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1. Molecular acclimation of Halobacterium salinarum to halite brine inclusions

Author: Charly Favreau, Alicia Tribondeau, Marie Marugan, François Guyot, Beatrice Alpha-Bazin, Arul Marie, Remy Puppo, Thierry Dufour, Arnaud Huguet, Séverine Zirah, Adrienne Kish, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Physiologie moléculaire et adaptation (PhyMA), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique des Plasmas (LPP), Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École polytechnique (X)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Milieux Environnementaux, Transferts et Interactions dans les hydrosystèmes et les Sols (METIS), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), CNRS-MITI program X-life program, Muséum National d’Histoire Naturelle program ATM, Sorbonne Université (graduate stipend CF), and ANR-21-CE49-0017,ExocubeHalo,Préservation des surfaces cellulaires des microorganismes halophiles comme biosignatures en exposition aux rayonnements spatiaux sur Exocube(2021)
Subjects: Plasma Physics (physics.plasm-ph), Microbiology (medical), Biological Physics (physics.bio-ph), FOS: Physical sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Physics - Biological Physics, Microbiology, Physics - Plasma Physics
Abstract: Halophilic microorganisms have long been known to survive within the brine inclusions of salt crystals, as evidenced by the change in color for salt crystals containing pigmented halophiles. However, the molecular mechanisms allowing this survival has remained an open question for decades. While protocols for the surface sterilization of halite (NaCl) have enabled isolation of cells and DNA from within halite brine inclusions, “-omics” based approaches have faced two main technical challenges: (1) removal of all contaminating organic biomolecules (including proteins) from halite surfaces, and (2) performing selective biomolecule extractions directly from cells contained within halite brine inclusions with sufficient speed to avoid modifications in gene expression during extraction. In this study, we tested different methods to resolve these two technical challenges. Following this method development, we then applied the optimized methods to perform the first examination of the early acclimation of a model haloarchaeon (Halobacterium salinarum NRC-1) to halite brine inclusions. Examinations of the proteome of Halobacterium cells two months post-evaporation revealed a high degree of similarity with stationary phase liquid cultures, but with a sharp down-regulation of ribosomal proteins. While proteins for central metabolism were part of the shared proteome between liquid cultures and halite brine inclusions, proteins involved in cell mobility (archaellum, gas vesicles) were either absent or less abundant in halite samples. Proteins unique to cells within brine inclusions included transporters, suggesting modified interactions between cells and the surrounding brine inclusion microenvironment. The methods and hypotheses presented here enable future studies of the survival of halophiles in both culture model and natural halite systems.
Published: 2023
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2. Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking

Author: Arul Marie, Jane C. Wheeler, Elise Dufour, Nicolas Goepfert, Clara Azémard, Antoine Zazzo, Séverine Zirah, Centre National de la Recherche Scientifique (CNRS), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), CONOPA - Instituto de Investigacion y Desarrollo de Camelidos Sudamericanos, Archéologie des Amériques (ArchAm), Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)
Subjects: 0301 basic medicine, Proteomics, Old World, Multivariate analysis, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SDV]Life Sciences [q-bio], Biophysics, Endangered species, Biochemistry, [SHS]Humanities and Social Sciences, 03 medical and health sciences, Metabolomics, Tandem Mass Spectrometry, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Animals, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], ComputingMilieux_MISCELLANEOUS, 030102 biochemistry & molecular biology, biology, South America, biology.organism_classification, Molecular network, 030104 developmental biology, Evolutionary biology, South american, Molecular networking, Multivariate Analysis, Camelids, New World, Camelid, Hair
Abstract: The proteomic analysis of hairs, yarns or textiles has emerged as a powerful method to determine species of origin, mainly used in archaeozoological research and fraud control. Differentiation between the South American camelid (SAC) species (the wild guanaco and vicuna and their respective domesticates the llama and alpaca) is particularly challenging due to poor database information and significant hybridization between species. In this study, we analysed 41 modern and 4 archaeological samples from the four SACs species. Despite strong similarities with Old World Camelidae, we identified 7 peptides specific to SACs assigned to keratin K86 and the keratin-associated proteins KAP13-1 and KAP11-1. Untargeted multivariate analysis of the LC-MS data permitted to distinguish SAC species and propose discriminant features. MS/MS-based molecular networking combined with database-assisted de novo sequencing permitted to identify 5 new taxonomic peptides assigned to K33a, K81 and/or K83 keratins and KAP19-1. These peptides differentiate the two wild species, guanaco and vicuna. These results show the value of combining database search and untargeted metabolomic approaches for paleoproteomics, and reveal for the first time the potential of molecular networks to highlight deamidation related to diagenesis and cluster highly similar peptides related to interchain homologies or intra- or inter-specific polymorphism. SIGNIFICANCE: This study used an innovative approach combining multivariate analysis of LC-MS data together with molecular networking and database-assisted de novo sequencing to identify taxonomic peptides in palaeoproteomics. It constitutes the first attempt to differentiate between hair fibres from the four South American camelids (SACs) based on proteomic analysis of modern and archaeological samples. It provides different proteomic signatures for each of the four SAC species and proposes new SAC taxonomic peptides of interest in archaeozoology and fraud control. SACs have been extensively exploited since human colonization of South America but have not been studied to the extent of their economic, cultural and heritage importance. Applied to the analysis of ancient Andean textiles, our results should permit a better understanding of cultural and pastoral practices in South America. The wild SACs are endangered by poaching and black-market sale of their fibre. For the first time, our results provide discriminant features for the determination of species of origin of contraband fibre.
Published: 2021
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3. Animal fibre use in the Keriya valley (Xinjiang, China) during the Bronze and Iron Ages: A proteomic approach

Author: Sébastien Lepetz, Clara Azémard, Antoine Zazzo, Abduressul Idriss, Séverine Zirah, Arul Marie, Corinne Debaine-Francfort, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Institut d'Archéologie et du Patrimoine du Xinjiang, Bureau du Patrimoine du Xinjiang, Laboratoire Chimie Appliquée à l'Art et à l'Archéologie, Avignon Université (AU), Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)-Université Paris Nanterre (UPN)-Université Panthéon-Sorbonne (UP1), ZAZZO, Antoine, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Archéologie de L'Asie centrale, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), and Archéozoologie et histoire des sociétés (AHS)
Subjects: Proteomics, 010506 paleontology, Archeology, Veterinary medicine, Bronze Age 35 36, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Iron Age, Pastoralism, engineering.material, 01 natural sciences, Caprinae, Prehistory, Bronze Age, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], 0601 history and archaeology, Bronze, keratin, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, [SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory, 060102 archaeology, biology, Sedentism, Xinjiang, 06 humanities and the arts, biology.organism_classification, textiles, Wool, engineering, animal fibres
Abstract: International audience; 18 Textile technology strongly advanced with sedentism and pastoralism. During prehistory, many 19 populations settled in central Eurasia, a place of extensive exchange and cultural contact. In the 20 Taklamakan desert, the dry climate enabled good preservation of ancient textiles. The study presented 21 here aimed to identify animal fibres from Bronze Age and Iron Age sites in the Keriya valley 22 (Xinjiang, China) using proteomics. A large corpus of 109 keratin extracts obtained from raw fibres or 23 textiles was analysed, enabling us to establish a corrected and improved list of peptide markers for the 24 identification of species, not only among the family Bovidae, but also for camels and humans. In total, 25 we were able to identify 97% of the sampled objects to the taxonomic level of tribe and 85% of 26 caprines to the level of genus. The assemblage was dominated by hair of sheep (57.8%) followed by 27 goat (16.5%), cattle (8.3%), camel (0.9%), human (0.9%) and non-differentiated Caprinae (sheep or 28 goat) (12.8%). The study showed a continuity between the two sites in this respect. It revealed a 29 choice of raw material linked to the function of the textile, with most woven textiles being made from 30 sheep's wool and most pelt being obtained from goat. Comparison with the bone assemblage of one of 31 the sites provided insight into the herd management strategies. The results confirm the heuristic 32 potential of the proteomic approach for the determination of archaeological fibres and for textiles 33 studies in general. Data are available via ProteomeXchange with identifier PXD012189. 34
Published: 2019
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4. Global Metabolomic Characterizations of Microcystis spp. Highlights Clonal Diversity in Natural Bloom-Forming Populations and Expands Metabolite Structural Diversity

