Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences and Medical School, Nanjing University, 163 Xianlin Avenue, Nanjing, 210093, China
| | - Junfeng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences and Medical School, Nanjing University, 163 Xianlin Avenue, Nanjing, 210093, China
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Lei Dong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences and Medical School, Nanjing University, 163 Xianlin Avenue, Nanjing, 210093, China; Chemistry and Biomedicine Innovative Center, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China.
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34
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Bacillus cereus Decreases NHE and CLO Exotoxin Synthesis to Maintain Appropriate Proteome Dynamics During Growth at Low Temperature. Toxins (Basel) 2020; 12:toxins12100645. [PMID: 33036317 PMCID: PMC7601483 DOI: 10.3390/toxins12100645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 12/02/2022] Open
Abstract
Cellular proteomes and exoproteomes are dynamic, allowing pathogens to respond to environmental conditions to sustain growth and virulence. Bacillus cereus is an important food-borne pathogen causing intoxication via emetic toxin and/or multiple protein exotoxins. Here, we compared the dynamics of the cellular proteome and exoproteome of emetic B. cereus cells grown at low (16 °C) and high (30 °C) temperature. Tandem mass spectrometry (MS/MS)-based shotgun proteomics analysis identified 2063 cellular proteins and 900 extracellular proteins. Hierarchical clustering following principal component analysis indicated that in B. cereus the abundance of a subset of these proteins—including cold-stress responders, and exotoxins non-hemolytic enterotoxin (NHE) and hemolysin I (cereolysin O (CLO))—decreased at low temperature, and that this subset governs the dynamics of the cellular proteome. NHE, and to a lesser extent CLO, also contributed significantly to exoproteome dynamics; with decreased abundances in the low-temperature exoproteome, especially in late growth stages. Our data therefore indicate that B. cereus may reduce its production of secreted protein toxins to maintain appropriate proteome dynamics, perhaps using catabolite repression to conserve energy for growth in cold-stress conditions, at the expense of virulence.
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35
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Rousset L, Alpha-Bazin B, Château A, Armengaud J, Clavel T, Berge O, Duport C. Groundwater promotes emergence of asporogenic mutants of emetic Bacillus cereus. Environ Microbiol 2020; 22:5248-5264. [PMID: 32815215 DOI: 10.1111/1462-2920.15203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 01/15/2023]
Abstract
Bacillus cereus is a ubiquitous endospore-forming bacterium, which mainly affects humans as a food-borne pathogen. Bacillus cereus can contaminate groundwater used to irrigate food crops. Here, we examined the ability of the emetic strain B. cereus F4810/72 to survive abiotic conditions encountered in groundwater. Our results showed that vegetative B. cereus cells rapidly evolved in a mixed population composed of endospores and asporogenic variants bearing spo0A mutations. One asporogenic variant, VAR-F48, was isolated and characterized. VAR-F48 can survive in sterilized groundwater over a long period in a vegetative form and has a competitive advantage compared to its parental strain. Proteomics analysis allowed us to quantify changes to cellular and exoproteins after 24 and 72 h incubation in groundwater, for VAR-F48 compared to its parental strain. The results revealed a significant re-routing of the metabolism in the absence of Spo0A. We concluded that VAR-F48 maximizes its energy use to deal with oligotrophy, and the emergence of spo0A-mutated variants may contribute to the persistence of emetic B. cereus in natural oligotrophic environments.
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Affiliation(s)
- Ludivine Rousset
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France.,INRAE, Pathologie Végétale, Montfavet, F-84140, France
| | - Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France
| | - Alice Château
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France
| | - Thierry Clavel
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France
| | - Odile Berge
- INRAE, Pathologie Végétale, Montfavet, F-84140, France
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36
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Horspool AM, Wang T, Scaringella YS, Taub ME, Chan TS. Human Liver Microsomes Immobilized on Magnetizable Beads: A Novel Approach to Study In Vitro Drug Metabolism. Drug Metab Dispos 2020; 48:645-654. [PMID: 32474441 PMCID: PMC7370995 DOI: 10.1124/dmd.120.090696] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/13/2020] [Indexed: 01/08/2023] Open
Abstract
Human liver microsomes (HLM) are a commonly used tool to study drug metabolism in vitro. Typical experiments conducted using suspensions of HLM can be challenging to separate from the incubation solution without lengthy ultracentrifugation steps. Magnetizable beads coated with silica (MGBS) were found to bind strongly to HLM, which could then be isolated and purified using a magnet. Binding of HLM to the MGBS (HLM-MGBS) was demonstrated to be mediated by strong interactions between microsomal phospholipids and MGBS, as artificially prepared phosphatidylcholine (PC) liposomes could be more efficiently captured by the MGBS. HLM-MGBS complexes retained functional cytochrome P450 and uridine-diphosphate-glucuronosyltransferase (UGT) activity as indicated by CYP2C8-mediated amodiaquine de-ethylation, CYP3A4-mediated midazolam 1'hydroxylation, UGT1A1-mediated glucuronidation of estradiol, UGT1A9-mediated glucuronidation of propofol, and UGT2B7-mediated glucuronidation of zidovudine. When comparing suspension HLM alone with HLM-MGBS complexes containing equivalent amounts of HLM, the intrinsic clearance (CLint) of CYP450 substrates was comparable; however, CLint of UGT1A1, UGT1A9, and UGT2B7 was increased in the HLM-MGBS system between 1.5- and 6-fold. HLM-MGBS used in an incubation could also be readily replaced with fresh HLM-MGBS to maintain the presence of active enzymes. Thus, HLM-MGBS demonstrate increased in vitro metabolic efficiency and manipulability, providing a new platform for determination of accurate metabolic parameters. SIGNIFICANCE STATEMENT: The following work describes the strong binding of HLM to magnetizable beads. In addition, the preservation of enzyme activity on the bound HLM provides a novel means to conduct preclinical metabolism studies.
