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Bagnols sur Ceze, France

Christie-Oleza J.A.,CEA Marcoule Nuclear Site
Molecular & cellular proteomics : MCP | Year: 2012

Roseobacters are generalist bacteria abundantly found in the oceans. Because little is known on how marine microorganisms interact in association or competition, we focused our attention on the microbial exoproteome, a key component in their interaction with extracellular milieu. Here we present a comparative analysis of the theoretically encoded exoproteome of twelve members of the Roseobacter group validated by extensive comparative proteogenomics. In silico analysis revealed that 30% of the encoded proteome of these microorganisms could be exported. The ratio of the different protein categories varied in accordance to the ecological distinctness of each strain, a trait reinforced by quantitative proteomics data. Despite the interspecies variations found, the most abundantly detected proteins by shotgun proteomics were from transporter, adhesion, motility, and toxin-like protein categories, defining four different plausible adaptive strategies within the Roseobacter group. In some strains the toxin-secretion strategy was over-represented with repeats-in-toxin-like proteins. Our results show that exoproteomes strongly depend on bacterial trophic strategy and can slightly change because of culture conditions. Simulated natural conditions and the effect of the indigenous microbial community on the exoproteome of Ruegeria pomeroyi DSS-3 were also assayed. Interestingly, we observed a significant depletion of the toxin-like proteins usually secreted by R. pomeroyi DSS-3 when grown in presence of a natural community sampled from a Mediterranean Sea port. The significance of this specific fraction of the exoproteome is discussed. Source


Armengaud J.,CEA Marcoule Nuclear Site
Expert Review of Proteomics | Year: 2010

This review describes how intimately proteogenomics and system biology are imbricated. Quantitative cell-wide monitoring of cellular processes and the analysis of this information is the basis for systems biology. Establishing the most comprehensive protein-parts list is an essential prerequisite prior to analysis of the cell-wide dynamics of proteins, their post-translational modifications, their complex network interactions and interpretation of these data as a whole. High-quality genome annotation is, thus, a crucial basis. Proteogenomics consists of high-throughput identification and characterization of proteins by extra-large shotgun MS/MS approaches and the integration of these data with genomic data. Discovery of the remaining unannotated genes, defining translational start sites, listing signal peptide processing events and post-translational modifications, are tasks that can currently be carried out at a full-genomic scale as soon as the genomic sequence is available. Proteomics is increasingly being used at the primary stage of genome annotation and such an approach may become standard in the near future for genome projects. Advantageously, the same experimental proteomic datasets may be used to characterize the specific metabolic traits of the organism under study. Undoubtedly, comparative genomics will experience a renaissance taking into account this new dimension. Synthetic biology aimed at re-engineering living systems will also benefit from these significant progresses. © 2010 Expert Reviews Ltd. Source


Guilbaud P.,CEA Marcoule Nuclear Site | Zemb T.,Marcoule Institute for Separative Chemistry
ChemPhysChem | Year: 2012

Reverse micelles? The transition from weak aggregation to water-poor reverse micelles triggered by the presence of extracted ion pairs is modeled using molecular dynamics simulations (see picture). The presence of the ion induces a polar/apolar segregation and the formation of a curved film microstructure consistent with the classical inverse micelle. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source


Armengaud J.,CEA Marcoule Nuclear Site
Current Opinion in Biotechnology | Year: 2016

Environmental biotechnology relies on the exploration of novel biological systems and a thorough understanding of the underlying molecular mechanisms. Next-generation proteomics based on the latest generation of mass analyzers currently allows the recording of complete proteomes from any microorganism. Interpreting these data can be straightforward if the genome of the organism is established, or relatively easy to perform through proteogenomics approaches if a draft sequence can be obtained. However, next-generation proteomics faces new, interesting challenges when the organism is distantly related to previously characterized organisms or when mixtures of organisms have to be analyzed. New mass spectrometers and innovative bioinformatics tools are reshaping the possibilities of homology-based proteomics, proteogenomics, and metaproteomics for the characterization of biological systems. Novel time- and cost-effective screening strategies are also possible with this methodology, as exemplified by whole proteome thermal profiling and subpopulation proteomics. The complexity of environmental samples allows for unique developments of approaches and concepts. © 2016 Elsevier Ltd. Source


Duvail M.,CEA Marcoule Nuclear Site | Guilbaud P.,CEA Marcoule Nuclear Site
Physical Chemistry Chemical Physics | Year: 2011

Coordination of nitrate anions with lanthanoid cations (Ln3+) in water, methanol and octanol-1 has been studied by means of molecular dynamics simulations with explicit polarization. Potential of mean force (PMF) profiles have been calculated for a mono-complex of lanthanoid nitrate (Ln(NO 3)2+) in these solvents using umbrella-sampling molecular dynamics. In pure water, no difference in the nitrato coordination to lanthanoids (Nd3+, Eu3+ and Dy3+) is observed, i.e. the nitrate anion prefers the monodentate coordination, which promotes the salt dissociation. Then, the influence of the nature of the solvating molecules on the nitrato coordination to Eu3+ has been investigated. PMF profiles point out that both monodenate and bidentate coordinations are stable in neat methanol, while in neat octanol, only the bidentate one is. MD simulations of Eu(NO3)3 in water-octanol mixtures with different concentrations of water have been then performed and confirm the importance of the water molecules' presence on the nitrate ion's coordination mode. © the Owner Societies. 2011. Source

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