Based on a strong collaboration developed through existing projects such as OUEST-Genopole®, GIS Institut de la Génomique marine, network of excellence « Marine Genomics Europe », the teams from Europole Mer have already played a leading role to organise, in France and in Europe, experimental marine biology research with an integrative approach as required by genomics.
See projects calls and their results
This strategy has placed France in a leadership positions in Europe and the GIS Europole Mer must pursue and reinforce this dynamic.
The implementation strategy of Research Area 1 over 2008-12 is based on the following actions
- To maintain an active animation between partners of the network of excellence "Marine Genomics Europe";
- To support this network of laboratories and their unique infrastructures, and to increase their capacity thanks to the Integrated Infrastructure Initiative (I3) Program of the 7th Framework Program of the European Union.;
- To develop an international PhD program in systemic marine biology around the University Pierre and Marie Curie and a few European Universities;
- To initiate an international program in experimental marine biology in order to promote research on marine models for fundamental biology and on improvement of cultivated species;
- To tighten links with the European Molecular Biology Laboratory (EMBL) through exchanges of expertise on services and activities common to both partners; and through collaborative projects between scientists from EMBL and GIS Europole Mer, in particular with co-supervised PhD thesis ;
- To host one or several chairs of excellence working on topcis related to Research Area 1.
LIPIDOMITO: Structural and functional chemistry of mitochondrial membrane lipids of marine bivavlves
In this third year, new trials and methodological set up were conducted to validate the quality of mitochondrial preparations and to characterize mitochondrial oxidative activities and functional properties in bivalves. Meantwhile, two experiments were performed in 2010, exposing oysters Crassostrea gigas to various physiological and stress situations including hypoxia/anoxia and dietary changes.
Larval metamorphosis in the invasive species Crepidula fornicata: from chemical ecology to genomics approach
Scientific coordinator: Frédérique Viard (ADMM Adaptation et Diversité en Milieur Marin UMR 7144, SBR)
Bacterial biofilms on biotic and abiotic surfaces in marine environment: search for adhesion and co-regulation factors using proteomic and analytical chemistry approaches.
The antibiofilm molecules secreted by Pseudoalteromonas 3J6 and D41 strains were partially purified. Four outer membranes proteins of Pseudoalteromonas D41 were identified as induced in biofilms. Consistently, qRT-PCR confirmed that their genes were differentially expressed in biofilms. Mutants of Pseudomonas aeruginosa lacking any of the homologous proteins showed altered biofilm formation. The response of the sponge Suberites domuncula to the bacterial communication molecule 3oxoC12-HSL was studied by proteomic and at the gene expression level (cDNA librairies and qRT-PCR). Several proteins involved in phagocytosis were overproduced in response to 3oxoC12-HSL
Polysaccharides are the most abundant and the most diverse renewable materials found on earth and in the oceans. Except polysaccharides used traditionally in food and non-food industry, the structure and the functionality of most of them are unknown and unexplored. Structural analyses of complex polysaccharides benefit strongly from the use of polysaccharides depolymerising enzymes: glycoside hydrolases (GH) and polysaccharides lyases (PL). The enzymes have the advantage to produce discrete series of oligosaccharides the characterisation of which is determinant to resolve the parent polysaccharides structures. In this project we propose to cross-over the chemical diversity of the polysaccharides with the marine biological diversity, as a source of enzymes, in order to highlight new GH and PL. We plan to implement a medium throughput screening tool. We will screen protein extracts from marine bacteria as well as targeted recombinant proteins against an original polysaccharides collections that we will set up.
The brown algae are a proven source of novel biomolecules and exhibit several additional features that make them prime targets for both applied and fundamental research. We recently proposed the filamentous brown alga Ectocarpus siliculosus as a model for this group of organisms and the complete genome sequence of this species has recently been completed at Genoscope. The aim of this project is to generate a user-friendly genome resource, based on this genome sequence that will allow this data to be efficiently exploited by the project partners and by the international community as a whole. To create this resource, we propose to 1) improve the large-scale assembly of the genome by assigning supercontigs to linkage groups using a genetic map, 2) improve the identification of transcribed regions using a whole genome tiling array approach, and 3) to create an internet-accessible genome database in Roscoff that will include high-quality, manually annotated gene models. The genome database will be designed so that it can evolve to include additional data in the future, such as expression analyses and mutant data.
Transcriptomic and functional analyses of the impact of reproduction on energetic and oxidative balances in the Pacific oyster Crassostrea gigas
The study of interactions between reproduction, energetic metabolism and oxidative stress of the Pacific oyster was performed over a whole reproductive cycle (task 1). This revealed a group of genes involved in energetic metabolism and oxidative stress showing whose relative expression increases during gametogenesis. Interestingly, relative expression of another cluster of genes as well as flow cytometry analyses showed differences between sexes. Histological analyses confirmed heritable differences between lines selected for high or low reproductive allocation, but the observed differences were much lower in 2009 than in 2008 (task 2), limiting the interest of further analyses. Finally, functional activity of the oyster AMPK? was first demonstrated and quantified by immunodetection (task 3). Analyses of this activity during a complete reproductive cycle are in progress.