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Affiliation(s)
- Alexander M Horspool
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut
| | - Ting Wang
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut
| | - Young-Sun Scaringella
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut
| | - Mitchell E Taub
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut
| | - Tom S Chan
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut
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Marichal L, Degrouard J, Gatin A, Raffray N, Aude JC, Boulard Y, Combet S, Cousin F, Hourdez S, Mary J, Renault JP, Pin S. From Protein Corona to Colloidal Self-Assembly: The Importance of Protein Size in Protein-Nanoparticle Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:8218-8230. [PMID: 32585107 DOI: 10.1021/acs.langmuir.0c01334] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein adsorption on nanoparticles is an important field of study, particularly with regard to nanomedicine and nanotoxicology. Many factors can influence the composition and structure of the layer(s) of adsorbed proteins, the so-called protein corona. However, the role of protein size has not been specifically investigated, although some evidence has indicated its potential important role in corona composition and structure. To assess the role of protein size, we studied the interactions of hemoproteins (spanning a large size range) with monodisperse silica nanoparticles. We combined various techniques-adsorption isotherms, isothermal titration calorimetry, circular dichroism, and transmission electron cryomicroscopy-to address this issue. Overall, the results show that small proteins behaved as typical model proteins, forming homogeneous monolayers on the nanoparticle surface (protein corona). Their adsorption is purely enthalpy-driven, with subtle structural changes. In contrast, large proteins interact with nanoparticles via entropy-driven mechanisms. Their structure is completely preserved during adsorption, and any given protein can directly bind to several nanoparticles, forming bridges in these newly formed protein-nanoparticle assemblies. Protein size is clearly an overlooked factor that should be integrated into proteomics and toxicological studies.
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Affiliation(s)
- Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
- Université Paris-Saclay, CEA, CNRS, I2BC, B3S, 91190 Gif-sur-Yvette, France
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Anouchka Gatin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
| | - Nolwenn Raffray
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
| | | | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, I2BC, B3S, 91190 Gif-sur-Yvette, France
| | - Sophie Combet
- Université Paris-Saclay, Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Fabrice Cousin
- Université Paris-Saclay, Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Stéphane Hourdez
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Team DYDIV, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Jean Mary
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Team DYDIV, Station Biologique de Roscoff, 29680 Roscoff, France
| | | | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
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Dubberstein D, Lidon FC, Rodrigues AP, Semedo JN, Marques I, Rodrigues WP, Gouveia D, Armengaud J, Semedo MC, Martins S, Simões-Costa MC, Moura I, Pais IP, Scotti-Campos P, Partelli FL, Campostrini E, Ribeiro-Barros AI, DaMatta FM, Ramalho JC. Resilient and Sensitive Key Points of the Photosynthetic Machinery of Coffea spp. to the Single and Superimposed Exposure to Severe Drought and Heat Stresses. FRONTIERS IN PLANT SCIENCE 2020; 11:1049. [PMID: 32733525 PMCID: PMC7363965 DOI: 10.3389/fpls.2020.01049] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/25/2020] [Indexed: 05/23/2023]
Abstract
This study unveils the single and combined drought and heat impacts on the photosynthetic performance of Coffea arabica cv. Icatu and C. canephora cv. Conilon Clone 153 (CL153). Well-watered (WW) potted plants were gradually submitted to severe water deficit (SWD) along 20 days under adequate temperature (25/20°C, day/night), and thereafter exposed to a gradual temperature rise up to 42/30°C, followed by a 14-day water and temperature recovery. Single drought affected all gas exchanges (including Amax ) and most fluorescence parameters in both genotypes. However, Icatu maintained Fv/Fm and RuBisCO activity, and reinforced electron transport rates, carrier contents, and proton gradient regulation (PGR5) and chloroplast NADH dehydrogenase-like (NDH) complex proteins abundance. This suggested negligible non-stomatal limitations of photosynthesis that were accompanied by a triggering of protective cyclic electron transport (CEF) involving both photosystems (PSs). These findings contrasted with declines in RuBisCO and PSs activities, and cytochromes (b559 , f, b563 ) contents in CL153. Remarkable heat tolerance in potential photosynthetic functioning was detected in WW plants of both genotypes (up to 37/28°C or 39/30°C), likely associated with CEF in Icatu. Yet, at 42/30°C the tolerance limit was exceeded. Reduced Amax and increased Ci values reflected non-stomatal limitations of photosynthesis, agreeing with impairments in energy capture (F0 rise), PSII photochemical efficiency, and RuBisCO and Ru5PK activities. In contrast to PSs activities and electron carrier contents, enzyme activities were highly heat sensitive. Until 37/28°C, stresses interaction was largely absent, and drought played the major role in constraining photosynthesis functioning. Harsher conditions (SWD, 42/30°C) exacerbated impairments to PSs, enzymes, and electron carriers, but uncontrolled energy dissipation was mitigated by photoprotective mechanisms. Most parameters recovered fully between 4 and 14 days after stress relief in both genotypes, although some aftereffects persisted in SWD plants. Icatu was more drought tolerant, with WW and SWD plants usually showing a faster and/or greater recovery than CL153. Heat affected both genotypes mostly at 42/30°C, especially in SWD and Icatu plants. Overall, photochemical components were highly tolerant to heat and to stress interaction in contrast to enzymes that deserve special attention by breeding programs to increase coffee sustainability in climate change scenarios.