Author: Marc Edery, Benjamin Marie, Arnaud Catherine, Charlotte Duval, Chakib Djediat, Arul Marie, Séverine Le Manach, Cécile Bernard, Séverine Zirah, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), and DUVAL, Charlotte
Subjects: Microbiology (medical), Cyanobacteria, Metabolite, lcsh:QR1-502, Biodiversity, Zoology, Photosynthesis, Freshwater ecosystem, Microbiology, lcsh:Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Metabolomics, cyanobacteria blooms, Microcystis, [CHIM] Chemical Sciences, Genotype, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Metabolome, [CHIM]Chemical Sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Genotyping, 030304 developmental biology, mass spectrometry, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, biology, 030306 microbiology, secondary metabolites, Cyanotoxin, biology.organism_classification, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, chemistry, chemiodiversity, aquatic environment
Abstract: Cyanobacteria are photosynthetic prokaryotes that are able to synthetize a wild rang of secondary metabolites exhibiting noticeable bioactivity, comprising toxicity. Microcystis represents one of the most common cyanobacteria taxa constituting the intensive blooms that arise nowadays in freshwater ecosystems worldwide. They produce numerous cyanotoxins (toxic metabolites), which are potentially harmful to Human health and aquatic organisms. In order to better understand the variations in cyanotoxins production between clones of the Microcystis, we investigate the diversity of several strains isolated from the same blooms, from different populations in various geographical area.Twenty-four clonal strains were compared by genotyping with 16S-ITS fragment sequencing and metabolites chemotyping using LC ESI-qTOF mass spectrometry. While, genotyping can only discriminate between the different species, the global metabolomes reveal clear discriminant molecular profiles between strains. These profiles can be clustered primarily according to their global metabolite content, then to their genotype, and finally to their sampling localities. A global molecular network of all metabolites highlights the production of a wide set of chemically diverse metabolites, comprising only few microcystins, but many aeruginosins, cyanopeptolins and microginins, along with a large set of unknown molecules. They represent the molecular biodiversity that still remain to be investigated and characterized at their structure as well as at their potential bioactivity or toxicity levels.
Published: 2019
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5. Binding Specificity of Native Odorant-Binding Protein Isoforms Is Driven by Phosphorylation and O-N-Acetylglucosaminylation in the Pig Sus scrofa

Author: Patricia Nagnan-Le Meillour, Alexandre Joly, Chrystelle Le Danvic, Arul Marie, Séverine Zirah, Jean-Paul Cornard, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Thales Research and Technology [Palaiseau], THALES, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrochimie Infrarouge et Raman - UMR 8516 (LASIR), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Université de Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 [UGSF], Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 [UGSF], Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 [LASIRE], Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL), INRA (French Institut National de Recherche Agronomique), CNRS (French Centre National de Recherche Scientifique), ENSCL, Nagnan-Le Meillour, Patricia, Université de Lille-Centre National de la Recherche Scientifique (CNRS), THALES [France], and Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Gene isoform, Endocrinology, Diabetes and Metabolism, odorant-binding protein, 030209 endocrinology & metabolism, Olfaction, lcsh:Diseases of the endocrine glands. Clinical endocrinology, law.invention, 03 medical and health sciences, pheromone, 0302 clinical medicine, law, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Receptor, Binding selectivity, ComputingMilieux_MISCELLANEOUS, lcsh:RC648-665, biology, Chemistry, phosphorylation, Binding protein, fluorescence spectroscopy, O-GlcNAc, CID-nano-LC-MS/MS, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, 030104 developmental biology, Biochemistry, Recombinant DNA, Odorant-binding protein, biology.protein, Phosphorylation
Abstract: International audience; Odorant-binding proteins (OBP) are secreted in the nasal mucus at the vicinity of olfactory receptors (ORs). They act, at least, as an interface between hydrophobic and volatile odorant molecules and the hydrophilic medium bathing the ORs. They have also been hypothesized to be part of the molecular coding of odors and pheromones, by forming specific complexes with odorant molecules that could ultimately stimulate ORs to trigger the olfactory transduction cascade. In a previous study, we have evidenced that pig olfactory secretome was composed of numerous olfactory binding protein isoforms, generated by O-GlcNAcylation and phosphorylation. In addition, we have shown that recombinant OBP (stricto sensu) produced in yeast is made up of a mixture of isoforms that differ in their phosphorylation pattern, which in turn determines binding specificity. Taking advantage of the high amount of OBP secreted by a single animal, we performed a similar study, under exactly the same experimental conditions, on native isoforms isolated from pig, Sus scrofa, nasal tissue. Four fractions were obtained by using strong anion exchange HPLC. Mapping of phosphorylation and O-GlcNAcylation sites by CID-nanoLC-MS/MS allowed unambiguous localization of phosphosites at S13 and T122 and HexNAc sites at S13 and S19. T112 or T115 could also be phosphorylated. BEMAD analysis suggested extra phosphosites located at S23, S24, S41, S49, S57, S67, and T71. Due to the very low stoichiometry of GlcNAc-peptides and phosphopeptides, these sites were identified on total mixture of OBP isoforms instead of HPLC-purified OBP isoforms. Nevertheless, binding properties of native OBP isoforms to specific ligands in S. scrofa were monitored by fluorescence spectroscopy. Recombinant phosphorylated OBP-Pichia isoforms bind steroids and fatty acids with slight differences. Native isoforms, that are phosphorylated but also O-GlcNAcylated show radically different binding affinities for the same compounds, which strongly suggests that O-GlcNAcylation increases the binding specificity of OBP isoforms. These findings extend the role of O-GlcNAc in regulating the function of proteins involved in many mechanisms of metabolic homeostasis, including extracellular signaling in olfaction. Data is available via ProteomeXChange with identifier PXD011371.
Published: 2019
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6. Identification of degraded bone and tooth splinters from arid environments using palaeoproteomics

Author: Séverine Zirah, Antoine Zazzo, Louise Le Meillour, Sophie Cersoy, Matthieu Lebon, Arul Marie, David Pleurdeau, Joséphine Lesur, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Laboratoire d'Archéologie Moléculaire et Structurale (LAMS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Histoire naturelle de l'Homme préhistorique (HNHP), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Centre de Recherche sur la Conservation (CRC ), Muséum national d'Histoire naturelle (MNHN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Perpignan Via Domitia (UPVD), LabEx BCDiv, MNHN, DIM-MAP, Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Proteomics, 010506 paleontology, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Computational biology, Oceanography, 01 natural sciences, Bone diagenesis, 03 medical and health sciences, Species identification, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Earth-Surface Processes, Ancient collagen, Bone decalcification, Paleontology, Arid, 030104 developmental biology, Africa, Arid environment, Identification (biology), Trypsin Digestion, Geology, ATR-FTIR
Abstract: International audience; The analysis of the skeletal remains of vertebrates in archaeological contexts provides information about human- animal relationship and their environment. Their taxonomic identification based on macroscopic observation is not always possible due to fragmentation and poor preservation. In recent years, proteomics has emerged as an alternative but there is clearly a lack of data in arid environment where diagenesis rapidly affects the integrity of bone proteins. Here, we report the efficiency of three protocols for protein extraction. The protocols used harsh (1 M HCl and 0.6 M HCl) and soft (Tris-EDTA) decalcification agents and were tested on unidentified splinters from the 2000 years-old site of Toteng, Botswana. The preservation of the organic phase was first estimated using attenuated total reflectance Fourier transform infrared spectroscopy and a set of samples with contrasted col- lagen contents were selected for palaeoproteomics. The extracted proteins were submitted to a bottom-up proteomic approach involving trypsin digestion followed by ultra-high-performance liquid chromatography coupled to mass spectrometry (UHPLC-MS). Our results identify Tris-EDTA buffer as the most suitable dec- alcification protocol for poorly preserved bones and propose a collagen content threshold of ~3% weight content for successful detection of peptides. This approach, combined with biogeographical and chronological reparti- tions of mammals in Africa allows refining taxonomic attributions for four out of nine splinters, leading to species identification. Data are available via ProteomeXchange with identifier PXD010725.
Published: 2018
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7. To be pastoralist or not to be? Tracing the introduction of domestic caprines in Southern Africa using Palaeoproteomics

Author: Louise Le Meillour, Joséphine Lesur, Sophie Cersoy, Arul Marie, Matthieu Lebon, Pleurdeau David, Severine Zirah, Antoine Zazzo, Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Centre de Recherche sur la Conservation (CRC ), Muséum national d'Histoire naturelle (MNHN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Perpignan Via Domitia (UPVD)
Subjects: [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2018

8. Physiological effects caused by microcystin-producing and non-microcystin producing Microcystis aeruginosa on medaka fish: A proteomic and metabolomic study on liver

