CNRS Integrative Biology of Marine Models
CNRS Integrative Biology of Marine Models
Goulitquer S.,French National Center for Scientific Research |
Potin P.,CNRS Integrative Biology of Marine Models |
Tonon T.,CNRS Integrative Biology of Marine Models
Marine Drugs | Year: 2012
Marine systems are very diverse and recognized as being sources of a wide range of biomolecules. This review provides an overview of metabolite profiling based on mass spectrometry (MS) approaches in marine organisms and their environments, focusing on recent advances in the field. We also point out some of the technical challenges that need to be overcome in order to increase applications of metabolomics in marine systems, including extraction of chemical compounds from different matrices and data management. Metabolites being important links between genotype and phenotype, we describe added value provided by integration of data from metabolite profiling with other layers of omics, as well as their importance for the development of systems biology approaches in marine systems to study several biological processes, and to analyze interactions between organisms within communities. The growing importance of MS-based metabolomics in chemical ecology studies in marine ecosystems is also illustrated. © 2012 by the authors; licensee MDPI.
Holzer G.,CNRS Lyon Institute of Functional Genomics |
Markov G.V.,CNRS Integrative Biology of Marine Models |
Laudet V.,University Pierre and Marie Curie
Current Topics in Developmental Biology | Year: 2017
Nuclear receptors (NRs) are a family of ligand-regulated transcription factors that modulate a wide variety of physiological functions in a ligand-dependent manner. The first NRs were discovered as receptors of well-known hormones such as 17β-estradiol, corticosteroids, or thyroid hormones. In these cases a direct activation of the receptor transcriptional activity by a very specific ligand, with nanomolar affinity, was demonstrated, providing a strong conceptual framework to understand the mechanism of action of these hormones. However, the discovery that some NRs are able to bind different ligands with micromolar affinity was a first sign that the univocal relationship between a specific receptor (e.g., TR) and a specific ligand (e.g., thyroid hormone) should not be generalized to the whole family. These discussions about the nature of NR ligands have been reinforced by the study of the hormone/receptor couple evolution. Indeed when the ligand is not a protein but a small molecule derived from a biochemical pathway, a simple coevolution mechanism between the ligand and the receptor cannot operate. We and others have recently shown that the ligands acting for a given NR early on during evolution were often different from the classical mammalian ligands. This suggests that the NR/ligand evolutionary relationship is more dynamic than anticipated and that the univocal relationship between a receptor and a specific molecule may be an oversimplification. Moreover, classical NRs can have different ligands acting in a tissue-specific fashion with significant impact on their function. This also suggests that we may have to reevaluate the pharmacology of the ligand/receptor couple. © 2017 Elsevier Inc.
Hehemann J.-H.,Massachusetts Institute of Technology |
Boraston A.B.,University of Victoria |
Czjzek M.,Paris-Sorbonne University |
Czjzek M.,CNRS Integrative Biology of Marine Models
Current Opinion in Structural Biology | Year: 2014
Marine algae contribute approximately half of the global primary production. The large amounts of polysaccharides synthesized by these algae are degraded and consumed by microbes that utilize carbohydrate-active enzymes (CAZymes), thus creating one of the largest and most dynamic components of the Earth's carbon cycle. Over the last decade, structural and functional characterizations of marine CAZymes have revealed a diverse set of scaffolds and mechanisms that are used to degrade agars, carrageenan, alginate and ulvan-polysaccharides from red, brown and green seaweeds, respectively. The analysis of these CAZymes is not only expanding our understanding of their functions but is enabling the enhanced annotation of (meta)-genomic data sets, thus promoting an improved understanding of microbes that drive this marine component of the carbon cycle. Furthermore, this information is setting a foundation that will enable marine algae to be harnessed as a novel resource for biorefineries. In this review, we cover the most recent structural and functional analyses of marine CAZymes that are specialized in the digestion of macro-algal polysaccharides. © 2014 Elsevier Ltd.