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Affiliation(s)
- Danielly Dubberstein
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
- Centro Univ. Norte do Espírito Santo (CEUNES), Dept. Ciências Agrárias e Biológicas (DCAB), Univ. Federal Espírito Santo (UFES), São Mateus, Brazil
| | - Fernando C. Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Ana P. Rodrigues
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
| | - José N. Semedo
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
- Unid. Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
| | - Isabel Marques
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
| | - Weverton P. Rodrigues
- Setor Fisiologia Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Univ. Estadual Norte Fluminense (UENF), Darcy Ribeiro, Brazil
- Centro de Ciências Agrárias, Naturais e Letras, Universidade Estadual da Região Tocantina do Maranhão, Estreito, Brazil
| | - Duarte Gouveia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Bagnols-sur-Cèze, France
| | - Magda C. Semedo
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
- Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
| | - Sónia Martins
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
- Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
| | - Maria C. Simões-Costa
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
| | - I. Moura
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
| | - Isabel P. Pais
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
- Unid. Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
| | - Paula Scotti-Campos
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
- Unid. Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
| | - Fábio L. Partelli
- Centro Univ. Norte do Espírito Santo (CEUNES), Dept. Ciências Agrárias e Biológicas (DCAB), Univ. Federal Espírito Santo (UFES), São Mateus, Brazil
| | - Eliemar Campostrini
- Setor Fisiologia Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Univ. Estadual Norte Fluminense (UENF), Darcy Ribeiro, Brazil
| | - Ana I. Ribeiro-Barros
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Fábio M. DaMatta
- Dept. Biologia Vegetal, Univ. Federal Viçosa (UFV), Viçosa, Brazil
| | - José C. Ramalho
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
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Anastasi C, Rousselle P, Talantikite M, Tessier A, Cluzel C, Bachmann A, Mariano N, Dussoyer M, Alcaraz LB, Fortin L, Aubert A, Delolme F, El Kholti N, Armengaud J, Fournié P, Auxenfans C, Valcourt U, Goff SVL, Moali C. BMP-1 disrupts cell adhesion and enhances TGF-β activation through cleavage of the matricellular protein thrombospondin-1. Sci Signal 2020; 13:13/639/eaba3880. [PMID: 32636307 DOI: 10.1126/scisignal.aba3880] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bone morphogenetic protein 1 (BMP-1) is an important metalloproteinase that synchronizes growth factor activation with extracellular matrix assembly during morphogenesis and tissue repair. The mechanisms by which BMP-1 exerts these effects are highly context dependent. Because BMP-1 overexpression induces marked phenotypic changes in two human cell lines (HT1080 and 293-EBNA cells), we investigated how BMP-1 simultaneously affects cell-matrix interactions and growth factor activity in these cells. Increasing BMP-1 led to a loss of cell adhesion that depended on the matricellular glycoprotein thrombospondin-1 (TSP-1). BMP-1 cleaved TSP-1 between the VWFC/procollagen-like domain and the type 1 repeats that mediate several key TSP-1 functions. This cleavage induced the release of TSP-1 C-terminal domains from the extracellular matrix and abolished its previously described multisite cooperative interactions with heparan sulfate proteoglycans and CD36 on HT1080 cells. In addition, BMP-1-dependent proteolysis potentiated the TSP-1-mediated activation of latent transforming growth factor-β (TGF-β), leading to increased signaling through the canonical SMAD pathway. In primary human corneal stromal cells (keratocytes), endogenous BMP-1 cleaved TSP-1, and the addition of exogenous BMP-1 enhanced cleavage, but this had no substantial effect on cell adhesion. Instead, processed TSP-1 promoted the differentiation of keratocytes into myofibroblasts and stimulated production of the myofibroblast marker α-SMA, consistent with the presence of processed TSP-1 in human corneal scars. Our results indicate that BMP-1 can both trigger the disruption of cell adhesion and stimulate TGF-β signaling in TSP-1-rich microenvironments, which has important potential consequences for wound healing and tumor progression.
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Affiliation(s)
- Cyril Anastasi
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Patricia Rousselle
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Maya Talantikite
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Agnès Tessier
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Caroline Cluzel
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Alice Bachmann
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Natacha Mariano
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Mélissa Dussoyer
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Lindsay B Alcaraz
- University of Lyon, Centre Léon Bérard, INSERM U1052, CNRS UMR 5286, Cancer Research Center of Lyon (CRCL), F-69373 Lyon, France
| | - Laëtitia Fortin
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Alexandre Aubert
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Frédéric Delolme
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France.,University of Lyon, ENS de Lyon, INSERM US8, CNRS UMS3444, SFR Biosciences, F-69366 Lyon, France
| | - Naïma El Kholti
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Jean Armengaud
- CEA Marcoule, Innovative Technologies for Detection and Diagnostics Laboratory (DRF/Joliot/DMTS/SPI/Li2D), F-30200 Bagnols-sur-Cèze, France
| | - Pierre Fournié
- Purpan University Hospital, Ophthalmology Department, F-31059 Toulouse, France.,University of Toulouse, CNRS UMR 5165, INSERM U1056, Epithelial Differentiation and Rheumatoid Autoimmunity Unit (UDEAR), F-31059 Toulouse, France
| | - Céline Auxenfans
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France.,Hospices Civils de Lyon, Tissue and Cell Bank, F-69437 Lyon, France
| | - Ulrich Valcourt
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France.,University of Lyon, Centre Léon Bérard, INSERM U1052, CNRS UMR 5286, Cancer Research Center of Lyon (CRCL), F-69373 Lyon, France
| | - Sandrine Vadon-Le Goff
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France
| | - Catherine Moali
- University of Lyon, CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), F-69367 Lyon, France.