Author: Hélène Huet, Benoit Sotton, Arul Marie, Claude Yéprémian, Arnaud Catherine, Charlotte Duval, Marc Edery, Alain Paris, Joëlle Vinh, Benjamin Marie, Séverine Le Manach, Lucrèce Mathéron, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), École nationale vétérinaire d'Alfort (ENVA), Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Neurobiologie et diversité cellulaire (NDC), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Xénobiotiques, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), ESPCI ParisTech-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), and Institut de Recherche pour le Développement (IRD)
Subjects: Fish Proteins, Male, Proteomics, 0301 basic medicine, Microcystis, Microcystins, Health, Toxicology and Mutagenesis, Oryzias, Fresh Water, Microcystin, 010501 environmental sciences, Toxicology, 01 natural sciences, Algal bloom, Microbiology, 03 medical and health sciences, Metabolomics, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Ecotoxicology, Microcystis aeruginosa, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, Ecosystem, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, chemistry.chemical_classification, biology, Aquatic animal, General Medicine, biology.organism_classification, Pollution, 030104 developmental biology, Liver, chemistry, Female
Abstract: Cyanobacterial blooms have become a common phenomenon in eutrophic freshwater ecosystems worldwide. Microcystis is an important bloom-forming and toxin-producing genus in continental aquatic ecosystems, which poses a potential risk to Human populations as well as on aquatic organisms. Microcystis is known to produce along with various bioactive peptides, the microcystins (MCs) that have attracted more attention notably due to their high hepatotoxicity. To better understand the effects of cyanobacterial blooms on fish, medaka fish (Oryzias latipes) were sub-chronically exposed to either non-MC-producing or MC-producing living strains and, for this latter, to its subsequent MC-extract of Microcystis aeruginosa. Toxicological effects on liver have been evaluated through the combined approach of histopathology and ‘omics’ (i.e. proteomics and metabolomics). All treatments induce sex-dependent effects at both cellular and molecular levels. Moreover, the modalities of exposure appear to induce differential responses as the direct exposure to the cyanobacterial strains induce more acute effects than the MC-extract treatment. Our histopathological observations indicate that both non-MC-producing and MC-producing strains induce cellular impairments. Both proteomic and metabolomic analyses exhibit various biological disruptions in the liver of females and males exposed to strain and extract treatments. These results support the hypothesis that M. aeruginosa is able to produce bioactive peptides, other than MCs, which can induce toxicological effects in fish liver. Moreover, they highlight the importance of considering cyanobacterial cells as a whole to assess the realistic environmental risk of cyanobacteria on fish.
Published: 2018
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9. Deep conservation of bivalve nacre proteins highlighted by shell matrix proteomics of the Unionoida Elliptio complanata and Villosa lienosa

Author: Jaison Arivalagan, Benjamin Marie, Arul Marie, Lucrèce Mathéron, Sophie Berland, Frédéric Marin, Gérard Bolbach, Molécules de Communication et Adaptation des Micro-Organismes ( MCAM ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Analyse, Interactions Moléculaires et Cellulaires ( LBM-E2 ), Laboratoire des biomolécules ( LBM UMR 7203 ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Département de Chimie - ENS Paris, École normale supérieure - Paris ( ENS Paris ) -École normale supérieure - Paris ( ENS Paris ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Département de Chimie - ENS Paris, École normale supérieure - Paris ( ENS Paris ) -École normale supérieure - Paris ( ENS Paris ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Biologie des Organismes et Ecosystèmes Aquatiques ( BOREA ), Université des Antilles ( UA ) -Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut de Recherche pour le Développement ( IRD ) -Muséum National d'Histoire Naturelle ( MNHN ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Funding from the Marie Curie European Union Seventh Framework Programme under grant agreement no. 605051., Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Analyse, Interactions Moléculaires et Cellulaires (LBM-E2), Laboratoire des biomolécules (LBM UMR 7203), Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Biogéosciences [UMR 6282] [Dijon] (BGS), and Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)
Subjects: Unionidae, 0301 basic medicine, Unionoida, [ SDV.BA.ZI ] Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Villosa lienosa, Biomedical Engineering, Biophysics, Life Sciences–Earth Science interface, Bioengineering, Biology, Proteomics, Biochemistry, bivalve, Evolution, Molecular, Biomaterials, 03 medical and health sciences, Paleontology, Calcification, Physiologic, proteomics, Animal Shells, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], shell nacre, Shell matrix, Animals, calcium carbonate, 14. Life underwater, Nacre, Mantle (mollusc), chemistry.chemical_classification, Extracellular Matrix Proteins, Elliptio, biology.organism_classification, biomineralization, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, chemistry, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], organic matrix proteins, Glycoprotein, Biotechnology, Biomineralization
Abstract: The formation of the molluscan shell nacre is regulated to a large extent by a matrix of extracellular macromolecules that are secreted by the shell-forming tissue, the mantle. This so-called ‘calcifying matrix’ is a complex mixture of proteins, glycoproteins and polysaccharides that is assembled and occluded within the mineral phase during the calcification process. Better molecular-level characterization of the substances that regulate nacre formation is still required. Notable advances in expressed tag sequencing of freshwater mussels, such as Elliptio complanata and Villosa lienosa , provide a pre-requisite to further characterize bivalve nacre proteins by a proteomic approach. In this study, we have identified a total of 48 different proteins from the insoluble matrices of the nacre, 31 of which are common to both E. complanata and V. lienosa . A few of these proteins, such as PIF, MSI60, CA, shematrin-like, Kunitz-like, LamG, chitin-binding-containing proteins, together with A-, D-, G-, M- and Q-rich proteins, appear to be analogues, if not true homologues, of proteins previously described from the pearl oyster or the edible mussel nacre matrices, thus forming a remarkable list of deeply conserved nacre proteins. This work constitutes a comprehensive nacre proteomic study of non-pteriomorphid bivalves that has enabled us to describe the molecular basis of a deeply conserved biomineralization toolkit among nacreous shell-bearing bivalves, with regard to proteins associated with other shell microstructures, with those of other mollusc classes (gastropods, cephalopods) and, finally, with other lophotrochozoans (brachiopods).
Published: 2017
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10. Gender-Specific Toxicological Effects of Chronic Exposure to Pure Microcystin-LR or Complex Microcystis aeruginosa Extracts on Adult Medaka Fish

Author: Chakib Djediat, Gérard Bolbach, Marc Edery, Séverine Le Manach, Gilles Clodic, Benjamin Marie, Cécile Bernard, Qin Qiao, Hélène Huet, Nour Khenfech, Arul Marie, Charlotte Duval, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École nationale vétérinaire d'Alfort (ENVA), Spectrométrie de Masse et Protéomique [IBPS] (IBPS-SPM), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and École nationale vétérinaire - Alfort (ENVA)
Subjects: 0301 basic medicine, Cyanobacteria, Proteomics, Microcystis, Microcystins, Oryzias, Microcystin-LR, 010501 environmental sciences, 01 natural sciences, Oogenesis, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, medicine, Environmental Chemistry, Animals, [CHIM]Chemical Sciences, Microcystis aeruginosa, 14. Life underwater, 0105 earth and related environmental sciences, biology, Glycogen, Hepatotoxin, General Chemistry, biology.organism_classification, 6. Clean water, Lakes, 030104 developmental biology, medicine.anatomical_structure, chemistry, 13. Climate action, Hepatocyte
Abstract: International audience; Cyanobacterial blooms often occur in freshwater lakes and constitute a potential health risk to human populations, as well as to other organisms. However, their overall and specific implications for the health of aquatic organisms that are chronically and environmentally exposed to cyanobacteria producing hepatotoxins, such as microcystins (MCs), together with other bioactive compounds have still not been clearly established and remain difficult to assess. The medaka fish was chosen as the experimental aquatic model for studying the cellular and molecular toxicological effects on the liver after chronic exposures (28 days) to environmentally relevant concentrations of pure MC-LR, complex extracts of MC producing or nonproducing cyanobacterial biomasses, and of a Microcystis aeruginosa natural bloom. Our results showed a higher susceptibility of females to the different treatments compared to males at both the cellular and the molecular levels. Although hepatocyte lysis increased with MC-containing treatments, lysis always appeared more severe in the liver of females compare to males, and the glycogen cellular reserves also appeared to decrease more in the liver of females compared to those in the males. Proteomic investigations reveal divergent responses between males and females exposed to all treatments, especially for proteins involved in metabolic and homeostasis processes. Our observations also highlighted the dysregulation of proteins involved in oogenesis in female livers. These results suggest that fish populations exposed to cyanobacteria blooms may potentially face several ecotoxicological issues.
Published: 2016
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11. Historical linseed oil/colophony varnishes formulations: Study of their molecular composition with micro-chemical chromatographic techniques