Ras M.,French National Institute for Agricultural Research |
Ras M.,CNRS Integrative Biology of Marine Models |
Steyer J.-P.,French National Institute for Agricultural Research |
Bernard O.,French Institute for Research in Computer Science and Automation
Reviews in Environmental Science and Biotechnology | Year: 2013
High rate outdoor production units of microalgae can undergo temperature fluctuations. Seasonal temperature variations as well as more rapid daily fluctuations are liable to modify the growth conditions of microalgae and hence affect production efficiency. The effect of elevated temperatures, above optimal growth temperatures, on growth is seldom reported in literature, but often described as more deleterious than low temperatures. Depending on the species, different strategies are deployed to counteract the effect of above optimal temperatures such as energy re-balancing and cell shrinking. Moreover, long term adaptation of certain species over generation cycles has also been proven efficient to increase optimal temperatures. Physical models coupled to biological kinetics are able to predict the evolution of temperature in the growth media and its effect on the growth rate, highlighting the downstream drastic economic and environmental impacts. Regarding the relative elasticity of microalgae towards temperature issues, cell mortality can depend on species or adapted species and in certain cases can be attenuated. These elements can complement existing models and help visualize the effective impacts of temperature on outdoor cultures. © 2013 Springer Science+Business Media Dordrecht.
Bothwell J.H.F.,Queen's University of Belfast |
Bothwell J.H.F.,Marine Biological Association of The United Kingdom |
Bothwell J.H.F.,CNRS Integrative Biology of Marine Models |
Griffin J.L.,The Hopkins Building
Biological Reviews | Year: 2011
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful analytical techniques available to biology. This review is an introduction to the potential of this method and is aimed at readers who have little or no experience in acquiring or analyzing NMR spectra. We focus on spectroscopic applications of the magnetic resonance effect, rather than imaging ones, and explain how various aspects of the NMR phenomenon make it a versatile tool with which to address a number of biological problems. Using detailed examples, we discuss the use of 1H NMR spectroscopy in mixture analysis and metabolomics, the use of 13C NMR spectroscopy in tracking isotopomers and determining the flux through metabolic pathways ('fluxomics') and the use of 31P NMR spectroscopy in monitoring ATP generation and intracellular pH homeotasis in vivo. Further examples demonstrate how NMR spectroscopy can be used to probe the physical environment of a cell by measuring diffusion and the tumbling rates of individual metabolites and how it can determine macromolecular structures by measuring the bonds and distances which separate individual atoms. We finish by outlining some of the key challenges which remain in NMR spectroscopy and we highlight how recent advances-such as increased magnet field strengths, cryogenic cooling, microprobes and hyperpolarisation-are opening new avenues for today's biological NMR spectroscopists. © 2010 The Authors. Biological Reviews © 2010 Cambridge Philosophical Society.
Dittami S.M.,Paris-Sorbonne University |
Dittami S.M.,CNRS Integrative Biology of Marine Models |
Eveillard D.,CNRS Nantes Atlantic Computer Science Laboratory |
Tonon T.,Paris-Sorbonne University |
Tonon T.,CNRS Integrative Biology of Marine Models
Molecular Ecology | Year: 2014
Increasing evidence exists that bacterial communities interact with and shape the biology of algae and that their evolutionary histories are connected. Despite these findings, physiological studies were and still are generally carried out with axenic or at least antibiotic-treated cultures. Here, we argue that considering interactions between algae and associated bacteria is key to understanding their biology and evolution. To deal with the complexity of the resulting 'holobiont' system, a metabolism-centred approach that uses combined metabolic models for algae and associated bacteria is proposed. We believe that these models will be valuable tools both to study algal-bacterial interactions and to elucidate processes important for the acclimation of the holobiont to environmental changes. © 2014 John Wiley & Sons Ltd.
Popper Z.A.,National University of Ireland |
Michel G.,CNRS Integrative Biology of Marine Models |
Herve C.,CNRS Integrative Biology of Marine Models |
Domozych D.S.,Skidmore College |
And 4 more authors.
Annual Review of Plant Biology | Year: 2011
All photosynthetic multicellular Eukaryotes, including land plants and algae, have cells that are surrounded by a dynamic, complex, carbohydrate-rich cell wall. The cell wall exerts considerable biological and biomechanical control over individual cells and organisms, thus playing a key role in their environmental interactions. This has resulted in compositional variation that is dependent on developmental stage, cell type, and season. Further variation is evident that has a phylogenetic basis. Plants and algae have a complex phylogenetic history, including acquisition of genes responsible for carbohydrate synthesis and modification through a series of primary (leading to red algae, green algae, and land plants) and secondary (generating brown algae, diatoms, and dinoflagellates) endosymbiotic events. Therefore, organisms that have the shared features of photosynthesis and possession of a cell wall do not form a monophyletic group. Yet they contain some common wall components that can be explained increasingly by genetic and biochemical evidence. Copyright © 2011 by Annual Reviews. All rights reserved.