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High-throughput proteotyping of bacterial isolates by double barrel chromatography-tandem mass spectrometry based on microplate paramagnetic beads and phylopeptidomics. J Proteomics 2020; 226:103887. [PMID: 32619772 DOI: 10.1016/j.jprot.2020.103887] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 12/18/2022]
Abstract
Tandem mass spectrometry-based proteotyping of microorganisms presents several advantages over whole-cell MALDI-TOF mass spectrometry: because a larger number of signals are recorded with better accuracy and precision, the approach allows for the identification of microorganisms at more resolved taxonomic levels, and can easily manage complex samples. Additionally, the use of SP3 paramagnetic beads for cell lysis and protein cleanup simplifies sample preparation for proteotyping. Based on these features, we have developed and tested a 96-well plate platform for high-throughput proteotyping of a large variety of bacteria. We evaluated the performance of the platform in terms of bacterial load and found no cross-contamination between wells. Likewise, phylopeptidomics analysis revealed no alteration in the relative quantifications of microorganisms. Finally, we applied this new format for rapid proteotyping of a large set of dental isolates using double-barrel chromatography coupled to tandem mass spectrometry, which maximizes the number of spectra per unit of time. The procedure allowed us to establish whether these isolates were pure strains or mixtures of strains and to identify the microorganisms at the most resolved taxonomic level. SIGNIFICANCE: The rapid and accurate identification of microorganisms is a clinical priority in medical diagnostics; however, specimens containing mixtures of microorganisms are difficult to analyze and the procedure is time-consuming. Tandem mass spectrometry proteotyping allows the fast identification of complex mixtures of microorganisms, known or unknown, and can also establish the biomass ratio of each component. We describe here a new workflow for preparing microbial samples in a 96-well-plate format for tandem mass spectrometry proteotyping and document its advantages and limitations. We demonstrate that this new format coupled to a highly efficient double-barrel LC-MS/MS system allows proteotyping of 96 isolates in 55 h.
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41
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Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host. NPJ Biofilms Microbiomes 2020; 6:23. [PMID: 32504001 PMCID: PMC7275042 DOI: 10.1038/s41522-020-0133-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 05/07/2020] [Indexed: 02/06/2023] Open
Abstract
Metaproteomics of gut microbiomes from animal hosts lacking a reference genome is challenging. Here we describe a strategy combining high-resolution metaproteomics and host RNA sequencing (RNA-seq) with generalist database searching to survey the digestive tract of Gammarus fossarum, a small crustacean used as a sentinel species in ecotoxicology. This approach provides a deep insight into the full range of biomasses and metabolic activities of the holobiont components, and differentiates between the intestine and hepatopancreatic caecum.
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42
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Bioactive Potential of Extracts of Labrenzia aggregata Strain USBA 371, a Halophilic Bacterium Isolated from a Terrestrial Source. Molecules 2020; 25:molecules25112546. [PMID: 32486092 PMCID: PMC7321072 DOI: 10.3390/molecules25112546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 01/15/2023] Open
Abstract
Previous studies revealed the potential of Labrenzia aggregata USBA 371 to produce cytotoxic metabolites. This study explores its metabolic diversity and compounds involved in its cytotoxic activity. Extracts from the extracellular fraction of strain USBA 371 showed high levels of cytotoxic activity associated with the production of diketopiperazines (DKPs). We purified two compounds and a mixture of two other compounds from this fraction. Their structures were characterized by 1D and 2D nuclear magnetic resonance (NMR). The purified compounds were evaluated for additional cytotoxic activities. Compound 1 (cyclo (l-Pro-l-Tyr)) showed cytotoxicity to the following cancer cell lines: breast cancer 4T1 (IC50 57.09 ± 2.11 µM), 4T1H17 (IC50 40.38 ± 1.94), MCF-7 (IC50 87.74 ± 2.32 µM), murine melanoma B16 (IC50 80.87 ± 3.67), human uterus sarcoma MES-SA/Dx5 P-pg (−) (IC50 291.32 ± 5.64) and MES-SA/Dx5 P-pg (+) (IC50 225.28 ± 1.23), and murine colon MCA 38 (IC50 29.85 ± 1.55). In order to elucidate the biosynthetic route of the production of DKPs and other secondary metabolites, we sequenced the genome of L. aggregata USBA 371. We found no evidence for biosynthetic pathways associated with cyclodipeptide synthases (CDPSs) or non-ribosomal peptides (NRPS), but based on proteogenomic analysis we suggest that they are produced by proteolytic enzymes. This is the first report in which the cytotoxic effect of cyclo (l-Pro-l-Tyr) produced by an organism of the genus Labrenzia has been evaluated against several cancer cell lines.