Author: Anna Lluveras-Tenorio, Jean-Yves Le Huerou, Agnès Lattuati-Derieux, Sophie Tirat, Stéphane Serfaty, Ilaria Degano, Jean-Philippe Echard, Arul Marie, Systèmes et Applications des Technologies de l'Information et de l'Energie (SATIE), École normale supérieure - Cachan (ENS Cachan)-Université Paris-Sud - Paris 11 (UP11)-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-École normale supérieure - Rennes (ENS Rennes)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche sur la Conservation (CRC ), Muséum national d'Histoire naturelle (MNHN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Cité de la musique-Philharmonie, Musée de la musique, Equipe Conservation Recherche, Musée de la Musique, Cité de la musique-Philharmonie de Paris-Cité de la musique-Philharmonie de Paris, Centre de Recherche pour la Conservation des Collections (CRCC), Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Cergy Pontoise (UCP), Université Paris-Seine, Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC), Université Paris-Seine-Université Paris-Seine-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM)-École normale supérieure - Rennes (ENS Rennes)-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan), and Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: food.ingredient, Chromatography, 010405 organic chemistry, Chemical structure, 010401 analytical chemistry, Size-exclusion chromatography, Ether, Raw material, [SHS.ART]Humanities and Social Sciences/Art and art history, 01 natural sciences, High-performance liquid chromatography, 0104 chemical sciences, Analytical Chemistry, [SPI.MAT]Engineering Sciences [physics]/Materials, chemistry.chemical_compound, Hydrolysis, food, chemistry, Linseed oil, Polymerization, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Organic chemistry, Spectroscopy
Abstract: International audience; Mixtures of siccative oil and Pinaceae resin were among the most widespread formulations used for varnishing in the 16th–18th centuries. The aim of this research is to study the molecular composition of different formulations of varnishes based on linseed oil and colophony. The mixtures were prepared by cooking both raw materials in different proportions, following the outlines of historical recipes gathered in treatises and manuscripts from that period. Size exclusion chromatography (SEC) evidenced the presence of numerous oligomeric compounds from linseed oil and colophony. Analysis using Electrospray-Quadrupole-Time of Flight mass spectrometer (ESI-Q-ToF) allowed the characterization of oligomeric compounds from colophony. In particular, structures of dimeric diterpenic acid units attached by ester, ether, anhydride or keto linkage are proposed. Concerning linseed oil, oxidized and chain-shortened triglycerides were characterized with High Performance Liquid Chromatography coupled with Electrospray-Quadrupole-Time of Flight mass spectrometer (HPLC–ESI-Q-ToF). SEC quantitation of compounds allowed us to assess the influence of the oil to colophony ratio on the molecular composition of the varnishes: oil polymerization appears to be minimized in favor of its hydrolysis in presence of colophony, whereas linseed oil seems to inhibit the formation of diterpenic dimers and trimers. In addition, analyses evidence the reaction of diterpenic acids with linseed oil compounds. In particular, we identified hybrid molecules formed by a diglyceride and a diterpenic acid. Addition products of a of a triglyceride and a diterpenic acid may also be present in the mixtures. These results bring new information about the molecular composition of varnishes made from linseed oil and colophony, and will improve the knowledge of historical varnishes. To this purpose, all analytical protocols were implemented on micro-samples so that they could be applied later on ancient artifacts.
Published: 2016
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12. Shell proteome of rhynchonelliform brachiopods

Author: Danièle Gaspard, Frédéric Marin, Maggie Cusack, Arul Marie, Françoise Immel, Nathalie Guichard, Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de recherche sur la Paléobiodiversité et les Paléoenvironnements ( CR2P ), Muséum National d'Histoire Naturelle ( MNHN ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Molécules de Communication et Adaptation des Micro-Organismes ( MCAM ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), School of Geographical and Earth Sciences, University of Glasgow, Work supported by the INTERRVIE Program (INSU, CNRS, France, campaign 2011–2012), the ADEQUA GDR, France (2008–2012) on pearl research and the COST Action Biomineralix (COST TD 0903, Nov. 2009–May 2014, http://www.cost.eu/domains_actions/cmst/Actions/TD0903)., Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Biomineralization, Proteomics, Proteome, Shell (structure), Brachiopods, Biology, Matrix (biology), Calcium Carbonate, Paleontology, chemistry.chemical_compound, Calcification, Physiologic, Animal Shells, Structural Biology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Shell, Animals, 14. Life underwater, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, Calcite, Minerals, Phylum, Marine invertebrates, Extracellular matrix, [ SDV.IB.BIO ] Life Sciences [q-bio]/Bioengineering/Biomaterials, Invertebrates, chemistry, Evolutionary biology, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Peptides
Abstract: 7 pages; International audience; Brachiopods are a phylum of marine invertebrates that have an external bivalved shell to protect their living tissues. With few exceptions, this biomineralized structure is composed of calcite, mixed together with a minor organic fraction, comprising secreted proteins that become occluded in the shell structure, once formed. This organic matrix is thought to display several functions, in particular, to control mineral deposition and to regulate crystallite shapes. Thus, identifying the primary structure of matrix proteins is a prerequisite for generating bioinspired materials with tailored properties. In this study, we employed a proteomic approach to identify numerous peptides that constitute the shell proteins, in three rhynchonellid brachiopods from different localities. Our results suggest that the shell protein repertoires identified thus far, differ from that of better known calcifying metazoans, such as molluscs.
Published: 2015
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13. Characterization of the teeth skeletal matrix from Arbacia lixula

Author: Julia Maxi Kanold, Françoise Immel, Arul Marie, Laurent Plasseraud, Gérard Alcaraz, Franz Brümmer, Frédéric Marin, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, F. Marin, F. Brümmer, A. Checa, G. Furtos, I.G. Lesci & L. Šiller, Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Molécules de Communication et Adaptation des Micro-Organismes ( MCAM ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] ( ICMUB ), Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, F. Marin, F. Brümmer, A. Checa, G. Furtos, I.G. Lesci & L. Šiller, Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Frédéric Marin, Franz Brümmer, Antonio Checa, Gabriel Furtos, Isidoro Giorgio, Lesci and Lidija Šiller, and Laffont, Rémi
Subjects: [SDV.IB.BIO] Life Sciences [q-bio]/Bioengineering/Biomaterials, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [ SDV.IB.BIO ] Life Sciences [q-bio]/Bioengineering/Biomaterials, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, ComputingMilieux_MISCELLANEOUS
Abstract: 15 pages; International audience
Published: 2015

14. Unveiling the evolution of bivalve nacre proteins by shell proteomics of Unionoidae

Author: Benjamin Marie, Frédéric Marin, Arul Marie, Sophie Berland, Lionel Dubost, Jaison Arivalagan, Laffont, Rémi, F. Marin, F. Brümmer, A. Checa, G. Furtos, I.G. Lesci & L. Šiller, Molécules de Communication et Adaptation des Micro-Organismes ( MCAM ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, F. Marin, F. Brümmer, A. Checa, G. Furtos, and I.G. Lesci & L. Šiller
Subjects: 0301 basic medicine, Proteomics, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], General Materials Science, 14. Life underwater, Mantle (mollusc), Bivalve shell, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Villosa, biology, Mechanical Engineering, Pearl oyster, Elliptio, biology.organism_classification, [ SDV.IB.BIO ] Life Sciences [q-bio]/Bioengineering/Biomaterials, [SDV.IB.BIO] Life Sciences [q-bio]/Bioengineering/Biomaterials, 030104 developmental biology, chemistry, Biochemistry, Mechanics of Materials, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Glycoprotein, Biomineralization
Abstract: The formation of the molluscan shell nacre is regulated to a large extent by a matrix of extracellular macromolecules that are secreted by the shell forming tissue, the mantle. This so called “calcifying matrix” is a complex mixture of proteins and glycoproteins that is assembled and occluded within the mineral phase during the calcification process. While the importance of the calcifying matrix to shell formation has long been appreciated, the molecular basis that dictates nacre formation remains largely uncharacterized.Recent expressed sequence tag (EST) investigations of the freshwater mussels (Elliptio complanata and Villosa leinosa) provide an opportunity to further characterize the proteins in the bivalve shell by a proteomic approach. In this study, we have identified a total of 15 proteins from their nacre insoluble matrices. Few of these proteins, such as Pif, MSI60, Nacrein-like, Shematrin, Kunitz-like containing, Papilin-like, LamG containing, Chitin-binding containing, M-rich and Q-rich proteins, appear to be analogs, if not true homologs, of proteins previously described from the pearl oyster or the edible mussel nacre matrices. This work constitutes a comprehensive EST-based nacre proteomic study of non-pteriomorphid bivalves that concretely gives us the opportunity to describe the molecular basis of deeply conserved nacre biomineralization toolkit within nacreous shell bearing bivalves.
Published: 2015

15. Proteomics of CaCO3 biomineral-associated proteins: how to properly address their analysis

Author: Arul Marie, Benjamin Marie, Frédéric Marin, Paula Ramos-Silva, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Section Computational Science, University of Amsterdam [Amsterdam] (UvA), Molécules de Communication et Adaptation des Micro-Organismes ( MCAM ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), and University of Amsterdam [Amsterdam] ( UvA )
Subjects: Proteomics, Biomineralization, Sample preparation, Nanotechnology, Computational biology, Biology, Biochemistry, Calcium Carbonate, 03 medical and health sciences, Calcification, Physiologic, Bleaching treatment, Animal Shells, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Calcifying extracellular matrix, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, Molecular Biology, Close contact, 030304 developmental biology, 0303 health sciences, 030302 biochemistry & molecular biology, Proteins, Animal proteomics, [ SDV.IB.BIO ] Life Sciences [q-bio]/Bioengineering/Biomaterials, Anthozoa, Extracellular Matrix, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Mollusca, Protein identification
Abstract: 8 pages; International audience; In a recent editorial (Proc. Natl. Acad. Sci., 2013 110, E2144-E2146) and elsewhere, questions have been raised regarding the experimental practices in relation to the proteomic analysis of organic matrices associated to the biomineralized CaCO3 skeletons of metazoans such as molluscan shells and coral skeletons. Indeed, although the use of new high sensitivity MS technology potentially allows to identify a greater number of proteins, it is also equally (or even more) sensitive to contamination of residual proteins from soft tissues, which are in close contact with the biomineral. Based on our own past and present experimental know-how-observations that are reproducible and coherent with the current understanding of extracellular biomineralization processes-we are convinced that a careful and appropriate cleaning of biominerals prior to any analysis is crucial for accurate proteomic investigations and subsequent pertinent interpretation of the results. Our goal is to alert the scientific community about the associated bias that definitely should be avoided, and to provide critical recommendations on sample preparation and experimental design, in order to better take advantage of the aptness of proteomic approaches aiming at improving our understanding of the molecular mechanisms in biomineralization.
Published: 2013
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16. Proteomic and profile analysis of the proteins laced with aragonite and vaterite in the freshwater mussel Hyriopsis cumingii shell biominerals