Nehr Z.,CNRS Integrative Biology of Marine Models
Plant signaling & behavior | Year: 2011
Ectocarpus siliculosus is being developed as a model organism for brown algal genetics and genomics. Brown algae are phylogenetically distant from the other multicellular phyla (green lineage, red algae, fungi and metazoan) and therefore might offer the opportunity to study novel and alternative developmental processes that lead to the establishment of multicellularity. E. siliculosus develops as uniseriate filaments, thereby displaying one of the simplest architectures among multicellular organisms. The young sporophyte grows as a primary filament and then branching occurs, preferentially at the center of the filament. We recently described the first morphogenetic mutant étoile (etl) in a brown alga, produced by UVB mutagenesis in E. siliculosus. We showed that a single recessive mutation was responsible for a defect in both cell differentiation and the very early branching pattern (first and second branch emergences). Here, we supplement this study by reporting the branching defects observed subsequently, i.e. for the later stages corresponding to the emergence of up to the first six secondary filaments, and we show that the branching process is composed of at least two distinct components: time and position. © 2011 Landes Bioscience
Michel G.,CNRS Integrative Biology of Marine Models |
Tonon T.,CNRS Integrative Biology of Marine Models |
Scornet D.,CNRS Integrative Biology of Marine Models |
Cock J.M.,CNRS Integrative Biology of Marine Models |
Kloareg B.,CNRS Integrative Biology of Marine Models
New Phytologist | Year: 2010
•Brown algal cell walls share some components with plants (cellulose) and animals (sulfated fucans), but they also contain some unique polysaccharides (alginates). Analysis of the Ectocarpus genome provides a unique opportunity to decipher the molecular bases of these crucial metabolisms.•An extensive bioinformatic census of the enzymes potentially involved in the biogenesis and remodeling of cellulose, alginate and fucans was performed, and completed by phylogenetic analyses of key enzymes.•The routes for the biosynthesis of cellulose, alginates and sulfated fucans were reconstructed. Surprisingly, known families of cellulases, expansins and alginate lyases are absent in Ectocarpus, suggesting the existence of novel mechanisms and/or proteins for cell wall expansion in brown algae.•Altogether, our data depict a complex evolutionary history for the main components of brown algal cell walls. Cellulose synthesis was inherited from the ancestral red algal endosymbiont, whereas the terminal steps for alginate biosynthesis were acquired by horizontal gene transfer from an Actinobacterium. This horizontal gene transfer event also contributed genes for hemicellulose biosynthesis. By contrast, the biosynthetic route for sulfated fucans is an ancestral pathway, conserved with animals. These findings shine a new light on the origin and evolution of cell wall polysaccharides in other Eukaryotes. © CNRS (2010). Journal compilation © New Phytologist Trust (2010).
Dittami S.M.,CNRS Integrative Biology of Marine Models
ISME Journal | Year: 2015
Like most eukaryotes, brown algae live in association with bacterial communities that frequently have beneficial effects on their development. Ectocarpus is a genus of small filamentous brown algae, which comprises a strain that has recently colonized freshwater, a rare transition in this lineage. We generated an inventory of bacteria in Ectocarpus cultures and examined the effect they have on acclimation to an environmental change, that is, the transition from seawater to freshwater medium. Our results demonstrate that Ectocarpus depends on bacteria for this transition: cultures that have been deprived of their associated microbiome do not survive a transfer to freshwater, but restoring their microflora also restores the capacity to acclimate to this change. Furthermore, the transition between the two culture media strongly affects the bacterial community composition. Examining a range of other closely related algal strains, we observed that the presence of two bacterial operational taxonomic units correlated significantly with an increase in low salinity tolerance of the algal culture. Despite differences in the community composition, no indications were found for functional differences in the bacterial metagenomes predicted to be associated with algae in the salinities tested, suggesting functional redundancy in the associated bacterial community. Our study provides an example of how microbial communities may impact the acclimation and physiological response of algae to different environments, and thus possibly act as facilitators of speciation. It paves the way for functional examinations of the underlying host–microbe interactions, both in controlled laboratory and natural conditions.The ISME Journal advance online publication, 26 June 2015; doi:10.1038/ismej.2015.104. © 2015 International Society for Microbial Ecology