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Cogne Y, Gouveia D, Chaumot A, Degli-Esposti D, Geffard O, Pible O, Almunia C, Armengaud J. Proteogenomics-Guided Evaluation of RNA-Seq Assembly and Protein Database Construction for Emergent Model Organisms. Proteomics 2020; 20:e1900261. [PMID: 32249536 DOI: 10.1002/pmic.201900261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 03/24/2020] [Indexed: 11/10/2022]
Abstract
Proteogenomics is gaining momentum as, today, genomics, transcriptomics, and proteomics can be readily performed on any new species. This approach allows key alterations to molecular pathways to be identified when comparing conditions. For animals and plants, RNA-seq-informed proteomics is the most popular means of interpreting tandem mass spectrometry spectra acquired for species for which the genome has not yet been sequenced. It relies on high-performance de novo RNA-seq assembly and optimized translation strategies. Here, several pre-treatments for Illumina RNA-seq reads before assembly are explored to translate the resulting contigs into useful polypeptide sequences. Experimental transcriptomics and proteomics datasets acquired for individual Gammarus fossarum freshwater crustaceans are used, the most relevant procedure is defined by the ratio of MS/MS spectra assigned to peptide sequences. Removing reads with a mean quality score of less than 17-which represents a single probable nucleotide error on 150-bp reads-prior to assembly, increases the proteomics outcome. The best translation using Transdecoder is achieved with a minimal open reading frame length of 50 amino acids and systematic selection of ORFs longer than 900 nucleotides. Using these parameters, transcriptome assembly and translation informed by proteomics pave the way to further improvements in proteogenomics.
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Affiliation(s)
- Yannick Cogne
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Duarte Gouveia
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Arnaud Chaumot
- INRAE, UR RiverLY Laboratoire d'écotoxicologie, Centre de Lyon-Villeurbanne, Villeurbanne, F-69625, France
| | - Davide Degli-Esposti
- INRAE, UR RiverLY Laboratoire d'écotoxicologie, Centre de Lyon-Villeurbanne, Villeurbanne, F-69625, France
| | - Olivier Geffard
- INRAE, UR RiverLY Laboratoire d'écotoxicologie, Centre de Lyon-Villeurbanne, Villeurbanne, F-69625, France
| | - Olivier Pible
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Christine Almunia
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
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Leprêtre M, Almunia C, Armengaud J, Le Guernic A, Salvador A, Geffard A, Palos-Ladeiro M. Identification of immune-related proteins of Dreissena polymorpha hemocytes and plasma involved in host-microbe interactions by differential proteomics. Sci Rep 2020; 10:6226. [PMID: 32277127 PMCID: PMC7148315 DOI: 10.1038/s41598-020-63321-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/27/2020] [Indexed: 12/04/2022] Open
Abstract
Biological responses of zebra mussel Dreissena polymorpha are investigated to assess the impact of contaminants on aquatic organisms and ecosystems. In addition to concentrate chemical contaminants in their tissues, zebra mussels accumulate several microorganisms such as viruses, protozoa and bacteria. In order to understand the molecular mechanisms involved in the defence against microorganisms this study aims at identifying immune proteins from D. polymorpha hemolymph involved in defence against protozoa and viruses. For this purpose, hemolymph were exposed ex vivo to Cryptosporidium parvum and RNA poly I:C. Differential proteomics on both hemocytes and plasma revealed immune proteins modulated under exposures. Different patterns of response were observed after C. parvum and RNA poly I:C exposures. The number of modulated proteins per hemolymphatic compartments suggest that C. parvum is managed in cells while RNA poly I:C is managed in plasma after 4 h exposure. BLAST annotation and GO terms enrichment analysis revealed further characteristics of immune mechanisms. Results showed that many proteins involved in the recognition and destruction of microorganisms were modulated in both exposure conditions, while proteins related to phagocytosis and apoptosis were exclusively modulated by C. parvum. This differential proteomic analysis highlights in zebra mussels modulated proteins involved in the response to microorganisms, which reflect a broad range of immune mechanisms such as recognition, internalization and destruction of microorganisms. This study paves the way for the identification of new markers of immune processes that can be used to assess the impact of both chemical and biological contaminations on the health status of aquatic organisms.
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Affiliation(s)
- Maxime Leprêtre
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO Stress Environnementaux et BIOsurveillance des milieux aquatiques, UFR Sciences Exactes et Naturelles, Campus du Moulin de la Housse, BP 1039, 51687, Reims, CEDEX, France
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, F-69100, Villeurbanne, France
| | - Christine Almunia
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Antoine Le Guernic
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO Stress Environnementaux et BIOsurveillance des milieux aquatiques, UFR Sciences Exactes et Naturelles, Campus du Moulin de la Housse, BP 1039, 51687, Reims, CEDEX, France
| | - Arnaud Salvador
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, F-69100, Villeurbanne, France
| | - Alain Geffard
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO Stress Environnementaux et BIOsurveillance des milieux aquatiques, UFR Sciences Exactes et Naturelles, Campus du Moulin de la Housse, BP 1039, 51687, Reims, CEDEX, France
| | - Mélissa Palos-Ladeiro
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO Stress Environnementaux et BIOsurveillance des milieux aquatiques, UFR Sciences Exactes et Naturelles, Campus du Moulin de la Housse, BP 1039, 51687, Reims, CEDEX, France.