Author: Laurent Bédouet, Yufei Ma, Jean-Pierre Andrieu, Qingling Feng, Arul Marie, Sophie Berland, Biologie des organismes marins et écosystèmes (BOME), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, Freshwater bivalve, Molecular Sequence Data, MESH: Bivalvia, Mineralogy, MESH: Amino Acid Sequence, engineering.material, Biology, Biochemistry, Calcium Carbonate, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Structural Biology, Chitin binding, Animal Shells, Vaterite, Animals, MESH: Animals, MESH: Proteins, 14. Life underwater, Amino Acid Sequence, 030304 developmental biology, 0303 health sciences, MESH: Molecular Sequence Data, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Aragonite, MESH: Proteomics, Proteins, General Medicine, Mussel, MESH: Animal Shells, Bivalvia, Calcium carbonate, chemistry, MESH: Calcium Carbonate, 030220 oncology & carcinogenesis, engineering, Pearl, Biomineralization
Abstract: International audience; Hyriopsis cumingii (Lea, Unionidae), a freshwater bivalve species widely distributed in China and commercially exploited for freshwater pearl production, was chosen as the reference model to investigate the protein signature in the organic scaffold matching calcium carbonate crystallization mode. This study takes advantage of different calcium carbonate habits production by the organism: aragonite in shell and pearl and vaterite in alternative pearl formation. Amino acid global composition and proteomics analysis have been undertaken to study the amino acid imbalance with respect to biominerals and microstructures. Forty peptides sequences were obtained by proteomics, of which ten are shared by all the different samples, nine are laced with aragonite; another nine with vaterite and twelve are related to pearls. Bioinformatics analysis allowed the peptides to be matched to the deduced protein sequences from EST databases and allowed functional assignment (e.g. scaffolding, strain strength, chitin binding or carbonic anhydrase function) to the proteins found in the different materials. Such panel of motifs tailored in vaterite and aragonite habits produced in a freshwater mollusk gives food for thought about organic control of the biomineralization processes.
Published: 2013

17. Kinetic features of L,D-transpeptidase inactivation critical for β-lactam antibacterial activity

Author: Louis B. Rice, Jean-Luc Mainardi, Arul Marie, Sébastien Triboulet, Mélanie Etheve-Quelquejeu, Vincent Dubée, Jean-Pierre Simorre, Michel Arthur, Laurent Gutmann, Lionel Dubost, Catherine M. Bougault, Jean-Emmanuel Hugonnet, Lauriane Lecoq, Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de biologie structurale ( IBS - UMR 5075 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: Bacterial Diseases, Imipenem, MESH: Peptidyl Transferases, Acylation, Enterococcus faecium, lcsh:Medicine, Pathogenesis, Substrate Specificity, MESH: Recombinant Proteins, chemistry.chemical_compound, MESH: Structure-Activity Relationship, Tetrahedral carbonyl addition compound, MESH : Structure-Activity Relationship, MESH : Ampicillin, polycyclic compounds, MESH : Bacterial Proteins, MESH: Enterococcus faecium, Bacterial Physiology, MESH : Enterococcus faecium, lcsh:Science, MESH: Bacterial Proteins, MESH: Imipenem, 0303 health sciences, Multidisciplinary, MESH : Substrate Specificity, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], MESH: Kinetics, Multi-Drug-Resistant Tuberculosis, Ceftriaxone, Streptococci, Recombinant Proteins, Bacterial Pathogens, Bacterial Biochemistry, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Infectious Diseases, Biochemistry, Lactam, Medicine, MESH : Kinetics, Antibacterial activity, Ertapenem, MESH : Imipenem, Research Article, medicine.drug, Drugs and Devices, MESH : Recombinant Proteins, Stereochemistry, Microbiology, beta-Lactam Resistance, Structure-Activity Relationship, 03 medical and health sciences, MESH : beta-Lactam Resistance, Bacterial Proteins, MESH : Peptidyl Transferases, medicine, Tuberculosis, Pharmacokinetics, Biology, Microbial Pathogens, MESH : Acylation, 030304 developmental biology, Gram Positive, MESH: Acylation, 030306 microbiology, lcsh:R, Bacteriology, biochemical phenomena, metabolism, and nutrition, MESH: beta-Lactam Resistance, MESH: Ceftriaxone, Kinetics, chemistry, Peptidyl Transferases, Ampicillin, lcsh:Q, MESH: Substrate Specificity, Peptidoglycan, MESH: Ampicillin, Penam, MESH : Ceftriaxone, [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract: International audience; Active-site serine D,D-transpeptidases belonging to the penicillin-binding protein family (PBPs) have been considered for a long time as essential for peptidoglycan cross-linking in all bacteria. However, bypass of the PBPs by an L,D-transpeptidase (Ldt(fm)) conveys high-level resistance to β-lactams of the penam class in Enterococcus faecium with a minimal inhibitory concentration (MIC) of ampicillin >2,000 µg/ml. Unexpectedly, Ldt(fm) does not confer resistance to β-lactams of the carbapenem class (imipenem MIC = 0.5 µg/ml) whereas cephems display residual activity (ceftriaxone MIC = 128 µg/ml). Mass spectrometry, fluorescence kinetics, and NMR chemical shift perturbation experiments were performed to explore the basis for this specificity and identify β-lactam features that are critical for efficient L,D-transpeptidase inactivation. We show that imipenem, ceftriaxone, and ampicillin acylate Ldt(fm) by formation of a thioester bond between the active-site cysteine and the β-lactam-ring carbonyl. However, slow acylation and slow acylenzyme hydrolysis resulted in partial Ldt(fm) inactivation by ampicillin and ceftriaxone. For ampicillin, Ldt(fm) acylation was followed by rupture of the C(5)-C(6) bond of the β-lactam ring and formation of a secondary acylenzyme prone to hydrolysis. The saturable step of the catalytic cycle was the reversible formation of a tetrahedral intermediate (oxyanion) without significant accumulation of a non-covalent complex. In agreement, a derivative of Ldt(fm) blocked in acylation bound ertapenem (a carbapenem), ceftriaxone, and ampicillin with similar low affinities. Thus, oxyanion and acylenzyme stabilization are both critical for rapid L,D-transpeptidase inactivation and antibacterial activity. These results pave the way for optimization of the β-lactam scaffold for L,D-transpeptidase-inactivation.
Published: 2013
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18. Proteomic strategy for identifying mollusc shell proteins using mild chemical degradation and trypsin digestion of insoluble organic shell matrix: a pilot study on Haliotis tuberculata

Author: Stéphanie Auzoux-Bordenave, Sophie Berland, Frédéric Marin, Arul Marie, Benjamin Marie, Laurent Bédouet, Christian Milet, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Study financed through the 'ATM Biomineralization' programme (2009-2012) supported by the French Ministry of Education and Research and the Muséum National d'Histoire Naturelle., Biologie des Organismes et Ecosystèmes Aquatiques ( BOREA ), Université des Antilles ( UA ) -Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut de Recherche pour le Développement ( IRD ) -Muséum National d'Histoire Naturelle ( MNHN ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Molécules de Communication et Adaptation des Micro-Organismes ( MCAM ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [UMR 6282] [Dijon] (BGS), and Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, Proteome, Lysine, Pilot Projects, Peptide, Applied Microbiology and Biotechnology, 03 medical and health sciences, chemistry.chemical_compound, Protein sequencing, Animal Shells, Mollusc shell, medicine, Trifluoroacetic acid, Animals, Trypsin, Abalone, Mollusc shell proteomics, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Haliotis asinina, biology, 030302 biochemistry & molecular biology, [ SDV.IB.BIO ] Life Sciences [q-bio]/Bioengineering/Biomaterials, biology.organism_classification, Extracellular Matrix, Enzyme, Solubility, chemistry, Biochemistry, Mollusca, Ladder sequencing, medicine.drug
Abstract: 13 pages; International audience; A successful strategy for the identification of shell proteins is based on proteomic analyses where soluble and insoluble fractions isolated from organic shell matrix are digested with trypsin with the aim of generating peptides, which are used to identify novel shell proteins contained in databases. However, using trypsin as a sole degradative agent is limited by the enzyme's cleavage specificity and is dependent upon the occurrence of lysine and arginine in the shell protein sequence. To bypass this limitation, we investigated the ability of trifluoroacetic acid (TFA), a low-specificity chemical degradative agent, to generate clusters of analyzable peptides from organic shell matrix, suitable for database annotation. Acetic acid-insoluble fractions from Haliotis tuberculata shell were processed by trypsin followed by TFA digestion. The hydrolysates were used to annotate an expressed sequence tag library constructed from the mantle tissue of Haliotis asinina, a tropical abalone species. The characterization of sequences with repeat motifs featured in some of the shell matrix proteins benefited from TFA-induced serial cutting, which can result in peptide ladder series. Using the degradative specificities of TFA and trypsin, we were able to identify five novel shell proteins. This pilot study indicates that a mild chemical digestion of organic shell matrix combined with trypsin generates peptides suitable for proteomic analysis for better characterization of mollusc shell matrix proteins.
Published: 2012
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19. The differential spatial distribution of secondary metabolites in Arabidopsis leaves reacting hypersensitively to Pseudomonas syringae pv. tomato is dependent on the oxidative burst