During this first year the main objectives were to acquire new genomic data and tools, to improve an in vitro test with hemocytes and vibrios, to analyze the genomes of vibrios and to perfect a method of mutagenesis in V. tapetis and V. aestuarianus. In order to measure the phagocytosis of bacteria by hemocytes, a new method with antibodies linked with fluorochromes has been developed. In order to obtain new sequences in Manila clam, a Suppression Subtractive Hybridization (SSH) was performed between hemocytes of challenged and control clams. The analysis of genome of Vibrio tapetis by MaGe (Génoscope®) shows several virulent factors inside genomic islands with taxonomic distances very close with vibrio but also with pathogenic human bacteria. The method of conjugation to introduce plasmids in V. tapetis and V. aestuarianus mutagenesis is now reliable and permitted to obtain the first mutants of V. tapetis.
Phlorotannin biosynthesis in model brown seaweeds using a two-pronged approach combining functional genomics and metabolic profiling (Phlorotann-ING).
This project aims to elucidate the pathway(s) of phlorotannin biosynthesis in brown seaweeds using an approach that combines molecular biology and genomics techniques with methods commonly used in chemistry, biochemistry and ecology. The scientific partners will study the biochemical function and regulation of the enzymes involved in phlorotannin biosynthesis with regard to the structural variability of the phenol compounds that are formed in wild seaweeds and in those cultivated under conditions of stress. This is the first project to associate the functional genomics studies that are currently underway on the brown seaweed model Ectocarpus silisculosus—whose genome has been sequenced and annotated (UMR 7139)—with the ecological, biochemical and chemical studies conducted at LEBHAM on two bio indicators on the Brittany coast, Sargassum muticum and Ascophyllum nodosum.
Search for evidences of molecular thermostability in hydrothermal and intertidal invertebrates using recombinant proteins approach
The hydrothermal annelid Alvinella pompejana is considered as one of the most thermotolerant eukaryotes on earth. To survive, it developped numerous physiological adaptations such as an increase of protein thermal properties. In Alvinella, previous in silico analysis showed a significant enrichment in hydrophobic and charged amino acids in its ribosomal proteins. In order to confirm the “thermostable” status of proteins from hydrothermal species, we propose to compare thermo-stability properties, structural characteristics and function of a targeted set of proteins between two hydrothermal annelids (A. pompejana and P. grasslei) and two molluscs (the hydrothermal mussel B. azoricus and the coastal species C. gigas). A complementary analysis of the relation “phenotype-genotype" on three polymorphic systems showing evidences of differential selection to temperature will be conducted on both A. pompejana and C. gigas in natural populations to better understand the effect of thermal selection that could be at the origin of ecological speciation mechanisms.
The goal of this one year project is to generate a transcriptomic profile of a functional photosymbiosis, which associates a heterotrophic host and a photosynthetic. The partnership Symsagittifera roscoffensis (acoele, metazoan) / Tetraselmis convolutae (unicellular green prasinophyte alga) offers the unprecedented possibility to access to the two aposymbiotic states and to the photosymbiotic entity without classical limitations of cross-contamination or low genetic material yields. Based on the controlled cultures of both partners in the SBR, this global transcriptomic approach will provide the first photosymbiotic standard obtained by in silico subtraction from the three pyrosequenced transcriptoms: the aposymbiotic alga, the aposymbiotic juvenile acoel and the symbiotic association. The bioanalysis should highlight the fine transcriptomic adjustments and explain the trophic relationship and pivotal adaptation to photosymbiosis. It must be noted that today, one does not know how photosynthetic activity is recruited/co-opted and controlled by heterothophic organisms during photosymbiosis, which represents 50 percent of marine photosynthesis. Deciphering such strategy of control of photosynthesis will also provide arguments for refining our knowledge on the historical mechanisms that lead to the primary and secondary endosymbioses (chloroplasts acquisition).
Role of the EsGRP1 protein in the extracellular matrix and in the morphogenesis of the brown alga Ectocarpus siliculosus (ECTOMEC).
The characterisation of the extracellular protein EsGRP1 was carried out by 1) completing the sequencing of EsGRP1, which showed an example of alternative splicing, and 2) producing antibodies against EsGRP1, which were used to immunolocalize EsGRP1 in the filaments of Ectocarpus siliculosus.In addition, in order to identify mutants altered in the composition of their extracellular matrix, the FTIR technique was tested on E. siliculosus filaments in the laboratory of Chantal Compère (Ifremer Brest). The experiments performed so far aiming at adjusting the technique to Ectocarpus were not conclusive.
The objective of the project is to better understand the functionality and the regulation of key genes involved in HUFA synthesis pathway in a marine fish species of aquaculture interest, the European sea bass (Dicentrarchus labrax). The work is based on the development of molecular tools combined with gene expression studies and biochemical approaches in order to investigate the expression and the activity of enzymes involved in PUFA bioconversion in fish fed different diets differing in HUFA content. Special attention is paid to FADS2 gene (fatty acid delta-6-desaturase) whose activity has been considered as the first limiting step in vertebrates. The first results obtained reveal specific features concerning FADS2 function and regulation which could explain the low capacity of HUFA synthesis in marine fish species.