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Pible O, Allain F, Jouffret V, Culotta K, Miotello G, Armengaud J. Estimating relative biomasses of organisms in microbiota using "phylopeptidomics". MICROBIOME 2020; 8:30. [PMID: 32143687 PMCID: PMC7060547 DOI: 10.1186/s40168-020-00797-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/05/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND There is an important need for the development of fast and robust methods to quantify the diversity and temporal dynamics of microbial communities in complex environmental samples. Because tandem mass spectrometry allows rapid inspection of protein content, metaproteomics is increasingly used for the phenotypic analysis of microbiota across many fields, including biotechnology, environmental ecology, and medicine. RESULTS Here, we present a new method for identifying the biomass contribution of any given organism based on a signature describing the number of peptide sequences shared with all other organisms, calculated by mathematical modeling and phylogenetic relationships. This so-called "phylopeptidomics" principle allows for the calculation of the relative ratios of peptide-specified taxa by the linear combination of such signatures applied to an experimental metaproteomic dataset. We illustrate its efficiency using artificial mixtures of two closely related pathogens of clinical interest, and with more complex microbiota models. CONCLUSIONS This approach paves the way to a new vision of taxonomic changes and accurate label-free quantitative metaproteomics for fine-tuned functional characterization. Video abstract.
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Affiliation(s)
- Olivier Pible
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRAE, F-30207, Bagnols-sur-Cèze, France
| | - François Allain
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRAE, F-30207, Bagnols-sur-Cèze, France
| | - Virginie Jouffret
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRAE, F-30207, Bagnols-sur-Cèze, France
| | - Karen Culotta
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRAE, F-30207, Bagnols-sur-Cèze, France
| | - Guylaine Miotello
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRAE, F-30207, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRAE, F-30207, Bagnols-sur-Cèze, France.
- Laboratory "Innovative technologies for Detection and Diagnostics", DRF-Li2D, CEA-Marcoule, BP 17171, F-30200, Bagnols-sur-Cèze, France.
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Marichal L, Klein G, Armengaud J, Boulard Y, Chédin S, Labarre J, Pin S, Renault JP, Aude JC. Protein Corona Composition of Silica Nanoparticles in Complex Media: Nanoparticle Size does not Matter. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E240. [PMID: 32013169 PMCID: PMC7075126 DOI: 10.3390/nano10020240] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 12/30/2022]
Abstract
Biomolecules, and particularly proteins, bind on nanoparticle (NP) surfaces to form the so-called protein corona. It is accepted that the corona drives the biological distribution and toxicity of NPs. Here, the corona composition and structure were studied using silica nanoparticles (SiNPs) of different sizes interacting with soluble yeast protein extracts. Adsorption isotherms showed that the amount of adsorbed proteins varied greatly upon NP size with large NPs having more adsorbed proteins per surface unit. The protein corona composition was studied using a large-scale label-free proteomic approach, combined with statistical and regression analyses. Most of the proteins adsorbed on the NPs were the same, regardless of the size of the NPs. To go beyond, the protein physicochemical parameters relevant for the adsorption were studied: electrostatic interactions and disordered regions are the main driving forces for the adsorption on SiNPs but polypeptide sequence length seems to be an important factor as well. This article demonstrates that curvature effects exhibited using model proteins are not determining factors for the corona composition on SiNPs, when dealing with complex biological media.
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Affiliation(s)
- Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
- Université Paris-Saclay, CEA, CNRS, NIMBE, Laboratoire Interdisciplinaire sur l’Organisation Nanométrique et Supramoléculaire, 91191 Gif-sur-Yvette, France; (S.P.); (J.-P.R.)
| | - Géraldine Klein
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
- Université Paris-Saclay, CEA, CNRS, NIMBE, Laboratoire Interdisciplinaire sur l’Organisation Nanométrique et Supramoléculaire, 91191 Gif-sur-Yvette, France; (S.P.); (J.-P.R.)
- UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), Institut Universitaire de la Vigne et du Vin, AgroSup Dijon, Université de Bourgogne Franche-Comté, rue Claude Ladrey, BP 27877, 21000 Dijon, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, 30207 Bagnols-sur-Cèze, France;
| | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
| | - Stéphane Chédin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
| | - Jean Labarre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
| | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, Laboratoire Interdisciplinaire sur l’Organisation Nanométrique et Supramoléculaire, 91191 Gif-sur-Yvette, France; (S.P.); (J.-P.R.)
| | - Jean-Philippe Renault
- Université Paris-Saclay, CEA, CNRS, NIMBE, Laboratoire Interdisciplinaire sur l’Organisation Nanométrique et Supramoléculaire, 91191 Gif-sur-Yvette, France; (S.P.); (J.-P.R.)