Author: Sejir Chaouch, Graham Noctor, Clara Simon, Serge Kauffmann, Bernard Bodo, Laure Didierlaurent, Kamal Massoud, Marie Garmier, Mathilde Langlois-Meurinne, Arul Marie, Floriant Bellvert, Patrick Saindrenan, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire de Chimie et Biochimie des Substances Naturelles, Centre National de la Recherche Scientifique (CNRS), Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire de chimie et biochimie des substances naturelles, Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre National de la Recherche Scientifique ( CNRS ), Institut de biologie moléculaire des plantes ( IBMP ), and Université de Strasbourg ( UNISTRA ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: 0106 biological sciences, Hypersensitive response, Indoles, Physiology, Metabolite, Arabidopsis, Pseudomonas syringae, Plant Science, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Glucosides, Coumarins, Gene Expression Regulation, Plant, Metabolome, Camalexin, Arabidopsis thaliana, ComputingMilieux_MISCELLANEOUS, Plant Diseases, Respiratory Burst, 030304 developmental biology, 0303 health sciences, biology, [ SDV.BC ] Life Sciences [q-bio]/Cellular Biology, biology.organism_classification, Plant Leaves, Thiazoles, Biochemistry, chemistry, Scopolin, Reactive Oxygen Species, Salicylic Acid, Signal Transduction, 010606 plant biology & botany
Abstract: Secondary metabolites (SMs) play key roles in pathogen responses, although knowledge of their precise functions is limited by insufficient characterization of their spatial response. The present study addressed this issue in Arabidopsis leaves by non-targeted and targeted metabolite profiling of Pseudomonas syringae pv. tomato (Pst-AvrRpm1) infected and adjacent uninfected leaf tissues. While overlap was observed between infected and uninfected areas, the non-targeted metabolite profiles of these regions differed quantitatively and clustering analysis underscores a differential distribution of SMs within distinct metabolic pathways. Targeted metabolite profiling revealed that infected tissues accumulate more salicylic acid and the characteristic phytoalexin of Arabidopsis, camalexin, than uninfected adjacent areas. On the contrary, the antioxidant coumarin derivative, scopoletin, was induced in infected tissues while its glucoside scopolin predominated in adjacent tissues. To elucidate the still unclear relationship between the accumulation of SMs and reactive oxygen species (ROS) accumulation and signalling, a catalase-deficient line (cat2) in which ROS signalling is up-regulated, was used. Metabolic analysis of cat2 suggests that some SMs have important interactions with ROS in redox homeostasis during the hypersensitive response to Pst-AvrRpm1. Overall, the study demonstrates that ROS availability influences both the amount and the pattern of infection-induced SM accumulation.
Published: 2010
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20. Proteomic analysis of the organic matrix of the abalone Haliotis asinina calcified shell

Author: Christian Milet, Lionel Dubost, Daniel J. Jackson, Bernard M. Degnan, Frédéric Marin, Benjamin Marie, Arul Marie, Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Molécules de Communication et Adaptation des Micro-Organismes ( MCAM ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Courant Research Centre Geobiology, Georg-August-University [Göttingen], School of Biological Sciences, University of Queensland [Brisbane], Biologie des Organismes et Ecosystèmes Aquatiques ( BOREA ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Muséum National d'Histoire Naturelle ( MNHN ) -Institut de Recherche pour le Développement ( IRD ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université des Antilles ( UA ), Work supported by grants AFSSET APR EST 2007 10, by an Australian Research Council grant, and by DFG funding., ANR ACCRO-EARTH BLAN06-2_159971, ANR 07 SEST CY ANOTOX 005,ANR ACCRO-EARTH BLAN06-2_159971, ANR 07 SEST CY ANOTOX 005, Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Georg-August-University = Georg-August-Universität Göttingen, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), ANR-06-BLAN-0347,ACCRO-Earth,Accidents in Climate Carbon cycle Regulation of the Earth(2006), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Biology, Proteomics, Bioinformatics, Biochemistry, 03 medical and health sciences, Extracellular, lcsh:QH573-671, Mantle (mollusc), [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, Molecular Biology, 030304 developmental biology, Alanine, chemistry.chemical_classification, 0303 health sciences, Viral matrix protein, Haliotis asinina, lcsh:Cytology, Research, 030302 biochemistry & molecular biology, biology.organism_classification, [ SDV.IB.BIO ] Life Sciences [q-bio]/Bioengineering/Biomaterials, chemistry, biology.protein, Whey Acidic Protein, Glycoprotein
Abstract: Background The formation of the molluscan shell is regulated to a large extent by a matrix of extracellular macromolecules that are secreted by the shell forming tissue, the mantle. This so called "calcifying matrix" is a complex mixture of proteins and glycoproteins that is assembled and occluded within the mineral phase during the calcification process. While the importance of the calcifying matrix to shell formation has long been appreciated, most of its protein components remain uncharacterised. Results Recent expressed sequence tag (EST) investigations of the mantle tissue from the tropical abalone (Haliotis asinina) provide an opportunity to further characterise the proteins in the shell by a proteomic approach. In this study, we have identified a total of 14 proteins from distinct calcified layers of the shell. Only two of these proteins have been previously characterised from abalone shells. Among the novel proteins are several glutamine- and methionine-rich motifs and hydrophobic glycine-, alanine- and acidic aspartate-rich domains. In addition, two of the new proteins contained Kunitz-like and WAP (whey acidic protein) protease inhibitor domains. Conclusion This is one of the first comprehensive proteomic study of a molluscan shell, and should provide a platform for further characterization of matrix protein functions and interactions.
Published: 2010
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21. Evolution of nacre: biochemistry and proteomics of the shell organic matrix of the cephalopod Nautilus macromphalus

Author: Frédéric Marin, Benjamin Marie, Laurent Bédouet, Lionel Dubost, Gilles Luquet, Gérard Alcaraz, Christian Milet, Arul Marie, Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Chimie et Biochimie des Substances Naturelles, Centre National de la Recherche Scientifique ( CNRS ), Biologie des organismes marins et écosystèmes ( BOME ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Phytopharmacie et Biochimie des Iteractions Cellulaires ( PBIC ), Etablissement National d'Enseignement Supérieur Agronomique de Dijon ( ENESAD ) -Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ), Financed by a PhD Fellowship from the Ministère Délégué à la Recherche et aux Nouvelles Technologies, (No. 15 351) accompanying the ACI JC3049. The 'Conseil Régional de Bourgogne' (Dijon, France) provided additional support for the acquisition of new equipment in the Biogeosciences research unit (UMR CNRS 5561)., ANR : ACCRO-Earth, BLAN06–2_159971,ACCRO-Earth, BLAN06–2_159971, Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre National de la Recherche Scientifique (CNRS), Biologie des organismes marins et écosystèmes (BOME), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Phytopharmacie et Biochimie des Iteractions Cellulaires (PBIC), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), ANR: ACCRO-Earth, BLAN06–2_159971,ACCRO-Earth, BLAN06–2_159971, Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie et biochimie des substances naturelles, Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), ANR-06-BLAN-0347,ACCRO-Earth,Accidents in Climate Carbon cycle Regulation of the Earth(2006), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)
Subjects: Proteome, Shell (structure), Proteomics, Biochemistry, Calcium Carbonate, 03 medical and health sciences, Paleontology, chemistry.chemical_compound, proteomics, evolution, Animals, 14. Life underwater, Amino Acid Sequence, Nautilus, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, Molecular Biology, Chromatography, High Pressure Liquid, 030304 developmental biology, Calcite, Nautilus macromphalus, 0303 health sciences, biology, 030302 biochemistry & molecular biology, Organic Chemistry, Proteins, biology.organism_classification, biomineralization, [ SDV.IB.BIO ] Life Sciences [q-bio]/Bioengineering/Biomaterials, Biological Evolution, Cephalopod, Calcium carbonate, chemistry, Chemical engineering, Solubility, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Molecular Medicine, Sequence Alignment, Biomineralization, mollusk shell nacre
Abstract: 12 pages; International audience; In mollusks, one of the most widely studied shell textures is nacre, the lustrous aragonitic layer that constitutes the internal components of the shells of several bivalves, a few gastropods, and one cephalopod: the nautilus. Nacre contains a minor organic fraction, which displays a wide range of functions in relation to the biomineralization process. Here, we have biochemically characterized the nacre matrix of the cephalopod Nautilus macromphalus. The acid-soluble matrix contains a mixture of polydisperse and discrete proteins and glycoproteins, which interact with the formation of calcite crystals. In addition, a few bind calcium ions. Furthermore, we have used a proteomic approach, which was applied to the acetic acid-soluble and -insoluble shell matrices, as well as to spots obtained after 2D gel electrophoresis. Our data demonstrate that the insoluble and soluble matrices, although different in their bulk monosaccharide and amino acid compositions, contain numerous shared peptides. Strikingly, most of the obtained partial sequences are entirely new. A few only partly match with bivalvian nacre proteins. Our findings have implications for knowledge of the long-term evolution of molluskan nacre matrices.
Published: 2009
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22. Nacre evolution: a proteomic approach