| | - Jean-Christophe Aude
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
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47
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Gobeaux F, Bizeau J, Samson F, Marichal L, Grillo I, Wien F, Yesylevsky SO, Ramseyer C, Rouquette M, Lepêtre-Mouelhi S, Desmaële D, Couvreur P, Guenoun P, Renault JP, Testard F. Albumin-driven disassembly of lipidic nanoparticles: the specific case of the squalene-adenosine nanodrug. NANOSCALE 2020; 12:2793-2809. [PMID: 31961354 DOI: 10.1039/c9nr06485k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the field of nanomedicine, nanostructured nanoparticles (NPs) made of self-assembling prodrugs emerged in the recent years with promising properties. In particular, squalene-based drug nanoparticles have already shown their efficiency through in vivo experiments. However, a complete pattern of their stability and interactions in the blood stream is still lacking. In this work we assess the behavior of squalene-adenosine (SQAd) nanoparticles - whose neuroprotective effect has already been demonstrated in murine models - in the presence of fetal bovine serum (FBS) and of bovine serum albumin (BSA), the main protein of blood plasma. Extensive physicochemical characterizations were performed using Small Angle Neutron Scattering (SANS), cryogenic transmission electron microscopy (Cryo-TEM), circular dichroism (CD), steady-state fluorescence spectroscopy (SSFS) and isothermal titration calorimetry (ITC) as well as in silico by means of ensemble docking simulations with human serum albumin (HSA). Significant changes in the colloidal stability of the nanoparticles in the presence of serum albumin were observed. SANS, CD and SSFS analyses demonstrated an interaction between SQAd and BSA, with a partial disassembly of the nanoparticles in the presence of BSA and the formation of a complex between SQAd and BSA. The interaction free energy of SQAd nanoparticles with BSA derived from ITC experiments, is about -8 kcal mol-1 which is further supported in silico by ensemble docking simulations. Overall, our results show that serum albumin partially disassembles SQAd nanoparticles by extracting individual SQAd monomers from them. As a consequence, the SQAd nanoparticles would act as a circulating reservoir in the blood stream. The approach developed in this study could be extended to other soft organic nanoparticles.
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Affiliation(s)
- Frédéric Gobeaux
- LIONS - NIMBE CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France.
| | - Joëlle Bizeau
- LIONS - NIMBE CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France.
| | - Firmin Samson
- LIONS - NIMBE CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France.
| | - Laurent Marichal
- LIONS - NIMBE CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France. and I2BC, JOLIOT, DRF, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Isabelle Grillo
- Institut Laue Langevin, 71 avenue des martyrs, B.P. 156, 38042 Grenoble Cedex 9, France
| | | | - Semen O Yesylevsky
- Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky 46, 03028 Kyiv, Ukraine
| | - Christophe Ramseyer
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030 Besançon Cedex, France
| | - Marie Rouquette
- Institut Galien Paris-Sud, UMR 8612, CNRS, Université Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, F-92296 Châtenay-Malabry Cedex, France
| | - Sinda Lepêtre-Mouelhi
- Institut Galien Paris-Sud, UMR 8612, CNRS, Université Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, F-92296 Châtenay-Malabry Cedex, France
| | - Didier Desmaële
- Institut Galien Paris-Sud, UMR 8612, CNRS, Université Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, F-92296 Châtenay-Malabry Cedex, France
| | - Patrick Couvreur
- Institut Galien Paris-Sud, UMR 8612, CNRS, Université Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, F-92296 Châtenay-Malabry Cedex, France
| | - Patrick Guenoun
- LIONS - NIMBE CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France.
| | - Jean-Philippe Renault
- LIONS - NIMBE CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France.
| | - Fabienne Testard
- LIONS - NIMBE CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France.
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48
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Biola-Clier M, Gaillard JC, Rabilloud T, Armengaud J, Carriere M. Titanium Dioxide Nanoparticles Alter the Cellular Phosphoproteome in A549 Cells. NANOMATERIALS 2020; 10:nano10020185. [PMID: 31973118 PMCID: PMC7074930 DOI: 10.3390/nano10020185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/11/2020] [Accepted: 01/16/2020] [Indexed: 12/02/2022]
Abstract
TiO2 nanoparticles (NPs) are one of the most produced NPs worldwide and are used in many consumer products. Their impact on human health, especially through inhalation, has been studied for more than two decades. TiO2 is known for its strong affinity towards phosphates, and consequently interaction with cellular phosphates may be one of the mechanisms driving its toxicity. In the present study, we used a phosphoproteomics approach to document the interaction of TiO2-NP with phosphoproteins from A549 human pulmonary alveolar epithelial cells. Cells were exposed to 21 nm anatase/rutile TiO2-NPs, then their phosphopeptides were extracted and analyzed using shotgun proteomics. By comparing the phosphoprotein content, phosphorylation status and phosphorylation sites of exposed cells with that of control cells, our results show that by affecting the phosphoproteome, TiO2-NPs affect cellular processes such as apoptosis, linked with cell cycle and the DNA damage response, TP53 being central to these pathways. Other pathways including inflammation and molecular transport are also affected. These molecular mechanisms of TiO2-NP toxicity have been reported previously, our study shows for the first time that they may derive from phosphoproteome modulation, which could be one of their upstream regulators.
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Affiliation(s)
| | - Jean-Charles Gaillard
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France;
| | - Thierry Rabilloud
- Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, IRIG-DIESE-LCBM-ProMD, F-38054 Grenoble, France;
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France;
- Correspondence: (J.A.); (M.C.)
| | - Marie Carriere
- Univ. Grenoble-Alpes, IRIG, SyMMES, CIBEST, F-38000 Grenoble, France;
- Correspondence: (J.A.); (M.C.)