Author: Michel Becchi, Bernard M. Degnan, Arul Marie, Benjamin Marie, Lionel Dubost, Frédéric Marin, Gilles Luquet, Daniel J. Jackson, Christian Milet, Isabelle Zanella-Cléon, Laurent Bédouet, Nathalie Le Roy, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie et biochimie des substances naturelles, Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Biologie des organismes marins et écosystèmes (BOME), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), School of Integrative Biology, University of Queensland [Brisbane], D. Kisailus, L. Estroff, H.S. Gupta, W.J. Landis & P.D. Zavattieri, Laffont, Rémi, D. Kisailus, L. Estroff, H.S. Gupta, W.J. Landis & P.D. Zavattieri, Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Chimie et Biochimie des Substances Naturelles, Centre National de la Recherche Scientifique ( CNRS ), Biologie des organismes marins et écosystèmes ( BOME ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de biologie et chimie des protéines [Lyon] ( IBCP ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), and Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0303 health sciences, Freshwater bivalve, Materials science, biology, Haliotis asinina, Unio pictorum, Macroevolution, biology.organism_classification, [ SDV.IB.BIO ] Life Sciences [q-bio]/Bioengineering/Biomaterials, 010603 evolutionary biology, 01 natural sciences, Cephalopod, [SDV.IB.BIO] Life Sciences [q-bio]/Bioengineering/Biomaterials, 03 medical and health sciences, Evolutionary biology, Biophysics, 14. Life underwater, Nautilus macromphalus, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: From an evolutionary viewpoint, the molluscan nacre constitutes a fascinating object. This microstructure appeared early, in the Lower Cambrian period, about 530 million years ago, and since then, has been kept unchanged until today. Nacre is restricted to the conchiferan mollusks, where it occurs in t least three main classes, bivalves, gastropods and cephalopods. The aim of the present study is to investigate whether all nacres are built from the same “macromolecular tools”, proteins of the nacre matrix. To this end, we studied three new nacre models, the freshwater bivalve Unio pictorum, the cephalopod Nautilus macromphalus, and the gastropod Haliotis asinina, to which we applied a combined biochemical and proteomic characterization of their respective nacre matrices. The results of our approach, that can be defined as “shellomics” (proteomics applied to shell proteins) shed a new light on the macroevolution of nacre matrix proteins and on the in vitro design of nacre-like biomaterials.
Published: 2009

23. The effect of molecules in mother-of-pearl on the decrease in bone resorption through the inhibition of osteoclast cathepsin K

Author: Laurent Bédouet, Marlène Gallet, Denis Duplat, Sophie Berland, Lionel Dubost, Michel Brazier, Christian Milet, Evelyne Lopez, Arul Marie, Marthe Rousseau, Saïd Kamel, Biologie des organismes marins et écosystèmes (BOME), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche sur les mécanismes de la résorption osseuse (UMRO), Université de Picardie Jules Verne (UPJV), Laboratoire de chimie et biochimie des substances naturelles, Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), and Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)
Subjects: Materials science, medicine.medical_treatment, Cathepsin K, Biophysics, Osteoclasts, Bioengineering, 02 engineering and technology, Bone resorption, Bone remodeling, Biomaterials, 03 medical and health sciences, chemistry.chemical_compound, Osteoclast, Materials Testing, medicine, Animals, Bone Resorption, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, Cells, Cultured, bone remodeling, 030304 developmental biology, Extracellular Matrix Proteins, 0303 health sciences, Protease, 021001 nanoscience & nanotechnology, Cathepsins, Ostreidae, Resorption, Papain, enzyme, medicine.anatomical_structure, Biochemistry, chemistry, nacre, Mechanics of Materials, bioactivity, osteoclast, Ceramics and Composites, Cortical bone, Rabbits, 0210 nano-technology
Abstract: International audience; This study evaluates the effect of the mother-of-pearl (nacre) organic matrix on mammalian osteoclast activity and on cathepsin K protease. Rabbit osteoclasts were cultured on bovine cortical bone slices in the presence of water-soluble molecules extracted from nacre of the pearl oyster Pinctada margaritifera. Osteoclast resorption activity was determined by quantification of the resorption surface area on bovine bone slices. Papain and cathepsin K, B and L inhibition tests were performed in the presence of the nacre water-soluble extracts. The active crude extract was fractionated by dialysis and reversed-phase high-performance liquid chromatography before electrospray mass spectrometry analysis of inhibitory fractions. The water-soluble molecules extracted from nacre decreased bone resorption without jeopardizing osteoclast survival. The hydrolytic activity of cysteine proteinases was reduced when the enzymes were incubated with the nacre water-soluble molecules. Trending towards characterization of the molecules involved, it appears that cathepsin K inhibitors remain in different nacre water-soluble organic matrix subfractions, composed of low molecular weight molecules. Mollusk shell nacre contains molecules capable of reducing osteoclast bone resorption activity by inhibiting cathepsin K, giving a new facet of the bioactivity of nacre as bone biomaterial.
Published: 2007
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24. Identification of low molecular weight molecules as new components of the nacre organic matrix

Author: Laurent Bédouet, Lionel Dubost, Jean Peduzzi, Karine Le Ny, Sophie Berland, Marthe Rousseau, Arul Marie, Filippo Rusconi, Evelyne Lopez, Denis Duplat, Biologie des organismes marins et écosystèmes (BOME), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), Acides nucléiques : dynamique, ciblage, et fonctions biologiques - Régulation et dynamique des génomes (ANDCFB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie et biochimie des substances naturelles, Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Spectrometry, Mass, Electrospray Ionization, Physiology, Electrospray ionization, Glycine, Peptide, 02 engineering and technology, Mother-of-pearl, Mass spectrometry, Biochemistry, Calcium Carbonate, Matrix (chemical analysis), Pinctada margaritifera, 03 medical and health sciences, Glycine-rich, Metabolites, Molecule, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Pinctada, Nacre, Molecular Biology, Chromatography, High Pressure Liquid, 030304 developmental biology, Alanine, chemistry.chemical_classification, 0303 health sciences, Chromatography, Repeats, 021001 nanoscience & nanotechnology, Small molecule, Crystallography, Membrane, chemistry, 0210 nano-technology, Peptides, Dialysis
Abstract: International audience; Nacre of Pinctada margaritifera displays a number of interesting biological activities on bone, mainly concentrated in a water-soluble organic matrix representing 0.24% of the nacre weight. Dialysis of that matrix through 8 kDa and 1 kDa cut-off membranes showed that 60% of it is made of small molecules of molecular masses below 1 kDa. Reversed-phase high-performance liquid chromatography of the small molecule fractions and subsequent electrospray ionization mass spectrometric analysis of 19 fractions thereof indicated the presence of at least 110 different molecules, in the range 100 Da-700 Da. Evidence for aggregate-forming properties of the small molecules was given. Amino acid analysis revealed that most of the small molecules were not peptides and tandem mass spectrometric gas-phase fragmentations clearly indicated a structural relationship between several molecules. Intriguingly, differences of a single Dalton between mono-charged ions peaks were observed. Further, approximately 40 analytes could be arranged in a ladder-like manner with mass spaces of 57 Da. Some of the water-soluble peptide sequences obtained after MS/MS fragmentation revealed that the 57 Da shift corresponds to the repetition of glycine residues. Furthermore, the exchange of glycine against alanine explains the 14 Da shift observed between some peptides. These data show for the first time that small molecules, especially peptides, are prevalent components of nacre. The molecular species described in this report might have a functional role in nacre.
Published: 2006
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25. Novel mechanism of resistance to glycopeptide antibiotics in Enterococcus faecium

Author: Arul Marie, J.-C. Quincampoix, Jean-Emmanuel Hugonnet, Louis B. Rice, Laurent Gutmann, Julie Cremniter, Nathalie Josseaume, Lionel Dubost, Jean-Luc Mainardi, Michel Arthur, Lecerf, Maxime, Laboratoire de Recherche Moléculaire sur les Antibiotiques, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR58-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Laboratoire de chimie et biochimie des substances naturelles, Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Medical and Research Services, Louis Stokes Cleveland Veterans Affairs Medical Center, This work was supported by the European Community (COBRA, contract LSHM-CT-2003-503335, 6th PCRD), the National Institute of Allergy and Infectious Diseases (Grant R01 AI45626), and the Fondation pour la Recherche Médicale., Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IFR58-Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Européen Georges Pompidou [APHP] ( HEGP ), Laboratoire de Chimie et Biochimie des Substances Naturelles, and Centre National de la Recherche Scientifique ( CNRS )
Subjects: Cytoplasm, MESH : Muramoylpentapeptide Carboxypeptidase, Enterococcus faecium, MESH : Models, Biological, Muramoylpentapeptide Carboxypeptidase, MESH : Drug Resistance, Bacterial, Biochemistry, Substrate Specificity, Muramoylpentapeptide carboxypeptidase, chemistry.chemical_compound, polycyclic compounds, Peptide bond, MESH: Enterococcus faecium, MESH : Anti-Bacterial Agents, MESH : Enterococcus faecium, MESH: Peptide Fragments, MESH : Peptidoglycan, Alanine, 0303 health sciences, MESH: Microbial Sensitivity Tests, MESH : Substrate Specificity, MESH: Peptidoglycan, Hydrolysis, Glycopeptides, MESH: Amino Acid Substitution, Glycopeptide, Anti-Bacterial Agents, Cross-Linking Reagents, MESH: Muramoylpentapeptide Carboxypeptidase, MESH: Hydrolysis, MESH : Cross-Linking Reagents, MESH : Cytoplasm, MESH : Glycopeptides, Stereochemistry, MESH: Alanine, MESH: Cross-Linking Reagents, Microbial Sensitivity Tests, Peptidoglycan, Biology, beta-Lactams, Models, Biological, Article, 03 medical and health sciences, MESH : Amino Acid Substitution, MESH : beta-Lactams, MESH : Hydrolysis, MESH: beta-Lactams, MESH: Anti-Bacterial Agents, Glycosyltransferase, Drug Resistance, Bacterial, MESH: Drug Resistance, Bacterial, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, 030304 developmental biology, MESH: Glycopeptides, 030306 microbiology, MESH: Cytoplasm, MESH : Peptide Fragments, MESH: Models, Biological, Cell Biology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Peptide Fragments, chemistry, Amino Acid Substitution, biology.protein, MESH: Substrate Specificity, MESH : Microbial Sensitivity Tests, MESH : Alanine, Bacteria
Abstract: International audience; Glycopeptides and beta-lactams are the major antibiotics available for the treatment of infections due to Gram-positive bacteria. Emergence of cross-resistance to these drugs by a single mechanism has been considered as unlikely because they inhibit peptidoglycan polymerization by different mechanisms. The glycopeptides bind to the peptidyl-D-Ala(4)-D-Ala(5) extremity of peptidoglycan precursors and block by steric hindrance the essential glycosyltransferase and D,D-transpeptidase activities of the penicillin-binding proteins (PBPs). The beta-lactams are structural analogues of D-Ala(4)-D-Ala(5) and act as suicide substrates of the D,D-transpeptidase module of the PBPs. Here we have shown that bypass of the PBPs by the recently described beta-lactam-insensitive L,D-transpeptidase from Enterococcus faecium (Ldt(fm)) can lead to high level resistance to glycopeptides and beta-lactams. Cross-resistance was selected by glycopeptides alone or serially by beta-lactams and glycopeptides. In the corresponding mutants, UDP-MurNAc-pentapeptide was extensively converted to UDP-MurNAc-tetrapeptide following hydrolysis of D-Ala(5), thereby providing the substrate of Ldt(fm). Complete elimination of D-Ala(5), a residue essential for glycopeptide binding, was possible because Ldt(fm) uses the energy of the L-Lys(3)-D-Ala(4) peptide bond for cross-link formation in contrast to PBPs, which use the energy of the D-Ala(4)-D-Ala(5) bond. This novel mechanism of glycopeptide resistance was unrelated to the previously identified replacement of D-Ala(5) by D-Ser or D-lactate.
Published: 2006
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26. Insights from shell proteome : biomineralization control and environmental adaptation in bivalves

Author: Arivalagan immanuel, Jaison Rathina Raj, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Museum national d'histoire naturelle - MNHN PARIS, Arul Marie, and Sophie Berland
Subjects: Proteomics, Biomineralization, Biominéralisation, Protéomique, Mollusk, Ecologie fonctionnelle, Mollusques, [SDV.BA]Life Sciences [q-bio]/Animal biology, Plasticité phénotypique, Phenotypic plasticity, Adaptation, Functional ecology
Abstract: In this study, the SMPs from four commercially important and divergent bivalve species crassostrea gigas (pacific oyster), Mya truncata (soft shell clam), Mytilus edulis (blue mussel) and Pecten maximus (king scallop) were extracted and analysed using standardized extraction protocol and proteomic pipeline. This enables us to identify critical elements of basic biomineralization tool kit for calcification process irrespective of their shell morphology, mineralogy and microstructure. In addition, it enables the identification of SMPs that are specific to calcite and aragonite mineralogies. The signifiant numbers of SMPs found species-specific were hypothesized as adaptation to their modus vivendi. In fact, the latter proteins possess immunity-related functions and fit into specific pathway, phenoloxidase, suggesting their role in defense against pathogen. The comparative study of shell proteome of mussels living in full marine condition, North Sea and the Iow saline Baltic Sea showed the modulation of the SMPs that constitute the basic biomineralization tool kit. Higher modulation of chitin related proteins and non-modulated protein such as carbonic anhydrase, EGF and fibronectin domain containing proteins points out the impaired scaffold and mineral nucleation process in Baltic mussel. The modulation of immunity related proteins denote the influence of biotic components. These investigations show the functional diversity of SMPs and their roles beyond shell formation in the bivalvesand put forth the idea that shell is dynamic, endowed with both biochemical and mechanical protection.; Le processus de biominéralisation confère aux organismes qui le développent une valeur adaptative. La coquille carbonatée des mollusques intègre les fonctions de protection biomécanique à différentes échelles. La coquille résulte de l'association de composés inorganiques et d'une matrice organique protéique, médiatrice du contrôle biologique de la minéralisation. L'analyse du protéome de la coquille chez 4 espèces de bivalves met en évidence deux patrons fonctionnels et leur degré de conservation phylogénétique : l'un lié au contrôle de la minéralisation stricto sensu ; l'autre à la protection immune. L'étude de populations vivant à l'état naturel en mer Baltique, dont les eaux présentent localement de fortes variations ioniques montre que le protéome intègre également l'impact de conditions environnementales limitantes. L'anthropocène impose un rythme adaptatif pressant aux organismes et la modification acido-basique des eaux océaniques est susceptible d'impacter sensiblement les organismes calcifiants. La signature de mécanismes adaptatifs du contrôle biologique de la biominéralisation se traduit dans le protéome de la coquille. Les implications sont particulièrement signifiantes dans un contexte d'intérêt de développement aquacole grandissant.
Published: 2017

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26 results on '"Arul Marie"'

1. Molecular acclimation of Halobacterium salinarum to halite brine inclusions

2. Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking

3. Animal fibre use in the Keriya valley (Xinjiang, China) during the Bronze and Iron Ages: A proteomic approach

4. Global Metabolomic Characterizations of Microcystis spp. Highlights Clonal Diversity in Natural Bloom-Forming Populations and Expands Metabolite Structural Diversity

5. Binding Specificity of Native Odorant-Binding Protein Isoforms Is Driven by Phosphorylation and O-N-Acetylglucosaminylation in the Pig Sus scrofa

6. Identification of degraded bone and tooth splinters from arid environments using palaeoproteomics

7. To be pastoralist or not to be? Tracing the introduction of domestic caprines in Southern Africa using Palaeoproteomics

8. Physiological effects caused by microcystin-producing and non-microcystin producing Microcystis aeruginosa on medaka fish: A proteomic and metabolomic study on liver

9. Deep conservation of bivalve nacre proteins highlighted by shell matrix proteomics of the Unionoida Elliptio complanata and Villosa lienosa

10. Gender-Specific Toxicological Effects of Chronic Exposure to Pure Microcystin-LR or Complex Microcystis aeruginosa Extracts on Adult Medaka Fish

11. Historical linseed oil/colophony varnishes formulations: Study of their molecular composition with micro-chemical chromatographic techniques

12. Shell proteome of rhynchonelliform brachiopods

13. Characterization of the teeth skeletal matrix from Arbacia lixula

14. Unveiling the evolution of bivalve nacre proteins by shell proteomics of Unionoidae

15. Proteomics of CaCO3 biomineral-associated proteins: how to properly address their analysis

16. Proteomic and profile analysis of the proteins laced with aragonite and vaterite in the freshwater mussel Hyriopsis cumingii shell biominerals

17. Kinetic features of L,D-transpeptidase inactivation critical for β-lactam antibacterial activity

18. Proteomic strategy for identifying mollusc shell proteins using mild chemical degradation and trypsin digestion of insoluble organic shell matrix: a pilot study on Haliotis tuberculata

19. The differential spatial distribution of secondary metabolites in Arabidopsis leaves reacting hypersensitively to Pseudomonas syringae pv. tomato is dependent on the oxidative burst

20. Proteomic analysis of the organic matrix of the abalone Haliotis asinina calcified shell

21. Evolution of nacre: biochemistry and proteomics of the shell organic matrix of the cephalopod Nautilus macromphalus

22. Nacre evolution: a proteomic approach

23. The effect of molecules in mother-of-pearl on the decrease in bone resorption through the inhibition of osteoclast cathepsin K

24. Identification of low molecular weight molecules as new components of the nacre organic matrix

25. Novel mechanism of resistance to glycopeptide antibiotics in Enterococcus faecium

26. Insights from shell proteome : biomineralization control and environmental adaptation in bivalves

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26 results on '"Arul Marie"'

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