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49
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Le Saux S, Aarrass H, Lai-Kee-Him J, Bron P, Armengaud J, Miotello G, Bertrand-Michel J, Dubois E, George S, Faklaris O, Devoisselle JM, Legrand P, Chopineau J, Morille M. Post-production modifications of murine mesenchymal stem cell (mMSC) derived extracellular vesicles (EVs) and impact on their cellular interaction. Biomaterials 2019; 231:119675. [PMID: 31838346 DOI: 10.1016/j.biomaterials.2019.119675] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 12/06/2019] [Indexed: 12/14/2022]
Abstract
In regards to their key role in intercellular communication, extracellular vesicles (EVs) have a strong potential as bio-inspired drug delivery systems (DDS). With the aim of circumventing some of their well-known issues (production yield, drug loading yield, pharmacokinetics), we specifically focused on switching the biological vision of these entities to a more physico-chemical one, and to consider and fine-tune EVs as synthetic vectors. To allow a rational use, we first performed a full physico-chemical (size, concentration, surface charge, cryoTEM), biochemical (western blot, proteomics, lipidomics, transcriptomics) and biological (cell internalisation) characterisation of murine mesenchymal stem cell (mMSC)-derived EVs. A stability study based on evaluating the colloidal behaviour of obtained vesicles was performed in order to identify optimal storage conditions. We evidenced the interest of using EVs instead of liposomes, in regards to target cell internalisation efficiency. EVs were shown to be internalised through a caveolae and cholesterol-dependent pathway, following a different endocytic route than liposomes. Then, we characterised the effect of physical methods scarcely investigated with EVs (extrusion through 50 nm membranes, freeze-drying, sonication) on EV size, concentration, structure and cell internalisation properties. Our extensive characterisation of the effect of these physical processes highlights their promise as loading methods to make EVs efficient delivery vehicles.
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Affiliation(s)
- Sarah Le Saux
- ICGM, Univ Montpellier, ENSCM, CNRS, Montpellier, France
| | - Hanna Aarrass
- ICGM, Univ Montpellier, ENSCM, CNRS, Montpellier, France
| | | | - Patrick Bron
- CBS, Univ Montpellier, INSERM, CNRS, Montpellier, France
| | - Jean Armengaud
- Laboratory «Innovative technologies for Detection and Diagnostics», CEA-Marcoule, DRF/JOLIOT/DMTS/SPI/Li2D, Bagnols-sur-Cèze, France
| | - Guylaine Miotello
- Laboratory «Innovative technologies for Detection and Diagnostics», CEA-Marcoule, DRF/JOLIOT/DMTS/SPI/Li2D, Bagnols-sur-Cèze, France
| | - Justine Bertrand-Michel
- MetaToul-LIPIDOMIQUE, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC) Inserm/Université Paul Sabatier UMR1048, Toulouse, France
| | - Emeric Dubois
- MGX-Montpellier GenomiX, IGF, CNRS, INSERM, Univ Montpellier, Montpellier, France
| | - Simon George
- MGX-Montpellier GenomiX, IGF, CNRS, INSERM, Univ Montpellier, Montpellier, France
| | - Orestis Faklaris
- Montpellier Ressources Imagerie, Biocampus, CNRS, INSERM, Univ Montpellier, Montpellier, France
| | | | | | - Joël Chopineau
- ICGM, Univ Montpellier, ENSCM, CNRS, Montpellier, France; Université de Nîmes, Nîmes, France
| | - Marie Morille
- ICGM, Univ Montpellier, ENSCM, CNRS, Montpellier, France.
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50
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Proteases as Secreted Exoproteins in Mycoplasmas from Ruminant Lungs and Their Impact on Surface-Exposed Proteins. Appl Environ Microbiol 2019; 85:AEM.01439-19. [PMID: 31540994 DOI: 10.1128/aem.01439-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/10/2019] [Indexed: 12/29/2022] Open
Abstract
Many mycoplasma species are isolated from the ruminant lungs as either saprophytes or true pathogens. These wall-less bacteria possess a minimal genome and reduced metabolic capabilities. Accordingly, they rely heavily on their hosts for the supply of essential metabolites and, notably, peptides. Seven of 13 ruminant lung-associated Mycoplasma (sub)species were shown to possess caseinolytic activity when grown in rich media and assessed with a quantitative fluorescence test. For some species, this activity was detected in spent medium, an indication that proteases were secreted outside the mycoplasma cells. To identify these proteases, we incubated concentrated washed cell pellets in a defined medium and analyzed the supernatants by tandem mass spectrometry. Secreted-protease activity was detected mostly in the species belonging to the Mycoplasma mycoides cluster (MMC) and, to a lesser extent, in Mycoplasma bovirhinis Analyzing a Mycoplasma mycoides subsp. capri strain, chosen as a model, we identified 35 expressed proteases among 55 predicted coding genes, of which 5 were preferentially found in the supernatant. Serine protease S41, acquired by horizontal gene transfer, was responsible for the caseinolytic activity, as demonstrated by zymography and mutant analysis. In an M. capricolum mutant, inactivation of the S41 protease resulted in marked modification of the expression or secretion of 17 predicted surface-exposed proteins. This is an indication that the S41 protease could have a role in posttranslational cleavage of surface-exposed proteins and ectodomain shedding, whose physiological impacts still need to be explored.IMPORTANCE Few studies pertaining to proteases in ruminant mycoplasmas have been reported. Here, we focus on proteases that are secreted outside the mycoplasma cell using a mass spectrometry approach. The most striking result is the identification, within the Mycoplasma mycoides cluster, of a serine protease that is exclusively detected outside the mycoplasma cells and is responsible for casein digestion. This protease may also be involved in the posttranslational processing of surface proteins, as suggested by analysis of mutants showing a marked reduction in the secretion of extracellular proteins. By analogy, this finding may help increase understanding of the mechanisms underlying this ectodomain shedding in other mycoplasma species. The gene encoding this protease is likely to have been acquired via horizontal gene transfer from Gram-positive bacteria and sortase-associated surface proteases. Whether this protease and the associated ectodomain shedding are related to virulence has yet to be ascertained.
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